Ⅰ. Introduction

ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Ⅰ. Introduction

Under the auspices of the National Committee of Planning and Development and the Chinese Academy of Sciences, the National Laboratory of Biomacromolecules was founded in 1989, and formally opened in Jan. 1991. Over the past decade, the NLB successfully completed many fundamental research projects of national significance, accumulated talents, equipments, technologies, and experiences in the area of protein science.

The NLB was repeatedly ranked exceptional in 1989, 1991, 1996, 2001 and 2004 in the evaluations of all National Laboratories in biological sciences organized by the Ministry of Science and Technology. In 1994, the 10th anniversary of the inauguration of the National Key Laboratories, the NLB was awarded one of the outstanding groups and was selected as one of the first five labs to undertake further reform. In 1996, the lab was commended as the outstanding lab by the Bureau of Human resources, Chinese Academy of Sciences. Because of its excellent performance, the NLB was one of the first to enter the knowledge innovation program implemented by Chinese Academy of Sciences in Beijing in 1999. In 2004, when celebrating 20th anniversary of inauguration of the National Laboratories, the NLB was again honored with a ‘Golden Bull’ award as an outstanding group in National Key Laboratories.

2003 has seen the change of leadership and Academic Committee of the NLB. Under the new leadership and academic committee, the NLB implemented a strategy ‘Dynamic, Open, Collaborative, and Competitive’, aiming to fulfill the important national needs and to reach frontlines of international science and technology. It is clear that the NLB will be continuously led by the Honorary Director, Prof. Chen-lu Tsou and other two senior academics Prof. Dong-cai Liang and Prof. Fu-yu Yang, built on the core of protein science, the NLB will actively pursue multidisciplinary study of protein 3-dimentional structure and function, structure and function of biological membrane and membrane proteins, function and folding principles of proteins, molecular basis of immunology and infectious diseases, molecular neurobiology, and systems biology. In the end of 2004, the NLB are carrying out 47 projects, with funds totaling 31.3 M, from various sources including the Ministry of Science and Technology, Chinese Academy of Sciences and other national funding agencies.

The NLB adheres to the concept ‘Human resource is the most precious resource’, puts the highest priority in management of human resources, combines the action of attracting and training, stabilizing and metabolizing. The NLB has recruited a large number of outstanding young and mid-aged scientists to play critical roles, among them are receivers of ‘Hundred Talents Plan’ of the Chinese Academy of Sciences, ‘National Outstanding Young Researcher Award’ from the National Science Foundation China, and ‘Cheng-gong’ professors of the Ministry of Education. A creative team based on graduate students and postdocs, led by first class scientist has emerged in the NLB.

The NLB has integrated existing equipments, systematically constructed key infrastructure, combining with the platform of protein science in the hosting Institute of Biophysics. The NLB has fully prepared and has built the sound foundation for establishment of the National Lab for Protein Sciences, further facilitate the systematic and large scale development of the protein sciences of our country.

National Laboratory of Biomacromelecules

Director Zihe Rao

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Ⅰ. 前言

生物大分子国家重点实验室于1989年经国家计划发展委员会和中国科学院批准成立，1991年1月通过验收并正式对外开放运行。在十几年的成长历程中，实验室承担了多项国家重大科研任务，在蛋白质科学研究领域已形成了人才、装备、技术、经验的综合优势并取得了骄人业绩。在国家科学技术部对全国生物学科国家重点实验室和部门开放实验室的历次评估中，生物大分子国家重点实验室分别于1989年、1991年、1996年、2001年和2004年五次被评为优秀；1994年我室被评为先进集体的同时被科技术部选为全国首批五个国家重点实验室试点单位之一；1996年我室又被中国科学院人事局评为先进集体；1999年作为优秀实验室首批进入了中国科学院在京区启动的生物科学的开放实验室知识创新试点。2004年在国家重点实验室成立二十周年之际，我室再度被国家科学技术部评为 “国家重点实验室计划先进集体”称号，荣获金牛奖。 2003 年实验室进行了室领导及学术委员会的换届，在新一届室领导和学术委员会的带领下本着“流动、开放、联合、竞争”的办室方针，面向国家发展战略需求和国际科技发展前沿，结合实验室多年来的工作积累，明确地提出了实验室的定位：实验室将继续在我国生物物理和生物化学界前辈科学家邹承鲁、梁栋材、杨福愉三位先生的指导和带领下，以蛋白质科学为核心，发挥多学科交叉综合的优势，结合人类健康相关的国家需求，围绕生物膜与膜蛋白功能与结构、蛋白质功能与折叠原理、蛋白质三维结构与功能，感染与免疫、系统生物学等重大科学问题开展原创性研究。截止 2004 年底实验室承担国家、科学院的在研任务 47 项，从科技部和中科院得到的运行经费和各课题组在研研究经费总额达 3130 万元。生物大分子国家重点实验室坚持“人才是第一资源”的理念，将人才工作作为各项工作的重中之重。实验室坚持引进与培养相结合、稳定与流动相统一的原则，广纳优秀人才加盟，引进了中国科学院“百人计划”入选者、国家杰出青年基金获得者和教育部“长江学者奖励计划”特聘教授等一大批优秀中青年科学工作者来室担当重任。形成了以一流领衔科学家为核心，以一批有突出贡献的中年学术骨干和青年创新人才为主体，以研究生、博士后为基础的金字塔形的创新人才队伍。生物大分子国家重点实验室在仪器设备方面整合了自有的仪器设备，依靠中科院生物物理研究所的蛋白质科学研究平台，通过学科调整和蛋白质科学关键仪器设备的系统性建设，将为建设蛋白质科学国家实验室奠定良好基础，并以此推进我国蛋白质科学研究走规模化、体系化的发展道路。

生物大分子国家重点实验室主任饶子和

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Ⅱ. Organization 1. Honorary Directors Chenlu Tsou Institute of Biophysics CAS Dongcai Liang Institute of Biophysics CAS Fuyu Yang Institute of Biophysics CAS

2. Director and Vice Directors Director Zihe Rao Institute of Biophysics CAS Vice Directors Tao Xu Institute of Biophysics CAS Weimin Gong Institute of Biophysics CAS Xianming Pan Institute of Biophysics CAS

3 Academic Council:

Chairman: Chihchen Wang Member of CAS Institute of Biophysics CAS Beijing

Members: Jun Yu Professor Institute of Genomics CAS Beijing Zhixin Wang Member of CAS Institute of Biophysics CAS Beijing Zhaohui Ye Member of CAS Wuhan Institute of Physics and Mathematics CAS Wuhan Xianen Zhang Professor Ministry of Science and Technology Beijing Boliang Li Professor Shanghai Institute for Biological Sciences CAS Shanghai Jiayang Li Member of CAS Institute of Genetics and Developmental Biology CAS Beijing Qishui Lin Member of CAS Shanghai Institutes for Biological Sciences CAS Shanghai Yunyu Shi Member of CAS School of Life Science, University of Science and Hefei Technology of China Fuchu He Member of CAS Academy of Military Medical Science Beijing Zihe Rao Member of CAS Institute of Biophysics CAS Beijing Tao Xu Professor Institute of Biophysics CAS Beijing Aike Guo Member of CAS Institute of Biophysics CAS Beijing Guangxia Gao Professor Institute of Microbiology CAS Beijing Wenrui Chang Professor Institute of Biophysics CAS Beijing Xiyun Yan Professor Institute of Biophysics CAS Beijing Boqin Qiang Member of CAS Institute of Basic Medical Research CAMS Beijing

Academic Secretary： Xiyun Yan

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Ⅱ. 机构 1. 名誉主任邹承鲁中科院生物物理所梁栋材中科院生物物理所杨福愉中科院生物物理所 2. 主任、副主任主任饶子和中科院生物物理所副主任徐涛中科院生物物理所龚为民中科院生物物理所潘宪明中科院生物物理所

3. 学术委员会

主任：王志珍中国科学院院士中科院生物物理所北京

委员： (以姓氏笔画为序) 于军研究员中科院北京基因组所北京王志新中国科学院院士中科院生物物理所北京叶朝辉中国科学院院士中科院武汉物理与数学研究所武汉张先恩研究员科技部北京李伯良研究员上海生命科学研究院上海李家洋中国科学院院士中科院遗传发育所北京林其谁中国科学院院士上海生命科学研究院上海施蕴渝中国科学院院士中国科技大学生命科学院合肥贺福初中国科学院院士军事医学科学院北京饶子和中国科学院院士中科院生物物理所北京徐涛研究员中科院生物物理所北京郭爱克中国科学院院士中科院生物物理所北京高光侠研究员中科院微生物所北京常文瑞研究员中科院生物物理所北京阎锡蕴研究员中科院生物物理所北京强伯勤中国科学院院士中国医学科学院基础所北京

学术秘书：阎锡蕴（兼）

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4 International Scientific Committee

The International Scientific Committee is composed of eminent overseas scientists whose expertise is in fields closely related to the research of the Laboratory. The purpose of the International Committee is to advise on the priorities and direction for research, to maintain international scientific dialogue and exchange, and to allow appraisal of the Laboratory against an international standard.

Chairman: Robert Huber (Nobel Prize Laureate) Max Plank Institute for Biochemistry (Germany)

Vice Chairman: Erwin Neher (Nobel Prize Laureate) Max Plank Institute for Biophysical Chemistry (Germany) Members: Giuseppina Barsacchi Laboratori di Biologia Celluare e dello Sviluppo (Italy) Guy Dodson University of York (UK) Khalid Iqbal NYS Institute for Basic Research (USA) Neil Isaacs University of Glasgow (UK) Jack Johnson The Scripps Research Institute (USA) David Stuart University of Oxford (UK) Joel Sussman The Weizmann Institute of Science (Israel) Michael G. Rossmann Purdue University, (USA) Jack Johnson The Scripps Research Institute (USA) Bi-Cheng Wang University of Georgia, (USA) Brian Matthews University of Oregon (USA) Louise N. Johnson University of Oxford (UK) Neil Isaacs University of Glasgow (UK) Johannes Frederik Gerardus Vliegenthart Bijvoet Center for Biomolecular Research (Netherlands) 5 Research Faculty

Chang Chen Hongyu Deng Zusen Fan Guangxia Gao Weimin Gong Haiying Hang Shigang He Guangju Ji Taijiao Jiang Tao Jiang Renjie Jiao Gang Jin Sarah Perrett Wei Liang Yingfang Liu Xianming Pan Zhihai Qin Zihe Rao Hong Tang Jie Tang Jinhui Wang Shengdian Wang Yi Wang Zhixin Wang Zhizhen Wang Zhongju Xiao Tao Xu Xiyun Yan Fuquan Yang Qinwei Yin Xianen Zhang Xujia Zhang 6 Senior Faculty Wenrui Chang Jianwen Chen Youguo Huang Guozhong Jing Dongcai Liang Jinfeng Wang Fuyu Yang Junmei Zhou Chenlu Tsou

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4. 国际科学委员会为了与国际同行保持经常联系，及时了解国际研究动向，掌握和确定研究战略，组织本实验室的国际同行评估，本实验室成立了由国外科学家组成的“国际科学委员会”。主席： Robert Huber (诺贝尔奖获得者) Max Plank Institute for Biochemistry (Germany) 副主席： Erwin Neher (诺贝尔奖获得者) Max Plank Institute for Biophysical Chemistry (Germany) 委员会成员： Giuseppina Barsacchi Laboratori di Biologia Celluare e dello Sviluppo (Italy) Guy Dodson University of York (UK) Khalid Iqbal NYS Institute for Basic Research (USA) Neil Isaacs University of Glasgow (UK) Jack Johnson The Scripps Research Institute (USA) David Stuart University of Oxford (UK) Joel Sussman The Weizmann Institute of Science (Israel) Michael G. Rossmann Purdue University, (USA) Jack Johnson The Scripps Research Institute (USA) Bi-Cheng Wang University of Georgia, (USA) Brian Matthews University of Oregon (USA) Louise N. Johnson University of Oxford (UK) Neil Isaacs University of Glasgow (UK) Johannes Frederik Gerardus Vliegenthart Bijvoet Center for Biomolecular Research (Netherlands) 5 实验室固定成员：(以拼音为序)

陈畅邓红雨范祖森高光侠龚为民杭海英何士刚姬广聚蒋太交江涛焦仁杰靳刚柯莎梁伟刘迎芳潘宪明秦志海饶子和唐宏唐捷王晋辉王盛典王毅王志新王志珍肖中举徐涛阎锡蕴杨福全殷勤伟张先恩张旭家

6 实验室资深人员：(以拼音为序) 常文瑞陈建文黄有国静国忠梁栋材王金凤杨福愉周筠梅邹承鲁

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Ⅲ. Management 1 Management of the NLB

The NLB is managed strictly according to the ‘Temporary Regulations of Establishment and Management of National Key Laboratories’. The director is responsible for running the NLB, and the academic committee is responsible for evaluation. The NLB is organized according to the research directions based on research unit. An academic conference is organized every year in Feb. to March. The director of the NLB presents a summary of the previous year and a proposal for running and expenditure of current year.

2. Academic committee

The Annual Meeting convened by the Academic Council provides a forum to discuss and appraise the research of the Laboratory. At this meeting, ongoing research projects are assessed, new research proposals are considered for approval, the accounts are inspected, the research achievements of the Laboratory are examined and the priorities and direction for future research are set.

3. Research directions

1) Protein science and catalytic enzyme

2) Three dimensional structure and function of bio-macro molecules

3) Biology of membrane molecules

4) Molecular basis of immunology and infectious diseases

5) Molecular neuroscience

4. Management of projects

Members of the NLB submits following materials to the secretary of the NLB: 1) All publications (a reprint and an electronic version) with the NLB in corresponding address, including papers, book chapters, and publications in national and international conferences 2) Photocopy of national and international awards received in past 12 months 3) Progress report (with a Chinese and an English version)

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Ⅲ. 管理 1 实验室管理实验室依据“国家重点实验室建设与管理暂行办法”对实验室进行全面管理。本室实行实验室主任负责制、学术委员会评审制；实验室采用以研究方向为导向，以研究组为基本科研单元的运行模式，每年 2-3 月间召开上年度学术年会。实验室主任就年度运行管理、经费使用提出可行方案，并向学术委员会汇报上年度的实验室工作总结。 2 学术委员会学术委员会结合本室学术年会每年召开全体会议一次，评议实验室的工作，内容包括确定实验室研究方向、制定及修改课题指南、审批课题申请、检查课题进展情况、监督经费使用、评审科研成果及审议学术活动计划等。 3 研究方向 1）蛋白质和分子酶学 2）生物大分子三维结构和功能 3）膜分子生物学 4）感染与免疫的分子基础 5) 分子神经生物学 4 课题管理实验室成员每年应按时向实验室秘书提交以下材料： 1) 当年发表的具有“生物大分子国家重点实验室”署名的全部著作目录（包括专著、论文，国际及全国性学术会议论文等），并提交版面清楚平整的论文单印本一式一份及论文电子版； 2) 当年获得国际、国家或省部级科技奖励的证书复印件一份； 3) 年度工作报告（中、英文各一份）的电子文档。报告格式按实验室秘书提供的文档模版填写。

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Ⅳ. Summary of Research in 2004

Inspired by the mortem of the NLB ‘rigorous, diligent, devoted’, all members are working extremely hard and the NLB is making great progresses in 2004. Especially in the aspect of grant application, the ‘the National Basic Research Program’: Structure and Function of Bio-membrane and Membrane Proteins, led by Dr. Tao Xu has been approved by the MOST, with a total of 25M. In the ‘the National Basic Research Program’: Human Liver Structural Proteomics and New Methods and Techniques of Proteomics, a sub-project: Human Liver Structural Proteomics, led by Dr. Wei-min Gong, has been approved, with a total of 9M. A project ‘Single Molecule Detection of Cell Membrane Protein CD146 and Molecular Recognition of Its Ligand and Signal Trunsduction in Living Cells’ led by Dr. Xi-yun Yan has been approved by the NSFC as a key research project. The NLB has been awarded the outstanding group and the ‘Golden Bull’ award; the project led by Dr. Wen-rui Chang: Three Dimensional Structure and Function of Photon Catching Complex of Algae Photosynthesis’ has won the 1st prize of Science and Technology in Beijing. This project has significant implication for the mechanism of photosynthesis and energy regeneration and usage. Dr. Zi-he Rao has been elected a member of Third World Academy and the outstanding personnel of 973. Dr. Wen-rui Chang has been awarded ‘He Liang and He Li’ award for progress of science and technology, and the outstanding personnel of 973. The NLB has won research grants totaling 29M. The NLB currently has 8 postdoc, 58 Ph.D. students and 45 Master students. 1 Research Funds Running expenditure from the MOST and CAS: 2.3M.

Total research grants: 29M. 2 Research Projects

There are 47 items of scientific research programs which are taking on in the NLB till the end of the year of 2004, including the National Basic Research Program (973), 2 items (13 projects); the National High Technology Research and Development Program of China (863), 7 items; the Key Technologies R&D Program, 3 items; 3 items of the Major Program of the National Natural Science Foundation of China, 2 items of the Key Program, 1 item of the National Science Fund for Distinguished Young Scholars, 1 item of the State Key Laboratories Development Program, 9 items of the General Program; 13 items of the Knowledge Innovation Program of Chinese Academy of Sciences, and so on.

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Ⅳ. 2004 年工作总结

生物大分子国家重点实验室在过去的一年里全室人员在严谨、勤奋、求精献身精神鼓舞下，团结协作，努力工作使得全室各项工作得以顺利开展，完成情况良好。特别是今年在项目申请方面由徐涛研究员作为首席科学家申报的《国家重点基础研究发展规划》973 项目：“生物膜和膜蛋白的结构与功能研究”获得科技部批准，项目总经费 2500 万元；在“973”项目：“人类肝脏结构蛋白质组和蛋白质组新技术新方法研究” 中，龚为民研究员申报的子课题：人类肝脏结构蛋白质组学研究获得批准，项目总经费 900 万元；阎锡蕴研究员关于“活细胞单分子探测细胞膜蛋白 CD146 及其配体的分子识别和信号传导机制”研究项目也获得了基金委重点项目经费的支持。在成果取得方面，生物大分子国家重点实验室被授予国家重点实验室计划先进集体荣誉称号并获金牛奖；常文瑞课题组主持完成的“藻类光合作用捕光复合物的三维结构与功能研究” 获北京市科学技术奖一等奖，该项成果对于光合作用的机理研究和可再生能源的开发利用具有重要意义；饶子和院士当选为第三世界科学院院士并获得 973 计划先进个人荣誉称号；常文瑞研究员获得了 2004 年度何梁何利基金科学与技术进步奖，973 计划先进个人荣誉称号等。在经费争取方面，我室今年在研科研项目经费总额达 2900 万元。在人才培养方面，实验室设有博士后流动站，在站博士后 8 人，在读博士生 58 人，硕士生 45 人。 1 经费科技部和中科院支持的运行经费：230 万元在研研究经费总额达 2900 万元。 2 项目

2004 年底实验室承担的在研任务 47 项，包括“973”计划主持项目 2 项，子课题 13 项；“863”计划课题 7 项；国家科技攻关计划课题 3 项；科技部基础研究快速反应支持项目 1 项；国家自然科学基金重大项目 3 项、重点项 2 项、国家杰出青年基金 1 项、优秀国家重点实验室基金 1 项、面上项目 9 项；中科院创新工程重大项目课题 4 项、创新工程重要方向项目课题 8 项、生物科学与技术研究特别支持项目 2 项。中科院创新工程领域前沿项目 1 项，院长基金特别支持项目1 项，院生物局特别支持项目1 项。

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3.GRADUATE STUDENTS ⑴ Post-Doctoral Fellows

Previous: Zhanfen Qin Xuesong Chen

Current: Hongmei Zhang Xianzhi Dong Jianqiang Ni Changcheng Yin

Chunling Zhang Xiaoxue Yan Tongbiao Zhao Yan Gan

⑵ Doctoral Students

Students Conferred with the Ph.D Degree in 2004:

Ling Yan Qiu Cui Lingyun Wang Chuanpeng Liu

Chuanxi Cai Zhenfeng Liu Feng Wang Caihong Yun

Yu Cao Yingang Feng Sun Huang Zhuo Li

Dongsheng Liu Yongfang Zhao Yunzheng Zhao

The National Laboratory of Biomacromolecules currently has 58 Doctoral students.

⑶ Master’s Students

Students Conferred with the Master Degree in 2004:Su Xu

The National Laboratory of Biomacromolecules currently has 45 Master’s students.

⑷ Student Awards

1) CAS Director’s Scholarships were awarded to Yi Jiang and Hanchi Yan

2) Second Class Di-Ao Scholarships were awarded to Guoping Ren

⑸ Graduate Student Supervisor Awards

1）Prof. Chihchen Wang was awarded a Procter & Gamble Outstanding Graduate Student Supervisor Award in 2004

2）Prof. Xiyun Yan was awarded a Procter & Gamble Outstanding Graduate Student Supervisor Award in 2004

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3 人才

⑴ 博士后

出站博士后：秦占芬陈雪松

在站博士后张红梅董先智倪建强尹长城张春玲

闫小雪赵同标甘燕

⑵ 博士生

2004 年取得博士学位 15 人:

闫玲崔球王凌云刘川鹏蔡传喜

柳振峰王锋云彩红曹禹冯银刚

黄隼李卓刘东升赵永芳赵云罡

在读博士生 58 人

⑶ 硕士生

2004 年取得硕士学位 1 人：徐苏

硕士生 45 人

⑷ 研究生获奖情况

博士生江轶、严汉池获中国科学院院长优秀奖

博士生任国平获中国科学院地奥奖学金二等奖

⑸ 研究生导师获奖情况

王志珍院士获中国科学院宝洁优秀研究生导师奖阎锡蕴研究员获中国科学院宝洁优秀研究生导师奖

12 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

4 Scientific Awards

(1) Wenrui Chang 1st Beijing municipal award of science and technology: Studies on 3D-structure of photosynthetic membrane proteins-Crystal structure and function of spinach major light harvesting complex (2) Zihe Rao Elected as member of the third world academy of science (3) National Key Laboratory of Biomacromolecules Named “Excellent Team of National Key Laboratory Program” and awarded Golden Cattle Trophy (4) Wenrui Chang Won Liliang He Progress Award of Science and Technology of year 2004 (5) Wenrui Chang Named Excellent Scientist of National Loboratory by Ministry of Science and Technology of China (6) Wenrui Chang Won “Award of Excellent Scientist of 973 project” from Ministry of Science and Technology of China (7) Wenrui Chang Won “Award of Excellent Scientist of 973 project” from Ministry of Science and Technology of China

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4 获奖情况

(1) 常文瑞等完成的“藻类光合作用捕光蛋白－色素复合物的三维结构与功

能研究”成果获北京市科学技术奖一等奖。（图一）

(2) 饶子和院士当选为第三世界科学院院士。

(3) 生物大分子国家重点实验室获“国家重点实验室计划先进集体”称号并获

金牛奖。

(4) 常文瑞研究员获 2004 年度何梁何利基金科学与技术进步奖。（图二）

(5) 常文瑞研究员获国家科技部颁发的“国家实验室先进个人”称号。（图三）

(6) 饶子和院士获国家科技部颁发“973 计划先进个人”奖。（图四）

(7) 常文瑞研究员获国家科技部颁发“973 计划先进个人”奖。（图五）

图一图二

图三图四图五

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5 International Exchance

(1) International Metting Held

10th International Conference on Crystallography Beijing China June, 2004 (2) Participation in International Meetings

Junmei Zhou Physical Aspects of Protein Folding Invited Speaker Time: 1/5-8/2004, Kyoto, Japan Topic: Folding and Chaperone Function of Escherichia Coli Trigger Factor Zihe Rao British Royal Society SARS Research Meeting Speaker Time: 1/12-15/2004, Landon, UK Topic: The The crystal structures of SARS virus main protease Mpro and its complex with an inhibitor Tao Xu Forty-eighth Research Meeting of Biophysics Society Speaker Time: 2/14-18/2004, Maryland, USA Topic: Regulation of Insulin Secretion by Extracellular ATP in Rat pancreatic beta cells Zihe Rao Sino-Japan SARS Research Meeting (organized by CAS) Speaker Time: 2/20-26/2004, Yokohama, Japan Topic: The The crystal structures of SARS virus main protease Mpro and its complex with an inhibitor Xiyun Yan The International Workshop on SARS Speaker Time: 2/23-24/2004, Japan Topic: Probing the structure of the SARS coronavirus using SEM Zihe Rao First Pacific Rim Conference on Protein Science Speaker Time: 4/14-20/2004, Yokohama, Japan Topic: The The crystal structures of SARS virus main protease Mpro and its complex with an inhibitor Sarah Perrett First Pacific Rim Conference on Protein Science Time: 4/14-18/2004, Japan Poster: Amyloid nucleation and hierarchical assembly of Ure2p fibrils Zihe Rao International Conference on SARS-one year after the (first) outbreak Speaker Time: 5/8-11/2004, Lubeck, German Topic: Structural Genomics Study of SARS coronavirus-The The crystal structures of SARS virus main protease Mpro and its complex with an inhibitor

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5 国际交流 (1)主办国际会议

第十届国际结晶学大会 2004 年 6 月中国北京

(2)参加国际会议

周筠梅 Physical Aspects of Protein Folding, Kyoto 时间：2004年1月5-8日，日本邀请报告：Folding and Chaperone Function of Escherichia coli Trigger Factor 饶子和英国皇家学会 SARS 研讨会大会报告时间：2004年1月12-15 日，英国伦敦题目：Structural genomics study of the SARS coronavirus ——The Crystal Structures of SARS Virus Main Protease Mpro and Its Complex with an Inhibitor 徐涛第 48 届生物物理学会年会专题报告时间：2004年2月14-18，美国（Maryland Baltimore）题目为：Regulation of Insulin Secretion by Extracellular ATP in Rat pancreatic beta cells 饶子和中-日 SARS 研讨会（中科院组团）大会报告时间：2004年2月20-26 日，日本题目：Structural genomics study of the SARS coronavirus ——The Crystal Structures of SARS Virus Main Protease Mpro and Its Complex with an Inhibitor 阎锡蕴 The International Workshop on SARS，Tokyo, Japan 时间：2004年2月23-24 日，日本题目：Probing the structure of the SARS coronavirus using SEM 饶子和 The 1st Pacific-Rim International Conference on ProteinScience 大会报告时间：2004年4月14-20 日，日本横滨题目：Structural genomics study of the SARS coronavirus ——The Crystal Structures of SARS Virus Main Protease Mpro and Its Complex with an Inhibitor 柯莎 The1st Pacific Rim Conference on Protein Science 时间：2004年4月14日-18 日，日本墙报: Amyloid nucleation and hierarchical assembly of Ure2p fibrils 饶子和 International Conference on SARS - one year after the (first)outbreak 大会报告时间：2004 年 5 月 8-11 日德国（Lubeck）题目：Structural genomics study of the SARS coronavirus —The Crystal Structures of SARS Virus Main Protease Mpro and Its Complex with an Inhibitor

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Qinwei Yin 2nd RNAi International Conference

Time: 5/10-13/2004, USA

Poster: Effective suppression of proliferation of human melanoma cells by a combination of siRNA molecules

Chih-chen Wang 4th International Workshop on the molecular biology of stress responses Invited Speaker

Time: 5/13-16/2004, Wuhan and Yichang, China

Topic: Dimerization by Domain Hybridization Bestows Chaperone and Isomerase Activities

Xianen Zhang 8th World Conference on Biosensors Speaker and Chair for enzyme sensors workshop

Time: 5/24-26/2004, Spain

Topic: Gene Technology: Opportunity in Biosensors

Zihe Rao Tenth International Conference on Crystallography Speaker

Time: 6/5-8/2004, Beijing, China

Topic: A perspective on Structural Genomics efforts in China-a report, review and revision

Wenrui Chang Tenth International Conference on Crystallography Invited Speaker

Time: 6/5-8/2004, Beijing, China

Topic: Crystal structure of spinach major light harvesting complex at 2.72 Å resolution

Junmei Zhou FASEB Conference: Protein Misfolding, Amyloid and Conformational Disease

Time: 6/12-17/2004, Colorado, USA

Poster: Amyloid nucleation and hierarchical assembly of Ure2 fibrils: role of Asn/Gln repeat and non-repeat regions of the prion domain

Sarah Perrett FASEB Conference: Protein folding in the cell

Time: 7/31-8/5/2004, Vermont, USA

Poster: Folding, misfolding and fibril formation of yeast prion protein Ure2

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殷勤伟第二届 RNAi 国际会议时间：2004年5月10-13 日，美国墙报：Effective suppression of proliferation of human melanoma cells by a combination of siRNA molecules

王志珍 4th International Workshop---On the molecular biology of stress responses,

Wuhan and Yichang

时间：2004 年 5 月 13-16 日

邀请报告：“Dimerization by domain hybridization bestows chaperone and

somerase activities”. 张先恩第八届世界生物传感器大会分组口头报告并主持酶传感器分会会场时间：2004年5月24-26 日，西班牙

题目：Gene Technology: Opportunity in Biosensors 饶子和第 10 届国际晶体学大会 ICCBM10 大会主席分会场报告时间：2004年6月5-8日，中国北京

题目：A perspective on Structural Genomics efforts in China – a report, review

and revision 常文瑞第十届国际结晶学大会大会特邀报告时间：2004年6月5-8日，中国北京

题目：Crystal structure of spinach major light harvesting complex at 2.72Å

resolution

周筠梅 FASEB Conference: Protein Misfolding, Amyloid and Conformational Disease,

Colorado 时间：2004年6月12日-17 日,美国

墙报: Amyloid nucleation and hierarchical assembly of Ure2 fibrils: role of

Asn/Gln repeat and non-repeat regions of the prion domain.

柯莎 FASEB Conference: Protein Folding in the Cell, Vermont 时间：2004年7月31日-8月5日,美国

墙报：Folding, misfolding and fibril formation of the yeast prion protein Ure2

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Xiyun Yan 2004 Asian-Pacific Rim Conference on Biology of Tumor Markers and 21th International Workshop on Tumor Markers Speaker Time: 8/21-25/2004, Xian, China Topic: A novel anti-CD146 antibody inhibits angiogenesis and tumor growth Wenrui Chang Thirteenth International Conference on Photosynthesis Invited Speaker Time: 8/29-9/3/2004, Canada Topic: Crystal structure of spinach major light harvesting complex at 2.72 Å resolution Zhihai Qin International Conference on Immune Escape of Tumors Speaker Time: 10/10-14/2004 Salzburg, Austria Topic: Diverse immunological mechanisms against transplanted and chemical carcinogen-induced tumors Zihe Rao Conference on Molecular Aspects and Prevention of SARS Speaker Time: 10/16-20/2004, Madrid, Spain Topic: Structural genomics study of the SARs-CoV. The crystal structure of the main protease and its inhibitors Xiyun Yan The first symposium between China and Japan on SARS Speaker Time: 10/17-18/2004, Beijing, China Topic: Generating SARS antibody library for SARS diagnosis and therapy Xianen Zhang 8th China-Japan-South Korea Enzyme Engineering Conference Speaker Time: 10/24-27/2004, Hangzhou, China Topic: A Muts-based Protein Chip for Detection of DNA Mutations Chih-chen Wang HUPO3rd Annual World Congress, Proteomics: decoding the genome Speaker

Time: 11/2004, Beijing, China Topic: Thiol-Protein Oxidoreductases as Molecular Chaperones Xiyun Yan Immunotherapy for the New Century Speaker Time: 11/15-19/2004, Havana, Cuba Topic: A novel anti-CD146 antibody inhibits angiogenesis and tumor growth Zihe Rao Structrral Genomics & Proteomics EU Projects Meeting Speaker Time: 12/1-4/2004, Spain Topic: A perspective on Structural Genomics efforts in China

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阎锡蕴 2004 亚太地区国际肿瘤生物学和医学暨第 21 届国际肿瘤标志物学术会议时间： 2004年8月21－25 日，中国西安

题目：A novel anti-CD146 antibody inhibits angiogenesis and tumor growth 常文瑞第十三届国际光合作用大会特邀报告时间：2004年8月29日-9月3日，加拿大

题目：Crystal structure of spinach major light-harvesting complex at 2.72Å

resolution 秦志海 “国际肿瘤免疫逃逸专题会议”上作专题报告

时间：2004 年 10 月 10 日-14 日，奥地利（Salzburg）

题目：Diverse immunological mechanisms against transplanted and chemical carcinogen-induced tumors. 饶子和 Molecular Aspects and Prevention of SARS 大会报告时间：2004 年 10 月 16-20 日西班牙马德里题目：Structural genomics study of the SARS-CoV. The crystal structure of the main protease and its inhibitors 阎锡蕴 The first symposium between China and Japan on SARS,Beijng China, 时间：2004 年 10 月 17-18 日，北京题目：Generating SARS antibody library for SARS diagnosis and therapy 张先恩第八届中日韩酶工程大会报告时间：2004 年 10 月 24-27 日，杭州题目：A MutS-based Protein Chip for Detection of DNA Mutations 王志珍 HUPO3rd Annual World Congress, Proteomics: decoding the genome 时间：2004 年 11 月，北京题目：“Thiol-Protein Oxidoreductases as Molecular Chaperones” 阎锡蕴 Immunotherapy for the New Century, Havana, Cuba, 时间：2004 年 11 月 15-19 日题目：A novel anti-CD146 antibody inhibits angiogenesis and tumor growth 饶子和 Structural Genomics & Proteomics EU Projects Meeting 时间：2004 年 12 月 1-4 日，西班牙题目：A perspective on Structural Genomics efforts in China

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⑶Visits Abroad

Tao Xu NIH, USA, 2/2004

Wenrui Chang Invited speech at Verona University, Italy

Wenrui Chang Invited speech at Sheffield University, UK

Xiyun Yan Tour to National Institute of Nanotechnology and Universities in Canada, sponsored by Ministry of Science and Technology of China, 9/30-10-13/2004 Xiyun Yan Tour to Daikin Company in Japan for the arrangement of research cooperation, 10/2004 Chih-chen Wang Medical School, Hong Kong University, 10/15/2004 Topic: Thiol-Protein Oxidoreductases as Molecular Chaperones Chih-chen Wang Chinese University of Hong Kong, 10/18/2004 Topic: Thiol-Protein Oxidoreductases as Molecular Chaperones ⑷Visitiors from the Taiwan Area and Abroad

David Westhead Doctor, Leeds University, UK Time: 2/16-22/2004 Jim Larrick Doctor, Panorama Research Institute, USA Time: 3/19-24/2004 Hoichi Yorinaka Vice President of Xiongben University, Japan Time: 3/29/2004 Tomomichi Ono Professor, Medical school, Xiongben University, Japan Time: 3/29/2004 T. Hoshino Rigaku Company, Japan Time: 3/31/2004 David Stipp Fortune magazine, USA Time: 5/26/2004 Orla M. Smith Valda Vinson Science journal, USA Time: 5/27/2004 Jack Johnson & Tianwei Lin Drs., The Scripps Research Institute Time: 6/3-4/2004 Tom Blundell Chair of School of Biological Sciences, University of Cambridge Time: 6/7/2004 Michael G Rossmann Doctor, Purdue University Time: 6/8/2004

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⑶对国外及港澳台地区的访问

徐涛美国 National Institutes of Health, 2004.2 常文瑞意大利 verona 大学邀请报告常文瑞英国 Sheffield 大学邀请报告阎锡蕴 2004年9月30日至10月13日, 受加拿大国家研究院国家纳米技术研究所（National Institute of NanoTechnology）的邀请,参加科技部组织的纳米科技代表团，访问了加拿大的有关研究机构和大学。阎锡蕴 2004 年 10 月，受日本大金公司邀请，访问该公司并开展 SARS 防治方面的研究。王志珍 2004 年 10 月 15 日香港大学医学院并做题为： “Thiol-Protein Oxidoreductases as Molecular Chaperones”报告王志珍 2004 年 10 月 15 日香港中文大学并做题为： “Thiol-Protein Oxidoreductases as Molecular Chaperones”报告

⑷来我室访问的外国和港澳台地区科学家

1、2004年2月16-22 日英国 Leeds 大学 David WESTHEAD 博士来访 2、2004年3月19-24 日美国 Panorama Research Institute 的 Jim Larrick 博士来访。 3 、2004年3月29日日本雄本大学 Hoichi Yorinaka 副学长与雄本大学药学院 Tomomichi Ono 教授等来访 4、2004年3月31日日本T. Hoshino 日本理学公司来访

5、2004年5月26日美国Fortune 杂志的 David Stipp 来访

6、2004年5月27日美国Science 杂志的 Orla M. Smith Valda Vinson 来访

7、2004 年 6 月 3-4 日美国 The Scripps Research Institute，Jack Johnson、林

天伟博士来访

8、2004年6月7日英国School of Biological Sciences, University

of Cambridge 的主席 Tom Blundell 博士来访

9、2004 年 6 月 8 日美国 Purdue University 的 Michael G Rossmann 博士来访

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John W. Kappler Member of British Royal Society, Investigator of Howard Hughes Medical Institute, Professor of National Jewish Medical research Center, Denver, Colorado, USA Time: 6/9-10/2004 Pjilippa Marrack Investigator of Howard Hughes Medical Institute, Professor of National Jewish Medical research Center, Denver, Colorado, USA Time: 6/9-10/2004 I. Raska Doctor, Pharmaceutical Institute, Academy of Sciences, Czech Time: 6/17/2004 British Visiting Group of Structural Genomics: Kim Watson, University of Reading; Dame Louise Johnson, University of Oxford; David Gillham, Syngenta Inc; Drake Eggleston, GlaxoSmithKline Inc; Peter Collins, Rigaku/MSC Inc; Paul Loeffen, University of Oxford; Jennifer Moynihan, University of Reading Yangxin Fu Professor, University of Chicago, USA Time: 7/2004 Speech topic: Tumor Immune Therapy Wenqin Xu Doctor, University of Washington, USA Time: 7/27/2004 Rongguang Zhang Argone National Laboratory, USA Time: 7/27/2004 Rudi Balling Director, German Research Center of Biotechnology Time: 7/27/2004 Zongchao Jia Doctor, Department of Chemistry, Queens University Time: 7/30/2004 Jie Zheng Professor, Department of Physiology and Membrane Biology, School of Medicine, University of California at Davis, USA Time: 8/2004 Topic: Molecular Motion of Ion Channel Zhinan Yin Professor of Immunology of Yale University, USA Time: 8/2004 Speech topic: T cell Function in Tumor Immunity Hospital Universitario de Canarias, Sapin Time: 9/1/2004 Kyogo Itoh Professor, Department of Immunology, School of Medicine, Kurume University, Japan Time: 9/12/2004 Takehisa Matsumoto Riken Inc., Japan Time: 10/25/2004 Visiting group from Academy of Sciences of Uzbekistan: seven people Time: 10/27/2004

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10、2004年6月9-10 日美国 Howard Hughes Medical Institute National，Jewish Medical and Research Center 的英国皇家科学院院士 John W. Kappler 和 Philippa Marrack 教授来访

11、2004年6月17日捷克科学院药物所 I. Raska 博士来访

12、2004 年英国结构基因组学使团来访（Dr Kim Watson The University of

Reading，Prof Dame Louise Johnson University of Oxford，Dr David GillhamSyngenta，

Dr Drake Eggleston GlaxoSmithKline，Dr Peter Collins Rigaku/MSC Inc，Dr Paul

Loeffen Oxford，Diffraction Limited，Dr Jennifer Moynihan The University of Reading）

13、2004 年 7 月份邀请 University of Chicago 大学傅阳心教授访问我所并做关于肿瘤免疫治疗的学术报告。

14、2004年7月27日美国University of Washington 的许文清博士来访

15、2004年7月27日美国Argone National Laboratory 的张荣光博士来访

16、2004年7月27日德国German Research Centre fro Biotechnology 的所长 Rudi Balling 来访

17、2004年7月30日加拿大女王大学生化系的贾宗超博士来访

18、2004年8月16日日本东京大学的 Aikichi Iwamoto 博士来访

19、2004年8月27日美国华盛顿大学 Fred Hutchinson Cancer Research Center 的

诺贝尔奖获得者 Leland H.Hartwell 校长来访

20、2004年8月，加州大学戴维斯分校医学院生理及膜生物学系教授郑来访，并做了题为 Molecular Motion of Ion Channel 的学术报告。

21、2004年8月，美国耶鲁大学免疫学教授尹芝南来我室访问并为全所做了

题为 T cell Function in Tumor Immunity 的报告。

22、2004年9月1日, Hospital Universitario de Canarias, Spain

23、2004年9月12日日本Kurume 大学医学部免疫系 Kyogo Itoh 教授来访

24、2004 年 10 月 25 日本 Takehisa Matsumoto、日本 Riken 公司来访 25、2004 年 10 月 27 日乌兹别克斯坦乌兹别克斯坦科学院 7 人来访

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Neil Isaascs, Richard Barron and Laurance Cogdell, Glasgow University Time: 10/29/2004 Gerhard Mterlik Professor, CEO, Diamond Inc, UK Time: 11/3/2004 Giovanni E. Mann Professor, Guy’s, King’s & St Thomas’ School of Biomedical Sciences Time: 11/2004 Vladimir Torchilin Chair of Department of Pharmaceutical Sciences, Northeastern University, USA Time: 11/12/2004 Visiting group Five people including Vice president of University of Tokyo Time: 11/22/2004 ⑸International Cooperation

Zhushen Fan Worked on tumor immunotherapy project in Dr. Yangxin Fu’s laboratory at University of Chicago Time: 2nd half of 2004 Zihe Rao with China-German Science Foundation Time: 4/2004-3/2007 Content: Structural Proteomics of SARS cornavirus Zihe Rao Within FP6 Time: 5/1/2004 Content: Sino-European Project on SARS Diagnostics and Antivirals Zihe Rao With Takehiko Sasazuki, President of International Medical Center of Japan Time: 12/7/2004 Content: Crystallographic analysis of important viral products, including structural analysis of the spike protein from SARS cornavirus as wellas several products from avian flu virus Zihe Rao With Teruo Kirkae, Director, Department of Infectious Diseases Research Institue, International Medical Center of Japan Time: 12/16/2004 Content: Crystallographic analysis of important viral products, including structural analysis of the spike protein from SARS cornavirus as wellas several products from avian flu virus Xiyun Yan With Andrew Bradbury, Professor, Los Alamos National Laboratory, USA Content: Establishment of high number and variety of SARS antibody library using a new phage vector Xiyun Yan With Kyogo Ito, Professor, Kurume University, Japan Content: immune activities of antigen surface positions

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26、2004 年 10 月 29 日.英国 Glasgow University 的 Neil Isaacs、Richard Barron 和

Laurance Cogdell 27、2004 年 11月3日英国Diamond 的 CEO Gerhard Materlik 教授来访 28、2004 年 11 月英国 Guy’s, King’s & St Thomas’ School of Biomedical Sciences 的 Giovanni E. Mann 教授来访

29、2004 年 11 月 12 日美国 Northeastern University Department of Pharmaceutical

Sciences 的 Chairman Vladimir P. Torchilin 来访 30、2004 年 11 月 22 日日本东京大学副校长等 5 人来访

⑸国际合作研究

1）范祖森：2004 年下半年到 University of Chicago 大学傅阳心教授实验室开展肿瘤免疫治疗的合作研究。 2）饶子和：合作方中德科学基金，时间 2004 年 4 月－2007 年 3 月合作内容

“Structural proteomics of SARS coronavirus” 3）饶子和：合作方第六欧盟框架计划，时间 2004年5月1日合作内容

“Sino-European Project on SARS Diagnostics and Antivirals （SARS 诊断及治疗的中—欧

合作计划项目(SEPSDA)）” 4）饶子和：合作方 Takehiko Sasazuki, President, International MedicalCenter of

Japan，时间 2004 年 12月7日合作内容：重要病毒的结构分析（crystallographic analysis of important viral products, including structural analysis of the spike protein from SARS coronavirus as well as several products from avian flu virus）

5）饶子和：合作方 Teruo Kirikae, Director, Department of Infectious Diseases Research

Institute, International Medical Center of Japan，时间 2004 年 12 月 16 日合作内容：重

要病毒的结构分析（crystallographic analysis of important viral products, including structural analysis of the spike protein from SARS coronavirus as well as several products from avian flu virus）

6）阎锡蕴与美国 Alamos 国家重点实验室的 Andrew Bradbury 教授合作，合作内容：利用新型噬粒载体构建大容量和多样性 SARS 抗体库。

7）阎锡蕴与日本 Kurume 大学 Kyogo Ito 教授合作，合作内容：开展抗原表位免疫活性的研究。

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Xiyun Yan With Daikin Company, Japan Content: inhibitory role of novel PTAF against SARS virus Junmei Zhou With Hirosh Kihara, Professor, Japan Time: 4/2004 and 12/2004 Content: Experiments at the station of X-rays small angle (15A). Tao Xu with Dr. Nils Brose, Max Plank Institue Content: the role of Munc13 in insulin secetion ⑹Domestic Meetings

Zihe Rao High Level Symposium on International Techniques of new medicine drug development and drug market Invited Speaker Time: 4/27/2004, Beijing Topic: Protein Science and Development of New Drugs Zihe Rao Zhongguancun Symposium Invited Speaker Time: 4/28/2004, Beijing Topic: Protein Science-from Aids to SARS Zihe Rao 7th National Conference of Enzymology Invited Speaker Time: 5/16/2004, Kunmin Topic: Protein Science is basic science as well as spring for industry- from Aids to SARS Wenrui Chang 7th National Conference of Enzymology Invited Speaker Time: 5/15-17/2004, Kunmin Topic: Studies on 3D-structure of photosynthetic membrane proteins-Crystal structure of spinach major light harvesting complex

Chih-chen Wang 7th National Conference of Enzymology Invited Speaker

Time: 5/15-17/2004, Kunmin

Topic: Dimerization by Domain Hybridization Bestows Chaperone and Isomerase Activities

Sarah Perrett 7th National Conference of Enzymology Speaker

Time: 5/15-17/2004, Kunmin Topic: Folding, misfolding and amyloid fibril formation of yeast prion protein Ure2

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8）阎锡蕴与日本大金公司合作，合作内容：研究新型网膜 PTAF 对 SARS 病毒的抑制作用。

9）周筠梅与日本关西医科大学的 Hirosh Kihara 教授合作，时间：2004年4月

和 12 月两次，合作内容：在 X-射线小角散射站（15 Å）进行实验。本工作获日本筑波高能物理所光子工厂的资助 10）徐涛与德国马普研究所 Dr. Nils Brose 合作，内容“Munc13 在胰岛素分泌中的作用”

⑹国内学术会议

饶子和国际新药开发技术与医药市场发展战略高层论坛特邀报告时间：2004年4月27日，北京题目：蛋白质科学与创新药物饶子和中关村论坛特邀报告时间：2004年4月28日，北京

题目：蛋白质科学—From AIDS to SARS 饶子和第七届全国酶学会特邀报告时间：2004年5月16日，昆明

题目：蛋白质科学是基础研究和生物产业的源泉—从 AIDS 到 SARS 常文瑞第七届全国酶学会议大会特邀报告时间：2004年5月15-17，昆明题目：Studies on 3D-structure of photosynthetic membrane proteins-Crystal structure of spinach major light harvesting complex 王志珍第七届全国酶学学术讨论会，昆明时间：2004年5月15-17，昆明

题目：“Dimerization by domain hybridization bestows chaperone and isomerase

activities”. Oral presentation. 柯莎第七届全国酶学学术讨论会大会报告时间：2004年5月15-17，昆明

题目：酵母 Prion 蛋白 Ure2 的折叠、错误折叠与淀粉样纤维的形成

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Yi Shi 7th National Conference of Enzymology Time: 5/16/2004, Kunmin Poster: The effect of hydrophobic fluorescent probe bis-ANS on the chaperone function of trigger factor and its dimerization Ming Bo 7th National Conference of Enzymology Time: 5/16/2004, Kunmin Poster: The glutathione peroxidase activity of yeast prion Ure2

Liling Zeng 7th National Conference of Enzymology Time: 5/16/2004, Kunmin Poster: The effect of C-domain on the in vivo chaperone function of trigger factor Huiyong Lian 7th National Conference of Enzymology Time: 5/16/2004, Kunmin Poster: Expression and purification of yeast chaperones Hsp104 and Ydj1 Yi Jiang 7th National Conference of Enzymology Time: 5/16/2004, Kunmin Poster: Amyloid nucleation and hierarchical assembly of Ure2 fibrils: role of Asn/Gln repeat and non-repeat regions of the prion domain Zihe Rao 1th Chinese International Workshop of Pharmacy Invited Speaker Time: 5/18/2004, Hangzhou Zihe Rao 1th Sino-German Symposium of Young Scientists in Chemistry and Biology Invited Speaker Time: 5/25/2004, Beijing Wei Liang 1th Chinese International Workshop of Pharmacy Time: 5/17-19/2004, Hangzhou Zihe Rao 2nd Chinese Proteomics Research Meeting Invited Speaker Time: 8/10-12/2004, Dalian Wei Liang “China’s Involvement in Imaging and Therapeutics”: Ceremony for starting publication and workshop Speaker Time: 9/3-6/2004, Beijing Topic: Guided Therapy of Tumors

29 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

石毅第七届全国酶学学术讨论会时间：2004年5月16日，昆明

墙报：疏水荧光探针 bis-ANS 对 trigger factor 分子伴侣功能及二聚化的影响。柏鸣第七届全国酶学学术讨论会时间：2004年5月16日，昆明

墙报：酵母 prion 蛋白 Ure2 的谷胱甘肽过氧化物酶活性。曾丽玲第七届全国酶学学术讨论会时间：2004年5月16日，昆明

墙报：C-domain 对 trigger factor 体内分子伴侣作用的影响。连惠勇第七届全国酶学学术讨论会时间：2004年5月16日，昆明

墙报：Expression and purification of yeast chaperones Hsp104 and Ydj1. 江轶第七届全国酶学学术讨论会时间：2004年5月16日，昆明

墙报：Amyloid nucleation and hierarchical assembly of Ure2 fibrils: role of Asn/Gln repeat and non-repeat regions of the prion domain. 饶子和国际药物制剂专题研讨会特邀报告时间：2004年5月18日，杭州题目：基于 SARS 蛋白质结构的药物设计饶子和第一届中德双边化学生物学青年学术会议特邀报告时间：2004年5月25日，北京题目：蛋白质科学是基础研究和生物产业的源泉梁伟第一届中国国际药剂学学术研讨会。时间：2004年5月17-19，杭州饶子和中国蛋白质组学第二届学术会议特邀报告时间：2004年8月10-12 日，大连题目：结构蛋白质组学研究进展梁伟《中国介入影像与治疗学》创刊暨学术研讨会时间：2004年9月3-6，北京题目：“肿瘤的靶向介入治疗”的大会发言

30 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Zihe Rao 3rd National representative conference of Chinese Crystallography Society and Research Meeting Invited Speaker Time: 9/17-24/2004, Chengdu Zihe Rao 8th Youth Scientific Symposium in Medicine and Health Invited Speaker Time: 10/10/2004, Beijing Zihe Rao 5th Youth Symposium of Chinese Scientific Association Invited Speaker Time: 11/2/2004, Beijing Tao Xu 6th Symposium of Biological Sciences Time: 11/1-6/2004, Chongqing Tao Xu Workshop of Biomembranes and Important Diseases Speaker Time: 12/23-26/2004, Sanya Topic: Intracellular membrane trafficking and regulation of blood glucose Zihe Rao Xiangshan Scientific Conference Invited Speaker

Time: 12/28-29/2004, Beijing

31 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

饶子和中国晶体学会第三次全国代表会暨学术会议时间：2004年9月17-24 日，成都饶子和第八届医药卫生青年科技论坛特邀报告时间：2004 年 10 月 10 日，北京题目：蛋白质结构：从 AIDS 到 SARS 饶子和中国科协第五届青年学术年会特邀报告时间：2004 年 11 月 2 日，北京题目：蛋白质产业和蛋白质基础研究徐涛第六届生命科学学术研讨会时间：2004 年 11 月 1-6 日，重庆徐涛生物膜与重大疾病学术研讨会时间：2004 年 12 月 23-26 日，三亚题目：细胞内膜转运和血糖调控饶子和香山科学会议大会报告时间：2004 年 12 月 28-29 日，北京题目：New progress in SARS basic research

32 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Ⅴ. Research Projects and Progress 1. Proteins and Molecular Enzymology Name Chih-chen Wang Position Professor, Member of CAS Research Topic Chaperones in Protein Folding Summary of Research 1. Conformational change of dimeric DsbC molecule induced by GdnHCl, A study by intrinsic fluorescence. Unfolding-refolding of E. coli DsbC, a homodimeric molecule, induced by GdnHCl was studied by intrinsic fluorescence. It is shown that the sulfur atoms of Cys 141 and Cys 163 are far apart from the indole ring of the single Trp (Trp 140), and cannot quench its fluorescence, while the potential quenchers are Met 136 and His 170. It was revealed that only Tyr 171, Tyr 38 and Tyr 52 among the eight Tyr residues, contribute to the bulk fluorescence of the molecule. The character of intrinsic fluorescence intensity changes induced by GdnHCl (equilibrium and kinetic data) and its parametric representation and the existence of an isobestic point of fluorescence spectra at different GdnHCl concentrations suggest the one step character of DsbC denaturation and its reversibility. 2. N-Terminal fluorophore labeling combined with donor-donor energy migration for study of the unfolding of dimeric DsbC. We have developed a valuable method for the N-terminal specific fluorescence labeling by using transamination combined with donor-donor energy migration (DDEM) to study unfolding/folding of a dimeric protein. Transamination provides a general approach for the selective fluorophore attachment to the N-terminal amino acid residues, and the dimeric structure of DsbC allows the introduction of two identical fluorophores, therefore we can take advantage of the DDEM method to trace its unfolding behavior. This combination strategy is useful to investigate conformational changes of other dimeric proteins under variable conditions. Great progresses can be expected when the specific labeling method is combined with DDEM at the single-molecule level. Moreover, this labeling approach can also be applied to non-dimeric protein molecules, and therefore broadens the scope of application for fluorescence spectroscopy. 3. Dimerization, zinc-finger, chaperone and thiol-protein oxidoreductases of DnaJ. 4. Translocation of α－Synuclein in E coli. 5. Protective action of protein disulfide isomerase on hypoxia in cells. 6. Suppression of chaperones on the amyloid formation of α－Synuclein.

Selected Publications 1. O. V.Stepanenko, I. M. Kuzenetsova, K. K. Turoverov*, C. J. Huang, and C. C. Wang*. Conformational change of dimeric DsbC molecule induced by GdnHCl: A study by intrinsic fluorescence. Biochemistry-USA 43, 5296-5303, (2004). 2. Xuejun Duan, Zhen Zhao, Jianping Ye, Huimin Ma*, Andong Xia*, Guoqing Yang, and Chih-chen Wang*. N-Terminal fluorephore labeling comined with donor-donor energy migration for study on unfolding of dimeric DsbC. Angew. Chem. Int. Ed. 43, 4216-4219, (2004).

33 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Ⅴ. 研究课题及进展 1.蛋白质和分子酶学

姓名王志珍

院士研究员副研究员长江学者百人计划国家杰出青年职称 √ √ □ □ □ □

研究方向分子伴侣和蛋白质折叠本年度工作简介 1. 测定内源荧光研究盐酸胍诱导的分子伴侣 DsbC 同源二聚体的构象变化分析了 DsbC 中色氨酸和酪氨酸残基的微环境。唯一的 Trp140 在两个单体之间没有能量传递，其荧光不为 Cys98-Cys101 和 Cys141-Cys163 的硫原子淬灭；但可能为 Met136 和 His170 淬灭。171、38 以及 52 位的酪氨酸残基是 DsbC 荧光的主要贡献者;其它 5 个酪氨酸的能量传递给 Trp140 获在它们之间传递。不同浓度盐酸胍诱导下的 DsbC 去折叠过程的平衡态内源荧光的变化，表明其去折叠过程为二态构象转变，没有检测到去折叠的平衡态中间体。动力学研究表明变性稀释重折叠与去折叠过程相可逆。 2. 用供体－供体能量转移（DDEM）技术研究 DsbC 同源二聚体的去折叠用乙醛酸将 DsbC 二个 N 末端的氨基转移生成 α 羰醛，利用 α 羰醛与肼的交联作用将荧光探针分子 BODIPY 特异地连接到 DsbC 的 N 末端，是一种新的荧光标记策略。用DDEM 技术计算 DsbC 不同程度去折叠后的能量转移效率探测分子到天然 DsbC 分子二个 N 末端间为 35Å（晶体中 29Å）；在 1.5M 盐酸胍中，二个 N 末端距离增加到 47Å，表明分子部分去折叠但尚未解离；6M 盐酸胍使大大超过 BODIPY 的临界距离，说明二体分子解离。Ｎ末端特异标记结合 DDEM 技术可成为双体蛋白质折叠研究的通用方法。 3．分子伴侣 DnaJ 的二聚化,锌指,巯基－蛋白质氧化还原酶性质的研究

4．α－Synuclein 在大肠杆菌中的转运 5．蛋白质二硫键异构酶对细胞缺氧损伤的保护作用

6．分子伴侣对α－Synuclein 形成纤维和淀粉样沉淀的抑制作用

获奖

王志珍 2004 年度中国科学院宝洁优秀研究生导师。任国平 2004 年度中国科学院地奥二等奖。

34 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Jun-Mei ZHOU Position Professor Research Topic Protein structure, function and folding Summary of Research 1) Structure and Function of the Chaperone and Foldase Trigger Factor Trigger factor (TF) has both chaperone and cis-trans prolyl isomerase activities and is the first chaperone encountered by the nascent polypeptide in bacteria. While ribosome-bound TF is monomeric, the function of the dimeric form, and the reason for the excess concentrations of TF in the cytosol, are unknown. We have shown that it is specifically the dimeric form of TF that is able to bind folding intermediates of a substrate protein and hold them in a conformation that is competent to be refolded in an ATPase-dependent manner by the Hsp70 system, DnaK/DnaJ/GrpE. This may represent a previously unrecognised function of TF as a cytosolic binding chaperone. 2) Function, Folding and Amyloid Formation of the Yeast Prion Protein Ure2 We have carried out a detailed study of the mechanism of amyloid fibril formation for the yeast prion protein Ure2 and a series of N-terminal deletion mutants using a combination of techniques. The results demonstrate the importance of both Gln/Asn repeat and non-repeat regions of the N-terminal prion domain in the process of amyloid nucleation, consistent with the importance of these regions for manifestation of the prion phenotype in vivo. We have also investigated the enzymatic properties of the Ure2 protein and demonstrated that Ure2 has glutathione-dependent peroxidase activity in both native and fibrillar forms. This work represents important progress in elucidation of the role of Ure2 in vivo. Further, establishment of an in vitro activity assay for Ure2 provides a valuable tool for the study of structure-function relationships.

Selected Publications 1. Zhu L, Qin ZJ, Zhou JM* & Kihara H. Unfolding kinetics of dimeric creatine kinase measured by stopped-flow small angle X-ray scattering. Biochimie 86:127-32 (2004). 2. Liu CP & Zhou JM.* Trigger factor-assisted folding of bovine carbonic anhydrase II. BBRC 313:509-15 (2004). 3. Jiang Y, Li H, Zhu L, Zhou JM* & Perrett S.* Amyloid nucleation and hierarchical assembly of Ure2p fibrils: Role of Asn/Gln repeat and non-repeat regions of the prion domain. J. Biol. Chem. 279:3361-3369 (2004). 4. Bai M, Zhou JM* & Perrett S* The yeast prion protein Ure2 shows glutathione peroxidase activity in both native and fibrillar forms. J. Biol. Chem. 279:5025-5030 (2004). 5. Liu CP, Perrett S & Zhou JM* (2005) Dimeric trigger factor stably binds folding-competent intermediates and cooperates with the DnaK-DnaJ-GrpE chaperone system to allow refolding. J. Biol. Chem. in press.

35 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名周筠梅

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向蛋白质的结构、功能与折叠本年度工作简介 1，Trigger Factor 的结构与分子伴侣功能 Trigger factor（TF）是大肠杆菌中新生肽链所遇到的第一个分子伴侣，具有肽基脯氨酰基顺反异构酶（PPIase）活性，在细胞内以三种状态存在：核糖体结合的单体、细胞质中游离的单体和二体。核糖体结合的 TF 帮助新生肽链折叠的机制已经研究的比较多，而细胞质中大量游离的 TF，特别是二体 TF 的功能尚不清楚。我们今年的研究结果表明只有二体 TF 能与蛋白质折叠的中间态紧密结合形成稳定的复合物，并维持折叠中间态具有继续折叠的构象；且只有那些被二体 TF 结合的折叠的中间体能够与 Hsp70 分子伴侣系统（DnaK/DnaJ/GrpE）相互作用，在 ATP 存在下，继续折叠为天然蛋白质。阐明了以前未意识到的，TF 可能作为细胞质内“结合分子伴侣”的作用。 2，酵母类 Prion 蛋白 Ure2 的功能、折叠和淀粉样纤维的形成我们应用 ThT 结合荧光和原子力显微镜技术，详细研究了酵母类 Prion 蛋白 Ure2 及一系列 N-端不同程度缺失突变体淀粉样纤维的形成。结果表明 Ure2 N-端 Prion 结构域中的 Gln/Asn 重复序列和非重复序列对淀粉样纤维形成的成核过程都是十分重要的。此结果与体内研究发现的这些区域对其形成表型的影响一致。我们还进一步研究了 Ure2 的酶学性质，发现天然 Ure2 和纤维形式的 Ure2 具有相同的谷胱甘肽过氧化物酶活性，本工作是阐明 Ure2 体内功能的重要进展。并且，在体外测定Ure2 活性方法的建立，为进一步研究Ure2 的结构和功能之间的关系提供了有用的工具。

本年度获奖情况

36 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Xian’en Zhang Position Professor Research Topic Molecular Recognition and Biosensors Summary of Research

The mismatch repair (MMR) system plays an important role in maintaining the stability of the genome and defects in the mammalian pathway for mismatch repair are associated with a strong predisposition to tumor development. So far, the detailed mechanism of interaction between MMR proteins is not well understood. Our recent research interests include multi-MMR protein interactions and MMR protein-DNA interactions, and exploring MMR molecules as biosensor recognition elements for effective detection of DNA mutations. The progress in the passed year is as follows:

1. The overexpression sytems of the proteins MutS and MutL have been established. 2. Four MutS fusion molecular systems have been constructed. Based on these fusions, two types of biochips have been built: protein chips and DNA chips, enabling the fast, specific and sensitive detection of DNA mutations, in combination of either fluorescence or enzymatic reaction. We have a number of publications on this aspect. 3. In the future we will focus on the structure-function relationships of protein-protein interactions related to DNA mismatch repair. Protein fusion technology and surface plasma resonance technology will be adopted to facilitate the research.

Selected Publications 1. LJ Bi, YF Zhou, XE Zhang*, ZP Zhang, CG Zhang and Anthony E. G. CASS. High Expression of Gene Encoding for MutL Fusion Protein and Research on Its Chaperon Function. Chinese Journal of Biochemistry and Molecular Biology 20(2): 149-155, (2004). 2. Li-Jun BI, Ya-Feng ZHOU, Xian-En ZHANG*, Jiao-Yu DENG, Ji-Kai WEN, Zhi-Ping ZHANG. Construction and Characterization of Different MutS Fusion Proteins as Recognition Elements of DNA Chip for Detection of DNA Mutations, Biosensors and Bioelectronics, 2004 in press. 3. Sun L, Dong Y, Zhou Y, Yang M, Zhang C, Rao Z, Zhang XE*. Crystallization and preliminary X-ray studies of methyl parathion hydrolase from Pseudomonas sp. WBC-3. Acta Crystallogr. D Biol. Crystallogr. 60(5): 954-6, (2004).

37 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名张先恩

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向分子识别与生物传感

本年度工作简介

一、课题组科研进展情况：

DNA 错配修复（Mismatch Repair，MMR）是细胞复制后的一种修复机制，具有维持 DNA 复制保真度，控制基因变异的作用。大量研究表明，DNA 错配修复基因缺陷会导致在 HNPCC 和散发性结肠癌等的发生。目前，DNA 错配修复的分子机制作为当今研究的热点也取得了一些进展，但修复过程中一些修复蛋白的具体作用，蛋白质之间的协同作用以及作用机制还存在争论。我们主要的研究工作包括 DNA 错配修复系统介导的基因突变检测方法研究，错配修复蛋白与 DNA 的作用及蛋白质之间协同作用研究。研究进展情况如下： 1，构建了 DNA 错配修复基因 mutS 和 mutL 的高效表达系统。 2，利用 MutS 蛋白对错配碱基的特异识别、结合功能，通过基因工程，构建一系列 MutS 融合蛋白，发展了基于 MutS 蛋白的基因突变检测蛋白质芯片和 DNA 芯片新方法。研究结果表明，基于 MutS 蛋白的蛋白质芯片和 DNA 芯片都能成功检测含有错配或未配对碱基的寡核苷酸片段及含有单个碱基错配的不同长度结核杆菌 rpoB 基因片段。 3，DNA 错配修复蛋白结构与功能的关系以及修复蛋白的协同作用研究。目前已经完成了 DNA 错配修复蛋白 MutS 融合分子系统的构建以及 mutL 基因的克隆、表达和纯化工作，为修复蛋白之间协同作用的动力学分析作准备。 MutS、MutL 和 MutH 的缺失突变和定点突变工作正在开展，该工作是确定 MutS 与 MutL、MutL 与 MutH 相互作用位点和关键氨基酸组成。

相关研究成果已经分别发表在国内外学术刊物上。

本年度获奖情况发表在 Analytical Chemistry 上的文章 “A MutS-based Protein Chip for Detection of DNA Mutations”获得 2004 年度“湖北省第十届自然科学优秀学术论文”特等奖。

38 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Wang Jinfeng Position Professor Research Topic NMR study of protein folding and solution structure Summary of Research We have accomplished the following studies during 2004: 1. Study of the folding pathway and mechanism of staphylococcal nuclease (SNase) (1) We studied the folding of the 1-79 residue fragment of SNase (SNase79). The residual α–helix and β–structures were determined. The β–turn Y27-Q30 was identified as a folding initiation site for SNase79. The conclusion was drawn that the cis/trans heterogeneity of the X-prolyl bond Q30-P31 determines whether the sequence region T13-V39 forms a native-like β–structure in SNase79. (2) We calculated the solution structure of [Pro-]SNase which has lost enzyme activity. The internal motions of [Pro-]SNase were analyzed. Analysis of the key factors that influence the enzyme function of proteins is in progress. (3) We determined the solution structure of the 1-140 residue fragment of SNase (SNase140). The NMR experiments for backbone dynamics were completed. The plasmid for two relevant fragments was constructed. (4) The C-terminal 121-143 residue fragment of SNase (SNaseα3) which contains the α-helix sub-domain of SNase was expressed and purified. Interaction between SNaseα3 and SNase121 was studied. A dramatic increase in enzyme activity of SNase121 and formation of native-like conformations of both fragments were observed. Study of the solution structure of the complex was started. 2. Structural genomics study (1) We calculated the solution structure of a 180-residue human translationally controlled tumor protein (TCTP). Determination of Ca2+ binding site on TCTP is in progress. (2) We calculated the solution structure of human programmed cell death 5 protein (PDCD5). We have expressed and purified the N-terminal 22-residue fragment of PDCD and determined its solution structure as an intact α–helix. (3) We obtained an initial solution structure of a protein from the human blood system which is a protein with unknown physiological function. (4) We calculated the solution structure of Ssh10b which is a member of Sac10b family from the hyperthermophilic archaeon Sulfolobus shibatae. Ssh10b was determined to be a dimer in aqueous solution.

Selected Publications (1) Human programmed cell death 5 protein has a helical-core and two dissociated structural regions. Dongsheng Liu, Yingang Feng, Yuan Cheng, Jinfeng Wang*. BBRC 2004, 318:391-396. (2) Searching for folding initiation sites of staphylococcal nuclease: A study of N-terminal short fragments. Jixun Dai, Xu Wang, Yingang Feng, Guibao Fan, Jinfeng Wang*. Biopolymers 2004, 75:229-241.

39 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名王金凤

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向本年度工作简介 2004 年内我组完成了如下方面的工作：

一、金黄色葡萄球菌酶（SNase）体外折叠路径和机制研究（1）完成了酶蛋白 N-末端 1－79 残基片段（SNase79）折叠研究。确定了α-螺旋和β-折叠的残余构象，β-转角 Y27－Q30 是折叠的起始位点，并阐明β-折叠是否在 SNase79 中形成取决于 Q30－P31 是处于 trans-构象还是 cis-构象。（2）确定了因 P42、P47 和 P117 突变而失活的 SNase 的溶液三维结构。完成了其内运动特性的研究。正在从构象变化及内运动变化角度分析失活的决定因素，以进一步探讨酶发挥功能机制。（3）确定了 N-末端 1－140 残基片段 SNase140 的溶液三维结构。完成了其内运动研究的实验。正在构建和表达两个相关片段，从而可以进一步分析 C-端几个氨基酸残基缺失对酶功能影响的决定因素。（4）成功地表达了 C-端 121－143 残基（即包含α3 亚结构域的残基）片段 SNase α3。并已开展 SNase α3 和 SNase121（1－121 残基片段）的相互作用研究。已观察到 SNase α3 和 SNase121 类天然构象的形成以及酶活的极大增加。正在解析复合体的三维结构。

二、与结构基因组研究相关的工作（1）解析了172 残基的人翻译控制的肿瘤蛋白质 TCTP 的溶液三维结构，正在进一步构建突变体以确定 Ca2+ 结合位点。（2）解析了人白血病细胞凋亡相关蛋白质 PDCD5 的溶液三维结构。并表达了 N- 端 22 残基片段和确定了这一独立α结构域构象。（3）初步解析了一个人血液系统未知结构功能蛋白质的三维结构。（4）解析了嗜热菌蛋白质 Ssh10b 双体的溶液三维结构。

本年度获奖情况

40 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Sarah Perrett Position Associate Professor Research Topic Protein Misfolding and Disease Summary of Research The yeast prion protein Ure2 forms amyloid-like filaments in vivo and in vitro. This ability depends on the N-terminal prion domain, which contains Asn/Gln repeats, a motif thought to cause human disease by forming stable protein aggregates. We compared the time course of structural changes monitored by thioflavin T (ThT) binding fluorescence and atomic force microscopy (AFM) for Ure2 and a series of prion domain mutants. AFM height images at successive time points during a single growth experiment showed the sequential appearance of at least four fibril types that could be readily differentiated by height, morphology and/or time of appearance. N-terminal deletion mutants showed an increased lag time, demonstrating that the intact N-terminal domain is required for efficient amyloid nucleation, consistent with its importance in prion formation in vivo. Further, the results show that Ure2 amyloid formation is a multistep process via a series of fibrillar intermediates. The C-terminal domain of Ure2 has homology to glutathione transferases (GSTs), but lacks typical GST activity. A recent study found that deletion of the Ure2 gene causes increased sensitivity to oxidants, while prion strains show normal sensitivity. Using steady-state kinetic methods, we succeeded in demonstrating glutathione-dependent peroxidase activity for Ure2, using a variety of substrates. The mutant 90Ure2, which lacks the unstructured N-terminal prion domain, showed kinetic parameters identical to WT, indicating that the prion domain does not contribute to the enzyme activity of Ure2. Interestingly, fibrillar aggregates showed the same level of activity as soluble protein, consistent with normal sensitivity towards oxidants of prion yeast strains. Demonstration that protection against oxidant toxicity is an inherent property of both native and amyloid forms of the Ure2 protein represents important progress in elucidation of its role in vivo. Further, establishment of an in vitro activity assay provides a valuable tool for the study of structure-function relationships of the Ure2 protein as both a prion and an enzyme.

Selected Publications 1． Jiang, Y., Li, H., Zhu, L., Zhou, J.M.* & Perrett, S.* Amyloid nucleation and hierarchical assembly of Ure2p fibrils: Role of Asn/Gln repeat and non-repeat regions of the prion domain. J. Biol. Chem. 279, 3361-3369, (2004) 2． Bai, M., Zhou, J.M.* & Perrett, S.* The yeast prion protein Ure2 shows glutathione peroxidase activity in both native and fibrillar forms. J. Biol. Chem. 279, 50025-50030, (2004) 3． Liu C.P., Perrett, S. & Zhou, J.M.* Dimeric trigger factor stably binds folding-competent intermediates and cooperates with the DnaK-DnaJ-GrpE chaperone system to allow refolding. J. Biol. Chem. (2005)in press.

41 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名柯莎

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ □ √ □ □ □

研究方向蛋白质错误折叠与疾病本年度工作简介在 2004 年度完成的工作主要有两方面： 1) Ure2 淀粉样纤维的成核以及分步组装酵母 Ure2 蛋白在体内和体外均易形成淀粉样纤维，其富含天冬酰胺和谷氨酰胺重复序列的 N 端（1-89）与 prion 性质密切相关。N 端的 15-42 位残基是夹在两段重复序列中的随机序列，相对疏水，在种间高度保守。我们以 ThT 结合荧光和原子力显微镜监测了 Ure2 及其 prion 结构域不同程度缺失的突变体在不同条件下淀粉样纤维形成过程。发现有原子力显微镜图象高度分别为 5、8、12、9 纳米、不同形态的纤维在 ThT 所追踪的平台期的不同时段出现。由原子力显微镜图象的高度还确认出 Ure2 的双体和寡聚体的存在。突变体 15Ure2 和 15–42Ure2 的纤维化也与野生型 Ure2 同样经由多个不同的纤维形态，但是与野生型相比它们与 ThT 结合荧光的延迟期更长， 15–42Ure2 与 ThT 的结合较弱。我们的工作表明该保守区对于淀粉样纤维形成的成核过程以及与 ThT 的结合过程都有重要作用，并且 Ure2 蛋白及其 N 端突变体的淀粉样化遵循经由多个纤维状中间体的分步组装机制。 2)酵母 prion 蛋白 Ure2 的谷胱甘肽过氧化物酶活性 Ure2 是酵母 prion [URE3]的前体蛋白形式，它与谷胱甘肽转硫酶（GST）具有同源性，却并不表现 GST 活性。最近有研究表明，缺失 Ure2 基因的酵母突变株表现出对重金属离子和氧化剂的敏感性增加，并推测 Ure2 可能具有潜在的谷胱甘肽过氧化物酶（GPx）活性。为了证明这种抗氧化剂毒性的保护作用是 Ure2 及

其 prion 形式的内在性质，我们分别以 CHP，H2O2，t-BH 为过氧化物底物，采用稳态动力学方法对 Ure2 的 GPx 活性进行了测定。其最适 pH 和最适温度分别为 pH 8 和 40 ºC。在双倒数作图中表现为米氏酶特性，其双底物反应动力学遵循顺序机制，而不是乒乓机制。这一点与 Ure2 归属于 GST 家族是一致的。缺失 N 端无结构的 PrD 结构域的突变体 90Ure2 具有与野生型 Ure2 相同的动力学常数。纤维化的 Ure2 聚集体也表现出与可溶的 Ure2 同等水平的 GPx 活性。Ure2 的 GPx 活性的证实是阐明其体内功能的重要进展。此外，体外活性测定方法的建立也为 Ure2 作为既是 prion 又是酶的蛋白质的结构与功能关系的研究提供了有价值的工具。

本年度获奖情况

(1)江轶获得 2004 年中科院院长优秀奖, (2)柏鸣已具有获得 2004 年所长奖学金一等奖的资格。

42 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

2. Three-dimensional Structure and Function of Biomacromolecules Name Dong-cai Liang Position Professor, Member of CAS Research Topic Structural Genomics Summary of Research A. Research projects and progress: 1. Structural genomics on proteins from human and T. tengcongensis 1) The expression of 26 genes were analyzed in detail;14 recombinant proteins were purified and 10 kinds of crystals (including microcrystals) were obtained. 2) X-ray diffraction data for 7 crystals were collected on our in-house Cu-anode X-ray source, and on the Beamline BL-6B Experimental Station (PF, Tsukuba, Japan). 3) The crystal structures of 5 proteins were solved using the methods of MAD, SAD/SIRAS and MR. The structures are listed below: a) KD93: The crystal structure of KD93, was determined using the MAD method. b) Calmodulin: Calmodulin plays a key role in transducing Ca2+ signals to different physiological effects. The crystal structure of a potato calmodulin (PCM6), the first three-dimensional structure of a plant calmodulin, was solved by the MR method. c) Insulin-like growth factor 1: The crystal structure of mini-IGF-1(2) was solved by the SAD/SIRAS method using our in-house X-ray source. d) Other unpublished results: The crystal structures of U123 and the C domain of U268 have just been solved. 2. Structural genomics on proteins in a two-component regulatory system Some proteins in a two-component regulatory system were chosen carefully as the targets of the structural genomics and structural biology project. B. Faculty and graduate students: Our group currently has three research faculty, one post-doctoral fellow and six graduate students. Two students were conferred with the Ph. D degree in 2004. C. Funds: Our work was supported by National Natural Science Foundation of China; 973 Project; 863 Program and CAS Major Innovation Program. Selected Publications Three papers were published in 2004. They are: 1. Jun-Feng Liu, Xin-Quan Wang, Zhan-Xin Wang, Jian-Rong Chen, Tao Jiang, Xiao-Min An, Wen-Rui Chang, Dong-Cai Liang*. Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells. Journal of Structural Biology 148, 370–374 (2004). 2. Cai-Hong Yun, Yue-Hua Tang, You-Min Feng, Xiao-Min An, Wen-Rui Chang, Dong-Cai Liang*. 1.42 A crystal structure of mini-IGF-1(2): an analysis of the disul.deisomerization property and receptor binding property of IGF-1 based on the three-dimensional structure. Biochemical and Biophysical Research Communications 326, 52–59 (2004). 3. Yun, C.H., Bai, J., Sun, D.Y., Cui, D.F., Chang, W.R., and Liang, D.C.* Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin. Acta Crystallogr. D. Biol. Crystallogr. 60 , 1214-1219 (2004).

43 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

2. 生物大分子三维结构和功能

姓名梁栋材

院士研究员副研究员长江学者百人计划国家杰出青年职称 √ √ □ □ □ □

研究方向结构基因组学研究本年度工作简介一、研究工作 1、人源及嗜热菌结构基因组方面： (1) 重点分析了 26 个基因的重组表达，纯化了 14 种重组蛋白，获得了 10 种蛋白的晶体(包括微晶)。 (2) 在本实验室铜靶光源，Mar-345 IP记录仪及在日本筑波 PF 光子工厂的 BL6B 光源上收集了 7 种晶体的衍射数据。 (3) 分别用多波长反常散射（MAD）、单波长反常散射SAD/SIRAS 方法和 MR 方法解析了 5 种蛋白质的晶体结构。解析的结构分别为： (a)KD93: KD93属于一个结构和功能未知的蛋白质家族。利用多波长反常散射技术(MAD)解析了这个蛋白质 1.9-Å 分辨率的晶体结构( J.S.B. 148 (2004) 370–374 ) (b)钙调素：钙调素直接或间接地参与了细胞内大多数重要的信号传导途径，我们用分子置换法解析了土豆钙调素 PCM6 的晶体结构( Acta Crys. D.. 60 (2004), 1214-1219 )。 (c)类胰岛素生长因子-1：我们用基于实验室光源的SAD/SIRAS 方法解析了 mini-IGF-1 (2)的晶体结构( B. B. R. C. 326 (2004) 52–59 )。 (d) U123 和 U268 C-结构域的结构解析工作刚刚完成。 2、开展 ”双因子调控系统” 的结构基因组研究。经过调研，选择一批有重要功能的双因子调控基因进行结构基因组和结构生物学研究。二、人员情况及人才培养：在职人员 3 名，博士后 1 名。2004 年毕业博士生 2 名，在读研究生 6 名。三、参加下列研究项目并从中获得研究经费：国家自然科学基金委青年基金 ( 项目编号 30200046)；重点项目 ( 项目编号 3130080 )；中科院创新工程重大项目 ( 项目编号 KSCX1-SW-17 )； “973” 项目(项目编号 2002CB713801 ) 和 “863” 项目 ( 项目编号 2002BA711A13) 本年度获奖情况

<藻类光合作用捕光蛋白－色素复合物的三维结构与功能研究> 2003 年度北京市科学技术奖一等奖(第四获奖人)

44 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Zihe Rao Position Professor, Member of CAS Research Topic Human disease related protein structure, function and drug design Summary of Research In 2004, Prof. Rao’s research group made good progress: we determined 26 three-dimensional protein structures; 26 papers were published in international SCI journals. Three patents were applied for. Our main achievements are as follows: 1. We analyzed two mutually overlapping fragments of FKBP52 (N (1-260) and C (145-459)) as well as the complex structure with the C-terminal pentapeptide from Hsp90. Based on the structures of the two overlapping fragments, the complete putative structure of FKBP52 can be defined. 2. Through analysis of the structure of the PTB domain of Dok1 and its complex with a phosphopeptide derived from RET receptor tyrosine kinase, we revealed the molecular basis for the specific recognition of RET by the Dok1 PTB domain. 3. We have determined the crystal structure of Pirin. The structure provides evidence that Pirin requires the participation of the metal ion for its interaction with Bcl-3 to co-regulate the NF-κB transcription pathway and the interaction with NFI in DNA replication. 4. We used the SARS Mpro structure, which we successfully determined in 2003, to design a series of inhibitors that are effective against four kinds of coronavirus, and analyzed the structures of the SARS Mpro and the porcine transmissible gastroenteritis virus (TGEV) Mpro in complex with these inhibitors. We have also analyzed the crystal structures of the SARS-CoV and mouse hepatitis virus (MHV) spike (S) protein fusion cores and proposed a conserved mechanism of membrane fusion involving the spike protein. Last year we obtained a European Union Framework 6 grant to carry out the Sino-European Project on SARS Diagnostics and Antivirals (SEPSDA). 5. We are highly effective in the purification of membrane proteins and structure analysis, as well as in the exploration of new technical methods.

Selected Publications 1. Wu B, Li P, Liu Y, Lou Z, Ding Y, Shu C, Ye S, Bartlam M, Shen B & Rao Z*. 3D structure of human FK506-binding protein 52: implications for the assembly of the glucocorticoid receptor/Hsp90/immunophilin heterocomplex. Proc. Natl. Acad. Sci. USA, 101(22): 8348-8353, (2004). 2. Bartlam M, Wang G, Yang H, Gao R, Zhao X, Xie G, Cao S, Feng Y & Rao Z*. Crystal Structure of an Acylpeptide Hydrolase/Esterase from Aeropyrum pernix K1. Structure, 12(8): 1481-1488, (2004). 3. Pang H, Bartlam M, Zeng Q, Miyatake H, Hisano T, Miki K, Wong LL, Gao GF & Rao Z*. Crystal Structure of Human Pirin: AN IRON-BINDING NUCLEAR PROTEIN AND TRANSCRIPTION COFACTOR. J. Biol. Chem., 279(2): 1491-1498, (2004). 4. Shi N, Ye S, Bartlam M, Yang M, Wu J, Liu Y, Sun F, Han X, Peng X, Qiang B, Yuan J* & Rao Z*. Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain. J. Biol. Chem., 279(6): 4962-4969, (2004). 5. Xu Y, Lou Z, Liu Y, Pang H, Tien P, Gao G.F & Rao Z*. Crystal structure of SARS-CoV spike protein fusion core. J. Biol. Chem., 279(47): 49414-49419, (2004).

45 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名饶子和

院士研究员副研究员长江学者百人计划国家杰出青年职称 √ √ □ □ □ □

研究方向与人类重大疾病相关的蛋白质结构、功能及药物设计本年度工作简介饶子和院士研究组包括了他在清华大学和中科院生物物理所的两个课题组， 2004 年科研进展顺利：共解析蛋白质三维结构 26 个，提交给国际蛋白质数据库（PDB）数据 17 个蛋白质结构信息；在国外发表 SGI 论文 26 篇，其中包括 Proc. Natl. Acad. Sci. USA 一篇、J. Biol. Chem.四篇、Structure 一篇、Biochemistry 两篇、Biophysical J.一篇。申请专利 3 项。毕业博士研究生 2 人；毕业硕士研究生 1 人；博士后出站 1 人。主要研究成果如下： 1、解析了 FKBP52 的两个相互交叠片段（N(1-260)和 C(145-459)）以及与 Hsp90 C 末端五肽复合物的晶体结构，基于这两个相互交叠结构域的结构，拼接得到 FKBP52 蛋白质全长的三维结构并推测了人 FKBP52 蛋白质的三维结构—— 糖皮质激素受体 Hsp90 免疫亲和素复合物结合模式。 2、通过解析 Dok1 PTB 结构域以及它与源自 RET 受体酪氨酸激酶的磷酸化多肽复合物的晶体结构，揭示出 Dok1 PTB 结构域对 RET 特异性识别的分子基础，并发现 Dok1 不识别源自 TrkA 和 IL-4 的多肽序列，可分别被 Shc 和 IRS1 识别。 3、解析了人 Pirin 晶体结构，这是一个可与 B 淋巴细胞癌基因编码的原癌蛋（Bcl-3）和核因子 I（NFI）反应的核蛋白。功能研究显示，Pirin 需要金属离子的参与同 Bcl-3 反应来共同调控 NF-κB 转录通路和在 DNA 复制过程中与 NFI 相互作用，因此由重金属的离子置换可建立起金属离子直接影响基因转录的一种新通路。 4、继去年成功解析了 SARS 冠状病毒主要蛋白酶（3CLpro）及其复合物的三维结构后，利用 SARS 冠状病毒主蛋白酶的晶体结构设计了一系列针对四种冠状病毒都有效的抑制剂；解析了 SARS 的主蛋白酶、猪的肠胃炎病毒主蛋白酶和上述抑制剂的晶体结构。还解析出 SARS-CoV S 蛋白融合核心的晶体结构，并以融合蛋白（S）为研究对象，解析出小鼠肝炎病毒（MHV）S 蛋白融合核心的晶体结构，提出 Spike 蛋白介导冠状病毒膜融合的分子机制。目前，我们与国内及欧洲的科学家们合作，共同获得了第六欧盟框架基金的支持，开展 SARS 诊断及治疗的中—欧合作计划(SEPSDA)。 5、今年研究组最大的亮点是膜蛋白研究方面的进展，我们在膜蛋白的高效、纯化、结构解析以及新技术方法的探索方面取得突破性的进展，为 2005 年成果的诞生奠定了坚实的基础。本年度获奖情况饶子和院士被评选为 2004 年国家重点基础研究发展计划（973 计划）先进个人

46 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Wenrui Chang Position Professor Research Topic 3D-Structure and function of photosynthesis membrane proteins Summary of Research

1. The first X-ray structure of LHC-II in icosahedral proteoliposome assembly at atomic detail was solved. One asymmetric unit of a large R32 unit cell contains ten LHC-II monomers. The 14 chlorophylls (Chl) in each monomer can be unambiguously distinguished as eight Chla and six Chlb molecules. Assignment of the orientation of the transition dipole moment of each chlorophyll has been achieved. All Chlb are located around the interface between adjacent monomers, and together with Chla they are the basis for efficient light harvesting. Four carotenoid-binding sites per monomer have been observed. The xanthophyll-cycle carotenoid at the monomer–monomer interface may be involved in the non-radiative dissipation of excessive energy, one of the photoprotective strategies that have evolved in plants. 2. The structures of some enzymes have also been solved and the results were published: the pH-profile structure of C-terminal despentapeptide nitrite reductase; the structure of potato calmodulin PCM6; the crystal structure of KD93 and the crystal structure of EFEa and its complex.

Selected Publications

1. Zhenfeng Liu, Hanchi Yan, Kebin Wang, Tingyun Kuang, Jiping Zhang, Lulu Gui, Xiaomin An & Wenrui Chang*. Crystal structure of spinach major light-harvesting complex at 2.72 Å resolution. Nature Vol 428, 287-292, (2004). 2. Wang F, Wang C, Li M, Gui LL, Zhang JP, Chang WR*. Crystallization and preliminary crystallographic analysis of earthworm fibrinolytic enzyme component B from Eisenia fetida. Acta Cryst. D 60, 933-935, (2004). 3. Hai-Tao Li, Chao Wang, Tschining Chang, Wen-Chang Chang, Ming-yih Liu, Jean Le Gall, Lu-Lu Gui, Ji-Ping Zhang, Xiao-Min An, Wen-Rui Chang*. pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes. BBRC 316, 107-113, (2004). 4. Chao Wang, Feng Wang, Mei Li, Yong Tang, Ji-Ping Zhang, Lu-Lu Gui, Xiao-Min An, Wen-Rui Chang*. Structural basis for broad substrate specificity of earthworm brinolytic enzyme component A. BBRC 325, 877-882, (2004).

47 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名常文瑞

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向光合膜蛋白的三维结构与功能研究本年度工作简介

1. 第一个以正二十面体蛋白脂质体形式堆积的高等植物主要捕光复合物 (LHC-II)的原子水平的晶体结构被解析。在该晶体的超大 R32 晶胞的一个不对称单位中含有 10 个 LHC-II 单体,每个单体内的 14 个叶绿素分子可以准确无误地确定为 8 个叶绿素a和6个叶绿素b,每个叶绿素分子的过渡偶极距方位均可确定。6 个叶绿素 b 分布在单体之间的界面上,与叶绿素 a 一起形成高效吸收光能的基础。每个单体的 4 个类胡罗卜素分子也被确定,一个参与叶黄素循环的类胡罗卜素分子位于单体之间的介面上,可能参与了植物在髙光照条件下过多激发能的非幅射耗散从而实现光保护的机制。

2. 一些重要功能酶的三维结构也被解析,其结果也己在不同学术刊物上发表：如去羧端 5 肤的亚硝酸还原酶的不同 pH 条件的晶体结构, 土豆植物钙调素 PCM6 的晶体结构,KD93 的晶体结构以及蚓激酶 EFEa 的高分辫率修正及其复合物的晶体结构等。

本年度获奖情况

1. “我国科学家破解膜蛋白晶体结构难题”入选“两院院士评选振邦杯 2004 年中国十大科技进展新闻” 2. 国家重点基础研究发展计划（973 计划）先进个人 3. 国家重点实验室计划先进个人 4. 何梁何利基金“科学与技术进步奖” 5. 2003 年度北京市科学技术奖一等奖

48 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Weimin Gong Position Professor Research Topic Structural Biology Summary of Research Bisphosphoglycerate mutase is a trifunctional enzyme of which the main function is to synthesize 2,3-bisphosphoglycerate, the allosteric effector of hemoglobin. Protein crystals were obtained and diffract to 2.5 Å, producing the first crystal structure of bisphosphoglycerate mutase. The enzyme remains a dimer in the crystal. The conformational changes in the backbone and the side chains of some residues reveal the structural basis for the different activities between phosphoglycerate mutase and bisphosphoglycerate mutase. The bisphosphoglycerate mutase-specific residue Gly-14 may cause the most important conformational changes, which makes the side chain of Glu-13 orient toward the active site. The positions of Glu-13 and Phe-22 prevent 2,3-bisphosphoglycerate from binding in the way proposed previously. In addition, the side chain of Glu-13 would affect the Glu-89 protonation ability responsible for the low mutase activity. Other structural variations, which could be connected with functional differences, were also examined. eIF3k, the smallest subunit of eukaryotic initiation factor 3 (eIF3), interacts with several other subunits of eIF3 and the 40 S ribosomal subunit. eIF3k is conserved among high eukaryotes and may play a unique regulatory role in higher organisms. We reported the crystal structure of human eIF3k, the first high-resolution structure of an eIF3 component. This novel structure contains two distinct domains, a HEAT repeat-like domain and a winged-helix-like domain. Through structural comparison and sequence conservation analysis, we show that eIF3k has three putative protein-binding surfaces and has potential RNA binding activity.

Selected Publications

1. L Liu, Z Wei, Y Wang, M Wan, Z Cheng & W Gong*. Crystal Structure of Human Coactosin-like Protein. J. Mol. Biol. 344: 317-323, (2004). 2. Y Wang, Z Wei, Q Bian, Z Cheng, M Wan, L Liu & W Gong*. Crystal Structure of Human Bisphosphoglycerate Mutase. J. Biol. Chem. 279(37): 39132-8, (2004) 3. Z Wei, P Zhang, Z Zhou, Z Cheng, M Wan, & W Gong*. Crystal Structure of Human eIF3k, the first structure of eIF3 subunits. J. Biol. Chem. 279(33): 34983-34990, (2004) 4. Z Zhou, X Song, Y Li & W Gong*. Unique Structural Characteristics of Peptide Deformylase from Pathogenic Bacterium Leptospira interrogans. J. Mol. Biol. 339(1): 207-215, (2004).

49 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名龚为民

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ √ √

研究方向结构生物学本年度工作简介本年度我们实验室在人类重要蛋白质、抗菌药物设计靶蛋白和植物防御蛋白等研究方面取得重要进展，根据这些蛋白的晶体结构和功能分析，共发表研究论文 9 篇，其中影响因子大于 5 的论文 4 篇，总影响因子 35。其中主要的研究结果如下。二磷酸甘油酸变位酶（BPGM）是一种三功能酶，其主要功能是合成血红蛋白的别构效应因子 2,3－BPG。从人脑 CDNA 文库中扩增出人二磷酸甘油酸变位酶基因并在大肠杆菌中表达，并测得 BPGM 的第一个晶体结构。人 BPGM 在晶体结构中以二体形式存在。BPGM 一些残基的主链与侧链的构象变化是构成 BPGM 与 dPGM 不同活性的结构基础。BPGM 特异性残基 Gly14 是诱导构象发生变化的重要因素，它使 Glu13 的侧链伸入活性中心，影响 Glu89 质子化，导致 BPGM 相对较低的变位酶活性。和 dPGM 相比，BPGM 中 Glu13 和 Phe22 的独特位置使催化残基 His11 附近的空间变小，不利于变位酶活性所要求的 2,3-BPG 中间体的转动，这可能是导致 BPGM 相对较低的变位酶活性的另一原因。 eIF3k 是真核翻译起始因子 3（eIF3）最小的亚基，它可以与 eIF3 的多个其他的亚基以及 40S 核糖体亚基相互作用。eIF3k 在高等真核生物（包括哺乳动物、昆虫和植物）中相当保守，在人体各器官中也普遍存在；但其却不存在于低等真核生物酵母的一些种类中。这说明 eIF3k 可能在高等生物中扮演着一个独特的角色。在这篇文章中，我们报道了 eIF3 第一个高分辨率的亚基结构，人类 eIF3k 亚基的晶体结构。此新型结构由两个不同的结构域（HAM 结构域和 WH 结构域）组成。蛋白质结构比较和氨基酸序列同源性分析表明，eIF3k 有 3 个可能的蛋白质结合表面，并且 eIF3k 可能有 RNA 结合活性。对 eIF3k 结构的解析和分析，为进一步了解 eIF3 复合物的结构和功能提供了关键信息。

本年度获奖情况

1）国务院政府特殊津贴； 2）新世纪百千万人才国家级人选

50 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Tao Jiang Position Professor Research Topic Crystal structure and functional study of biomacromolecules Summary of Research 1. To understand the processes involved in the catalytic mechanism of pyridoxal kinase (PLK), we determined the crystal structures of PLK.AMP-PCP-pyridoxamine, PLK.ADP.PLP, and PLK.ADP complexes. Comparison of these structures revealed that PLK exhibits different conformations during its catalytic process. After the binding of AMP-PCP (an analogue that replaces ATP) and pyridoxamine to PLK, this enzyme retains a conformation similar to that of the PLK.ATP complex. The distance between the reacting groups of the two substrates is 5.8 A, indicating that the position of ATP is not favorable for spontaneous transfer of its phosphate group. However, the structure of the PLK.ADP.PLP complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands at the active site. Therefore, it appears that after binding of both substrates, the enzyme-substrate complex requires changes in the protein structure to enable the transfer of the phosphate group from ATP to vitamin B(6). Furthermore, a conformation of the enzyme-substrate complex before the transition state of the enzymatic reaction was also hypothesized.

2. (R)-roscovitine is a selective inhibitor of Cyclin-dependent kinases (CDKs). Recent biochemical investigations have shown that (R)-roscovitine interacts with PLK selectively. We determined the crystal structure of PLK in complex with (R)-roscovitine. Structural analysis revealed that roscovitines bind in the pyridoxal binding site, rather than in the anticipated ATP-binding site. This affords a better understanding of the catalysis mechanism of PLK and could aid in the design of roscovitine derivatives displaying strict selectivity for either PLK or CDKs.

Selected Publications 1. Li MH, Kwok F, Chang WR, Liu SQ, Lo SC, Zhang JP, Jiang T*, Liang DC. Conformational changes in the reaction of pyridoxal kinase. J. Biol. Chem. 279 (17), 17459-65 (2004).

2. Liu JF, Wang XQ, Wang ZX, Chen JR, Jiang T, An XM, Chang WR, Liang DC*. Crystal structure of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells. J. Struct. Biol. 148(3), 370-4 (2004).

51 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名江涛

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向生物大分子晶体结构与功能研究本年度工作简介 1. 为了阐明吡哆醛激酶的催化反应过程，我们解析了 PLK -AMP-PCP- pyridoxamine、PLK-ADP-PLP 和 PLK-ADP 三种复合物的结构，结构比较表明吡哆醛激酶在催化过程中有不同的构象。结合 AMP-PCP 和 Pyridoxamine 后，酶的构象和复合物 PLK-ATP 的构象相似，两种底物的反应基因之间的距离为 5.8Å，表明 ATP 的位置不利于其磷酸基因的转移，然而在复合物 PLK-ADP-PLP 中，酶本身以及结合位点都发生很大的构象变化。因此，在结合了两种底物后，酶的构象改变以利于磷酸基团从 ATP 转移到 VB6。此外，文中提出了转移反应之前酶和两种底物相互作用模型（pre-reaction state model）。

2. (R)-roscovitine 是细胞周期依赖激酶的选择性抑制剂，最近的生物学研究表明， (R)-roscovitine 可以和 PLK 选择性的结合，我们解析了 PLK 和(R)-roscovitine 复合物的晶体结构，结构分析表明 roscovitine 结合在 PLK 的吡哆醛结合位点，而不是我们预先推测的 ATP 结合位点，这有助于我们了解 PLK 的催化机理，并且能够帮助我们设计对 PLK 或 CDK 更具有选择性的 roscovitine 的衍生物。

本年度获奖情况

52 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Liang Wei Position Associate Professor Research Topic Targeting delivery system of bio-macromolecular drug Summary of Research Permeation peptides, cell penetrating peptides (CCPs), or protein transduction domains (PTDs), including the Tat-peptide basic domain, have been intensely studied recently after early observations demonstrated rapid translocation properties, seemingly independent of receptor-mediated endocytosis, into various cell types. The ability of permeation peptides to cross cell membranes is specially promising for drug delivery, since one major barrier to successful therapies and imaging is the need for membrane translocation. A variety of multicationic oligomers, including arginine-rich peptides, as simple as 7-11 consecutive arginines are known to be more effective. Cargoes ranging in size from metal chelates, fluorescent dyes and proteins to iron oxide nanoparticles and liposomes can be delivered into cells, although the detailed mechanisms and subcellular localizations remain poorly understood and may differ, depending on cargo size, cell type, CPP sequence, and other experimental variables. We are attempting to develop a new strategy for siRNA delivery into cells using arginine octamer peptides (R8) attached to the PEG-liposome surface (R8-liposomes). One assumes that liposomes formulated using a charge neutral ratio of DOTAP/siRNA, adding 3% mol PEG-DSPE, post-inserting 0.5-1% mol R8-PEG-PE on the outer membrane of liposomes will provide an effective transfection system in vitro or in vivo. In this case, siRNA containing R8-liposomes should be nontoxic, and prevent aggregation and decrease adsorption of serum proteins and interaction with non-target cells. The presence of R8 increases the uptake capacity of siRNA into cells and subsequent accumulation in the cytoplasm compartment and enhances siRNA functions. We have examined cellular uptake and distribution of Rh-PE labeled liposomes with and without R8 attached by fluorescence microscopy. We have also compared transfection efficiency by using siRNA containing R8-liposomes and lipofectamine 2000-siRNA complexes in the presence of serum proteins or in their absence. Finally, we are testing the toxicity of siRNA containing R8-liposomes and siRNA-free R8-liposomes and the biologic activity of siRNA using RT-PCR and western blotting assay. The results provide new insights into the potential applications of R8-liposomes for delivery of siRNA.（In preparation for publication.）

Selected Publications

1. LIANG Wei*, DAVALIAN Dariush, TORCHILIN Vladimir P. The interaction of a novel peptoid enhancer ⎯ oligomer of arginine with bovine submaxillary mucin. Acta Pharm Sinica. 2004, 39(12): 1011-1017. 2. LIANG Wei*, Wang Ya-Qin, DAVALIAN Dariush. A Novel HIV-1 Therapeutic Target: Tat transactivator Protein. Prog. Biochem. Biophys. 2004, 31(9): 772-776. 3. LIANG Wei*, Wang Ya-Qin, LIU Xing-Jun. Targeting intervention for tumor therapy. Chin J Inetrv Imaging Ther. 2004, 1(1): 31-36.

53 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名梁伟

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ □ √ □ □ □

研究方向生物大分子药物的定向输送系统和药物作用靶标的筛选本年度工作简介实验室组建已基本完成，部分研究工作已开展。根据本实验室研究工作的需要及符合我所将来发展的要求，我们建立了蛋白质与多肽的定位修饰技术；适合生物大分子药物输送的自组装纳米制备技术；检验和鉴定生物大分子药物功能的分子生物学和细胞生物学评价技术。已完成和正在进行的研究工作有：

1、基于 HIV-1 病毒 TAT 蛋白碱性氨基酸区域的 TAT49-57 的寡肽是一段核定位信

号肽且具有不依赖内吞机制迅速穿透生物膜的功能，TAT49-57 这一特点尤其适合作

为核酸类物质的胞内输送的载体。在 TAT49-57 寡肽的基础上，我们筛选出了比其穿膜能力更强的由 8-12 个精氨酸组成的寡聚体。构建了八聚精氨酸联接的 PEG 化磷脂自组装胶束并实现了将其定量地插入到包载 hmd2 siRNA 的长循环脂质体的脂双层的外层膜上，三种不同肺癌细胞株体外转染试验显示其转染效率显著高于目前广泛使用的基因转染试剂 Lipofectamine 2000，且毒性明显低于 Lipofectamine 2000, 对 Lipofectamine 2000 转染无效的肺鳞癌成功地实现了靶基因的沉默和相关基因 P53 的高表达。 2、基于 PEG 化磷脂自组装胶束的前列腺素 E1 制剂已申请国家发明专利且通过初审（申请号：200410057147.0），其药动学和药效学试验正在进行中。 3、检定出特异性识别肺肿瘤细胞的肽类配基的序列；稳定的抗肿瘤药物高包载量的 PEG 化磷脂纳米胶束的筛选工作已完成；细胞内药物含量的测定方法已建立；原位肺癌动物模型的建立正在预试中。

本年度获奖情况

54 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

3. Molecular Membrane Biology Name FuyuYang Position Professor, Member of CAS Research Topic A novel member from lysosome-Chymotrysinogen B is involved in Apoptosis Summary of Research

A protease which can convert Bid into its active form (t Bid) inducing cytochrome c release through mitochondrial outer membrane has been isolated and purified from rat liver lysosomes. Peptide mass fingerprinting and biochemical analysis identified this protease as Chymotrypsin B (Ctr b), a robust and stable serine endopeptidase previously known as a digestive enzyme with expression restricted to the pancreas. Our results clearly demonstrate that intracellular Ctr b is lysosomally localized and it is conceivable that it can be leaked into the cytosol as a pro-apoptotic molecule.

Selected Publications

1 Yongfang Zhao,Xiaoxuan Fan, FuyuYang* and Xujia Zhang* Gangliosides modulate the activity of the plasma membrane Ca2+-ATPase from porcine brain synaptosomes. Arch. Biochem. Biophysics 427, 204-212, (2004).

2 Xiaoping Wang, Xuehai Han and Fuyu Yang* Critical segment of apocytochrome c for its insertion into membrane. Mol. Cell. Biochem. 262, 61-69, (2004).

55 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

3. 膜分子生物学

姓名杨福愉

院士研究员副研究员长江学者百人计划国家杰出青年职称 √ √ □ □ □ □

研究方向生物膜的结构与功能本年度工作简介

一、与张旭家博士等合作研究神经节苷脂、脂筏（lipid rafts）对细胞质膜、肌浆网膜 Ca2+-ATP 酶构象与活性的影响（详见张旭家的报告）二、溶酶体－线粒体途径诱发细胞凋亡的研究在研究 Bid 诱发线粒体通过外膜释放细胞色素 c（Cyt.c）过程中发现溶酶体含有多种蛋白酶能酶介 Bid→tBid 从而使 Cyt.c 从线粒体中释放并引起凋亡。我们经长期研究从大鼠肝溶酶体中分离纯化一种蛋白因子，称

之为 LBCP（Lysosomal Bid Cleavage Protease）。通过 LC-MS/MS 分析、酶切位点、生化特点等测定，初步确定 LBCP 为 Chymotrypsinogen B。这一结果进一步结合 Bioinformatics 并用 RT－PCR 等方法得到了验证。 Chymotrypsinogen 一般都认为仅分布于胰脏。我们从大鼠肝溶酶体中发现它的存在，经活化后它能酶切 Bid－tBid 并能使线粒体外膜的透性发生改变释出 Cyt c. 诱发凋亡。迄今国内外未见类似报道。

本年度获奖情况

56 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Tao Xu Position Professor Research Topic The Molecular Mechanism of Membrane Trafficking Summary of Research We have made progress in the following four aspects: 1) A new pathway of exocytosis regulation. We have determined that PKC could increase the sensitivity of regulated exocytosis, which is the first evidence that Ca2+-sensing of secretion could be regulated by phosphorylation. By using kinetic model to analyze the effects of PKC on the exocytosis dynamics, we concluded that PKC increased the exocytosis sensitivity by reducing the Ca2+ binding sites on the sensor protein without changing other kinetics parameters. The reduction of the Ca2+ binding site reduced the threshold of the Ca2+ need for secretion, and increased the fusion probability of vesicles far from the voltage gated calcium channel. 2) The investigation on the exocytosis of secretory lysosome The anti-infection, anti-virus, anti-tumor and anti-transplant effects of Natural killer cells (NK cells) depend on the exocytosis of “secretory lysosome”. We find that mass secretory lysosmes are produced in NK cells after target cell recognition. PKC but not Golgi apparatus is found to be involved during this process. 3) The development of detection method of single vesicle activities in live cells The study of vesicle transport and trafficking within cells is a hot topic. Previous researches were mainly focused on monitoring two-dimensional movement of vesicle within live cells. We have combined three-dimensional deconvolution fluorescence microscopy technique and single particle trafficking technique, which enable us to monitorl movements of single vesicle within PC-12 cells. 4） The dynamics of single GLUT4 vesicle in live cells GLUT4 is critically important in the blood sugar homeostasis. Evidences prove the defect of GLUT4 transport is linked to type II diabetes. The molecular mechanism by which GLUT4 storage vesicle (GSV) synthesizes and cycles is not clear. We have specifically labeled GSVs with green fluorescent protein. Using total internal reflection fluorescence microscopy, we have monitored the movements of GSV within the live cell and studied the characteristics of those movements. This result provides the basis for further investigation of the molecular mechanism of GSV movement.ther investigation of the molecular mechanism of GSV movement. Selected Publications [1]Hua Yang, Huisheng Liu, Zhitao Hu, Hongliang Zhu, and Tao Xu*. PKC-induced sensitization of Ca2+-dependent exocytosis is mediated by reducing the Ca2+-cooperativity in pituitary gonadotropes. Journal of General Physiology. (Accepted) [2]Dongfang Liu, Liang Xu, Fan Yang, Dongdong Li, Feili Gong, and Tao Xu*. Rapid biog enesis and sensitization of secretory lysosomes in NK cells mediated by target-cell recognition. PNAS. (In Press) [3]Qun-Fang Wan, Yongming Dong, Hua Yang, Xuelin Lou, Jiuping Ding, Tao Xu*. Protein Kinase Activation Increases Insulin Secretion by Sensitizing the Secretory Machinery to Ca2+. Journal of General Physiology. Vol.124:1-11. (2004) [4]Chen Hong LI, Li BAI, Dong Dong LI, Sheng XIA, Tao XU*. (2004) Dynamic tracking and Mobility analysis of single GLUT4 storage Vesicle in live 3T3-L1 Cells. Cell Research. (In Press) [5]Xia S, Xu L, Bai L, Xu ZQ, Xu T*. Labeling and dynamic imaging of synaptic vesicle-like microvesicles in PC12 cells using TIRFM. Brain Research. Vol.997(2):159-64. (2004) [6]DD Li, J Xiong, AL Qu, and T Xu*. Three-dimensional tracking of single secretory granules in live PC12 cells. Biophysical Journal. Vol.87(9):1991-2001. (2004)

57 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名徐涛

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ √ √ √

研究方向膜转运的分子机制本年度工作简介我们主要在以下四个方向取得了具有代表性的成果。 1) 发现了一条新的调控分泌的机制我们发现 PKC 可以显著增强分泌对钙离子的敏感性，从而首次证明了分泌的钙离子传感可被蛋白磷酸化所调控。为了进一步揭示蛋白磷酸化调节钙离子传感器的内在机理，我们利用动力学模型拟合，分析 PKC 对钙触发分泌的动力学特性的影响。我们发现 PKC 减少钙离子传感器上的钙离子结合位点，从而增强分泌对钙的敏感性；但动力学参数并没有显著的变化。钙离子结合步骤数目的减少意味着分泌所需钙离子的阀值的降低；同时距离钙离子通道的较远囊泡，分泌的可能性也提高了。该文章已被 JGP 接受。 2) 分泌型溶酶体分泌活动的调控机制研究自然杀伤细胞(Natural killer cells, NK)的抗感染，抗病毒，抗肿瘤以及移植排斥效应有赖于一种叫做"分泌型溶酶体"的分泌活动。我们发现 NK 细胞在杀伤靶细胞时需要大量重新生成分泌型溶酶体，其快速产生的过程不涉及高尔基体但需要 PKC 的参与。此工作已被 PNAS 接受，有关工作还在进一步研究和整理中。 3) 发展了活细胞单个囊泡活动的检测方法随着显微成像技术和活体细胞荧光标记技术的发展，直观观察和研究分泌囊泡的胞内转运过程已经成为目前细胞分泌研究的热点之一。但是国际上关于这方面的研究工作一直局限于分泌囊泡在细胞内二维平面内的运动，我们发展了三维荧光反卷积显微成像技术和单微粒跟踪技术成功地跟踪了 PC-12 细胞中单个分泌囊泡在全细胞范围内的三维运动过程并揭示了其运动规律，为以后深入阐明分泌囊泡转运过程中涉及的分子机制提供了技术基础。这一研究成果发表在 Biophys. J 上，同时配发了特约评论文章，对该工作给予好评。 4）活细胞中单个 GLUT4 囊泡动力学研究葡萄糖转运子 4(Glucose Transporter 4, GLUT4)在人体整体糖的平衡中起到了重要的作用，有越来越多的证据表明 II 型糖尿病与 GLUT4 的转运障碍有关。目前，储存 GLUT4 的囊泡(GLUT4 storage vesicles，GSV)的生成和循环途径及其分子机制尚不清楚。我们采用 EGFP 特异地标记了 GSV 并运用全内反射荧光显微技术（TIRFM）研究了 GSV 在活细胞内的动态运动及其规律。此研究结果已发表在 Cell Research 杂志上，为进一步揭示 GSV 运动的分子基础奠定了基础。本年度获奖情况

58 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name James Q. Yin Position Professor Research Topic RNAi and Functional Genomics Summary of Research SiRNA and miRNA can efficiently induce mRNA cleavage and/or translational repression at the posttranscriptional level in a sequence-specific manner. Recently, it has been demonstrated that these small RNAs guide genome modification in mammalian cells. However, their ability to direct cognate DNA methylation has been confirmed so far only in plants, and their function and mode of silencing are still elusive. We have reported that small RNAs derived from intron regions of the p53 gene (p53-sRNA) can target homologous DNA sequence in the promoter region of the heat shock protein 70.1 (hsp70.1) gene in both MCF7 and HeLa cells. Vector-based small RNA repressed expression of the hsp70.1 gene at the transcriptional level. Western blot analysis indicated that the expression of heat shock protein 70, a protein related to cell survival, was greatly reduced or completely inhibited owing to the promoter methylation of the hsp70.1 gene. These findings reveal that the expression of the p53 gene can regulate cell activities at both protein and RNA levels, suggesting that p53-sRNA may be a novel strategy for therapeutic gene silencing of tumor cells in human beings. Similarly, we also discovered several siRNAs from an intron of BRCA1 and their target mRNAs by using bioinformatics, and confirmed their existence in human cells with Northern blot analysis. Our results demonstrated that these siRNAs could regulate gene expression by different modes of action. In addition, my research group conducted some experiments concerning the development of red blood cells. The primary findings showed that there was a separation of apoptotic nuclei from survival cytoplasm. DNA microarray data showed that enzymes associated with cell apoptosis and survival display differential synthesis in pro-erythroblast and late-stage erythroblast cells. Moreover, we are documenting data concerning the effects of SMAD3-siRNA on liver fibrosis, and the inhibitory roles of hdm2-siRNA on lung cancer cells.

Selected Publications

1. Tan FL& Yin JQ*. RNAi, a new therapeutic strategy against viral infection. Cell Res. 14(6), 460-6 (2004). 2. Liu TG, Yin JQ*, Shang BY, Min Z, He HW, Jiang JM, Chen F, Zhen YS, Shao RG. Silencing of hdm2 oncogene by siRNA inhibits p53-dependent human breast cancer. Cancer Gene Ther. 11(11), 748-56 (2004). 3. Tan FL & Yin JQ*. RNAi, a new strategy for the treatment of cancers. Frontier Bioscience. 2005 in press.

59 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名殷勤伟

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ √ □

研究方向 RNAi 技术和功能基因组学本年度工作简介近年来,从植物到人类的细胞中发现了一类内源性的、长度约 22 个核苷酸的非编码 RNA,称为小 RNA。小RNA 可由内源性基因编码，位于编码基因间区或编码基因的内含子或外显子区,通过 RNA 聚合酶 II 而被转录,其前体含有冒状结构和多聚腺苷酸。它们在指导 mRNA 分子的转译抑制、降解断裂或其它形式的调节通路中发挥重要作用。目前已经知道小 RNA 可以发挥多种功能,如组织器官的定向发育、细胞生长分化的时空调节、信号通路的开启和关闭、细胞周期的监测与调控、学习与记忆、肿瘤的发生与凋亡、肥胖和衰老等。在 2004 年，我研究组采用生物信息学技术在 p53 和 BRCA1 基因的内含子中发现了具有调节功能的小 RNA 分子，经 RT-PCR 和 Western Blot证明这些小 RNA 分子能够以序列特异的方式沉默相应的靶基因。来源于 p53 基因内含子的小 RNA 能够诱导 Hsp70－1 基因操纵子的甲基化从而抑制 Hsp70－1 基因的表达。尽管寻找小 RNA 的靶基因是件非常困难的任务，但幸运的是BRCA1 内含子的小 RNA 却有许多靶基因。来源于BRCA1 基因内含子的小 RNA 能以不同的方式作用于靶基因从而调节那些基因的表达。这些小 RNA 分子亦能引起肿瘤细胞的行为和形态学的变化，进一步的深入而系统的研究在进行中。总之，根据其它实验室的研究结果和我们的发现，可以提出如下假说：单一的小 RNA 能有多个不同的靶基因。同样，多个不同的小 RNA 亦可与同一个 mRNA 分子相结合并调控其生物活性。随着编码基因的表达，从内含子和外显子剪切出的小 RNA 可以与其上下游的靶子 mRNA 的不同结构区域结合，从而指导转译抑制、切割降解或甲基化。小 RNA 的发现丰富了人们对蛋白质合成控制的认识，补充了在 RNA 水平对靶 mRNA 分子进行更迅速和有效的调节，展现了细胞内基因表达调控全方位多层次的网络系统。此外，我研究组还发现了红细胞核质凋亡分离的现象并在研究探讨可能的分子机制。我研究组也在研发 SMAD3－siRNA 对肝硬化的防治作用和 hdm－2－siRNA 对肺癌细胞的生长抑制作用。

本年度获奖情况

60 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Huang Youguo Position Professor Research Topic Activity and Conformation of Membrane Proteins Summary of Research Main results on activity and conformation change of MRP1, a typical transmembrane protein, obtained in 2004, were as follows: 1. The relationship between MRP1 activities and its NBD conformational changes MIANS, a sulfhydryl-reactive fluorescence, was used to label the cysteines of MRP1 (multidrug resistance protein), and the results indicated that an increase in fluorescence intensity and a large emission blue shift took place after two Cys residues of MRP1 reacted with MIANS, which demonstrated that labeled Cys residues in MRP1 reside in a relatively hydrophobic environment. The experimental results obtained from fluorescence resonance energy transfer further uncover that two Cys residues of MRP1 modified by MIANS located in the vicinity of its NBDs, of which one lies close to NBD1, and the other near NBD2. ATP, ADP and anticancer drugs can all reduce the rate of reaction of MRP1 with MIANS. The collisional quenchers, acrylamide, l-, and Cs+ were used to assess local environments of MIANS bound to MRP1 and the results showed that the region around the MIANS-labeled cysteine is positively charged. Both MIANS and NEM, which are sulfhydryl-reactive reagents, inhibited MRP1 ATPase activity, whereas anticancer drugs activated it. These results demonstrated that all nucleotides and drugs could induce changes in conformation of the NBDs in MRP1. Nucleotides can bind directly to NBDs, but drugs may react first with TMDs, which in turn alters the accessibility of the two Cys residues bound by MIANS and affects MRP1 ATPase activity, which is coupled with the transport of its substrates. Taken together, the above experimental results provide direct evidence for further study on the coupling of translocation of the transported species to hydrolysis of ATP in MRP1. 2. Fluorescent modified phosphatidylcholine floppase activity of reconstituted multidrug resistance-associated protein MRP1 Multidrug resistance-associated protein (MRP1) may function as a floppase in human red blood cells to translocate phosphatidylserine and/or phosphatidylcholine from inner membrane leaflet to outer leaflet. Here we report that the purified and reconstituted MRP1 protein into asolectin proteoliposomes is mainly in an inside-out configuration and possesses the ability to flop a fluorescent labeled phosphatidylcholine (NBD-PC) from outer leaflet (protoplasmic) to inner leaflet (extracytoplasmic). The reconstituted MRP1 protein retains endogenous ATPase activity. ATP hydrolysis is required for the flopping since removal of ATP and/or Mg2+ inhibits the translocation of NBD-PC. Further evidence to support this conclusion is that the translocation of NBD-PC is inhibited by vanadate, which traps ATP hydrolysis product ADP in the nucleotide binding domains. In addition, the translocation of NBD-PC by proteoliposomes containing MRP1 protein is in a glutathione-dependent manner, similar to the process of translocating anticancer drugs such as daunorubicin. Verapamil, vincristine, vinblastine, doxorubicin and oxidized glutathione partially inhibited the translocation of NBD-PC, whereas MK 571, an inhibitor of MRP1 protein, inhibited the translocation almost completely. Taken together, the purified and reconstituted MRP1 protein possesses the ability to flop NBD-PC from outer to inner leaflet of the proteoliposomes. Selected Publications 1. Huang, Z. and Huang, Y.* The relationship between MRP1 activities and its NBD conformational changes. Sci. China. C Life Sci. 47(5):425-433, 2004. 2. Huang, Z., Chang, X., Riordan, J.R., Huang, Y.* Fluorescent modified phosphatidylcholine floppase activity of reconstituted multidrug resistance-associated protein MRP1. Biochim. Biophys. Acta. 1660(1-2):155-163, 2004.

61 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名黄有国

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向膜蛋白的活性和构象本年度工作简介本年度在多药耐药蛋白 MRP1 的活性和构象变化的关系方面取得的主要研究结果如下：

1、MRP1 的 NBDs 结构域的构象变化与其转运药物的 ATP 酶活性相关用专一性标记蛋白分子中半胱氨酸(Cys)的荧光探针 MIANS 标记 MRP1(multidrug resistance protein)的实验结果表明，MIANS 与 MRP1 中的 2 个 Cys 结合，结合后不仅荧光强度增加，而且发射波长蓝移，表明所标记的位点处于相对疏水的环境，荧光共振能量转移实验进一步表明，MIANS 标记的 Cys 与 MRP1 核苷酸结合结构域(NBDs)很接近，其中 1 分子 MIANS 标记在 NBD1 附近，另一分子标记在 NBD2 附近，ATP，ADP 以及化疗药物能阻止 MIANS 对 MRP1 的标记，猝灭剂丙烯酰胺、Cs和I对MIANS-MRP1 荧光猝灭实验又表明，MIANS 标记的 Cys 位点处于一个带正点电荷的区域，同时，巯基结合试剂 MIANS 和 NEM 对 MRP1 ATP 酶的活性具有明显的抑制，而化疗药物却有明显的激活作用，上述实验结果提示，核苷酸和化疗药物都能引起 MRP1 的 NBDs 的构象变化，核苷酸可直接与 NBDs 结合，而化疗药物可能通过改变 MRP1 的跨膜结构域(TMDs)的构象进而影响 NBDs 的构象，从而调控 MRP1 ATP 酶的活性并影响对化疗药物的转运，结果对于深入揭示 MRP1 的 ATP 的结合和水解与其转运化疗药物之间的偶联提供了较直接的实验证据。

2、MRP1 的磷脂翻转酶活性可能与药物转运相关用纯化的 MRP1 蛋白的重建实验表明，重建 MRP1 具有翻转 NBD-PC（磷脂酰胆碱荧光类似物）的活性。除去 ATP 和 Mg2+可抑制其转运活性，进一步的实验表明，与 NBD 结合的 vanadate 亦抑制 NBD-PC 的转运。MRP1 的 NBD-PC 的转运与其它一些药物的转运具有相似性即依赖于 glutathione，而且 MRP1 的专一性抑制剂 MK571 可完全抑制其转运活性。上述实验结果表明，重建 MRP1 具有转运 NBD-PC 的能力，这种转运亦可能与肿瘤细胞的多药耐药性有关。综上，MRP1 是 1992 年才确认的一种多药耐药蛋白，越来越多的证据表明，它如同 MDR 一样参与了肿瘤多药耐药性调控。

本年度获奖情况

62 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Chen Jianwen Position Professor Research Topic Caveolae and multi-drug resistance Summary of Research 1. Cholesterol is a key lipid in mediating the enzyme activity or signaling pathway of many proteins on the plasma membrane in mammalian cells. We demonstrated for the first time that after overexpressing caveolin-1, the plasma membrane cholesterol level was decreased by about 12% and 30% for doxorubicin-sensitive and doxorubicin-resistant Hs578T breast cancer cells, respectively. However, the total cholesterol level in both cell lines was increased by about 10%. By measuring fluorescence and flow cytometry using the fluorescence dyes 1,6-diphenyl-1,3,5-hexatriene and Merocyanine 540, we found that overexpressing caveolin-1 resulted in a similar increase in membrane fluidity and loosening of lipid packing density as cholesterol depletion by 1 mM methyl-b-cyclodextrin (MbCD) or 2-hydroxypropyl-b-cyclodextrin (HbCD). Moreover, we found that the transport activity of P-gp was significantly inhibited by 1 mM MbCD or HbCD, which is also similar to the inhibitory effect of caveolin-1 overexpression. Our data demonstrated for the first time that the reduction of the plasma membrane cholesterol level induced by overexpressing caveolin-1 may indirectly inhibit P-gp transport activity by increasing plasma membrane fluidity. 2. Caveolin-1, the principal component of caveolae, is a 21–24 kDa integral membrane protein. The interaction of the caveolin-1 scaffolding domain with signaling molecules can functionally inhibit the activity of these signaling proteins. Little is known about how caveolin-1 influences the expression of Pglycoprotein (P-gp), an ABC transporter encoded by multi-drug resistance (MDR1) gene. To elucidate the possible mechanism between caveolin-1 and P-gp expression, we overexpressed caveolin-1 in Hs578T/Dox breast adenocarcinoma cells, a multidrug resistant line, and then selected single clone cells with high levels of caveolin-1 expression. Both Western blot and confocal microscopy analyses showed that caveolin-1 was markedly overexpressed in the transfectants, while P-gp protein was almost abolished. Reverse transcription polymerase chain reaction also showed that the expression of P-gp mRNA was significantly suppressed in the transfectants. This was confirmed further by Northern blot analysis. Moreover, through measuring the changes of drug resistance and P-gp transport activity in the transfectants, we found that overexpression of caveolin-1 reversed drug resistance of transfectants and lowered their P-gp transport activity to the level of Hs578T/S. Taken together, our results indicate that such suppression of P-gp in the transfectants overexpressing caveolin-1 may occur at the transcriptional level. Selected Publications 1. Yu-hong Pang and Jian-wen Chen*. Anisodamine Causes the Changes of Structure and Function in the Transmembrane Domain of the Ca2+-ATPase from Sarcoplasmic Reticulum. Biosci. Biotechol. Biochem 68 (1), 126-131, 2004. 2. Chuanxi CAI and Jianwen CHEN*. Overexpression of Caveolin-1 Induces Alteration of Multidrug Resistance in Hs578T Breast Adenocarcinoma Cells. Int. J. Cancer 111, 522–529, 2004. 3. Chuanxi Cai, Hua Zhu, and Jianwen Chen*. Overexpression of Caveolin-1 Increases Plasma Membrane Fluidity and Reduces P-glycoprotein Function in Hs578T/Dox Biochem.Biophys.Research.Communication 320, 868–874, 2004. 4. Hua Zhu, Chuanxi Cai, Jianwen Chen*. Suppression of P-glycoprotein gene expression in Hs578T/Dox by the overexpression of caveolin-1. FEBS Letters 576, 369–374, 2004.

63 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名陈建文

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向 Caveolae 和多药耐药性

本年度工作简介

1．胆固醇在介导哺乳动物细胞质膜上存在的许多蛋白的酶活和信号途径中是一个很关键的脂分子。我们的研究首次证明了在过表达 caveolin-1 后，对阿霉素药物敏感和耐药的乳腺癌细胞 Hs578T 的质膜胆固醇水平分别降低了 12%和 30%。但是，两种细胞的总胆固醇水平都增大了约 10%。通过流式方法测定 DPH 和 MC 540 的荧光，我们发现 caveolin-1 的过表达会引起膜流动性的增加和脂分子堆积密度的减低，这与用 1 mM MbCD或 HbCD 去除胆固醇的处理后得到的结果是相似的。并且，我们发现 P-gp 的转运活性明显受到 1 mM MbCD或 HbCD 的抑制，这与过表达 caveolin-1 后的抑制程度也是相似的。我们的数据第一次表明，由于过表达 caveolin-1 而导致的质膜胆固醇水平的降低可能通过增加膜流动性的方式间接抑制了 P-gp 的转运活性。

2．Caveolin-1，作为 caveolae 的主要组成成分，是一个 21-24 KDa的整合膜蛋白。Caveolin-1 的 scaffolding 结构域与信号分子的相互作用通常会抑制这些信号蛋白的活性。目前关于 caveolin-1 是如何影响 P 型糖蛋白(P-gp)，一种多药耐药基因(MDR1)编码的 ABC 转运蛋白的表达，了解的还不是很清楚。为了阐明 caveolin-1 与 P-gp 表达之间可能的机制，我们在 Hs578T/Dox 这种多药耐药的乳腺癌细胞系中过表达了 caveolin-1 并筛选了高表达量的单克隆细胞。Western blot 和 confocal 实验的结果都显示 caveolin-1 大量过表达于转染细胞中，但是 P-gp 蛋白基本已经消失。反转录聚合酶链反应实验表明在转染细胞中 P-gp 的 mRNA 转录受到了明显的抑制。Northern blot实验也进一步证明了这一结果。并且，通过测定转染细胞中 P-gp 的耐药性和转运活性的变化，我们发现 caveolin-1 的过表达逆转了转染细胞的耐药性以及使 P-gp 的转运活性降低到 Hs578T/S 的水平。我们的结果表明在过表达 caveolin-1 的转染细胞中， P-gp 的这种抑制可能发生在转录水平上。

本年度获奖情况

64 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Zhang Xujia Position Professor Research Topic Molecular Biology of Membrane Proteins Summary of Research 1. Electron microscopic study of V-ATPase from mung bean a. The vacuolar H+-ATPase from mung bean (Vigna radiate L.) was purified to homogeneity. The purified complex contained all the reported subunits from mung bean, but also showed a 40 kDa subunit. The excised 40 kDa band was also processed for HPLC/MS/MS peptide mapping. A peptide sequence obtained, YPPYQAIFSK, shows identity with the d subunit of Arabidopsis thaliana. This then strongly suggests that the band at 40 kDa represents the d subunit of the V-ATPase from mung bean. b. Subcomplexes (Vo) with or without subunit d were purified and reconstituted into soybean liposomes. The Vo subcomplex containing subunits a and c is a passive proton channel driven by K+/valinomycin mediated membrane potential and inhibited by bafilomycin A1 or DCCD, while the Vo subcomplex containing subunits a, c and d is not. This result suggested that the subunit d was just above the center of the c ring, like a “cap” to regulate the H+ translocation across the membrane. 2. Sphingolipids regulate the plasma membrane Ca2+-ATPase from erythrocyte ghosts a. In contrast to the effect of sphingolipids on the PMCA from porcine brain synaptosomes, the sphingolipids GM1, GM2, GM3 and GD1b greatly stimulate the PMCA, but Asiola-GM2 has no apparent effect. This result suggests that the regulation of the PMCA by sphingolipids is isoform dependence, in view of the fact that porcine brain synaptosomes contain PMCA1 - PMCA4, but the erythrocyte ghosts contain mainly PMCA4. b. The mechanism by which the gangliosides regulate the PMCA was systemically studied. The activities of the PMCA in the presence of CaM, polypeptide and calpain were measured. The results demonstrated that gangliosides stimulate the PMCA via their direct interactions with the c-termini of the PMCA, subsequently releasing active sites. Interestingly, GM2 stimulated the enzyme at lower concentrations, but inhibited it at higher concentrations. This result suggests that GM2 interacts with two regions of the PMCA: one located at the c-termini, the other at the self-inhibition region of the PMCA. Selected Publications 1. Yongfang Zhao, Xiaoxuan Fan, Fuyu Yang,* and Xujia Zhang*. Gangliosides modulate the activity of the plasma membrane Ca2+-ATPase from porcine brain synaptosomes. Archives of Biochemistry and Biophysics 427, 204-212, (2004). 2. Zhuo Li, Xujia Zhang*. Electron-microscopic structure of the V-ATPase from mung bean. Planta 219, 948-954, (2004).

65 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名张旭家

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ □ □

研究方向膜蛋白的结构与功能本年度工作简介一、绿豆 V-ATPase 电镜单颗粒的结构研究 V-ATPase 是一种多亚基复合物。在上一年获得绿豆 V-ATPase 电镜结构后，开始研究每一种亚基的空间定位及其功能。 1、首次发现绿豆V-ATPase 包含一个与膜结合的 40kDa 的亚基，生化实验表明该

条多肽是 Vo 的亚基。用串联质谱鉴定出它与植物 V-ATPase 的 d 亚基高度同源。

表明该多肽是绿豆 V-ATPase 的 d 亚基，我们称之谓 dmb。

2、在不同条件下分离纯化包含 d 亚基和不含 d 亚基的两种 Vo 亚复合物。分别将

其重组到大豆磷脂制成的的脂质体，发现 d 亚基的有或无直接对应 Vo 亚复合物

被动质子转运活性的关闭或开放状态，提出 Vo 被动质子转运通道可能位于 c 亚基环的中央孔，d 亚基则相当于一个“盖子”控制通道的开闭。考虑 d 亚基广泛存在于 V-ATPase 中，该模型可能具有广泛意义。二、神经节苷脂对质膜 Ca2+-ATPase(PMCA)的调控既上一年发现神经节苷脂对脑中 PMCA 具有调控作用的基础上，开始系统地研究神经节苷脂与 PMCA 的作用机理，包括与不同亚型 PMCA 的作用。 1、神经节苷脂 GM1、GM2、GM3 和 GD1b 对从血中提取的 PMCA 都有激活效应，而 Asialo-GM1 对 PMCA 没有作用。这一结果与我们以前从脑中提取的 PMCA 完全相反，表明神经节苷脂对 PMCA 的调控与 PMCA 的亚型相关，因为脑中 PMCA 包含 PMCA1～PMCA4,而血中主要为 PMCA4。 2、进一步研究了神经节苷脂对 PMCA 作用的机理。通过限制性酶切、钙调素竞争、短肽竞争等实验证明了神经节苷脂是通过与 PMCA的c末端的直接相互作用，从而使 PMCA 处于开放状态，进而激活 PMCA。另外，高浓度 GM2 抑制 PMCA 活性。机理研究表明，GM2 与 PMCA 的两个结构域相互作用：低浓度时作用于 PMCA 的 c 末端，从而激活 PMCA；而高浓度时，作用于 PMCA 的自抑制位点，进而抑制 PMCA 的活性。

本年度获奖情况

66 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

4. Molecular Basis of Infection and Immunity Name Yan Xiyun Position Professor Research Topic Identification of novel targets using an antibody-based approach Summary of Research 1. Identification of novel tumor targets and their specific antibodies. After identifying CD146 as a novel target in tumor angiogenesis, we investigated new aspects of CD146 function: (1) CD146 plays a critical role in trophoblast invasion; (2) CD146 expression is reduced in the pregnancy disorder preeclampsia; (3) the function of CD146 in cell signal transduction and neuron development; (4) identification of CD146 ligands; (5) evaluation of soluble CD146 as a marker for diagnosis of diseases. 2. SARS epitope library and SARS antibody library: (1) Image of three-dimensional appearance of SARS-CoV virus particles using SEM; (2) SARS peptide and SARS antibody libraries were constructed, from which several SARS antibodies were selected and evaluated for anti- SARS therapy. 5. Imaging of single molecule behavior in living cells, especially visualization of the dynamic behaviour of the membrane protein CD146 and its ligands in living cells by means of nanotechnology.

Selected Publications

1. Lin, Y., Yan, X.Y.*, Cao, W.H., Wang, C.Y., Xie, S.S. & Feng, J. Probing the Structure of the SARS Coronavirus Using Scanning Electron Microscopy. Antiviral Therapy 9: 169-171, (2004). 2. Liu, Q., Yan, X.Y.*, Li, Y., Zhang, Y., Zhao, X. & Shen, Y. Preeclampsia is Associated with the Failure of Melanoma Cell Adhesion Molecule (MCAM/CD146) Expression by Intermediate Trophoblast. Lab Invest84: 221-228 (2004) 3. Lin,Y.,Yan, X.Y.* Progression and Direction of Humanized Antibody Research. Chinese Journal of Biotechnology 20: 1-4, (2004) 4. Qin Liu, Xingang Zhao, Ying Zhang, Yi Shen, Yixun Liu, Xiyun Yan*. Melanoma cell adhesion molecule (MCAM/CD146) is a critical molecule in trophoblast invasion. Prog. Biochem. Biophys. 31(4): 309-312, (2004) 5. HAN Wei, ZHANG Pan-he, CAO Wu-chun, YANG Dong-ling, Yoshio Okamoto, Shigeharu Taira, YAN Xi-Yun*. The inactivation effect of photocatalytic titanium apatite filter on SARS Virus. Prog. Biochem. Biophys. 31(11): 982-985, (2004)

67 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

4. 感染与免疫的分子基础

姓名阎锡蕴

院士研究员副研究员百人计划国家杰出青年职称 □ √ □ √ □

研究方向疾病相关新型靶分子及其抗体的功能研究本年度工作简介 1．肿瘤靶分子及其抗体的新功能研究继 2003 年发现肿瘤血管新靶标 CD146 之后，我们深入研究了 CD146 的新功能，发现（1）在胚胎植入过程中 CD146 分子是影响滋养层细胞侵入行为的关键分子；（2）妊娠疾病先兆子痫胎盘 CD146 分子的表达明显下调；（3）CD146 分子参与细胞信号传导；（4）寻找 CD146 配体；（5）研究 CD146 分子在神经免疫系统中的分布及功能；（6）可溶性 CD146 分子在疾病诊断中的意义。另外，鉴定了一个新的肿瘤靶分子 T2-2 的分布及体内外功能；完成了抗人肿瘤相关抗原 HerB2 的免疫毒素 ScFv-Trail 及 ScFv-TNF-α 的构建表达和功能研究。 2．SARS 病毒抗原表位库和抗体库的研究利用超高分辨率扫描电镜报道了SARS病毒的三维立体结构；建立了SARS 冠状病毒BJ01株抗原表位库和SARS抗体库，获得SARS冠状病毒特异抗体并完成抗体的高效表达、纯化及中和活性实验。发现新型光触媒钛羟基磷灰石网膜PTAF 对SARS 病毒生长具有明显的抑制作用。 3.纳米材料与技术在细胞生物学研究的初探 2004 获得国家自然科学“纳米科技”基础研究领域重点项目支持，利用纳米技术探测 CD146 分子在活细胞信号传递过程中的单分子行为；并探讨纳米材料对基因扩增和基因转化的影响。

专利：2004 年申请发明专利 1 项；获得专利授权 1 项。

本年度获奖情况

2004 年培养的博士生荣获以下奖励： 1）2004 年中国科学院院长优秀奖 2）2004 年宝洁奖学金

68 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Zhihai Qin Position Professor Research Topic Interferon–γ、tumor stroma and tumor rejection Summary of Research

As a new lab founded in the middle of 2004, we have now 3 PhD students, 3 visiting scientists, 1 research assistant and 1 technician. Three laboratories have been established for cell culture, molecular cloning and basic immunological experiments. The interest of our group is focused on the role of IFN-γ on tumor stroma cells during an immune response mediated tumor rejection. Research has begun on the following aspects: 1）Generation of conditional knockout mice (Jing Jiang, Yu Lu and Wei Yang). Mice with an IFN-γ receptor deficiency specifically on different tumor stoma cells, such as fibroblasts or endothelial cells will be generated in collaboration with the Experimental Animal Institute of the Chinese Academy of Medical Sciences. 2）Establishment of a three-dimensional co-culture system of mouse fibroblasts and tumor cells (Shuibai Liu and Chunhai Zhou). To analyze the interaction between tumor cells and fibroblasts in vitro, we are going to establish a 3D co-culture system. A series of mouse embryonic fibroblast and tumor infiltrating fibroblast cell lines from IFN-γR knockout mice have been established. We will reconstitute the expression of IFN-γR on these cells and investigate tumor/fibroblast interaction in the presence or absence of IFN-γ. 3）Improvement of in vivo cytokine detection assays (Bin Li). 4）Investigation of the role of inflammatory cytokines, such as IFN-γ and TNF, during the process of chemical carcinogenesis (Zhiguang Li and Xiangyue Zhang).

Selected Publications 1. Qin, Z., and T. Blankenstein. A cancer immunosurveillance controversy. Nat Immunol 5:3, (2004). 2. Kim, H. J., T. Kammertoens, M. Janke, O. Schmetzer, Z. Qin, C. Berek, and T. Blankenstein. Establishment of early lymphoid organ infrastructure in transplanted tumors mediated by local production of lymphotoxin alpha and in the combined absence of functional B and T cells. J Immunol 172:4037, (2004) 3. Wu, T. H., C. N. Pabin, Z. Qin, T. Blankenstein, M. Philip, J. Dignam, K. Schreiber, and H. Schreiber. Long-Term Suppression of Tumor Growth by TNF Requires a Stat1- and IFN Regulatory Factor 1-Dependent IFN-gamma Pathway but Not IL-12 or IL-18. J Immunol 172:3243, (2004)

69 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名秦志海

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ √ □

研究方向 IFN-γ，肿瘤间质细胞与肿瘤的免疫排斥本年度工作简介

作为新建实验室，本年度我们的工作重点是科研队伍的组建，实验室建设和一些前期实验准备工作。本课题组现有博士研究生两名、硕转博士生一名、进修生三名、助研和实验员各一名。经过半年多时间的努力，我们现已建立起细胞培养室、分子生物学和免疫学三个实验室，并开始正常运行。围绕 IFN-γ，肿瘤间质细胞与肿瘤免疫排斥的关系这一主攻方向，我们从以下几个方面开展了工作： 1)构建肿瘤间质细胞特异性 IFN-γ受体基因敲除小鼠（蒋静、陆宇、杨薇）。为分析一些与肿瘤免疫排斥相关的效应因子，如 IFN-γ等对成纤维细胞和血管内皮细胞的作用，我们拟构建转基因小鼠。现已完成了部分 IFN-γ受体基因表达质粒的构建，将与中国医学科学院动物所合作，进一步构建转基因小鼠。 2 建立体外肿瘤细胞与间质细胞的 3D 共培养体系，研究其相互作用（刘树柏、周春海)。我们已从 IFN-γR 基因敲除小鼠体内分离、建成多种胚胎成纤维细胞系列和浸润肿瘤组织的成纤维细胞系列。同时，我们正在重建这些细胞对 IFN-γR 的表达。为近一步分析时间与剂量等因素对 IFN-γ作用的影响，我们利用 Tet-on/off 系统对该基因在培养体系内的表达进行了调控。 3)建立高敏感度的体内细胞因子检测方法（李冰）。为分析免疫反应过程中， IFN-γ、IL4 及 TNF 等细胞因子在体内的变化，我们正在建立高敏感度的细胞因子检测方法。 4)分析细胞因子在肿瘤免疫监视过程中的作用机制（李志广、张香月）。现已引进数种基因敲除小鼠，如：IFN-γR、TNF-R1、TNF-R2、和 TNF-R1/R2 双基因敲除小鼠等，拟分析 IFN-γ 和 TNF 在化学物如甲基胆蒽和二甲苯蒽等在小鼠体内致癌过程中的作用及免疫反应机制。

本年度获奖情况

70 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Haiying Hang Position Professor Research Topic Cell Cycle Checkpoint Protein Complex Summary of Research DNA damage arises during normal cellular metabolic processes or when cells are exposed to genotoxic agents. Cells respond to DNA damage by activating an intricate network of cell cycle checkpoint proteins and DNA repair factors. Mutations in these genes often lead to cancer development. One of the major tasks in this area is to identify key proteins in this network and discover their roles in cell cycle checkpoint control, DNA repair and tumor-prevention. Our current work focuses on a newly identified cell cycle checkpoint protein complex Rad9-Rad1-Hus1 (9-1-1 complex). We have successfully created rad1 and rad9 knockout cells and mice. Our studies with these cells have shown that rad1 and rad9 play essential roles in ensuring normal replication as well as S/M cell cycle checkpoint controls. We are also performing experiments to find out if deletion of rad1 or rad9 causes tumors in mice.

Selected Publications

71 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名杭海英

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ √ □

研究方向细胞周期检查点蛋白质的结构的结构与功能本年度工作简介在正常的细胞代谢活动中或当细胞暴露于遗传毒性因子时，会发生基因组 DNA 的损伤。细胞依赖由细胞周期调控蛋白和 DNA 修复蛋白组成的复杂系统对 DNA 的损伤进行控制和修复。当这些基因发生突变时，常常会导致癌症的发生。 Hus1、Rad1 和 Rad9 是细胞周期调控家族中的新成员，是 DNA 损伤修复系统中必不可少的组成成分。据认为这三种蛋白通过形成三分子复合体（9-1-1 复合体）,帮助细胞对抗遗传毒性压力,包括对细胞周期进行调控和对 DNA 的损伤进行修复等。但是，目前还不完全清楚 9-1-1 复合体在细胞周期调控和 DNA 修复中的作用机制,更不了解它是否有抑制肿瘤发生的功能。我们建立了小鼠基因敲除细胞(rad1-/-和 rad9-/-),并发现 rad1 和 rad9 均是调控 DNA 正常复制和 S/M 细胞周期检查点所必需的。我们还建立了 rad1 和 rad9 基因敲除小鼠,并正在利用这些小鼠检验 rad1 和 rad9 是否为抑癌基因。

本年度获奖情况

72 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Jie Tang Position Professor Research Topic Molecular Immunology Summary of Research

1. Functional studies of lymphocyte cell surface proteins CD72 is a regulatory receptor on B cells that suppresses B cell activation. Its function is closely related to a tyrosine phosphotase, SHP-1, which is associated with CD72 in nonactivated B cells. Upon CD72 ligand engagement, SHP-1 dissociates from CD72 so that its suppression of B cell receptor signaling is released. The function of CD72 can be regulated on the transcriptional level since multiple splicing variants of CD72 mRNA exist in mouse B cells. The relationship between CD72 splicing variants and B cell function is our primary interest. We have cloned five novel CD72 splicing variants and expressed them in mammalian cells. Their association with SHP-1 and their functions in B cell activation will be studied in COS and WEHI cell lines.

2. Antibody therapy of immune system related disease Sepsis is one of the major immune system related diseases. To suppress the abnormal immune response is our main approach to treat this disease. We will develop monoclonal antibodies against HMGB-1, which is a cytokine that functions at a late stage in the immune response to infections. We have expressed HMGB-1 in E.coli and established a functional assay using purified recombinant protein. Animal immunization is underway. With the anti-HMGB-1 antibody, we will study the role of HMGB-1 in a murine sepsis model and validate this protein as a target for human sepsis.

Selected Publications

73 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名唐捷

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ √ □

研究方向分子免疫学本年度工作简介（一）B 细胞特异性受体信号转导调控的研究。 CD72 是 B 细胞特异性受体，在 B 细胞成熟与活化的各个阶段都有表达。在 CD72 的胞内区上有两个免疫受体酪氨酸抑制性基序（ITIM）。每个 ITIM 内的酪氨酸被磷酸化后可与蛋白酪氨酸磷酸酯酶 SHP-1 的一个 SH2 结合性结构域相结合。在 B 细胞活化前，CD72 上的酪氨酸被磷酸化，SHP-1 与 CD72 结合，控制 BCR 的酪氨酸磷酸化水平，进而抑制BCR 介导的信号转导。当CD72 与其配体结合后， CD72 上的酪氨酸去磷酸化，SHP-1与 CD72 分离，从而解除了对BCR 信号转导的抑制。我们的工作是在 pre-mRNA 剪切水平上研究对 CD72 功能的调控。我们发现 CD72 在不同细胞和细胞活化的不同阶段剪切类型有变化，有些剪切类型会导致 CD72 上的第二个 ITIM 缺失，或者两个 ITIM 之间的距离增大，还有一些类型由于缺失跨膜区而不能在膜上表达。这些类型对 CD72 功能的影响是我们进一步研究的课题。（二）以 HMGB1 为靶点开发治疗败血症的单克隆抗体药物。在败血症的小鼠模型中，HMGB1 发挥后期调控因子的作用。在注射过 LPS 后 24 小时内加入抗 HMGB1 的多克隆抗体，就能阻断 LPS 伤害作用，明显增强生还比率。相比之下，HMGB1 较其它细胞因子在效应时间上明显靠后，因此它给我们拓宽了治疗时间的范围，相当于给我们开了一个全新的、高效的治疗窗口。拮抗 HMGB1 的药物开发，将是利用这个新窗口的关键。但人源的 HMGB1 与鼠源的 HMGB1 有 98%以上的同源性，导致鼠对人的 HMGB1 具有免疫耐受性，从而无法从正常小鼠或大鼠中得到单克隆抗体。由于鸡在进化中和哺乳动物差别比较大，在其体内产生抗人源 HMGB1 抗体的几率要大得多，已有文献证明确实能够免疫鸡得到具有中和活性的抗 HMGB1 抗体。我们掌握的鸡源性单克隆抗体筛选技术，主要是利用分子生物学方法从免疫后的鸡脾中构建抗体文库，并用酵母展示方法筛选特异性抗体。目前我们已完成了抗原的表达与纯化工作，建立了HMGB1 活性鉴定体系，并开始对鸡进行免疫。酵母展示系统在本实验室也已建立起来，在许多方面还有了进一步改进。

本年度获奖情况

74 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

Name Fan Zusen Position Professor Research Topic Molecular Mechanisms of Tumorigenesis, Killing mechanisms and Cancer Immunotherapy Summary of Research I. Molecular mechanisms of tumorigenesis Cell cycle control and tumorigenesis are at the frontier of cancer research. pp32 was recently confirmed as a new tumor suppressor. We identified eight pp32-associated proteins using the yeast two-hybrid system and confirmed their real interactions with histone H3, TRAP1 and RYBP. pp32 inhibits cell growth through binding to histone H3 and RYBP. The results will be prepared for publication. The interaction between pp32 and TRAP1 is under investigation. II. CTL-mediated killing mechanism against cancers CTL and NK cells are important effector cells in immune responses against viruses, intracellular bacteria and tumors. They kill their target cells through granule contents, including perforin and granzymes. Human granzymes A, B, K, M and H and their inactive forms were expressed and purified. We are studying their molecular pathways to induce apoptosis and compare with known pathways of granzyme A and B, which will provide natural drugs for cancer immunotherapy. III. Cancer immunotherapy NK cells are innate effector cells that play an important role in the defense against virally infected and transformed cells. We demonstrated that the TNF superfamily member LIGHT is a critical ligand for activation of NK cells. HVEM is expressed on NK cells and its engagement with LIGHT mediates NK cell activation. The activated NK cells can trigger activation and maturation of tumor specific CD8+ T cells at its priming phase in vivo and in vitro. NK cells can directly prime CTL responses to bridge innate and adaptive immunity for breaking the tolerance of CD8+ cells inside tumors, which may provide new guidance for cancer immunotherapy. This work is being reviewed for Nature Medicine.

Selected Publications

Zusen Fan, Ping Yu, Yang Wang, May lynne Fu, Youjin Lee, Yugang Wang, Wenhua Liu, Yonglian Sun, Yang-Xin Fu*. Natural killer activation by LIGHT primes tumor specific CD8+ T cell immunity to reject established tumors. Nature Medicine (under review).

75 ANNUAL REPORT NATIONAL LABORATORY OF BIOMACROMOLECULES 2004

姓名范祖森

院士研究员副研究员长江学者百人计划国家杰出青年职称 □ √ □ □ √ □

研究方向肿瘤发生的分子基础、杀伤机理及免疫治疗

本年度工作简介 1. 肿瘤发生的分子基础原癌基因和抑癌基因如何调节细胞生长分化及癌变机理，一直成为细胞生物学及肿瘤学研究的热点。pp32 被证实为新抑癌基因，但 pp32 如何调节细胞生长及发挥抑癌作用的机制尚未阐明。我们发现 pp32 与 SET 等蛋白形成 SET 复合体，参与颗粒酶 A 介导的细胞凋亡。以 pp32 为诱饵蛋白，采用酵母双杂交系统筛选出 8 个与 pp32 相作用的蛋白，其中组蛋白 H3, RYBP 和 TRAP1 与 pp32 的相互作用已被证实。并阐明了 pp32 与 H3 及 RYBP 结合, 抑制了基因转录, 进而阻止了细胞生长。部分结果将于近期内整理发表。正进一步研究 pp32 如何通过其作用蛋白 TRAP1 参与 TNFR 信号及 pRb 调节途径调控细胞生长分化，并从结构与功能的关系上，以期阐明 pp32 抑制细胞生长的机制。 2．肿瘤的杀伤机理 CTL 和 NK 细胞诱导的杀伤作用是机体抗病毒感染和抗肿瘤的主要效应途径。介导细胞杀伤的颗粒内容物为颗粒酶和导致膜损伤的穿孔素与颗粒素，各种颗粒酶如何协同诱导靶细胞凋亡以及穿孔素和颗粒素如何辅助颗粒酶进入细胞并如何发挥其特有的杀伤作用，均尚未搞清。我们已表达纯化了穿孔素和颗粒素及各种颗粒酶 A、B、K、M 和 H 及其突变体。正在探讨颗粒酶 K、M 和 H 在 CTL 介导肿瘤杀伤中的作用，并鉴定其作用底物，分析其与颗粒酶 A、B 杀伤途径的异同，阐明其杀伤机制，为抗肿瘤及抗病毒药物的研制提供理论基础和新思路。 3．肿瘤的免疫治疗 NK 细胞作为先天免疫的效应细胞在抗病毒及抗肿瘤中发挥重要作用。NK 细胞如何被活化和激发过继免疫反应尚不清楚。我们发现 TNF 超家族成员 LIGHT 是 NK 活化的重要配体，NK 表面表达 HVEM 受体并与其配体 LIGHT 结合介导 NK 细胞活化，体外及动物实验研究表明激活的 NK 细胞可以通过 IFN-γ 直接活化肿瘤特异性 CTL 介导有效的肿瘤杀伤，从而证明 NK 细胞是沟通先天免疫与过继免疫的桥梁。该研究论文正在 Nature Medicine 杂志审稿。在此基础上将深入探讨如何在肿瘤局部高效地表达 LIGHT 激发 NK 细胞的活性，为临床有效地介导肿瘤的免疫治疗提供新的免疫药物和理论基础。

本年度获奖情况

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Ⅵ. 论文索引 List of Publications

1 LIU ZF, YAN HC, WANG KB et al. and CHANG WR*. Crystal structure of spinach major light-harvesting complex at 2.72 angstrom resolution. NATURE, 2004, 428:287-292

3 DUAN XJ, ZHAO Z, YE JP et al. and MA HM*, XIA AD*, WANG CC*. Donor–Donor Energy-Migration Measurements of Dimeric DsbC Labeled at Its N-Terminal Amines with Fluorescent Probes: A Study of Protein Unfolding. ANGEW CHEM INT EDIT, 2004, 43:4216-4219.

4 PENG H, BARTLAM MARK, ZENG QH et al. and RAO ZH*. Crystal structure of human pirin - An iron-binding nuclear protein and transcription cofactor. J BIOL CHEM, 2004, 279:1491-1498.

5 SHI N, YE S, BARTLAM M et al. and RAO ZH*, YUAN JG*. Structural basis for the specific recognition of RET by the Dok1 phosphotyrosine binding domain. J BIOL CHEM, 2004, 279:4962-4969.

7 WEI ZY, ZHANG P, ZHOU ZC et al. and GONG WM*. Crystal structure of human eIF3k, the first structure of eIF3 subunits. J BIOL CHEM, 2004, 279:34983-34990.

8 LI MH, KWOK F, CHANG WR et al. and JIANG T*. Conformational changes in the reaction of pyridoxal kinase. J BIOL CHEM, 2004, 279:17459-17465.

9 WANG YL, WEI ZY, BIAN Q et al. and GONG WM*. Crystal structure of human bisphosphoglycerate mutase. J BIOL CHEM, 2004, 279:39132-39138.

10 XU YH, LIU YW, LOU ZY et al. and RAO ZH*. Structural basis for coronavirus-mediated membrane fusion: Crystal structure of MHV spike protein fusion core. J BIOL CHEM, 2004, 279:30514-30522.

11 XU YH, LOU ZY, LIU YW et al. and RAO ZH*. Crystal structure of SARS-CoV spike protein fusion core. J BIOL CHEM, 2004, 279:49414-49419.

12 BAI M, ZHOU JM*, PERRETT S* et al. The yeast prion protein Ure2 shows glutathione peroxidase activity in both native and fibrillar forms. J BIOL CHEM, 2004, 279:50025-50030.

13 BARTIAM M, WANG GG, YANG HT et al. and RAO ZH*. Crystal Structure of an Acylpeptide Hydrolase/Esterase from Aeropyrum pernix K1. STRUCTURE, 2004,

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12:1481-1488.

14 LIN Y, YAN XY*, CAO WC et al. Probing the structure of the SARS coronavirus using scanning electron microscopy. ANTIVIR THER, 2004, 9:287-289.

15 ZHOU ZC, SONG XM, LI YK et al. and GONG WM*. Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans. J MOL BIOL, 2004, 339:207-215.

16 LIU L, WEI ZY, WANG YL et al. and GONG WM*. Crystal structure of human coactosin-like Protein. J MOL BIOL, 2004, 344:317-323.

17 WAN QF, DONG YM, YANG H et al. and XU T*. Protein Kinase Activation Increases Insulin Secretion by Sensitizing the Secretory Machinery to Ca2+. J GEN PHYSIOL, 2004, 124:653-662.

18 LIU BB, BARTLAM MARK, GAO RJ et al. and RAO ZH*. Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the Archaeon Pyrococcus horikoshii. BIOPHYS J, 2004, 86:420-427.

19 LI DD, XIONG J, QU AL et al. and XU T*. Three-dimensional tracking of single secretory granules in live PC12 cells. BIOPHYS J, 2004, 87:1991-2001.

20 CAI CX, CHEN JW*. Overexpression of caveolin-1 induces alteration of multidrug resistance in Hs578T breast adenocarcinoma cells. INT J CANCER, 2004, 111:522-529.

21 LIU JH, WANG ZX*. Kinetic analysis of ligand-induced autocatalytic reactions.. BIOCHEM J, 2004, 379:697-702.

22 SU X, QING SB, PAN XM*. Thermal and conformational stability of Ssh10b protein from archaeon Sulfolobus shibattae. BIOCHEM J, 2004, 382:433-440.

23 STEPANENKO OV, KUZNETSOVA IM, TUROVEROV KK* et al. andWANG CC*. Conformational change of the dimeric DsbC molecule induced by GdnHCl. A study by intrinsic fluorescence. BIOCHEMISTRY-US, 2004, 43:5296-5303.

24 XU YH, ZHU JQ, LIU YW et al. and RAO ZH*, GAO GF*. Characterization of the heptad repeat regions, HR1 and HR2, and design of a fusion core structure model of the spike protein from severe acute respiratory syndrome (SARS) coronavirus. BIOCHEMISTRY-US, 2004, 43:14064-14071.

25 LI XM, LIU XQ, LOU ZY et al. and RAO ZH*, LIU YW*. Crystal Structure of Human Coactosin-like Protein at 1.9 A Resolution. PROTEIN SCI, 2004, 13:2845-2851.

26 ZHU L, QIN ZJ, ZHOU JM*. Unfolding kinetics of dimeric creatine kinase measured by stopped-flow small angle X-ray scattering. BIOCHIMIE, 2004, 86:127-132.

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27 FENG YM, HUANG S, ZHANG WZ et al. and JING GZ*. The effects of amino acid replacements of glycine 20 on conformational stability and catalysis of staphylococcal nuclease. BIOCHIMIE, 2004, 86:893-901.

28 ZHU H, CAI CX, CHEN JW* et al. Suppression of P-glycoprotein gene expression in Hs578T/Dox by the overexpression of caveolin-1. FEBS LETT, 2004, 576:369-376.

29 LIU JF, WANG XQ, WANG ZX et al. and LIANG DC*. Crystal sturcture of KD93, a novel protein expressed in human hematopoietic stem/progenitor cells. J STRUCT BIOL, 2004, 148:370-374.

30 ZHOU L, ZHANG XJ*. Electron-microscopic structure of th V-ATPase from mung bean. PLANTA, 2004, 219:948-954.

31 PANG H, LIU YG, HAN XQ et al. and RAO ZH*. Protective humoral responses to severe acute respiratory syndrome-associated coronavirus: implications for the design of an effective protein-based vaccine. J GEN VIROL, 2004, 85:3109-3113.

32 WANG WN, PAN XM, WANG ZX*. Kinetic analysis of zymogen autoactiviation in the presence of a reversible inhibitor. EUR J BIOCHEM, 2004, 271:4638-4645.

33 CAI CX, ZHU H, CHEN JW*. Overexpression of caveolin-1 increases plasma membrane fluidity and reduces P-glycoprotein function in Hs578T/Dox. BIOCHEM BIOPH RES CO, 2004, 320:867-874.

34 LIU CP, ZHOU JM*. Trigger factor-assisted folding of bovine carbonic anhydrase II. BIOCHEM BIOPH RES CO, 2004, 313:509-515.

35 LI HT, WANG C, CHANG TN et al. and CHANG WR*. pH-profile crystal structure studies of C-terminal despentapeptide nitrite reductase from Achromobacter cycloclastes. BIOCHEM BIOPH RES CO, 2004, 316:107-113.

36 LIU DS, FENG YG, CHENG Y et al. and WANG JF*. Human programmed cell death 5 protein has a helical-core and two dissociated structural regions. BIOCHEM BIOPH RES CO, 2004, 318:391-396.

37 BERNINI A, SPIGA O, CIUTTI A et al. and NICCOLAI N*. Prediction of quaternary assembly of SARS coronavirus peplomer. BIOCHEM BIOPH RES CO, 2004, 325:1210-1214.

38 WANG C, WANG F, LI M et al. and CHANG WR*. Structural basis for broad substrate specificity of earthworm fibrinolytic enzyme component A. BIOCHEM BIOPH RES CO, 2004, 325:877-882.

39 DAI JX, WANG X, FENG YG et al. and WANG JF*. Searching for folding initiation sites of staphylococcal nuclease: A study of N-terminal short fragments. BIOPOLYMERS, 2004, 75:229-241.

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40 HUANG ZH, CHANG XB, RIORDAN JR et al. and HUANG YG*. Fluorescent modified phosphatidylcholine floppase activity of reconstituted multidrug resistance-associated protein MRP1. BBA-BIOMEMBRANES, 2004, 1660:155-163.

41 XIA S, XU L, BAI L et al. and XU T*. Labeling and dynamic imaging of synaptic vesicle-like microvesicles in PC12 cells using TIRFM. BRAIN RES, 2004, 997:159-164.

42 ZHAO YF, FAN XX, YANG FY et al. and YANG FY, ZHANG XJ*. Gangliosides modulate the activity of the plasma membrane Ca2+-ATPase from porcine brain synaptosomes. ARCH BIOCHEM BIOPHYS, 2004, 427:204-212.

43 FENG J, WANG Q, WU YS et al. and ZHANG JP*. Triplet excitation transfer between carotenoids in the LH2 complex from photosynthetic bacterium Rhodopseudomonas palustris. PHOTOSYNTH RES, 2004, 82:83-94.

44 ZHOU ZC, GONG WM*. Co-crystallization of Leptospira interrogans peptide deformylase with a potent inhibitor and moleculara-replacement schemes with eight subunits in an asymmetric unit. ACTA CRYSTALLOGR D, 2004, 60:137-139.

45 CHANG SJ, SONG XM, YAN M et al. and GONG WM*. Purification, characterization and preliminary crystallographic studies of a cysteine protease from Pachyrrhizus erosus seeds. ACTA CRYSTALLOGR D, 2004, 60:187-189.

46 WANG F, WANG C, LI M et al. and CHANG WR*. Crystallization and preliminary crystallographic analysis of earthworm fibrinolytic enzyme component B from Eisenia fetida. ACTA CRYSTALLOGR D, 2004, 60:933-935.

47 YUAN CH, BAI J, SUN YD et al. and LIANG DC*. Structure of potato calmodulin PCM6: the first report of the three-dimensional structure of a plant calmodulin. ACTA CRYSTALLOGR D, 2004, 60:1214-1219.

48 LIU L, WANG YL, ZHANG P et al. and GONG WM*. Expression, purification and preliminary crystallographic studies of human coactosin-like protein. ACTA CRYSTALLOGR D, 2004, 60:1651-1653.

49 SUN L, DONG YJ, ZHOU YF et al. and ZHANG XE*. Crystallization and preliminary X-ray studies of methyl parathion hydrolase from Pseudomonas sp. WBC-3. ACTA CRYSTALLOGR D, 2004, 60:954-956.

50 HU HY, WANG GG, YANG HT et al. and RAO ZH*, JIN C*. Crystallization and preliminary crystallographic analysis of a native chitinase from the fungal pathogen Aspergillus fumigatus YJ-407. ACTA CRYSTALLOGR D, 2004, 60:939-940.

51 LIU BB, LI XM, GAO RJ et al. and RAO ZH*. Crystallization and preliminary X-ray analysis of inorganic pyrophosphatase from the hyperthermophilic archaeon Pyrococcus horikoshii OT3. ACTA CRYSTALLOGR D, 2004, 60:577-579.

52 SHI N, LIU YW, NI MH et al. and RAO ZH*. Expression, crystallization and preliminary X-ray studies of the recombinant PTB domain of mouse dok1 protein.

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ACTA CRYSTALLOGR D, 2004, 60:334-336.

53 XU YH, SU N, QING L et al. and RAO ZH*. Crystallization and preliminary crystallographic analysis of heptad repeat complex of SARS coronavirus Spike protein. ACTA CRYSTALLOGR D, 2004, 60:2377-2379.

54 XU YH, BAI ZH, QIN L et al. and RAO ZH*. Crystallization and Preliminary Crystallographic analysis of fusion Core of spike protein of the murine coronavirus mouse hepatitis virus (MHV). ACTA CRYSTALLOGR D, 2004, 60:2013-2015.

55 WANG YL, CHENG ZJ, LIU L et al. and GONG WM*. Cloning, purification, crystallization and preliminary crystallographic analysis of human phosphoglycerate mutase. ACTA CRYSTALLOGR D, 2004, D60:1893-1894.

56 SONG XM, ZHOU ZC, WANG J et al. and GONG WM*. Purification, characterization and preliminary crystallographic studies of a novel plant defensin from Pachyrrhizus erosus seeds. ACTA CRYSTALLOGR D, 2004, D60:1121-1124.

57 LI X, LIU X, ZHAO Y et al. and RAO ZH*. Crystallization and preliminary crystallographic studies of human coactosin-like protein (CLP). ACTA CRYSTALLOGR D, 2004, 60:2387-2388.

58 HAN XQ, BARTLAM M, JIN YH et al. and RAO ZH*. The expression of SARS-CoV M gene in P. Pastoris and the diagnostic utility of the expression product. J VIROL METHODS, 2004, 122:105-111.

59 WANG XP, HAN XH, YANG FY*. Critical segment of apocytochrome c for its insertion into membrane. MOL CELL BIOCHEM, 2004, 262:61-69.

60 PENG YH, CHEN JW*. Anisodamine causes th changes of structure and function in the transmembrane domain of th Ca2+-ATPase from sacroplasmic reticulum. BIOSCI BIOTECH BIOCH, 2004, 68:126-131.

61 HUANG ZH, HUANG YG*. The relationship between MRP1 activities and its NBD conformational changes. SCI CHINA SER C, 2004, 47:425-433.

62 ZHOU JM*. Prion Diseases and The "Protein only" Hypothesis. PROG BIOCHEM BIOPHYS, 2004, 31:95-105.

63 LIU Q, ZHAO XG, ZHANG Y et al. and YAN XY*. Melanoma cell adhesion molecule (MCAM/CD146) is a critical molecule in trophoblast invasion. PROG BIOCHEM BIOPHYS, 2004, 31:309-312.

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Ⅶ. 代表性论文选编（影响因子大于 4）

Selected Publications

1 LIU ZF, YAN HC, WANG KB et al. and CHANG WR*. Crystal structure of spinach major light-harvesting complex at 2.72 angstrom resolution. NATURE, 2004, 428:287-292 ……………………………………………………………………………………… 87

2 WU BL, LI PY, LIU YW et al. and RAO ZH*. 3D structure of human FK506-binding protein 52: Implications for the assembly of the glucocorticoid receptor/Hsp90/immunophilin heterocomplex. P NATL ACAD SCI USA, 2004, 101:8348-8353. ……………………………………………………………………………………… 93

4 PENG H, BARTLAM MARK, ZENG QH et al. and RAO ZH*. Crystal structure of human pirin - An iron-binding nuclear protein and transcription cofactor. J BIOL CHEM, 2004, 279:1491-1498. ………………………………………………………………………………………103

5 SHI N, YE S, BARTLAM M et al. and RAO ZH*, YUAN JG*. Structural basis for the specific recognition of RET by the Dok1 phosphotyrosine binding domain. J BIOL CHEM, 2004, 279:4962-4969. ………………………………………………………………………………………111

6 JIANG Y, LI H, ZHU L et al. and ZHOU JM*, PERRETT S*. Amyloid nucleation and hierarchical assembly of Ure2p fibrils - Role of asparagine/glutamine repeat and nonrepeat regions of the prion domain. J BIOL CHEM, 2004, 279:3361-3369. ………………………………………………………………………………………119

7 WEI ZY, ZHANG P, ZHOU ZC et al. and GONG WM*. Crystal structure of human eIF3k, the first structure of eIF3 subunits. J BIOL CHEM, 2004, 279:34983-34990. ………………………………………………………………………………………128

8 LI MH, KWOK F, CHANG WR et al. and JIANG T*. Conformational changes in the reaction of pyridoxal kinase. J BIOL CHEM, 2004, 279:17459-17465. ………………………………………………………………………………………136

9 WANG YL, WEI ZY, BIAN Q et al. and GONG WM*. Crystal structure of human bisphosphoglycerate mutase. J BIOL CHEM, 2004, 279:39132-39138. ………………………………………………………………………………………143

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10 XU YH, LIU YW, LOU ZY et al. and RAO ZH*. Structural basis for coronavirus-mediated membrane fusion: Crystal structure of MHV spike protein fusion core. J BIOL CHEM, 2004, 279:30514-30522. ………………………………………………………………………………………150

11 XU YH, LOU ZY, LIU YW et al. and RAO ZH*. Crystal structure of SARS-CoV spike protein fusion core. J BIOL CHEM, 2004, 279:49414-49419. ………………………………………………………………………………………159

12 BAI M, ZHOU JM*, PERRETT S* et al. The yeast prion protein Ure2 shows glutathione peroxidase activity in both native and fibrillar forms. J BIOL CHEM, 2004, 279:50025-50030. ………………………………………………………………………………………165

13 BARTIAM M, WANG GG, YANG HT et al. and RAO ZH*. Crystal Structure of an Acylpeptide Hydrolase/Esterase from Aeropyrum pernix K1. STRUCTURE, 2004, 12:1481-1488. ………………………………………………………………………………………171

14 LIN Y, YAN XY*, CAO WC et al. Probing the structure of the SARS coronavirus using scanning electron microscopy. ANTIVIR THER, 2004, 9:287-289. ………………………………………………………………………………………179

15 ZHOU ZC, SONG XM, LI YK et al. and GONG WM*. Unique structural characteristics of peptide deformylase from pathogenic bacterium Leptospira interrogans. J MOL BIOL, 2004, 339:207-215. ………………………………………………………………………………………182

16 LIU L, WEI ZY, WANG YL et al. and GONG WM*. Crystal structure of human coactosin-like Protein. J MOL BIOL, 2004, 344:317-323. ………………………………………………………………………………………191

17 WAN QF, DONG YM, YANG H et al. and XU T*. Protein Kinase Activation Increases Insulin Secretion by Sensitizing the Secretory Machinery to Ca2+. J GEN PHYSIOL, 2004, 124:653-662. ………………………………………………………………………………………198

18 LIU BB, BARTLAM MARK, GAO RJ et al. and RAO ZH*. Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the Archaeon Pyrococcus horikoshii. BIOPHYS J, 2004, 86:420-427. ………………………………………………………………………………………208

19 LI DD, XIONG J, QU AL et al. and XU T*. Three-dimensional tracking of single secretory granules in live PC12 cells. BIOPHYS J, 2004, 87:1991-2001. ………………………………………………………………………………………216

20 CAI CX, CHEN JW*. Overexpression of caveolin-1 induces alteration of multidrug resistance in Hs578T breast adenocarcinoma cells. INT J CANCER, 2004, 111:522-529. ………………………………………………………………………………………227

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21 LIU JH, WANG ZX*. Kinetic analysis of ligand-induced autocatalytic reactions.. BIOCHEM J, 2004, 379:697-702. ………………………………………………………………………………………235

22 SU X, QING SB, PAN XM*. Thermal and conformational stability of Ssh10b protein from archaeon Sulfolobus shibattae. BIOCHEM J, 2004, 382:433-440. ………………………………………………………………………………………241

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Ⅷ. Future Prospects

With the support of the Ministry of Science and Technology and the Chinese Academy of Sciences, the NLB will continuously carry out. Taking full advantage of current resources and focusing incremental resources, to develop a 1st class platform for protein sciences, including systems for high-throughput protein expression, for antibody research and development, for functional analysis of proteins, for structural genomics, for proteomics, for innovations of key technologies. Built on the core of protein science, the NLB will actively pursue multidisciplinary study of protein 3-dimentional structure and function, structure and function of biological membrane and membrane proteins, function and folding principles of proteins, molecular basis of immunology and infectious diseases, molecular neurobiology, nano-biology, computational biology, and systems biology, protein and multipeptide drugs, to generate a large number of breakthroughs to advance the fundamental understanding of basic principles of science and to meet the strategic need of the Nation.

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Ⅷ. 今后发展方向

在科技部和中科院的支持下，生物大分子国家重点实验室将一如既往地坚持“流动、开放、联合、竞争”的办室方针；坚持定期评估、优胜劣汰、强强联合的管理机制。充分利用现有资源，集中投入增量经费，分阶段、有重点地建设包括高通量蛋白质表达与抗体研发系统、蛋白质功能分析研究系统、结构基因组学研究系统、蛋白质组学研究系统、关键技术自主创新系统的国际一流的蛋白质科学研究平台，并在此基础上以蛋白质科学为核心，发挥多学科交叉综合的优势，积极筹备以蛋白质三维结构与功能研究、生物膜和膜蛋白功能与结构研究、蛋白质功能与折叠原理研究、感染与免疫的分子基础、分子神经生物学、纳米生物学与微纳仿生、计算生物学和系统生物学、蛋白质药物与多肽药物等领域为主要研究方向的蛋白质科学国家实验室。并取得一批重大原创性成果，和一批与国家战略需求相关的重大成果。

86 articles Crystal structure of spinach major light- harvesting complex at 2.72 A˚ resolution

Zhenfeng Liu1, Hanchi Yan1, Kebin Wang2, Tingyun Kuang2, Jiping Zhang1, Lulu Gui1, Xiaomin An1 & Wenrui Chang1

1National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, People’s Republic of China 2Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, 20 Nanxincun, Xiangshan, Beijing 100093, People’s Republic of China

......

The major light-harvesting complex of photosystem II (LHC-II) serves as the principal solar energy collector in the photosynthesis of green plants and presumably also functions in photoprotection under high-light conditions. Here we report the ﬁrst X-ray structure of LHC-II in icosahedral proteoliposome assembly at atomic detail. One asymmetric unit of a large R32 unit cell contains ten LHC-II monomers. The 14 chlorophylls (Chl) in each monomer can be unambiguously distinguished as eight Chla and six Chlb molecules. Assignment of the orientation of the transition dipole moment of each chlorophyll has been achieved. All Chlb are located around the interface between adjacent monomers, and together with Chla they are the basis for efﬁcient light harvesting. Four carotenoid-binding sites per monomer have been observed. The xanthophyll-cycle carotenoid at the monomer–monomer interface may be involved in the non-radiative dissipation of excessive energy, one of the photoprotective strategies that have evolved in plants.

Light harvesting is the primary process in photosynthesis. In green LHC-II organized in an icosahedral particle includes initial phasing plants, the function of harvesting solar energy is fulfilled by a series by the single isomorphous replacement (SIR) method plus phase of light-harvesting complexes in the thylakoid membrane of chloro- refining and extending by the real-space averaging method9. Data plasts. LHC-II, the most abundant integral membrane protein in collection, phasing and refinement statistics are listed in Table 1. chloroplasts, exists as a trimer and binds half of the thylakoid The high-quality electron density map enabled us to trace 94% of chlorophyll molecules. Every monomeric LHC-II comprises a polypeptide of about 232 amino-acid residues, 13–15 Chla and Chlb molecules1,3–4carotenoids2 and one tightly bound phospholipid3. Besides the light-harvesting function, LHC-II has also been shown to Table 1 Data collection, phasing and refinement statistics Data set Native (1) Native (2) K2HgI4 (derivative) function in the non-radiative dissipation of excess excitation energy ...... 4,5 formed under high-light conditions . It has a crucial role in mini- Resolution (A˚ ) 50–3.5 25–2.7 50–3.5 mizing the damaging effects of excess light by operating this photo- R merge* 0.087 (0.112) 0.082 (0.368) 0.100 (0.131) protective mechanism as light intensity becomes increasingly Completeness (%) 97.9 (95.5) 90.8 (79.6) 80.5 (83.2) ,I/j . 6.1 (2.1) 14.4 (2.5) 6.4 (3.3) saturating. Moreover, LHC-II also takes part in regulating the SIR phasing statistics distribution of excitation energy to photosystems II and I (ref. 6). No. of heavy atom sites 10 The structure of LHC-II from pea has been determined by R cullis (centric/acentric)† 0.66/0.69 Phasing power (centric/acentric)† 1.13/1.67 electron crystallography at 3.4 A˚ resolution parallel to the mem- Resolution (A˚ ) 15–5.0 brane plane, and at about 4.9 A˚ resolution perpendicular to this FOM† 0.36 7 Phase refinement and extension statistics plane . This model revealed some basic structural features of Resolution (A˚ ) 10–2.72 LHC-II, including three transmembrane a-helices (helices A, B FOM† 0.922 (0.801) and C) and a short amphipathic helix (helix D), 12 chlorophyll Correlation coefficient‡ 0.967 (0.765) R factor‡ 0.128 (0.468) tetrapyrroles with roughly determined locations and orientations, Structure refinement statistics and two carotenoids. A more detailed structural picture of LHC-II, Resolution 10–2.72 with an unambiguous determination of the identity of the chloro- Reflections (working set) 179,170 phylls (Chla or Chlb) and the orientation of their transition dipole Reflections (test set) 9,326 R work/R free (%) 19.4/22.1 moments, would be beneficial for a better understanding of the r.m.s.d. bond length (A˚ ) 0.0124 basic functional mechanism of LHC-II. We have obtained this r.m.s.d. bond angle (8) 2.257 Coordinate error (A˚ )§ information by solving the structure of LHC-II at higher resolution Luzzati§ 0.28 using X-ray crystallography. SigmaA§ 0.28 In our model of the X-ray structure of LHC-II at 2.72 A˚ Number of non-hydrogen atoms Protein 16,619 resolution, we provide the basis for investigating quantitatively Cofactors 11,720 Water 699 the underlying mechanism of the light-harvesting process and its ...... adjustment in LHC-II. We also reveal for the first time an elegant Numbers in parentheses correspond to values in the highest resolution shell. arrangement of membrane proteins in the icosahedral proteolipo- *Rmerge ¼ SjShjI j,h– , I h . j/S jS h , I h . , where h are unique reflection indices, I j,h are intensities of symmetry-related reflections and ,I h . is the mean intensity. Reflections with some assembly, and show that membrane proteins can be crystal- I . 2.0 £ j I in native (1) and derivative data sets were used in the R merge calculation, whereas lized in a way that differs from those described in ref. 8. the 23.0 £ j I cutoff was applied in the native (2) data set. †FOM (figure of merit), Rcullis (centric) and phasing power determined by programs from the CCP4 suite (see Methods). 2 ‡Correlation coefficient¼ Shð, Fo .2jFojhÞð, Fc .2jFcjhÞ=½Shð, Fo .2jFojhÞ Shð, Fc . 2 1=2 Structure determination 2jFcjhÞ ;R factor ¼ ShjFo 2 Fcj=ShFo, where h are the unique reflection indices, F o are the observed structure factors and F c are the structure factors calculated from inversion of the non- Crystallization of trimeric LHC-II isolated from Spinacia oleracea crystallographic symmetry-averaged map. is described briefly in the Methods. Structure determination of §From Luzzati plot and SigmaA analysis, as determined with CNS (see Methods). 87 287 NATURE | VOL 428 | 18 MARCH 2004 | www.nature.com/nature © 2004 Nature Publishing Group articles the 232 amino acids and accurately locate the 14 chlorophylls and 4 adjacent trimers, functioning as a bridge. The hydrophobic fatty- carotenoids within one monomeric LHC-II. For the 14 chloro- acid chains of DGDG extend into the membrane interior, inter- phylls, assignment of the orientation of the Qx and Qy transition acting with hydrophobic residues and pigments of LHC-II. Other dipolar moments was accomplished by proper positioning of the lipids that are expected to fill the gaps between LHC-II trimers and chlorophyll head groups. Ten chlorophylls were modelled with to form a spherical lipid-bilayer vesicle are mostly disordered. complete phytyl chains, but phytyl chains for the remaining four In the crystal lattice (Fig. 2b), LHC-IIs are assembled and packed chlorophylls could be only partially modelled. With the help of in a manner different from those in ‘Type I’ and ‘Type II’ three- 2F o–F c and F o–F c electron-density maps (Fig. 1a, b), all 14 dimensional (3D) crystals of membrane proteins as originally chlorophylls were unambiguously characterized as eight Chla and proposed in ref. 8. The LHC–DGDG proteoliposomes assume the six Chlb. The resulting Chla/b molar ratio of 1.33 is consistent with shape of closed spheres, presumably originating from curved, small the value determined by earlier biochemical analyses1,2.Three patches of two-dimensional (2D) membrane–protein crystals. Both carotenoids were identified as two luteins and one neoxanthin, the outer and inner surfaces of each proteoliposome are hydro- and the fourth member was interpreted as a mixed density involving philic. The contacts between two proteoliposomes in the crystal the xanthophyll-cycle carotenoids. In addition, two lipids, one lattice are polar interactions provided by the hydrophilic stromal detergent molecule and about 70 water molecules per monomer surfaces of LHC-IIs. The hydrophobic intramembranous surfaces of have been positioned. Figure 1c, d shows two regions of the LHC-II trimers are sheltered from crystal packing by the hydro- electron-density map calculated with the phases at 2.72 A˚ phobic chains of lipids. We categorize this novel kind of 3D crystal resolution. as a ‘Type III’ membrane-protein crystal.

Icosahedral proteoliposome and crystal packing The apoprotein and LHC-II trimer ¼ In the T 1 icosahedral particle (Fig. 2a), 20 LHC-II trimers are The polypeptide main chain of each monomeric LHC-II was organized in a closed ‘532’ point group symmetry, with their central continuously traced from Ser 14 to Gly 231. The secondary structure C3 axis serving as the icosahedral C3 axis and oriented radially model of spinach LHC-II reported here (Fig. 3a) is similar to the towards the sphere centre. One C3 axis and two C2 axes of the electron crystallographic model of LHC-II from pea7. Between the icosahedron superpose with the crystallographic axes. These trimers primary structures of spinach and pea LHC-II, 89% of the 232 form a spherical shell with an outer diameter of about 261 A˚ and an ˚ amino acids are conserved. However, deviations in the residue inner diameter of about 160 A. They are oriented in the shell with range, length, turns and orientation between helices in the two their ﬂat lumenal surface facing the interior of the sphere and the species were observed7 (Fig. 3a). We also found a typical amphi- less ﬂat stromal surface facing outwards, taking part in the contacts pathic short 310-helix located in the BC loop region and named it with other particles in the crystal. The interactions between two helix E. Helix E has a length close to that of helix D and is related to adjacent trimers are mediated mainly by two digalactosyl diacyl- helix D by the internal pseudo-C2 axis. It is inclined with respect to glycerol (DGDG) molecules and two pairs of chlorophylls through the membrane plane by an angle of about 308. In the following EC van der Waals contacts. They are all located near the icosahedral C2 loop, the polypeptide folds into two short antiparallel strands that axis. The digalactosyl head group of each DGDG is simultaneously are stabilized by an inter-strand ionic pair (Asp 111–His 120) and hydrogen bonded to the lumenal-surface amino acids from two some hydrogen bonds. The basic structural and functional unit of LHC-II is the trimer. The whole trimerization region covers the amino-terminal domain, the carboxy terminus, the stromal end of helix B, several hydrophobic residues from helix C and also the pigments and lipid bound to these parts of the polypeptide chain (Fig. 3b). Chla 614, Chla 613, xanthophyll-cycle carotenoid, phosphatidylglycerol (PG), Chlb 601 and Chla 602 from one monomer together with Chlb 607, Chlb 609 and Chla 603 from the neighbouring monomer line up from the periphery of the trimer to the core region near the central C3 axis at

Figure 1 Electron-density map at 2.72 A˚ resolution. a, Chla and b, Chlb. Grey cage,

2Fo–Fc density (1.5 £ j level); cyan cage, Fo–Fc density (4.0 £ j level). No residual Figure 2 Organization and packing of the icosahedral particles. a, Schematic drawing of 2Fo–Fc or Fo–Fc density appears beside Chla C7-methyl, while strong 2Fo–Fc and one-half of the LHC-II–DGDG proteoliposome viewed along the c axis of the hexagonal Fo–Fc densities show up at the position of Chlb C7-formyl if it is omitted. c, N-terminal cell. b, Packing diagram of ‘Type III’ membrane-protein crystal, showing the contacts region including binding sites for a Chlb (cyan) and a phospholipid coordinated to a Chla between icosahedral spherical particles in the hexagonal cell. Prosthetic groups are (green). d, Two antiparallel polypeptide strands in the EC loop region with one Chlb bound. omitted for clarity. The N-terminal domain and AC loop region located at the stromal

In c and d,2Fo–Fc densities (1.5 £ j level) are shown as a purple cage. surface are involved in the crystal packing. 88 288 © 2004 Nature Publishing Group NATURE | VOL 428 | 18 MARCH 2004 | www.nature.com/nature articles the interface between monomers, forming extensive hydrophobic resulting in the clustering of Chlb molecules in this region, which interactions. Six Chla (Chla 602 and Chla 603 from each monomer) may facilitate the efficient energy transfer between these chloro- constitute the core of the trimer. Our observations directly reveal phylls. It was suggested by functional investigations that Gln 131 is the structural role of PG in stabilizing the LHC-II trimer and clearly involved in the selective binding of Chlb molecules to LHC-II12,13.As indicate that hydrophobic interactions dominate the associations for the selective binding of Chla, we notice that the environment between monomers within a trimer. It was shown that removal of surrounding the C7-methyl groups of Chla molecules is mostly the first 49 or 51 amino-acid residues of the polypeptide by nonpolar. Hydrophobic repulsion or steric hindrance may be the proteolytic cleavage led to loss of PG and complete dissociation factors affecting the binding affinity of Chlb to these Chla-binding of the trimer into monomers, and that hydrolysis of the PG by sites. phospholipase A2 has a similar effect in breaking down the LHC-II trimer3. Chlorophyll arrangement for efficient light harvesting The chlorophylls in LHC-II are vertically distributed into two layers within the membrane, each layer lying close to the stromal or Chlorophyll-binding sites lumenal surface (Fig. 4a). Inside a monomer, the layer close to the In a crystallographic asymmetric unit, the individual chlorophyll- stromal surface contains eight chlorophylls (five Chla and three binding sites in each LHC-II monomer are occupied by one type of Chlb), which surround the central helices A and B more or less chlorophyll (either Chla or Chlb). No mixed binding sites were evenly to form an elliptical ring (Fig. 4b). The average centre-to- observed. All central ligands of the 14 chlorophylls have been centre distance between two neighbouring chlorophylls is about identified as side chains of seven amino-acid residues, two backbone 11.26 A˚ , with a maximum of 12.79 A˚ and a minimum of 9.74 A˚ . carbonyls, four water molecules and the phosphodiester group of Each chlorophyll inside this layer can find its symmetric mate 7 a PG (Supplementary Table 1; a comparison with a previous model related by the internal pseudo-C2 axis. The remaining six chloro- is also included). This coordination mode of Chla 611 to PG is phylls (three Chla and three Chlb) are arranged in the layer close to the second case of its kind since its first discovery in photosystem I the lumenal surface. They form two separate clusters comprising (ref. 10). On the other side, the phosphodiester group of PG forms a four chlorophylls (three Chlb and one Chla) and a Chla–Chla dimer hydrogen-bonding and ionic interaction with the side chains of (Fig. 4c). Among them, Chlb 606 and Chla 604 are associated with Tyr 44 and Lys 182 respectively (Fig. 1c). the smallest centre-to-centre distance (8.05 A˚ ) in LHC-II. The The polypeptide backbone NH and side chains also form hydro- shortest distance between two chlorophyll layers is about 13.89 A˚ 1 gen bonds with the C7-formyl groups (Chlb) and the C13 -keto (Chlb 609 to Chlb 606). groups of several chlorophylls (Supplementary Table 1). These Another interesting feature of this chlorophyll arrangement is the interactions will not only strengthen the linkage between pigments enrichment of Chlb molecules around helix C and at the interface and protein, but also influence the absorption characteristics of between monomers (Fig. 4a). All six Chlb molecules are located in chlorophylls as shown previously11. Except for Chlb 601, nearly all this region, with five of them belonging to one monomer and the Chlb in the complex are selectively hydrogen-bonded to the poly- remaining one (Chlb 601) from the neighbouring monomer. peptide or to the coordinated water of Chlb 607 through their Chlb 601 (II) and Chlb 609 (I) (distance, 11.79 A˚ ) are the closest C7-formyls. The amide side chain of Gln 131 interacts with three associated couple of chlorophylls between adjacent monomers Chlb molecules. One hydrogen bond is formed through the inter- within a trimeric LHC-II, indicating that this Chlb-rich region is action of its C ¼ O with the coordinated water of Chlb 606, and two of critical importance in energy equilibrating inside a functional additional hydrogen bonds are formed by its NH2 interacting with trimer. the C7-formyls of Chlb 607 and Chlb 609. Moreover, the C7-formyl In the trimeric LHC-II, all 24 chlorophylls from the stromal layer of Chlb 606 is hydrogen-bonded to the coordinated water of Chlb are organized into two irregular circular rings (Fig. 4d). The inner 607. All these interactions bring three Chlb into close proximity, ring located in the core region of a trimer is composed of six Chla molecules that are thought to have an important role in inter- monomeric energy transfer14. The remaining nine Chla and nine Chlb (those covered by the yellow circular ring in Fig. 4d) form the outer ring and are arranged in a mosaic pattern, with three Chlb alternating with three Chla. This new pigment arrangement would favour the efficient absorption of incident light energy from all directions in a broad spectral region and the transfer of the excitation energy to the nearest exit, the putative terminal fluorescence emitter Chla 612 (Supplementary Table 2), in a few steps and at high rates. Energy transfer between two lumenal clusters are much less efficient than those within a stromal layer, as they are separated by larger distances (Fig. 4e). We infer that these lumenal chlorophyll clusters might serve as upstream energy collectors, absorbing energy and transmitting it to the stromal chlorophylls in a relatively independent way. The energy absorbed by the stromal chlorophylls is quickly focused on Chla 612/Chla 611 and is further Figure 3 Secondary structure of monomeric LHC-II apoprotein and trimerization. View in transmitted to the neighbouring LHCs or reaction centres. parallel with the membrane plane. a, The vertical line indicates the approximate direction of the membrane normal and the position of the pseudo-C2 axis. Helices are labelled A–E. Carotenoids as light-harvesting antennae Helix E is newly defined, whereas others are labelled as before7. The angle between the The two central carotenoids with all-trans configurations are bound central axis of each helix and the membrane normal is shown in parentheses, with the in the grooves on both sides of the supercoil (helices A and B) to residue range marked below each value. b, The interface between two adjacent form a cross-brace. They are assigned as lutein molecules (Fig. 4). monomers is shown. Colour code: yellow, amino-acid residues; green, Chla; cyan and Best fit with the electron density is achieved when the b-rings of blue, Chlb; magenta, xanthophyll-cycle carotenoids; pink, PG; red, water; maroon, Ca both lutein molecules are oriented towards the lumenal surface and traces of N-terminal (Ser 14–Asp 54) and C-terminal (Asp 215–Gly 231) polypeptide the e-rings point to the stromal surface. The polyene chains of lutein chain. The vertical line represents the local C3 axis of an LHC-II trimer. 620 and lutein 621 are inclined with respect to the membrane normal 89 289 NATURE | VOL 428 | 18 MARCH 2004 | www.nature.com/nature © 2004 Nature Publishing Group articles by angles of about 598 and 628, respectively. Both ring-shaped end neoxanthin to Chlb 606 and Chlb 608 is highly possible. There is groups of these two lutein molecules interact with four internal experimental evidence to suggest that singlet excitation energy of homologous segments of the polypeptide15 located on both ends of luteins is transferred exclusively to Chla molecules and not to helices A and B through van der Waals contacts and hydrogen Chlb21. Neoxanthin was found to transfer its energy mostly towards bonds. Their polyene chains are firmly fixed in two elongated Chlb21,22. It can be concluded that lutein and neoxanthin found in narrow hydrophobic cavities on both sides of the supercoil, provid- LHC-II may function as effective accessory light-harvesting anten- ing strong and rigid linkage between helices A and B. They are nae, absorbing light in the blue–green spectral region as a comp- indispensable for proper in vitro folding of LHC-II into stable lement to Chla/b absorbing in the red region. This is in addition to complexes16–19. their obvious structural role as well as their photoprotective role of The third carotenoid, shaped like a bent-over hook, is located in quenching triplet chlorophylls and singlet oxygen7. the Chlb-rich region around helix C and is assigned as 9 0 -cis neoxanthin (Fig. 4). Its polyene chain forms an angle of about 588 Structure-based non-photochemical quenching model with the membrane normal. A value of about 57 ^ 1.58 derived The fourth carotenoid we discovered in LHC-II is located at the from linear dichroism spectra20 confirms our assignment. The monomer–monomer interface. The polyene chain of this caroten- epoxycyclohexane ring of neoxanthin hangs over the chlorin ring oid has an all-trans configuration and forms a small angle (348) with of Chla 604 and is hydrogen-bonded to the hydroxyl of Tyr 112 via the membrane normal. As shown in Fig. 3b, a hydrophobic pocket is 0 its C3 -hydroxyl. Side chains of Leu 134, Met 135, Val 138 from formed at the interface by several chlorophylls, hydrophobic resi- helix C and Trp 71 from helix B as well as chlorin rings and phytyl dues from the polypeptide and the PG. Part of the polyene chain of chains of Chlb 606 and Chlb 608 form a hydrophobic cleft this carotenoid together with one of its end groups is accommo- that accommodates the hook-shaped polyene chain of neoxanthin. dated inside this pocket. The opposite end group sticks outside the Thisbindingsitehasbeenshowntobehighlyselectivefor binding pocket and faces the chlorin plane of Chlb 601 at the neoxanthin17,19. The cyclohexane ring of neoxanthin on the other stromal side. The two ring-shaped end groups of this carotenoid end stretches into the exterior solvent region and exhibits weak exhibit distinct electron densities (one flat and the other bulgy electron density. between C-5 and C-6). This observation led to our original assign- The rate of singlet excitation energy transfer between carotenoids ment of this carotenoid as an antheraxanthin, an intermediate in the and chlorophylls is correlated with the mutual orientation between xanthophyll cycle. However, later carotenoid composition analysis them, the centre-to-centre intermolecular distance and the closest revealed that the major component of xanthophyll-cycle caroten- distance between two conjugated parts (Supplementary Table 3). Six oids in the LHC-II preparation used for crystallization is violax- Chla are found to be in favourable orientations and distances with anthin. We propose that the electron density may be interpreted by a respect to two luteins for efficient singlet energy transfer from lutein mixed binding of different xanthophyll-cycle carotenoids at this to Chla. The data also show that efficient energy transfer from site. The end group at the lumenal side points to the cavity formed

Figure 4 Pigments in the LHC-II trimer and monomer. a, Stereo view showing the pigment Chlorophylls are represented by three atoms: the central magnesium atom and two arrangement pattern in the LHC-II trimer. View along the membrane normal from the nitrogen atoms. The connecting line between the two nitrogens deﬁnes the directions of stromal side. Monomers are labelled I–III. For clarity, the chlorophyll phytyl chains and the Qy transition dipole. Green, Chla nitrogen; blue, Chlb nitrogen; grey, magnesium; lipids are omitted. Green, Chla; blue, Chlb; yellow, lutein; orange, neoxanthin; magenta, purple and blue ellipse, approximate monomer area. The magenta numerical note near xanthophyll-cycle carotenoids. b, c, Pigment pattern in a monomer at the stromal and the dark line connecting two chlorophylls indicates the centre-to-centre distance (A˚ ) lumenal sides, respectively. Colour designation the same as in a. d, e, Arrangement of between them. chlorophylls within a LHC-II trimer at the stromal and lumenal sides, respectively. 90 290 © 2004 Nature Publishing Group NATURE | VOL 428 | 18 MARCH 2004 | www.nature.com/nature articles

around the local C3 axis, suggesting that this cavity might be the energy-trapping sites. As a consequence, the potential damaging docking site for violaxanthin de-epoxidase23. effect of excess energy would be avoided. A The xanthophyll cycle was proposed to have a major role in adjusting the efficiency of light harvesting4,24,25. It involves the Methods conversion of violaxanthin into zeaxanthin through antherax- The LHC-II was isolated according to the protocol described previously30. A single step of anthin. It was suggested that zeaxanthin molecules can act as direct gel filtration chromatography with Hiload 16/60 Superdex 200 pg column (Pharmacia quenchers of excess excitation by accepting singlet energy trans- Biotech) was added to improve sample purification, ensuring crystallization 26,27 reproducibility. The purified LHC-II was solubilized in a solution containing 0.8% ferred from chlorophyll . We observed that at least three chloro- 21 n-nonyl-b-D-glucoside (BNG) (Anatrace) and 2 mg ml DGDG (Lipid Products) to a phylls are close to the xanthophyll-cycle carotenoids and adopt final concentration of 4 mg ml21 chlorophyll (about 8 mg ml21 protein) and mixed with favourable orientations for efficient singlet excitation transfer from the crystallization solution containing 66.5 mM HEPES-NaOH pH 7.5, 0.9–1.1 M citrate chlorophylls to the xanthophyll-cycle carotenoids (Supplementary trisodium and 0.2% N,N-bis-(3-D-gluconamidopropyl)deoxycholamide (DBC) Table 3). In addition, we noticed that the distance between Chla 613 (Anatrace) in a ratio of 3.0:1.8 (v/v). The resulting drop was equilibrated against a well of ˚ 1 ml crystallization solution at 291–293 Kusing the sitting-drop vapour-diffusion method. and Chla 614 is smaller than 10 A, and their mutual orientation is Green tabular crystals appeared a week later and grew to a maximum size of about close to an irregular distribution (Fig. 4e; Supplementary Table 2). 0.5 £ 0.5 £ 0.05 mm after one month. Heavy-atom derivative was prepared by soaking the crystal for about 24 h in artificial mother liquor (50 mM HEPES-NaOH pH 7.5, 0.6% These features agree well with the characteristics of statistical pair 21 energy trap28. We speculate that this pair of Chla molecules might BNG, 0.1% DBC, 1.5 mg ml DGDG, 1.09 M citrate trisodium) containing 0.5 mM K2HgI4, followed by a backsoaking procedure for about 3–5 h in heavy-atom-free also function as an excitation energy quencher, which would mother liquor. A cryoprotectant (50 mM HEPES-NaOH pH 7.5, 0.4% BNG, 0.15% DBC, enhance the quenching effect of the xanthophyll-cycle carotenoids. 1.0 mg ml21 DGDG, 1.15 M citrate trisodium, 11% saturated sucrose) was introduced to Here we propose a structure-based non-photochemical quench- the crystal by soaking for a few minutes and then the crystal was flash-frozen for the X-ray ing(NPQ)modelconcerningLHC-II(Fig.5).Efficientnon- diffraction experiment. The first native data set and the derivative data set were collected at PF (Tsukuba, Japan) beamline BL6B and the second native data set was collected at BSRF photochemical energy-transfer pathways are established upon (Beijing, China) beamline 3W1A. A large crystal-to-detector distance (250–350 mm) and aggregation of LHC-II trimers mediated by DGDG, so that the a small oscillation (0.58) are necessary for reducing the overlap of reflections in the large excitation energy is able to escape from one trimer to the adjacent diffraction angle region. Data were processed with Denzo and Scalepack31. A typical trimer via these pathways. The following step is the migration of the icosahedral ‘532’ point group symmetry was found by calculating self-rotation function with GLRF32. We inferred that there is only one T ¼ 1 icosahedral particle residing in a excitation to the trapping site (the xanthophyll-cycle carotenoids primitive rhombohedral unit cell by analysing the crystal packing. The icosahedron is and/or Chla 613–Chla 614 pair), where the non-radiative dissipa- oriented with one of its ‘32’ subgroups superposing with the crystallographic ‘32’ point tion of excitation energy happens. This explains the NPQ observed group. Each crystallographic asymmetric unit contains one-sixth of the icosahedron. upon incorporation of LHC-II into the liposomes containing Ten heavy-atom sites were located using SnB33 in direct method mode at 5 A˚ . The 29 arrangement of heavy atoms in the unit cell also abides with the icosahedral ‘532’ DGDG . Conformational change induced by the protonation of symmetry, confirming our judgement based on self-rotation function and crystal packing photosystem II proteins including LHC-II was found to be necess- analysis. The initial SIR phase was calculated with MLPHARE of the CCP4 suite34 at 5 A˚ . ary for NPQ4,25. Among the seven lumen-exposed acidic residues in Phase refinement and extension was performed according to the standard molecular replacement real-space averaging protocol9. The NCS matrix was derived from the output our structure, four of them (Glu 94, Asp 111, Glu 207 and Asp 211) 35 form ion pairs with basic residues. The protonation of these acidic of GLRF and improved by IMP . A molecular envelope enclosed by two icosahedral C3 axes and one icosahedral C5 axis covering an icosahedral asymmetric unit with a thickness residues under low lumenal pH conditions may trigger the confor- of about 50 A˚ was generated by MAMA35. Electron density was calculated using FFT mational changes of helix D and the BC loop. The linker chloro- (CCP4) and density averaging was performed with AVE35. The SFALL program (CCP4) phylls (Chla 614 and Chlb 605) at the trimer–trimer interface was used to calculate F c and a c from the averaged density map. The correlation coefficient (Fig. 5) are coordinated to these regions of polypeptide chain. and R factor were calculated using Rstats (CCP4). The a c were combined with the initial SIR phases a b using SigmaA (CCP4) and a new electron-density map was calculated with ˚ ˚ They may be moved and reoriented to promote the non-photo- the F o and the combined phases. Phases were extended from 5.0 A to 3.5 A using a step size chemical energy transfer and/or the quenching effect of the putative of 0.05 A˚ , and then to 2.72 A˚ with 0.02 A˚ step size. Phase refinement was performed for ten iterative cycles in each extension step. The final averaged electron-density map was of high quality, and the backbone was traced without much difficulty. Most of the pigments are clearly defined in the map. The electron-density map was interpreted using the program O36. The polypeptide model was built with the help of a published primary sequence of Lhcb1 (ref. 37). The crystals mainly contain two highly homologous polypeptides, Lhcb1 and Lhcb2. Differences between the two polypeptides are confined to the N-terminal region, which may account for the weakness of the electron density in the region before Ser 14. Structure refinement was performed with CNS38. At initial stages, two rounds of NCS-constrained simulated annealing (torsion angle dynamics protocol) were performed at 3.5 A˚ , followed by positional refinement. After the resolution was extended to 2.72 A˚ , the NCS constraint was switched to restraint mode and the restraint was gradually released at final stages. The individual B factors were refined using 10–2.72 A˚ data. Peaks above 3.0 £ j in the F o–F c electron density map were picked as candidates for water molecules, after the R factor was reduced to below 23%. Stereochemical restraints were introduced between chlorophylls and their central ligands during refinement. The final model was evaluated with PROCHECK39 and all ten monomers have good geometry with only one Ramachandran outlier (Val 119) per monomer, the backbone carbonyl of which coordinates a chlorophyll. Secondary structures of polypeptides were analysed with STRIDE40. Figures 1c, d and 2b was prepared with program O36. All other figures were prepared with Molscript41 and Raster3d42. Received 29 October 2003; accepted 27 January 2004; doi:10.1038/nature02373.

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USA 96, 34. CCP4 Collaborative Computational Project, The CCP4 suite: programs for protein crystallography. 10056–10061 (1999). Acta Crystallogr. D 50, 760–763 (1994). 13. Remelli, R., Varotto, C., Sandona`, D., Croce, R. & Bassi, R. Chlorophyll binding to monomeric light- 35. Jones, T. A. in Molecular Replacement (eds Dodson, E. J., Gover, S. & Wolf, W.) 92–105 (SERC harvesting complex. A mutation analysis of chromophore-binding residues. J. Biol. Chem. 274, Daresbury Laboratory, Warrington, 1992). 33510–33521 (1999). 36. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models 14. Gradinaru, C. C. et al. The flow of excitation energy in LHCII monomers: implications for the in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 structural model of the major plant antenna. Biophys. J. 75, 3064–3077 (1998). (1991). 15. Bassi, R., Sandona`, D. & Croce, R. 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H. M. V., Pascal, A. A., Grondelle, R. V. & Amerongen, H. V. Identifying the pathways of energy transfer between carotenoids and chlorophylls in LHCII and CP29. A Supplementary Information accompanies the paper on www.nature.com/nature. multicolor, femtosecond pump-probe study. J. Phys. Chem. B 104, 9330–9342 (2000). 22. Croce, R., Mu¨ller, M. G., Bassi, R. & Holzwarth, A. R. Carotenoid-to-chlorophyll energy transfer in Acknowledgements We thank D. C. Liang and the late P. S. Tang for their efforts in initiating recombinant major light-harvesting complex (LHC-II) of higher plants. I. femtosecond transient this project; X. C. Gu for discussions; N. Sakabe and K. Sakabe at PF (Tsukuba, Japan) and the absorption measurements. Biophys. J. 80, 901–915 (2001). staff at BSRF (Beijing, China) for their support during data collection at the synchrotron facilities. 23. Hieber, A. D., Bugos, R. C. & Yamamoto, H. Y. Plant lipocalins: violaxanthin de-epoxidase and This research was financially supported by the National Key Research Development Project of zeaxanthin epoxidase. Biochim. Biophys. Acta 1482, 84–91 (2000). China, the National Natural Science Foundation of China, the National Key Special Research 24. Demmig-Adams, B. & Adams, W. W. Photoprotection and other responses of plants to high light Program and the Knowledge Innovation Program of the Chinese Academy of Sciences. stress. Annu. Rev. Plant Physiol. Plant Mol. Biol. 43, 599–626 (1992). 25. Gilmore, A. M. Mechanistic aspects of xanthophyll cycle-dependent photoprotection in higher plant chloroplasts and leaves. Physiol. Planta. 99, 197–209 (1997). Competing interests statement The authors declare that they have no competing financial 26. Frank, H. A. et al. Photophysics of the carotenoids associated with the xanthophyll cycle in interests. photosynthesis. Photosynth. Res. 41, 389–395 (1994). 27. Ma, Y. Z., Holt, N. E., Li, X. P., Niyogi, K. K. & Fleming, G. R. Evidence for direct carotenoid Correspondence and requests for materials should be addressed to W.R.C. involvement in the regulation of photosynthetic light harvesting. Proc. Natl Acad. Sci. USA 100, ([email protected]). Coordinates and structure factors have been deposited in the Protein 4377–4382 (2003). Data Bank under accession code 1RWT.

92 292 © 2004 Nature Publishing Group NATURE | VOL 428 | 18 MARCH 2004 | www.nature.com/nature 3D structure of human FK506-binding protein 52: Implications for the assembly of the glucocorticoid receptor͞Hsp90͞immunophilin heterocomplex

Beili Wu*†‡, Pengyun Li*†‡, Yiwei Liu*†, Zhiyong Lou*†, Yi Ding*†, Cuiling Shu§, Sheng Ye*†, Mark Bartlam*†, Beifen Shen§¶, and Zihe Rao*†¶

*Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China; †National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China; and §Beijing Institute of Basic Medical Science, Beijing 100850, China

Edited by Timothy A. Springer, Harvard Medical School, Boston, MA, and approved April 14, 2004 (received for review September 17, 2003) FK506-binding protein 52 (FKBP52), which binds FK506 and pos- we have determined the structures of two overlapping fragments sesses peptidylprolyl isomerase activity, is an important immu- of FKBP52: N(1–260) [(1–260)a (space group P21) and N(1– nophilin involved in the heterocomplex of steroid receptors with 260)b (space group P212121)], and C(145–459). Based on these heat-shock protein 90. Here we report the crystal structures of two two structures, we have defined the whole putative structure of overlapped fragments [N(1–260) and C(145–459)] of FKBP52 and FKBP52, which is architecturally similar to FKBP51 except that the complex with a C-terminal pentapeptide from heat-shock the orientations between different domains are diverse. The protein 90. Based on the structures of these two overlapped structural alterations give the clues for the differential effects of fragments, the complete putative structure of FKBP52 can be FKBP52 and FKBP51. We have also determined the structure of defined. The structure of FKBP52 is composed of two consecutive C(145–459) in complex with the C-terminal pentapeptide FKBP domains, a tetratricopeptide repeat domain and a short (MEEVD) from Hsp90. The complex structure maps out the helical domain beyond the final tetratricopeptide repeat motif. Key binding pocket in the TPR domain and reveals several key structural differences between FKBP52 and FKBP51, including the residues involved in Hsp90 binding. relative orientations of the four domains and some important residue substitutions, could account for the differential functions Methods of FKBPs. Protein Expression and Purification. Codons 1–260 [N(1–260)] and 145–459 [C(145–459)] of human FKBP52 were cloned into the mmunophilins are proteins possessing peptidylprolyl isomer- His-6-tag expression plasmid pET28a(ϩ) (Novagen). N(1–260) Iase (PPIase) domains that bind immunosuppressant drugs. was overexpressed in Escherichia coli strain BL21 (DE3), and the According to their binding affinity for different drugs, immu- selenomethionine-labeled C(145–459) was produced by expres- nophilins have been divided into two families: FK506-binding sion in methionine-deficient E. coli strain B834 (DE3). The proteins (FKBPs), which bind FK506 and rapamycin, and cyclo- soluble proteins were purified by using Ni2ϩ-nitrilotriacetic acid philins, which bind cyclosporin A (1, 2). agarose (Qiagen, Valencia, CA) and chromatography on Super- FKBP52 is an immunophilin belonging to the FKBP family, dex 75 and Resource Q (Pharmacia). with a molecular mass of 52 kDa, and was first discovered as a component of an inactive steroid receptor͞heat-shock pro- Crystallization. The protein solution of N(1–260) used for crys- tein 90 (Hsp90) complex (3). The assembly pathway of steroid tallization contained 20 mM Tris (pH 8.0), 150 mM NaCl, and receptors involves multiple chaperone and cochaperone proteins such as Hsp90, Hsp40, Hsp70, Hsp70/90 organizing 20 mg/ml protein. Crystals were obtained by using the hanging- protein (Hop), and P23 (4–6). Matured steroid receptor drop vapor-diffusion technique with reservoir solutions con- complexes contained Hsp90 and at least one immunophilin: taining 28–31% polyethylene glycol 6000, 3–5% DMSO, and FKBP52, another FKBP (FKBP51), the cyclosporin A-binding 100 mM Tris [pH 8.0 for N(1–260)a] and 200 mM calcium protein cyclophilin 40 (Cyp40), or the protein phosphatase 5 chloride, 20% polyethylene glycol 3350 [for N(1–260)b] in a ␮ ␮ (PP5). These cochaperones all possess tetratricopeptide repeat drop formed by mixing 1 l of protein solution and 1 lof (TPR) domains, which form the binding sites for Hsp90 (7). reservoir solution at 291 K. Crystals of C(145–459) were grown ͞ The C-terminal MEEVD sequence motif of Hsp90 has been by using a reservoir solution of 100 mM Tris, pH 8.0 2.2–2.4 ͞ shown to be critical for the binding of Hsp90 to various M ammonium sulfate 2–4% (vol/vol) ethanol. Protein con- TPR-containing proteins (8). centration was 10 mg/ml in 20 mM Tris, pH 8.0/100 mM NaCl/5 Immunophilins are not required for steroid receptors to bind mM DTT. Crystals of the C(145–459)͞MEEVD complex hormones in vitro (5, 9, 10), but they are known to influence (protein/peptide, 1:1.5) were grown by using a reservoir solu- steroid signaling pathways. Receptor-associated FKBP52 and tion of 1.2 M sodium citrate (pH 6.7). PP5 are suggested to play a role in the shuttling of steroid receptors between cytoplasm and nuclear compartments (7, 11–13). Overexpression of FKBP51 may be responsible for the This paper was submitted directly (Track II) to the PNAS office. low hormone-binding affinity of glucocorticoid receptor in both Abbreviations: PPIase, peptidylprolyl isomerase; FKBP, FK506-binding protein; Hsp, heat- ͞ human and squirrel monkey (14–16). Although FKBP52 and shock protein; Hop, Hsp70 90 organizing protein; Cyp40, cyclophilin 40; PP5, protein Ϸ phosphatase 5; TPR, tetratricopeptide repeat; FK1, first FKBP domain of FKBPs; FK2, second FKBP51 share 75% sequence similarity (Fig. 1a), they affect FKBP domain of FKBPs. hormone binding by glucocorticoid receptor in opposing man- Data deposition: The atomic coordinates and structure factors for N(1–260) (space group ners and have different Hsp90-binding characteristics. It is not P21), C(145–459), and C(145–459)͞MEEVD have been deposited in the Protein Data Bank, clear what structural features are responsible for these functional www.pdb.org (PDB ID codes 1Q1C, 1P5Q, and 1QZ2, respectively). differences between FKBP52 and FKBP51. The crystal structure ‡B.W. and P.L. contributed equally to this work. of FKBP51 has been solved recently, as well as that of the PPIase ¶To whom correspondence may be addressed. E-mail: [email protected] or domain of FKBP52 (16, 17). FKBP52 is difficult to crystallize [email protected]. because of its instability in solution. To overcome this problem, © 2004 by The National Academy of Sciences of the USA

8348–8353 ͉ PNAS ͉ June 1, 2004 ͉ vol. 101 ͉ no. 22 www.pnas.org͞cgi͞doi͞10.1073͞pnas.0305969101 93 Fig. 1. (a) Sequence alignment of human FKBP52 (hFKBP52) and human FKBP51 (hFKBP51). Amino acids with high consensus are shown in red. Human FKBP52 shares 60% amino acid sequence identity and 75% similarity with human FKBP51. Four domains are indicated by different underlines: single underline, FK1 domain; double underline, FK2 domain; thick underline, TPR domain; dashed underline, calmodulin-binding domain. (b) The final N(1–260) model contains residues 21–257. (c) The final C(145–459) model contains residues 145–427. (d) The overall structure of FKBP52 has been defined based on the superposition of overlapped regions of N(1–260) and C(145–459). (e) Stereo view of the structural comparison between FKBP51 (blue) and FKBP52 (yellow) shows their similar structural architectures but the different orientations of their corresponding domains.

Data Collection and Processing. X-ray data were collected from a Results and Discussion single C(145–459) crystal to 2.7 Å at 90 K. Multiwavelength N(1–260), C(145–459), and Putative FKBP52 Structures. FKBP52 can anomalous diffraction data were collected on a charge-coupled be divided into four domains according to sequence analysis device detector at the BL41XU beamline of SPring-8 (Hyogo, (17). Two overlapped segments of FKBP52 [designated N(1– Japan). Data sets were indexed and scaled by using HKL2000 (18). 260) and C(145–459)] have been cloned, expressed, purified, and X-ray data of N(1–260)a were collected at the 13th beamline at crystallized. N(1–260) includes the first two FKBP domains Beijing Synchrotron Radiation Facility (Beijing, China) to 1.9 Å. [named FK1 (first FKBP domain of FKBPs) and FK2 (second Data of N(1–260)b were collected on a Rigaku (Tokyo) RU2000 ␣ FKBP domain of FKBPs)], whereas C(145–459) is composed of rotating Cu K anode source to 2.0 Å. Data sets were processed the second FKBP domain, the TPR domain, and a calmodulin- by using DENZO and SCALEPACK (18). The data for the C(145– binding domain. The final refined N(1–260) model contains 459)͞MEEVD complex were collected to 3.0 Å at the Advanced residues 21–257 of FKBP52 (Fig. 1b), whereas the C(145–459) Photon Source (Argonne, IL) and processed by using HKL2000. model contains residues 145–427 (Fig. 1c). Based on the superposition of overlapped regions of N(1–260) and C(145–459), the Structure Determination and Refinement. All 12 possible selenium sites of C(145–459) were found and refined at a 2.8-Å resolution overall structure of FKBP52 has been clearly defined (Fig. 1d). The FKBP domains of FKBP52 both consist of a five- to by using SOLVE (19), which produced a mean figure of merit of Ϸ six-stranded antiparallel ␤-sheet, which is wrapped around a 0.56. After density modification with RESOLVE (20), 50% of all ␣ the residues of C(145–459) were automatically traced into the short -helix with a right-handed twist, and are similar to those experimental density map; the remaining residues were traced of FKBP51, FKBP12, and macrophage infectivity potentiator manually by using O (21). CNS (22) was used for refinement and protein (16, 23, 24) (Fig. 2a). The TPR domain of FKBP52 is addition of solvent molecules. Structures of N(1–260)a and all helical and consists of three units of a consensus 34-aa

␣ BIOPHYSICS N(1–260)b were solved by molecular replacement using CNS. The motif. Each single unit consists of two consecutive -helices ␣ ␣ structures of the FKBP52 N-terminal domain (residues 24–140) containing 12–15 residues (except 1 and 3, containing 21 Ϸ (PDB ID code 1N1A) and the N-terminal fragment of C(145– and 23 residues, respectively) that cross at an angle of 20° to 459) (residues 149–255) were used as starting models. This each other. The organizational pattern of the FKBP52 TPR model was subjected to rigid-body refinement, and manual domain is similar to those of FKBP51, Cyp40, PP5, and Hop ␣ ␣ adjustments were made to the model in O. Water molecules were (8, 16, 25, 26). There is an additional -helix ( 7) in the C added by using CNS. The structure of the C(145–459)͞MEEVD terminus beyond the final TPR motif that contains the cal- complex was solved by molecular replacement with CNS, with modulin-binding site (Fig. 2b). The overall structure of C(145–459) as the search model. Data collection, processing, FKBP52 is very similar to that of FKBP51 except for their and refinement statistic are given in Table 1. relative domain orientations (16) (Fig. 1e). The rms deviations

Wu et al. PNAS ͉ June 1, 2004 ͉ vol. 101 ͉ no. 22 ͉ 8349 94 Table 1. Data collection and reﬁnement statistics C(145–459) N(1–260)a N(1–260)b C(145–459)–MEEVD

Data collection

Space group C2221 P21 P212121 C2221 Unit cell a͞b͞c, Å 114.4͞143.1͞171.2 48.8͞42.2͞79.1 45.1͞59.5͞103.2 111.6͞144.4͞170.8 ␣͞␤͞␥, ° 90.0͞90.0͞90.0 90.0͞102.3͞90.0 90.0͞90.0͞90.0 90.0͞90.0͞90.0 Wavelength, Å (peak) 0.9798 (edge) 0.9800 (remote) 0.900 1.2800 1.5418 0.9793 Resolution, Å 50.0–2.7 50.0–2.7 50.0–2.8 20.0–1.9 50.0–2.4 50.0–3.0 Completeness, % 100.0 (99.8) 100.0 (99.9) 100.0 (100.0) 99.2 (98.3) 99.9 (99.9) 98.7 (98.8) Reﬂections Total 291,352 291,742 258,271 72,917 78,753 169,154 Unique 38,801 38,872 34,752 24,881 11,441 27,894 Redundancy 7.5 7.5 7.4 2.9 6.9 6.1

Rmerge, %* 6.4 (32.9) 5.0 (34.4) 6.2 (42.2) 10.1 (40.1) 9.3 (31.4) 9.7 (58.9) I͞␴(I) 11.9 (4.2) 13.8 (4.7) 11.5 (4.0) 8.3 (2.7) 8.9 (5.4) 6.5 (1.9) Reﬁnement statistics Resolution, Å 50.0–2.8 20.0–1.9 50.0–2.4 50.0–3.0 R factor, %† Working set 21.4 20.8 21.6 23.0 Test set 28.4 24.7 27.3 28.7 Rms deviation Bonds, Å 0.013 0.019 0.007 0.008 Angles, ° 1.7 1.9 1.5 1.4 Ramachandran plot, %‡ Most favored 82.0 89.9 85.2 78.7 Allowed 16.9 9.1 12.3 16.9 Generously allowed 0.7 0.5 2.5 3.3 Disallowed 0.4 0.5 0.0 1.0

*Rmerge ϭ⌺h⌺l ͉ Iih Ϫ͗Ih͘ ͉͞⌺h⌺l ͗Ih͘, where ͗Ih͘ is the mean of the observations Iih of reflection h. † Rwork ϭ⌺(ʈFobs͉ Ϫ Fcalcʈ)͞⌺͉Fobs͉; Rfree is the R factor for a subset (10%) of reflections that was selected before refinement calculations and not included in the refinement. ‡Ramachandran plots were generated by using PROCHECK (14). between corresponding FK1, FK2, and TPR domains are 0.6, insertion of one residue (Lys-234) in the 221–242 loop and five 0.9, and 1.0 Å, respectively, for all C␣ atoms. residues (Gly-195, Glu-196, Met-197, Leu-198, and Asp-199) in The FK1 and FK2 domains of FKBP52 are linked by a highly the 192–199 loop, which both flank the binding pocket of FK2, hydrophilic hinge (residues 139–148), and the FK506-binding pushes the loops into the binding pocket. The large and extended pocket of FK1 is oriented Ϸ180° from the putative FK506- side chains of Lys-232, Glu-233, and Phe-235 (corresponding to binding pocket of FK2. Residues 140–142 form an antiparallel Ser-118, Pro-119, and Lys-121 of FK1, respectively) block the ␤-strand that interacts with residues 150–152 in the ␤1 strand of opening of the pocket and change the electrostatic state, in FK2. This loop is stabilized by the formation of a hydrogen-bond addition to the insertions mentioned above. We conclude that network with the side chains of neighboring residues (Fig. 3a). alterations in loops surrounding the binding pocket and substi- The extensive interactions in the hinge region suggest that the tution of residues important for the substrate binding account for flexibility of the hinge is restrained. The side chains of several the loss of the PPIase activity of FK2. Previously, a deletion residues in the interface (Met-48, Ile-49, Ile-154, and Arg-157) mutant (deletion of Asp-195, His-196, and Asp-197) of FKBP51 form a hydrophobic core, together with those of Asp-141, has shown that the FK2 domain relates to progesterone receptor Leu-142, Ile-150, Ile-151, and Arg-210. Although a small differ- preference and target protein interaction (16). Presumably, FK2 ence is found in the orientation between FK1 and FK2 of domains of FKBP proteins may result from a duplication event. N(1–260)a and N(1–260)b, which have different crystal packing, During evolution, FK2 domains lost their PPIase activity but act the conformations of the loop are mostly the same, as well as the as organizers of different domains and provide interaction hydrogen-bond interactions and the hydrophobic cores. These interfaces with other target proteins such as Hsp90 and steroid tight interactions and the rigid hinge stabilize the relative receptors. orientation of FK1 and FK2 and restrict the great change of this orientation. Structure of the C(145–459)͞MEEVD Complex. The overall structure The FK1 domain is responsible for the PPIase activity of of the peptide-bound C(145–459) is similar to that of the free FKBP52, whereas the FK2 domain shows no PPIase activity (27, protein. The peptide binds in a cavity formed by the ␣1, ␣3, and 28). Detailed structural information for FK1 has been reported ␣5 helices of the TPR domain. Of the three molecules in the (17). FK2 is architecturally similar to FK1 despite sharing only asymmetric unit, two (molecules A and B) bind the MEEVD 32% sequence identity but lacks the large bulge-splitting strand peptide, whereas the third (molecule C) does not. The peptide- ␤4 of FK1 (Fig. 2a). FK1 contains 14 residues directly related to binding pockets in molecules A and B are composed of exactly substrate binding, yet only five residues are conserved in FK2. In the same residues, namely Lys-282, Asn-324, Met-327, Lys-354, FK1, Ile-87 and Tyr-113 form highly conserved hydrogen bonds and Arg-358 (Fig. 3 b and c). Some interactions are important with substrates, and Trp-90 provides a platform for substrate to stabilize the binding of the peptide and are conserved in binding (17), whereas in FK2 the corresponding residues are both molecules. In particular, there is a hydrogen bond formed substituted by Pro-201, Phe-232, and Leu-204, respectively. The between Lys-282 and Met-1, and two hydrogen bonds are

8350 ͉ www.pnas.org͞cgi͞doi͞10.1073͞pnas.0305969101 Wu et al. 95 of molecule C is blocked by the FK2 domain of another molecule C, which explains why this molecule does not bind the peptide. Previous mutation analysis and crystal structures of TPR domains have identified residues in Hop, Cyp40, and PP5 that are essential for Hsp90 binding (8, 25, 26, 29, 30). Comparing these proteins with FKBP52, the key residues for binding Hsp90 are conserved, which suggests a functional similarity between these proteins.

Comparison with the Structure of FKBP51. Although the overall architectures of FKBP52 and FKBP51 are very similar, the relative orientations of their four domains are distinctly different (Fig. 1e). Superimposing the structures of FKBP52 and FKBP51 by using the FK2 domain as the reference, we observe that domain FK1 of FKBP51 is rotated at an angle (␪ ϭ 24°, ␻ ϭ 33°) relative to FK1 of FKBP52. The hinge linking FK1 and FK2 is stabilized by extensive hydrogen bonds and hydrophobic interactions in both FKBP proteins. The different hinge conformations of these two proteins and specific interactions in the interface between FK1 and FK2, together with a different hydrophobic core, may account for their different orientations. Thr-143 and Arg-206 of FKBP52 form four pairs of hydrogen bonds with Asp-141, Glu-144, and Glu-146. In FKBP51, the corresponding residues are Phe-143 and Lys-204, which do not form hydrogen bonds. Additionally, the side chains of Ile-154 and Arg-157 in FKBP52 (corresponding to Thr-152 and Lys-155 of FKBP51, respectively) provide tighter hydrophobic interactions. Available evidence suggests that the hinge may be involved in the interaction between FKBP52 and Hsp90. Thr-143 of FKBP52 has been identified as the major phosphorylation site for casein kinase II, and it is known that casein kinase II-phosphorylated FKBP52 does not bind to Hsp90 (31). Furthermore, Thr-143 is changed to Phe-143 in FKBP51, which may have a differential effect on the Hsp90 binding. The TPR domain orientation of FKBP52 is considerably different from that of FKBP51. There are fewer hydrogen bonds and hydrophobic interactions in the interface between FK2 and TPR domains, as well as the loop linking FK2 and TPR domains. Considering the flexibility of this area, it is likely that the different orientations of TPR domains are due to different crystal packing. Fig. 2. Stereo view of the superposition of FK and TPR domains. (a) Two FKBP The TPR domain chimera and truncation experiments have domains of FKBP51 and FKBP52 were superimposed onto FKBP12. FKBP12 shown that the TPR domain of FKBP51 requires appropriate (green), 51-FK1 (blue), and 52-FK1 (red) are similar. The structures of 51-FK2 downstream sequences for Hsp90 binding, but the TPR do- (cyan) and 52-FK2 (yellow) are more closed than the others. (b) TPR domains main of FKBP52 does not. Additionally, the C-terminal region are superimposed onto the TPR domains of FKBP52. FKBP52 is shown in yellow, FKBP51 is shown in cyan, Hop is shown in green, Cyp40 is shown in purple, and of FKBP51, which functionally interacts with the TPR domain PP5 is shown in pink. The conformations of all the TPR domains are similar, to permit Hsp90 binding, confers preferential association with containing six ␣-helices (␣1–␣6). The orientations of the extra ␣-helix (␣7) are progesterone receptor (32, 33). Comparing the TPR domain different. (c) Superposition of the structures of TPR domains and the ␣7- structures of FKBP52 and FKBP51 (Fig. 2), most residues in helixes of FKBP51 (blue) and FKBP52 (yellow). Gln-333, Phe-335, and Ala-365 the binding interface between FKBP52 and Hsp90 are strictly of FKBP52 are replaced by Arg-331, Tyr-333, and Leu-363 in FKBP51, which may conserved, with the exception of Gln-333, Phe-335, and Ala- be responsible for the differential binding pattern of FKBPs to Hsp90. The side 365 (corresponding to Arg-331, Tyr-333, and Leu-363 of chain of Ile-400 of FKBP52, corresponding to Ala-398 of FKBP51, will clash with FKBP51, respectively). The substitutions of Gln to Arg and Phe-369, and this may cause the different orientations of the ␣7-helix. Ala to Leu results in changes to the electronic state and steric relationship of the interaction interface, which would account for the differential binding pattern of FKBPs to Hsp90. formed between Lys-354, Arg-358, and Glu-2. Nevertheless, Superimposing the TPR domains and the extra seventh ␣-helix BIOPHYSICS the orientations of the peptides in these two molecules are (␣7) of FKBPs, it can be observed that structural architectures different. Additional amino acids N-terminal to this peptide of TPR domain are very similar. However, the ␣7-helix of sequence in Hsp90 also contribute to the binding and render FKBP52 shifts away by Ͼ30° from the Hsp90-binding interface specificity to the interaction between the TPR and Hsp90 (8). relative to FKBP51 (Fig. 2). The different orientations of the As a consequence, the binding between the MEEVD peptide ␣7-helix in FKBPs can be explained by the side chain of Ile-400 and C(145–459) is not strong, which may account for the (corresponding to Ala-398 in FKBP51) in the ␣7-helix of different observed binding modes. In the unit cell, the pocket FKBP52, which would otherwise clash with the phenyl group of molecule A faces the pocket of molecule B, and there is of Phe-369 in the FKBP51 conformation. The more compact enough space for the peptides to fill in, but the binding pocket orientation of the C terminus of FKBP51 may result in the

Wu et al. PNAS ͉ June 1, 2004 ͉ vol. 101 ͉ no. 22 ͉ 8351 96 Fig. 3. (a) Stereo view of the hydrogen bonds between FK1 and FK2 of FKBP52. Hydrogen bonds at the interface of FK1 and FK2 form a complicated network, which stabilizes the conformation. Residues in FK1 are shown in red, residues in FK2 are shown in yellow, and residues in the loop are shown in white. (b and c) Stereo view of the MEEVD peptide bound to molecules A (b)andB(c) of C(145–459). The omit electron-density map is contoured at 0.7 ␴ above the mean. Residues of the peptide are shown in white, and residues of the TPR domain are shown in yellow. Residues involved in important interactions are shown in ball-and-stick representation. Hydrogen bonds are shown as dotted lines. proximity and direct interaction with Hsp90, which is consis- FKBP51 could explain their differential effects on Hsp90 tent with previous studies. binding. Conclusions We thank Xuemei Li, Yuna Sun, and Wei Zheng (Z.R. group) for technical A detailed structural analysis of FKBP52 and the complex with assistance; Min Yao (Hokkaido University, Sapporo, Japan), Rongguang the MEEVD peptide has revealed the essential basis for the Zhang, Andrzej Joachimiak (Advanced Photon Source, Argonne, IL), loss of PPIase activity of the FK2 domain and the key residues Fei Sun, Feng Xu, and Feng Gao (Z.R. group) for assistance with data for Hsp90 binding. We observe a number of interesting collection; and Dr. R. B. Sim for critical reading of the manuscript. The structural variances between FKBP52 and FKBP51, including peptide MEEVD was a gift from Yuzhang Wu (Third Military Medical the relative orientations of corresponding domains and some University, Chongging, China). This work was supported by Project 863 important residue substitutions. The very real differences in Grant 2002BA711A12, Project 973 Grant G1999075600, and National orientation between the FK1 and FK2 domains in FKBP52 and Natural Science Foundation of China Grant 30221003.

1. Dolinski, K., Muir, S., Cardenas, M. & Heitman, J. (1997) Proc. Natl. Acad. Sci. 6. Morishima, Y., Kanelakis, K. C., Silverstein, A. M., Dittmar, K. D., Estrada, L. USA 94, 13093–13098. & Pratt, W. B. (2000) J. Biol. Chem. 275, 6894–6900. 2. Galat, A. (1993) Eur. J. Biochem. 216, 689–707. 7. Riggs, D. L., Roberts, P. J., Chirillo, S. C., Cheung-Flynn, J., Prapapanich, V., 3. Sanchez, E. R. (1990) J. Biol. Chem. 265, 22067–22070. Ratajczak, T., Gaber, R., Picard, D. & Smith, D. F. (2003) EMBO J. 22, 1158–1167. 4. Pratt, W. B. & Toft, D. O. (1997) Endocr. Rev. 18, 306–360. 8. Scheufler, C., Brinker, A., Bourenkov, G., Pegoraro, S., Moroder, L., Bartunik, 5. Cheung, J. & Smith, D. F. (2000) Mol. Endocrinol. 14, 939–946. H., Hartl, F. U. & Moarefi, I. (2000) Cell 101, 199–210.

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Fluorescence Spectroscopy

Donor–Donor Energy-Migration Measurements of Dimeric DsbC Labeled at Its N-Terminal Amines with Fluorescent Probes: A Study of Protein Unfolding**

Xuejun Duan, Zhen Zhao, Jianping Ye, Huimin Ma,* Andong Xia,* Guoqiang Yang, and Chih-Chen Wang*

Fluorescence resonance energy transfer (FRET) is a powerful technique for the determination of distances between two fluorophores. The overall geometry of protein structures[1–4] and the conformational changes of a molecule under different conditions can be studied by this method if appropriate sites of the molecule are labeled with fluorescence donor and acceptor probes. Nevertheless, it is rather difficult to specifically introduce two different fluorophore groups into one molecule,[2] especially into a homodimeric biomacromolecule that has two identical reactive sites. Different from the conventional FRET technique, donor–donor energy migration (DDEM) takes advantage of certain fluorescence probes that display an overlap of their absorption and emission spectra and are therefore able to transfer energy between themselves.[2–4] Energy transfer in this case is a reversible process and can be measured through analysis of the time- resolved depolarization of the fluorescence emission (as donor–donor energy migration results in additional depolarization). As only one type of probe is required, DDEM simplifies greatly not only the labeling operation but also the theoretical analysis and the time-resolved measurements and has been widely used to study the steady-state conformational changes of biomacromolecules. DsbC (1), a member of the Dsb family in the periplasm of Gram-negative bacteria, is a thiol-protein oxidoreductase that displays molecular chaperone activity.[5–7] The DsbC molecule is a V-shaped homodimer consisting of two 23.4-kDa subunits.[8] Each subunit is composed of a C-terminal thiore-

[*] X. Duan, Dr. J. Ye, Prof. Dr. H. Ma, Prof. Dr. A. Xia, Prof. Dr. G. Yang Center for Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing 100080 (China) Fax : (+ 86)106-255-9373 E-mail: [email protected] [email protected] Z. Zhao, Prof. C.-C. Wang National Laboratory of Biomacromolecules Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 (China) Fax : (+ 86)106-487-2026 E-mail: [email protected] [**] This work was supported by the National Natural Science Foundation of China (Grant no. 20375044), the Ministry of Science and Technology of China, and the Chinese Academy of Sciences. We thank Dr. Rudi Glockshuber (Eidgenössische Technische Hoch- schule, Hönggerberg, Switzerland) for the generous gift of pDsbC plasmid. Supporting information for this article is available on the WWW under http://www.angewandte.org or fromthe author.

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99 Angewandte Chemie doxin-like domain and a N-terminal domain, which is responsible for dimerization and is essential for the chaperone activity of the molecule.[8,9] The V-shaped structure of homodimeric DsbC led us to apply the DDEM method to explore its unfolding and dissociation behavior and to understand further its structure–function relationship. In this context, the two N-terminal amino groups of DsbC are the sites of choice at which to link two identical probes; however, the labeling of other amino groups, such as e-amino groups of lysine residues, and the nonspecific modification of groups other than amino groups could also occur. Several new methods for the introduction of fluorescent probes into proteins have recently been developed to improve the specificity of labeling.[10–12] The most common approach is to engineer a pair of reactive cysteine residues to provide two thiol handles for conjugation.[2,13] Alternatively, a ketone handle, produced through the introduction of an unnatural keto-containing amino acid, can be labeled with hydrazide-functionalized fluorophores with no observed cross-reactivity.[1, 13] Herein, we describe a general method for the specific Figure 1. Specific modification of the N-terminal amino groups of labeling of N-terminal groups through a transamination dimeric DsbC (1): a) transamination reaction with glyoxylate; b) coupling with 2; c) reduction with sodiumcyanoborohydride. The separa- reaction, in which the N-terminal amino group of a protein tion between the central B atomof the BODIPY FL dye and the termi- molecule is converted into a reactive carbonyl group, which is nal N atomof the hydrazide group of the linker armin 2 is 7.8 (cal- then treated with a hydrazide-containing fluorophore. As the culated with CS Chem3D software). BODIPY FL = 4,4-difluoro-5,7- intermediate in transamination reactions involves the partic- dimethyl-4-bora-3a,4a-diaza-s-indacene-3-propionic acid. ipation of an adjacent peptide bond, only the conversion of the terminal amino group occurs without modification of the internal amino groups on lysine residues.[14–17] Subsequently, the conformational changes of dimeric DsbC during unfolding (induced by guanidine hydrochloride (GuHCl)) were studied by DDEM. The fluorescent dye BODIPY FL (shown as the hydrazide derivative 2 in Figure 1) was employed as the probe owing to its high fluorescence quantum yield, its insensitivity to solvent polarity and pH, and its Förster radius of 57 .[2,13,18] The N- terminal amino groups of 1 were modified as shown in Figure 1 by a) a transamination reaction in the presence of [14,17] glyoxylate and CuSO4, b) coupling of the product 3 with BODIPY FL hydrazide (2), and c) reduction of the imine groups to the more stable amine form 4 of the labeled product. Sodium cyanoborohydride instead of borane-pyri- Figure 2. Absorption spectra of DsbC labeled with BODIPY. DsbC (1) dine was used as the reducing agent owing to its better was modified in the presence (solid line, 4, 1.2 mm) and absence [19] selectivity for imines and the absence of quenching effects (dashed line, 1.0 mm) of glyoxylate. The inset shows the excitation m on the fluorescence from the BODIPY dye (data not shown). (lem = 535 nm) and emission (lex =467 nm) spectra of 4 (4.1 m ); In a similar procedure, 1 was also labeled by following the 5-nmexcitation and emission slits were used. transamination step carried out in the absence of glyoxylate. As shown in Figure 2, the absorption spectrum of the protein modified in the presence of glyoxylate exhibits a main peak at agreement with the theoretical value of m/z 47410 expected 280 nm characteristic of native protein and a less intense band for DsbC with two N-terminal BODIPY labels 4, was at 505 nm for the BODIPY moiety,[13] whereas the absorption detected with a mass error < 0.3%.[20] Although the presence profile for the protein modified in the absence of glyoxylate of a small amount of DsbC modified on only one N-terminal shows only one band for native protein; this indicates that the amino group cannot be ruled out, it should not affect the BODIPY-labeled DsbC 4 can be prepared only through a DDEM measurements, especially in dilute solution. The transamination process carried out in the presence of efficiency with which fluorophores are incorporated into glyoxylate. DsbC is about 9%, which is ascribed to the limited To confirm further that the DsbC molecule had been accessibility of the N termini of the DsbC molecule. specifically labeled with BODIPY, 4 was also examined by The fluorescence spectra of 4 display an excitation band at MALDI TOF mass spectrometry. A peak at m/z 47300, in 505 nm and an emission band at 510 nm (see Figure 2 inset),

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100 Communications

which are almost the same as that for the free BODIPY dye[13] based on energy-transfer measurements.[2–4,21] The rate w of and indicate that the attachment of the fluorophore to DsbC energy transfer between two interacting fluorophores is does not alter its spectral properties. On the other hand, 4 expressed by Equation (1) according to the Förster energy- shows the same circular dichroism spectrum as that of the transfer mechanism:[2,3,21] [20] native DsbC, which suggests that the introduction of 3 1 R 6 BODIPY does not affect the secondary structure of the w ¼ hk2i 0 ð1Þ protein. The native DsbC, the partially denatured DsbC 2 t R formed in the presence of GuHCl (1.5m), and the fully denatured DsbC formed in the presence of GuHCl (6m) and (t = fluorescence lifetime, R0 = Förster radius (57 Æ 1 [2,18] 2 dithiothreitol (0.1m), all labeled with BODIPY, displayed for BODIPY), and hk i = orientation factor, for which an [20] 2 near-identical fluorescence-decay profiles, which were average value of =3 is usually taken; the parameter w obtained fitted to a single exponential function with a satisfactory from DDEM measurements and the values of R estimated by low value of c2 in the range of 1.17–1.38. The fluorescence Equation (1) are summarized in Table 1). lifetime (t) in each of the three cases was about 6.7 ns (calculated based on I(t) = Ae(t/t)) and indicate that the Table 1: Results fromDDEM measurements [a] fluorescence lifetime of BODIPY in BODIPY-labeled DsbC 1 DsbC w [ns ] t [ns] R [] Rc [] is unaffected by the extent of denaturing of the protein (Table 1).On the other hand, the decay rates of fluorescence Native 0.569 6.7 46 35 Partially denatured 0.141 6.7 58 47 anisotropy r(t) show a variation with different extents of Fully denatured – 6.6 – – denaturing of DsbC (Figure 3). The initial decay of r(t) of the fully denatured DsbC is much slower than that of the native [a] The parameter w was obtained fromthe best-fit curves based on r(t) = Aexp(2wt) + B; the value of c2 for each fitting was in the range of DsbC. The fast decay of the fluorescence anisotropy from the 1.077–1.422. The interfluorophore distance R in 4 denatured to different native DsbC suggests that the observed emission is not from extents was calculated according to Equation (1). Rc is the corrected the originally excited BODIPY fluorophore. The other value of R. The data quoted are the average of two independent adjacent fluorophore in the same DsbC molecule could experiments. contribute to the observed emission by an energy-transfer mechanism and thereby lead to the fast depolarization. This is an experimental hallmark of donor–donor energy-migration The calculated interfluorophore distances in the native processes.[4] and partially denatured DsbC are 46 and 58 , respectively, The interfluorophore distance R is defined as the distance and contain a contribution from the length of the linker group between the centers of two fluorophores and can be estimated of the BODIPY dye (Figure 1). Moreover, it is reasonable to

Figure 3. a)–c) Polarized fluorescence decays of Ik(t) and I?(t) and d)–f) anisotropy decays (along with the best-fit curves and the weighted residu- als) of 4 (4.1 mm) at various extents of denaturing of the DsbC protein; a),d) native DsbC; b),e) denatured in GuHCl (1.5m); c),f) denatured in m m GuHCl (6 ) with dithiothreitol (DTT, 0.1 ). Ik(t) and I?(t) represent the intensities of the fluorescence observed with the emission polarizer ori- entated parallel and perpendicular, respectively, to the excitation polarizer. All measurements were carried out at 273 K.

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101 Angewandte Chemie assume an averaged right-angled geometry between the two absorption spectra/molar absorptivities of the fluorescent probe 2 linker groups attached to the N termini of DsbC.[21] The (e = 80000m1 cm1 at 505 nm)[2] and the dimeric protein 1 (e = m1 1 [22] corrected value R for the native DsbC is thus 35 (Table 1), 32340 cm at 280 nm). As a control, the same procedure was c performed with DsbC in the absence of glyoxylate. which is in agreement with the value of 29 measured from the crystal structure of the protein.[8] Similarly, the corrected Received: March 22, 2004 distance between the two N termini in the partially denatured Revised: May 10, 2004 [Z460072] DsbC is 47 , which is markedly longer than 35 in the native protein. The much longer distance measured between Keywords: amines · analytical methods · energy transfer · the two N termini in a partially denatured molecule indicates . fluorescent probes · protein folding that the unfolding of DsbC in the presence of GuHCl (1.5m) renders the molecule more loose and flexible but not dissociated (Table 1). The very slow decay of the fluorescence [1] S. Weiss, Science 1999, 283, 1676 –1683. anisotropy of the fully denatured DsbC could only arise from [2] J. Karolin, M. Fa, M. Wilczynska, T. Ny, L. B.-. Johansson, the rotation of the probe molecule together with the fluctua- Biophys. J. 1998, 74, 11 –21. tion of the conformation of DsbC rather than from DDEM [3] T. Ikeda, B. Lee, S. Kurihara, S. Tazuke, S. Ito, M. Yamamoto, J. Am. Chem. Soc. 1988, 110, 8299 –8304. processes. The interfluorophore distance in this case, which is [4] H. Otto, T. Lamparter, B. Borucki, J. Hughes, M. P. Heyn, far longer than the critical distance R0 of BODIPY and could Biochemistry 2003, 42, 5885 –5895. not be determined by DDEM measurements, implies the [5] D. Missiakas, S. Raina, J. Bacteriol. 1997, 179, 2465 –2471. dissociation of the dimeric molecule in the fully denatured [6] D. Missiakas, C. Georgopoulos, S. Raina, EMBO J. 1994, 13, protein. 2013 –2020. In summary, we have developed a valuable method, which [7] J. Chen, J. L. Song, S. Zhang, Y. Wang, D. F. Cui, C. C. Wang, J. Biol. Chem. , 274, 19601 –19605. consists of N-terminal-specific fluorescence labeling through 1999 [8] A. A. McCarthy, P. W. Haebel, A. Törrönen, V. Rybin, E. N. a transamination reaction followed by DDEM measurements, Baker, P. Metcalf, Nat. Struct. Biol. 2000, 7, 196 –199. to study the unfolding/folding processes of a dimeric protein. [9] X. X. Sun, C. C. Wang, J. Biol. Chem. 2000, 275, 22743 –22749. The transamination step provides a general approach for the [10] V. W. Cornish, D. R. Benson, C. A. Altenbach, K. Hideg, W. L. selective attachment of a fluorophore to N-terminal amino Hubbell, P. G. Schultz, Proc. Natl. Acad. Sci. USA 1994, 91, acid residues, and the dimeric structure of DsbC allows the 2910 –2914. introduction of two identical fluorophores so that the DDEM [11] R. L. Lundblad, Chemical Reagents for Protein Modification, 2nd ed., CRC Press, Boca Raton, 1991. method can be used to trace its unfolding behavior. This [12] T. J. Tolbert, C. H. Wong, Angew. Chem. 2002, 114, 2275 –2278; combined strategy is useful to investigate conformational Angew. Chem. Int. Ed. 2002, 41, 2171 –2174. changes of other dimeric proteins under variable conditions. [13] R. P. Haugland, Handbook of Fluorescent Probes and Research An important development would be to combine the specific Products, 9th ed., Molecular Probes, Inc., Eugene, 2002, labeling method with DDEM measurement at the single- pp. 104 –110. molecule level. Furthermore, this labeling approach could [14] P. Wu, L. Brand, Methods Enzymol. 1997, 278. 321 –330. also be extended to nondimeric protein molecules and would [15] R. Q. He, C. L. Tsou, Biochem. J. 1992, 287, 1001 –1005. [16] B. Hammack, S. Godbole, B. E. Bowler, J. Mol. Biol. 1998, 275, therefore broaden the scope of application of fluorescence 719 –724. spectroscopy. [17] H. B. F. Dixon, R. Fields, Methods Enzymol. 1972, 25, 409 –419. [18] J. Karolin, L. B.-. Johansson, L. Strandberg, T. Ny, J. Am. Chem. Soc. 1994, 116, 7801 –7806. [19] R. F. Borch, M. D. Bernstein, H. D. Durst, J. Am. Chem. Soc. Experimental Section 1971, 93, 2897 –2904. General: DsbC (1) was prepared as reported previously[7, 9] from [20] See Supporting Information. plasmid pDsbC, which contains the full-length DsbC precursor gene. [21] A. A. Deniz, T. A. Laurence, G. S. Beligere, M. Dahan, A. B. Glyoxylate was purchased from Acros. BODIPY FL hydrazide was Martin, D. S. Chemla, P. E. Dawson, P. G. Schultz, S. Weiss, Proc. purchased from Molecular Probes, Inc. MALDI TOF mass spec- Natl. Acad. Sci. USA 2000, 97, 5179 –5184. trometry was performed on a Bruker BIFLEX III instrument. [22] A. Zapun, D. Missiakas, S. Raina, T. E. Creighton, Biochemistry 3: DsbC (1; 1 mg) was dissolved in an aqueous solution of sodium 1995, 34, 5075 –5089. m m acetate (2 mL; 1 , pH 5.5) containing glyoxylate (0.1 ) and CuSO4 (5 mm) and was stirred for 1 h at 296 K. The reaction was quenched through the addition of ethylenediaminetetraacetic acid diammonium salt to a final concentration of 20 mm followed by dialysis against sodium phosphate buffer (0.1m, pH 7.4). 4: BODIPY FL hydrazide (2; 200 mL; 1.96 mm in MeOH) and concentrated HCl (to a final concentration of 0.5m) were consec- utively added to 3, and the mixture was stirred for 1 h at 296 K in the dark. Sodium cyanoborohydride (5 equiv relative to the protein; Sigma) was then added and the solution was incubated overnight at 277 K. The mixture was applied onto a Sephadex G-25 column to remove any remaining free BODIPY dye and the excess reducing reagent. The protein fraction 4, which displays an absorbance at both 280 and 505 nm, was collected and then thoroughly dialyzed against phosphate buffer. The efficiency of labeling was calculated from the

Angew. Chem. Int. Ed. 2004, 43, 4216 –4219 www.angewandte.org 2004 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim 4219

102 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 2, Issue of January 9, pp. 1491–1498, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Crystal Structure of Human Pirin AN IRON-BINDING NUCLEAR PROTEIN AND TRANSCRIPTION COFACTOR*

Received for publication, September 9, 2003, and in revised form, October 13, 2003 Published, JBC Papers in Press, October 22, 2003, DOI 10.1074/jbc.M310022200

Hai Pang‡§, Mark Bartlam‡§, Qinghong Zeng‡§, Hideyuki Miyatake¶, Tamao Hisano¶, Kunio Miki¶, Luet-Lok Wongʈ, George F. Gao‡**, and Zihe Rao‡ ‡‡ From the ‡Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, School of Life Sciences and Engineering, Beijing, Beijing 100084, China, the ¶Theoretical Structural Biology Laboratory, RIKEN Harima Institute, SPring-8, Hyogo 679-5148, Japan, the ʈDepartment of Chemistry, Inorganic Chemistry Laboratory, South Parks Road, Oxford OX1 3QR, United Kingdom, and the **Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, United Kingdom

Pirin is a newly identified nuclear protein that inter- factor (NFI)1 and to the oncoprotein B cell lymphoma 3-encoded acts with the oncoprotein B-cell lymphoma 3-encoded (Bcl-3) in vivo (1, 3), suggesting that it is a transcription cofac- (Bcl-3) and nuclear factor I (NFI). The crystal structure tor. NFI is known to stimulate DNA replication and RNA of human Pirin at 2.1-Å resolution shows it to be a mem- polymerase II-driven transcription (4). Bcl-3 is a distinctive ber of the functionally diverse cupin superfamily. The member of the I␬B family, which inhibits the transcription structure comprises two ␤-barrel domains, with an factor NF-␬B by preventing NF-␬B nuclear translocation and Fe(II) cofactor bound within the cavity of the N-terminal DNA binding. However, there is also evidence that Bcl-3 pref- domain. These findings suggest an enzymatic role for erentially binds to NF-␬B p50 or p52 homodimers to stimulate Pirin, most likely in biological redox reactions involving transcription (5). The functional nature of this difference be- oxygen, and provide compelling evidence that Pirin re- tween I␬B (inhibiting) and Bcl-3 (enhancing) is not known, but quires the participation of the metal ion for its interac- it is clear that they bind to different protein partners. Pirin is tion with Bcl-3 to co-regulate the NF-␬B transcription one of four binding partners of Bcl-3, together with Bard1, pathway and the interaction with NFI in DNA replica- Tip60, and Jab1, and can be sequestered into quaternary com- tion. Substitution of iron by heavy metals thus provides a novel pathway for these metals to directly influence plexes with Bcl-3, p50, and DNA (3). These four Bcl-3-interact- gene transcription. The structure suggests an interesting protein partners, which do not share any sequence homol- ing new role of iron in biology and that Pirin may be ogy, might play some crucial role in regulating the function of involved in novel mechanisms of gene regulation. Bcl-3 and I␬B. Indeed, both Pirin and Bcl-3 are localized in the nucleus, and the potential roles of Pirin in NF-␬B-dependent transcriptional regulation are implicated in a number of exper- Pirin is a newly identified nuclear protein that is widely iments (6–10). expressed in dot-like subnuclear structures in human tissues, Here we report the crystal structure of human Pirin to 2.1-Å in particular liver and heart (1). Pirins are highly conserved resolution. Understanding of the Pirin structure is of critical among mammals, plants, fungi, and even prokaryotic organ- importance in elucidating and understanding its function, in isms and have been assigned as a sub-family of the cupin particular its interaction with the I␬B family of proteins in its superfamily based on both structure and sequence homology (1, role as a transcription cofactor. 2). The cupin superfamily is among the most functionally di- EXPERIMENTAL PROCEDURES verse of any protein family described to date, with both enzy- Cloning, Expression, Purification, and Crystallization—The com- matic and non-enzymatic members included (2). This cupin plete gene fragment encoding human Pirin protein was subcloned into ␤ superfamily is grouped according to a conserved -barrel fold pET-28a expression vector from a human liver cDNA library, and the and two characteristic sequence motifs. Study of Pirin reveals human Pirin was highly expressed as a soluble protein in Escherichia two cupin domains from its primary sequence that are consist- coli strain BL21(DE3) with a 6-residue His tag attached to its N ter- ent with other members of the superfamily. minus. Purification of the Pirin protein was carried out through an The exact functions of Pirins are not yet known. No enzy- affinity chromatography Co-NTA His Bind column (Qiagen) followed by size-exclusion chromatography on a Superdex 75 column (Amersham matic activity has been described, but human Pirin has been Biosciences). Crystals of Pirin were grown using the hanging drop- found to bind to the nuclear factor I/CCAAT box transcription vapor diffusion method from a solution containing 25 mg/ml Pirin in 14% polyethylene glycol 20000, 0.1 M MES, pH 6.5, at 16 °C. For phase determination, a selenomethionyl derivative was produced and crystal- * This work was supported by Grants G1999075600 (Project 973) and lized under similar conditions. The Pirin crystals belong to the space 2002BA711A12 (Ministry of Science and Technology, China) for the group P2 2 2 with unit cell parameters a ϭ 42.28, b ϭ 67.12, c ϭ Human Structural Genomics Initiative. The costs of publication of this 1 1 1 106.39 Å, ␣ ϭ ␤ ϭ ␥ ϭ 90°. article were defrayed in part by the payment of page charges. This Structure Determination—Data sets were collected at three wave- article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. lengths from a single selenomethionine derivative crystal at 100 K on The atomic coordinates and structure factors (code 1J1L) have been deposited in the Protein Data Bank, Research Collaboratory for Struc- tural Bioinformatics, Rutgers University, New Brunswick, NJ 1 The abbreviations used are: NFI, nuclear factor I; Bcl-3, B-cell (http://www.rcsb.org/). lymphoma 3; MES, 4-morpholineethanesulfonic acid; AAS, atomic ab- § These authors contributed equally to this work. sorption spectrophotometry; r.m.s., root mean square; araC, 1-␤-D-ar- ‡‡ To whom correspondence should be addressed. Tel.: 86-010-6277- abinofuranosylcytosine; Ni-ARD, nickel-binding dioxygenase, acireduc- 1493; Fax: 86-010-6277-3145; E-mail: [email protected]. tone dioxygenase; 2-OG, 2-oxoglutarate.

This paper is available on line at http://www.jbc.org 1491 103 1492 Crystal Structure of Human Pirin

TABLE I Data collection and refinement statistics The numbers in parentheses correspond to the highest resolution shell.

MAD peak MAD edge MAD remote Wavelength (Å) 0.9795 0.9799 0.9817 Resolution limit (Å) 50.0–2.1 (2.18–2.10) 50.0–2.1 (2.18–2.10) 50.0–2.1 (2.18–2.10) Total reflections 95,485 95,271 94,836 Unique reflections 30,975 30,927 30,894 Completeness 90.5 (81.5) 90.4 (81.4) 89.9 (79.8) a Rmerge 5.0 (27.5) 5.0 (28.8) 5.0 (29.3) I/␴ (I) 7.3 (1.9) 7.0 (1.8) 6.8 (1.8) Resolution range 50.0–2.1 b Rwork 20.6 b Rfree 24.9 Number of protein atoms 2,244 Number of water molecules 187 r.m.s. deviation Bonds (Å) 0.006 Angles (°) 1.35 Average B factor (Å2) Protein 21.28 Water 29.35 Ramachandran plot Favored (%) 88.6 Allowed (%) 11.4 a ϭ⌺⌺  Ϫ͗ ͘⌺ ⌺ ͗ ͘ ͗ ͘ Rmerge h l Iih Ih h I Ih , where Ih is the mean of the observations Iih of reflection h. b ϭ⌺ʈ  Ϫ  ʈ ⌺  ϭ Rwork ( Fp(obs) Fp(calc) )/ Fp(obs) ; Rfree R factor for a selected subset (5%) of the reflections that was not included in prior refinement calculations. beamline BL44B2 of SPring-8. Data were collected to 2.1-Å resolution Structural Overview—Pirin is composed of two structurally using energies corresponding to the peak (␭ ϭ 0.9795 Å) and edge 1 similar domains arranged face to face (Fig. 1, b and c). The core (␭ ϭ 0.9799 Å) of the experimentally determined selenium K-edge, and 2 of each domain comprises two antiparallel ␤-sheets, with eight a low energy remote wavelength (␭ ϭ 0.9817 Å). All processing, scaling, 3 ␤ and merging of datasets were performed using the HKL2000 package strands forming a -sandwich. The fold of each domain is very (11). Initial phases were calculated to 2.5-Å resolution with SOLVE (12) similar, and the two domains can be superimposed with an from seven heavy atom sites, and RESOLVE (13) was used for density r.m.s. difference of 1.3 Å for 64 equivalent residues. The N- modification and phase extension to 2.1 Å. The Pirin model was built terminal domain (residues 3–134) additionally features four using ARP/wARP (14) and O (15) and was subsequently refined with ␤-strands, and the C-terminal domain (residues 143–290) also CNS (16) using the low energy remote data. An initial round of simu- ␤ ␣ lated annealing was followed by alternate cycles of manual rebuilding includes four additional -strands and a short -helix. The two and minimization. The final model contains 288 residues, 188 water domains are cross-linked, with ␤1 forming part of one sheet of molecules, and an Fe2ϩ ion. The position of the metal ion was evident as the C-terminal domain, and strands ␤25 and ␤26 forming an ␴ Ϫ 2ϩ a peak greater than 16 in the Fo Fc map. The Fe ion was refined extension of one sheet of the N-terminal domain. The C-terminal 2 at full occupancy with a temperature factor of 17.5 Å . The coordinating ␣ 56 ⑀ 58 ⑀ 101 ⑀ 103 ⑀ -helix packs against the outer surface of the N-terminal domain atoms His N 2, His N 2, His N 2, and Glu O 2 have temper- ␤ ature factors of 10.8, 18.1, 12.9, and 13.8 Å2, respectively. -barrel. The two domains are joined by a short linker of 10 Identification of the Metal Ion—The metal ion bound in the N-termi- amino acids (residues 134–143) that contains a single turn of a nal domain of Pirin was confirmed to be iron by atomic absorption 310 helix. Four additional 310 helices are located in the structure. spectrophotometry (AAS). The AAS experiments were performed in the Similar cavities are found in each domain. In the N-terminal Tsinghua Analysis Center using a Carl Zeiss Technology Analytic Jena 2ϩ 2ϩ domain, the cavity contains a metal binding site with a single AAS 6 Vario instrument. The presence of the metal ions Mg ,Ca , 2ϩ Mn2ϩ,Fe2ϩ,Co2ϩ,Ni2ϩ,Cu2ϩ, and Zn2ϩ were analyzed. The results Fe ion located at about 6 Å from the protein surface (Fig. 1d). indicated that, after Co2ϩ-affinity chromatography, only Fe2ϩ remained The C-terminal domain cavity is more compact than the N- in the protein solution after gel-filtration chromatography on a Super- terminal domain and is closed by the ␤-strand formed by resi- dex-75 column (Amersham Biosciences) and equilibration in 20 mM dues 6–12. The C-terminal domain does not contain any metal Tris-HCl (pH 8.0) and 150 mM NaCl. binding site. RESULTS AND DISCUSSION Pirin Is a Member of the Cupin Superfamily—It has been Structure Determination—The structure of human Pirin was predicted that Pirin belongs to the cupin superfamily on the basis determined using the multiple-wavelength anomalous disper- of primary sequence (2). From a Dali (17) search for structural sion method from a single selenomethionine derivative crystal. similarity, the Pirin structure was confirmed to closely resemble Details of the data collection and structure refinement are members of the cupin superfamily (Fig. 2, a–f), particularly the given in Table I. The asymmetric unit of the Pirin crystal structures of quercetin 2,3-dioxygenase (18), glycinin g1 (19), and contains one monomer. The electron density map is of high phosphomannose isomerase (20). As with Pirin, these three pro- quality such that 288 out of 290 residues could be built. No teins are bicupins with two germin-like ␤-barrel domains. Pirin density was observed for the two N-terminal residues, but the also contains the two characteristic sequences of the cupin su- remainder of the Pirin molecule, including the C-terminal end perfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG- of the polypeptide chain, is well defined (Fig. 1a). Two cis- (X)2-H-(X)3-N separated by a variable stretch of 15–50 amino proline residues could be identified in the structure (Pro31 and acids (Fig. 2g). These motifs are best conserved in the N- Pro50). The final model of the structure contains 288 residues, terminal domain (residues 49–71 and residues 88–105) where 188 water molecules, and 1 Fe2ϩ ion. The presence of iron was the conserved histidine and glutamic acid residues correspond established by atomic absorption spectrophotometry, and to the metal-coordinating residues. The C-terminal domain quantitative measurements showed that there is 1 mol of Fe2ϩ motifs (residues 178–199 and residues 216–230) lack the metal per mol of protein. binding residues normally associated with the cupin fold. 104 Crystal Structure of Human Pirin 1493

FIG.1.The Pirin structure. a, a stereo diagram of the Pirin structure shown asaC␣ trace. Every 20th residue is labeled. The top view (b) and side view (c)of the Pirin structure are shown. The structure is colored from N-terminal (blue)to C-terminal (red). The metal ion is shown as a large gray sphere, and the coordinating groups and water molecules are shown as ball-and-stick models. d, a stereo diagram showing the electron density map in the metal binding site. The metal ion is coordinated by three histidines, one glutamate, and two water molecules. The omit map is contoured at 1.8 ␴.

The cupin superfamily has possibly the widest range of bio- main can be superimposed onto the N-terminal domain of Pirin chemical functions of any superfamily identified to date (2). It with an r.m.s. difference of 1.5 Å for 84 equivalent residues. is comprised of both enzymatic and non-enzymatic members, The Cu-binding site of quercetin 2,3-dioxygenase, formed by 3 which have either one or two cupin domains. The cupin fold histidines, a glutamic acid residue and a single water molecule, comprises a motif of six to eight antiparallel ␤-strands located matches the metal site of Pirin. The three histidines of Pirin within a conserved ␤-barrel structure (2). The variety of bio- (His56, His58, and His101) are structurally equivalent to those of chemical functions is reflected by the low sequence homology quercetin 2,3-dioxygenase (His66, His68, and His112). Similarly, shared among the cupin superfamily members (Fig. 2g). A the phosphomannose isomerase structure can be superimposed BLAST search for proteins homologous to human Pirin re- onto that of Pirin with an r.m.s. difference of 1.3 Å for 71 vealed significant conservation between mammals, plants, and equivalent residues. Phosphomannose isomerase is a zinc-con- prokaryotes, particularly within the N-terminal domain (1). taining enzyme, and its metal binding site, comprising two Interestingly, sequence alignment of human Pirin and related histidines and two glutamic acid residues, also matches the proteins reveals two clusters that are highly conserved metal site of Pirin. throughout all aligned sequences. These sequence clusters, Regardless of the overall structural similarity between its corresponding to residues 52–70 (cluster 1) and 88–106 (cluster two domains, the C-terminal domain of Pirin shows interesting 2), include the four metal coordinating residues of human Pi- differences from the N-terminal domain. Notably, the C-termi- rin, which are strictly conserved among all aligned sequences. nal domain of Pirin does not contain a metal binding site and Pirin (Fig. 2a) and the bicupin metalloenzymes quercetin its sequence does not contain the conserved metal-coordinating 2,3-dioxygenase (Fig. 2b) and phosphomannose isomerase (Fig. residues. Several members of the cupin superfamily do not 2d) show similarities in the overall fold. Quercetin 2,3-dioxy- contain the metal-coordinating residues, including the tran- genase is a copper-containing enzyme, and its N-terminal do- scription factor araC from Escherichia coli (21). araC is a single 105 1494 Crystal Structure of Human Pirin

FIG.2.A comparison between Pirin and similar structures. a, Pirin structure; b, quercetin 2,3-dioxygenase structure (PDB code: 1JUH); c, glycinin g1 structure (PDB code: 1FXZ); d, phosphomannose isomerase structure (PDB code: 1PMI); e, oxalate oxidase (germin) structure (PDB code: 1FI2); f, araC dimer structure (PDB code: 2ARC). g, structure-based sequence alignment of Pirin with related structures. PIRIN-N, N-terminal domain of Pirin; PIRIN-C, C-terminal domain of Pirin; 2,3QD-N, N-terminal domain of quercetin 2,3-dioxygenase; 2,3QD-C, C-terminal 106 Crystal Structure of Human Pirin 1495

FIG.3.The metal binding site. Metal binding sites of Pirin (a), quercetin 2,3-dioxygenase (PDB code: 1JUH, b), phosphomannose isomerase (PDB code: 1PMI, c), and oxalate oxidase (PDB code: 1FI2, d). domain member of the cupin family and binds arabinose for 2.15 Å (Table II). A structure-based sequence alignment shows activation of transcription. There are notable similarities be- that the metal binding motif is highly conserved within a tween the C-terminal domain of Pirin and araC. In araC, the number of other cupin superfamily members (Fig. 2g). The arabinose binding site is located within the ␤-barrel and is metal binding domain of Pirin is most structurally similar to closed by an N-terminal domain arm. The ␤-barrel of the C- that in germin, a Mn2ϩ-containing oxalate oxidase in which the terminal domain of Pirin is also closed by the N-terminal ␤1 metal is also octahedrally coordinated by three histidines, a strand. However, in the absence of arabinose, the N-terminal glutamic acid and two water molecules (22). As with quercetin arm of araC becomes disordered, suggesting that it is impor- 2,3-dioxygenase, the three histidines in oxalate oxidase (His88, tant for ligand stability. A detailed analysis of the arabinose His90, and His137) are structurally equivalent to those in Pirin binding residues in the araC structure shows that the C-ter- (His56, His58, and His101). One notable difference between Pirin minal domain of Pirin is unlikely to bind arabinose. and related metalloproteins of the cupin superfamily is the The Metal Binding Site—Surprisingly, a single Fe2ϩ ion is location of the coordinating Glu residue. Quercetin 2,3-dioxy- located in the Pirin N-terminal domain where it is coordinated genase (Fig. 3b), phosphomannose isomerase (Fig. 3c), and by 3 histidine residues (His56, His58, and His101) through their oxalate oxidase (Fig. 3d) all contain a conserved Glu residue in N⑀2 atoms, and one glutamic acid (Glu103) through the O⑀2 the equivalent structural position to residue 63 of Pirin. How- atom (Fig. 3a). The metal binding site is exposed to the solvent, ever, this residue is not conserved in Pirin and the coordinating and the octahedral coordination environment is completed by Glu residue is instead located in position 103 on ␤-strand 10. two water molecules, with metal-ligand distances of 2.24 and The structure of a nickel-binding dioxygenase, acireductone domain of quercetin 2,3-dioxygenase; PROGLYCININ, glycinin g1; PMI-N, N-terminal domain of phosphomannose isomerase; PMI-C, C-terminal domain of phosphomannose isomerase; OXALATE, oxalate oxidase (germin); ARAC, araC. Only the regions adjacent to the two characteristic conserved cupin sequences are shown. The two conserved cupin sequence motifs are shaded in gray, and metal coordinating residues are shown in green boxes. The secondary structure elements relate to the Pirin N-terminal domain structure. 107 1496 Crystal Structure of Human Pirin

TABLE II Metal-donor atom distances and temperature factors

Distance to metal ion Temperature factor

ÅÅ2 Fe2ϩ 17.5 His56 N⑀2 2.07 10.8 His58 N⑀2 2.12 18.1 His101 N⑀2 2.32 12.9 Glu103 O⑀2 2.28 13.8 Water 1 2.24 19.1 Water 2 2.15 22.4 dioxygenase (Ni-ARD) from Klebsiella pneumoniae, was recently determined by NMR and its active site modeled by comparative homology modeling (23). It was suggested that ARD might also be a member of the cupin superfamily. The Ni2ϩ ion in ARD was predicted to be coordinated by six ligands, namely three histidine residues, a glutamic acid, and two water molecules. The spatial arrangement of ligand groups in the Ni-ARD model is similar to that of Pirin and germin, with an average distance of 2.1 Å between the metal and donor atoms. Potential Functions of Pirin—The bound metal ion may play an important role in Pirin function by stabilizing the N-terminal cupin domain structure and/or by imparting enzymatic activity to the protein. The iron found in the structure is the metal cofactor in numerous enzymes spanning a wide spectrum of activities. Metal-dependent Transcriptional Regulation—Pirins are putative transcription cofactors. Heavy metals are known to play an important role in the transcriptional regulation of eukaryotic and prokaryotic genes (24–29). Pirin is newly identified in this study to be a metal-binding protein, and, interestingly, the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts ⅐ ⅐ FIG.4.A model of the Pirin Bcl-3 (p50)2 complex (A and B). The as a cofactor for the transcription factor NFI, the regulatory ankyrin repeat domain of Bcl-3 is shown as a ribbon model colored red. mechanism of which is generally believed to require the assist- The Pirin structure is shown as a ribbon model with the N-terminal ance of a metal ion (30). Our structural data support the hy- domain colored blue and the C-terminal domain colored green. The (p50) homodimer is shown as a ribbon model with one p50 molecule pothesis that the bound iron of Pirin may participate in this 2 colored orange and the other colored yellow. transcriptional regulation by enhancing and stabilizing the formation of the p50⅐Bcl-3⅐DNA complex. Metals have been implicated directly or indirectly in the NF-␬B family of tran- lated to these enzymes, but 2-OG-dependent monooxygenases scription factors that control expression of a number of early have a highly conserved HX(D/E) . . . H motif, with the two his- response genes associated with inflammatory responses, cell tidines and one aspartate or glutamate forming a facial triad, growth, cell cycle progression, and neoplastic transformation leaving three coordination sites on the octahedral Fe(II) center (30). However, most metal-dependent transcription factors are for the binding of 2-OG and oxygen. Because the metal binding

DNA-binding proteins that bind to specific sequences when the site in Pirins has a highly conserved His3Glu set of ligands, with metal binds to the protein. Pirin, on the other hand, appears to only two potentially vacant coordination sites on the Fe(II), Pi- function differently and bind to the transcription factor⅐DNA rins are unlikely to be 2-OG-dependent monooxygenases. The complex. other members of the cupin superfamily thought to contain iron

The His3Glu ligand environment and octahedral geometry of are dioxygenases, and a phylogenetic analysis of cupins placed the metal-binding site in Pirin are well suited for the binding of Pirins in the same clade as cysteine dioxygenases (2). Dioxygen- heavy metal ions. The Fe(II) cofactors in non-heme iron pro- ases require electron transfer cofactor proteins, and the genes teins such as Pirin are labile, and therefore substitution of iron encoding the various proteins of a dioxygenase system are gen- in Pirin by other metal ions offers a novel mechanism by which erally grouped together into an operon. Although no open reading heavy metals can directly interfere with gene transcription. frames encoding such cofactor proteins have been found on either Potential Enzymatic Activity of Pirins—The Fe2ϩ binding site the 5Ј or 3Ј sides of the human Pirin gene (1), this aspect war- in Pirin closely resembles that found in germin, the archetypal rants further investigation. cupin. Germin is a manganese-containing protein that has been Model of a Pirin⅐Bcl-3 Complex—The oncoprotein Bcl-3 is a shown to be an oxalate oxidase and superoxide dismutase (22, distinctive member of the I␬B family of NF-␬B inhibitors and is 31). We found that Pirin does not possess either superoxide located predominantly in the nucleus. It has the properties of a dismutase or oxalate oxidase activity, but we cannot rule out transcriptional co-activator and acts as a bridging factor be- oxidase activity with other substrates. Recently, a number of tween NF-␬B/Rel and nuclear co-regulators. Pirin is known to 2-oxoglutarate (2-OG)-dependent iron monooxygenases, includ- be one of several binding partners that can associate with Bcl-3 ing clavaminic acid synthase 1 (32), hypoxia-inducible factor (33, (3) to form part of a larger quaternary complex on NF-␬B DNA 34), and factor-inhibiting hypoxia-inducible factor, were sug- binding sites. Four binding partners of Bcl-3 have so far been gested to be members of the cupin superfamily on the basis of identified, namely Pirin, Jab1, Bard1, and Tip60. There are no sequence and structure homology (35). Pirin is structurally re- apparent shared sequence motifs in these four cofactors re- 108 Crystal Structure of Human Pirin 1497

quired for interaction with Bcl-3, and the only common prop- important step toward understanding the function of these erties between them is that they are nuclear proteins and proteins. Our work shows that human Pirin is a monomer with associate with gene regulators. two cross-linked ␤-barrel domains. Pirin is confirmed to be a The structure of the Bcl-3 ankyrin repeat domain (ARD) is member of the cupin superfamily on the basis of primary se- elongated and is comprised of seven ankyrin (ANK) repeats quence and structural similarity. The presence of a metal bind- (36). Its central ankyrin repeats are similar to those of I␬B␣, ing site in the N-terminal ␤-barrel of Pirin, which is highly with the key difference that Bcl-3 has a seventh ankyrin repeat conserved among Pirins, may be significant in its role in regu- at the C terminus in place of the PEST region of I␬B␣. Mu- lating NFI DNA replication and NF-␬B transcription factor tagenesis studies of Bcl-3 indicated that all seven ankyrin activity. Fe(II) was surprisingly found to be bound to Pirin and repeats are required for binary interaction with Pirin, whereas could impart enzymatic activity to the protein. Substitution of interactions with Jab1 or Bard1 require only five repeats (3). iron by other heavy metals also offers a direct mechanism for Pirin and Bcl-3 can also be sequestered into quaternary com- heavy metals to influence gene transcription. This novel path- plexes with p50 and DNA, and Pirin is known to increase the way may be relevant in the toxicity and other effects of these DNA binding by Bcl-3⅐p50. As with Pirin, all seven ankyrin metals. Finally, the structure of Pirin strongly suggests that a repeats are required for the Bcl-3⅐p50 interaction (3). The stoi- new role of iron in biology, namely regulating DNA replication chiometry of the complex is not known, but Bcl-3 is able to and gene transcription at the level of the DNA complexes, recognize at least two proteins simultaneously (3). should be added to the list of the many vital functions of this Because the structures of I␬B␣/NF-␬B (p65/p50 heterodimer) metal in living organisms. ␬ (37, 38) complex and NF- B p50 homodimer (39) are known, Acknowledgments—We are grateful to Feng Gao, Fei Sun, and and to understand the interaction between Pirin, Bcl-3, and Zhiyong Lou from the Rao laboratory for assistance, and to p50, we modeled the complex of these two proteins using pro- Rongguang Zhang and Andrzej Joachimiak from the Advanced Photon tein-protein docking techniques (Fig. 4, A and B). A Bcl-3⅐(p50) Source (Argonne National Laboratory) for help with data collection. We 2 thank Zhi Xing of the Tsinghua Analysis Center for help with atomic complex was constructed using the structures of the absorption spectrophotometry. Critical discussions with Neil Isaacs I␬B␣⅐NF-␬B complex and the ankyrin repeat domain (ARD) of (Glasgow University, UK) and David Stuart (Oxford University, UK) Bcl-3. The Bcl-3 ARD structure and the (p50)2 homodimer were are greatly appreciated. ␬ ␣⅐ ␬ superimposed onto the I B NF- B complex. Pirin was then REFERENCES ⅐ docked to the Bcl-3 (p50)2 complex using the program FTDOCK 1. Wendler, W. M., Kremmer, E., Forster, R., and Winnacker, E. L. (1997) J. Biol. (40). The surface of Pirin has a large acidic patch on the Chem. 272, 8482–8489 N-terminal domain surface formed by residues 77–82, 97–103, 2. Dunwell, J. M., Culham, A., Carter, C. E., Sosa-Aguirre, C. R., and Goodenough, P. W. (2001) Trends Biochem. Science 26, 740–746 and 124–128. We suggest that this acidic patch could interact 3. 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110 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 6, Issue of February 6, pp. 4962–4969, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Structural Basis for the Specific Recognition of RET by the Dok1 Phosphotyrosine Binding Domain*

Received for publication, October 7, 2003, and in revised form, November 5, 2003 Published, JBC Papers in Press, November 7, 2003, DOI 10.1074/jbc.M311030200

Ning Shi‡§, Sheng Ye‡, Mark Bartlam‡, Maojun Yang§, Jing Wu§, Yiwei Liu‡, Fei Sun‡, Xueqing Han‡, Xiaozhong Peng§, Boqing Qiang§, Jiangang Yuan§¶, and Zihe Rao‡ʈ From the ‡Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100084 and the §National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College, National Human Genome Center, Beijing 100005, China

Dok1 is a common substrate of activated protein-ty- been identified as the highly phosphorylated 62-kDa protein rosine kinases. It is rapidly tyrosine-phosphorylated in that interacts with ras GTPase-activating protein in chronic response to receptor tyrosine activation and interacts myelogenous leukemia progenitor cells and v-Abl-transformed with ras GTPase-activating protein and Nck, leading to preB cells (1, 2). The expression of v-Abl or the chimeric protein inhibition of ras signaling pathway activation and the p210bcr-Abl in chronic myelogenous leukemia cells has been c-Jun N-terminal kinase (JNK) and c-Jun activation, re- shown to lead to constitutive Dok1 phosphorylation (1, 2). Re- spectively. In chronic myelogenous leukemia cells, it has cent studies have shown that Dok1 is a common substrate of shown constitutive phosphorylation. The N-terminal activated protein-tyrosine kinases such as v-Abl (2), v-Src (3), phosphotyrosine binding (PTB) domain of Dok1 can rec- BCR (4), EphRs (5), RET (6), and integrin ␤ (7). It is rapidly ognize and bind specifically to phosphotyrosine-con- tyrosine-phosphorylated in response to receptor tyrosine acti- taining motifs of receptors. Here we report the crystal vation in various cell systems. structure of the Dok1 PTB domain alone and in complex Dok1 contains an N-terminal pleckstrin homology (PH)1 do- with a phosphopeptide derived from RET receptor tyro- main followed by a central phosphotyrosine binding (PTB) do- sine kinase. The structure consists of a ␤-sandwich composed of two nearly orthogonal, 7-stranded, antiparallel main and a proline- and tyrosine-rich C-terminal tail. The PH ␤-sheets, and it is capped at one side by a C-terminal domain is known to bind to acidic phospholids and localize ␣-helix. The RET phosphopeptide binds to Dok1 via a proteins to the plasma membrane, whereas the PTB domain is surface groove formed between strand ␤5 and the C- known to mediate protein-protein interactions by binding to terminal ␣-helix of the PTB domain. The structures phosphotyrosine-containing motifs (8). The C-terminal part of reveal the molecular basis for the specific recognition Dok1 contains multiple tyrosine phosphorylation sites. When of RET by the Dok1 PTB domain. We also show that phosphorylated, they become potential docking sites for Src Dok1 does not recognize peptide sequences from TrkA homology 2-containing proteins such as ras GTPase-activating and IL-4, which are recognized by Shc and IRS1, protein and Nck, leading to inhibition of ras signaling pathway respectively. activation and the c-Jun N-terminal kinase (JNK) and c-Jun activation, respectively (6). The many proteins that have been identified to contain PTB Protein-protein interactions play key roles in signal trans- domains fall into two major groups. The first group contains duction. These interactions are often mediated by adapter pro- PTB domains that have primary sequence similarity to the Shc teins, which simultaneously associate with several kinases of a PTB domain. The second group contains insulin receptor sub- signaling pathway, forming an ordered module that permits strate (IRS)-like proteins such as IRS, Dok, and SNT/FRS2, sequential activation of each enzyme and by anchoring pro- which contain PTB domains with limited sequence similarity to teins, which are tethered to subcellular structures and localize the Shc PTB domain but similar binding characteristics (9). their complement of enzymes close to their site of action. The The Dok1 PTB domain belongs to the second group. It is 17% docking protein Dok1 appears to function as an adapter. It has identical in sequence to the IRS PTB domain and was supposed to recognize sequences containing the NKLpY motif (10). To better understand the PTB domain specificity of Dok and the * This work was supported by National Sciences Foundation of China (Grants 30200045 and 30221003); the National Program for Key Basic interaction between Dok1 and RET, we have determined the Research Project (“973” Grants G1999075602 and G1999011902); and x-ray crystal structure of the murine Dok1 PTB domain alone the National High Technology Research and Development Program and in complex with a phosphopeptide derived from RET. (“863” Grant 2002BA711A12). The costs of publication of this article were defrayed in part by the payment of page charges. This article must MATERIALS AND METHODS therefore be hereby marked “advertisement” in accordance with 18 Peptide Synthesis and Binding Studies—The following peptides U.S.C. Section 1734 solely to indicate this fact. The atomic coordinates and structure factors (code 1P5T) have been were synthesized by Sigma: the Shc-specific TrkA Tyr(P)-490 (Ac- deposited in the Protein Data Bank, Research Collaboratory for Struc- HIIENPQpYFSDAGGK-NH2), the IRS1-specific IL-4R Tyr(P)-497 (Ac- tural Bioinformatics, Rutgers University, New Brunswick, NJ LVIAGNPApYRSGGK-NH2), RET Tyr(P)-1062 (Ac-STWIEN- (http://www.rcsb.org/). ¶ To whom correspondence may be addressed. Tel.: 86-10-65296411; Fax: 86-10-65240529; E-mail: [email protected]. 1 The abbreviations used are: PH, pleckstrin homology; PTB, phos- ʈ To whom correspondence may be addressed: Laboratory of Struc- photyrosine binding; JNK, c-Jun N-terminal kinase; IRS, insulin recep- tural Biology, School of Life Science and Engineering, Tsinghua Uni- tor substrate; MES, 4-morpholineethanesulfonic acid; PIPES, 1,4- versity, Beijing 100084, P. R. China. Tel.: 86-10-6277-1493; Fax: 86-10- piperazinediethanesulfonic acid; pY, phosphotyrosine; MEN, multiple 6277-3145; E-mail: [email protected]. endocrine neoplasia.

4962 This paper is available on line at http://www.jbc.org 111 Structural Basis for the Recognition of RET by Dok1 4963

TABLE I X-ray data collection, phasing, and refinement statistics Numbers in parentheses correspond to the highest resolution shell (2.59–2.50 Å).

MAD data Data set RET peptide complex Peak Edge Remote Wavelength (Å) 0.9798 0.9800 0.9000 0.9000 Resolution (Å)50–2.5 50–2.5 50–2.5 50–2.5

Space group P212121 P212121 Unit Cell a/b/c (Å) 41.1/56.2/99.6 45.5/55.7/99.1 Reflections Total 52658 49486 55735 44613 Unique 8330 (780)a 8423 (740)a 8238 (670)a 8410 (764)a Redundancy 7.2 (4.8)a 7.1 (3.9)a 7.3 (2.5)a 5.3 (4.2)a Completeness (%) 99.0 (94.5)a 97.6 (89.0)a 96.6 (80.1)a 91.0 (85.7)a a a a a Rmerge 0.106 (0.348) 0.102 (0.361) 0.108 (0.460) 0.104 (0.349) Mean I/␴(I) 6.5 (1.7)a 5.6 (1.6)a 5.4 (1.3)a 13.4 (2.7)a

Refinement statistics Resolution range (Å) 50.0–2.5 50.0–2.5 b Rwork/Rfree (%) 21.8/26.5 21.3/27.7 r.m.s.d.c from ideal values Bonds (Å) 0.014 0.016 Angles (°) 1.78 2.07 Number of atoms Protein 1689 1811 Water 16 17 Ramachandran plot Most favored (%) 86.7 82.8 Additionally allowed (%) 12.7 16.1 a ϭ⌺⌺ ͉ Ϫ͗ ͘ ͉ ⌺ ⌺ ͗ ͘ ͗ ͘ Rmerge h I IIh Ih / h I Ih , where Ih is the mean of the observations Iih of reflection h. b ϭ⌺ʈ ͉ Ϫ ͉ ʈ ⌺͉ ͉ ϭ Rwork ( Fp(obs) Fp(calc) )/ Fp (obs) ; Rfree R factor for a selected subset (5%) of the reflections that was not included in prior refinement calculations. c r.m.s.d., root mean square deviation.

KLpYGMSDGGK-NH2) and RET Tyr-1062 non-phosphopeptide (Ac- Data Collection and Structure Determination—Data were collected STWIENKLYGMSDGGK-NH2). A C-terminal GGK extension was from a flash-frozen crystal after soaking the crystal in a reservoir added to each of the peptides for coupling to the CM5 chip via the lysine solution containing 20% (v/v) glycerol. The MAD data were collected at side chain amino group. Binding analyses of the Dok1 PTB domain and the BL41XU beamline at SPring-8. Three different wavelengths were the peptides were performed using a Biosensor BIAcore instrument used to obtain the multiwavelength anomalous diffraction data: 0.9798 (BIACORE 1000) (BIAcore) according to the manufacturer’s instruc- Å (peak), 0.9800 Å (edge), and 0.9000 Å (remote). Data were integrated, tions. CM5 research grade sensor chips (BIAcore) were used. All buffers scaled, and merged using the HKL programs DENZO and SCALE- were filtered before use. The peptide concentration of 200 ␮g/ml and a PACK (12). Crystals of the Dok1 PTB domain belong to the space ␮ ϳ ϭ ϭ ϭ contact time of 13.3 min at a flow rate of 3 l/min gave 200 resonance group P212121, with unit cell parameters a 41.1 Å, b 56.2 Å, c units. Three phosphopeptides were coupled to different flow cells of the 99.6 Å, ␣ ϭ ␤ ϭ ␥ ϭ 90°, containing two molecules per asymmetric CM5 chip, respectively. A reference surface was generated simulta- unit. Three selenium sites were located and refined at 2.5-Å resolu- neously under the same conditions but without peptide injection and tion using SOLVE (13), which produced a mean figure of merit of 0.32. used as a blank to correct for instrument and buffer artifacts. All After auto-modeling with RESOLVE (14), about 50% of all the resi- measurements were conducted in HEPES-buffered saline buffer (10 mM dues were easily modeled into the experimental map. The remaining HEPES, pH 7.4, containing 0.15 M NaCl, 3 mM EDTA, and 0.005% residues were traced manually with O (15). CNS (16) was used for Tween 20) at a flow rate of 20 ␮l/min at 25 °C. After each measurement, refinement and the addition of solvent molecules. the chip surface was regenerated with 5 ␮lof6M guanidine-HCl (pH Data from the RET peptide complex crystals were collected at a 7.0) buffer at a flow rate of 10 ␮l/min at 25 °C. The Dok1 PTB domain wavelength of 0.9000 Å at the BL41XU beamline at SPring-8. The ␮ was injected at variable concentrations at 20 l/min flow rate, and crystal also belonged to the space group P212121, containing two mole- binding to the peptides immobilized on the chip was monitored in real cules per asymmetric unit, but with different unit cell parameters, a ϭ time. Response curves were prepared by subtracting the signal gener- 45.5 Å, b ϭ 55.7 Å, c ϭ 99.1 Å, ␣ ϭ ␤ ϭ ␥ ϭ 90°. The structure of the ated from the control flow cell. Kinetic parameters were determined complex was phased by molecular replacement using CNS with the using the software BIA evaluation 3.0. model of the free Dok1 PTB domain as the starting model. The RET Protein Expression, Purification, and Crystallization—The His- phosphopeptides bound to the Dok1 PTB domain were located using an Ϫ tagged murine Dok1 PTB domain (residues 154–266) was expressed Fo Fc difference electron density map. Model building and fitting and purified by Ni2ϩ-chelation chromatography. The N-terminal His were carried out using O, and refinement and addition of water mole- tag was removed by thrombin digestion, and the protein was purified cules were performed using CNS. Data collection, processing, and re- as described previously.2 Se-Met-substituted Dok1 PTB domain was finement statistics are given in Table I. The complex model consists of produced in the methionine auxotrophic Escherichia coli strain B834 residues 154–256 of mouse Dok1, the 10 residues of the RET phos- (DE3) (Novagen). Crystals of Se-Met-derived Dok1 PTB domain were phopeptide, and 17 water molecules. Model quality was checked with grown in a hanging drop by mixing 1 ␮l of protein solution (7 mg/ml, PROCHECK (17). 10 mM MES (pH 6.5), 50 mM NaCl, 10 mM DTT) and 1 ␮l of reservoir Coordinates—Coordinates and structure factors for the Dok1 PTB solution containing 28% (v/v) polyethylene glycol 6000, 0.1 M MES domain have been deposited in the Protein Data Bank (accession num- (pH 6.0), 10 mM dithiothreitol (DTT). Crystals of Dok1 PTB domain in ber 1P5T). Coordinates and structure factors for the Dok1 PTB domain a complex with RET peptide were grown by the same method using 1 and RET peptide complex have been deposited in the Protein Data ␮l of protein solution (10 mg/ml, 1 mM RET peptide, 10 mM MES (pH Bank (accession number 1EUF). 6.5), 50 mM NaCl, 10 mM DTT) with 1 ␮l of reservoir solution (30% (v/v) polyethylene glycol 6000, 0.1 M PIPES (pH 6.0), 10 mM dithio- RESULTS AND DISCUSSION threitol (DTT)). The resulting crystals grew after 1 week at 16 °C. Specificity of Phosphopeptide Binding—Affinity analysis was performed by means of surface plasmon resonance. The syn- 2 N. Shi, submitted for publication. thetic peptides derived from TrkA (residues 483–494), IL-4R 112 4964 Structural Basis for the Recognition of RET by Dok1

FIG.1. Biosensor analysis of the Dok1 PTB domain with immobilized phosphopeptides. Five different concentrations of Dok1 PTB domain were injected over three flow cells with different phosphopeptides and the reference flow cell. The sensorgram shows the relative response in resonance units (RU) after background subtraction versus time in seconds are recorded for the following peptide: RET (a), TrkA (b), and IL-4R (c). The concentrations of PTB domain are indicated by numbers in the corresponding graphs.

(residues 489–499), and RET (residues 1054–1064) were cou- with Se-Met derivative data. Final statistics for the structure pled to the sensor chip, CM5 of BIAcore, and various concen- are given in Table I. The electron density was of good quality trations of Dok1 PTB domain solutions were run over the chip. and well defined for most of the structure. The final model

The dissociation constant (Kd) of binding of RET phosphopep- consists of residues 154–256 of mouse Dok1 in chain A, resi- tide to the Dok1 PTB domain was determined to be 3.2 ␮M from dues 154–254 in chain B, and 16 water molecules. The PTB the data in Fig. 1a. Measurements made in the presence of domain of Dok1 adopts a “PH domain-like” fold, with seven 100–500 ␮M of its non-phosphorylated counterpart were un- strands forming a ␤-sandwich composed of two nearly orthog- changed. However, no binding could be detected for immobi- onal antiparallel ␤-sheets (Fig. 2a). The ␤-sandwich is capped lized Trka and IL-4 peptides (Fig. 1, b and c), indicating bind- at one end by a C-terminal ␣-helix. ing specificity of the Dok1 PTB domain to the receptor. Structure of the Dok1 PTB Domain-RET Peptide Com- Structural Overview—The native structure of the Dok1 PTB plex—To gain further insight into the molecular basis for the domain was determined by MAD phasing to 2.5-Å resolution binding properties of the Dok1 PTB domain, we determined the 113 Structural Basis for the Recognition of RET by Dok1 4965

FIG.2.Overall structure of dok1 PTB domain. a, ribbon stereo diagram showing the fold of the Dok1 PTB domain (green) and the orientation of the bound RET phosphopeptide (white). The ribbon diagram was generated with the program BOBSCRIPT (11). b, structure-based sequence alignments of the nine Doks and hIRS1 PTB domains. Sequences of mouse Dok1-(147–264), human dok1-(147–264), mouse Dok2-(144–259), human Dok2-(141–257), mouse Dok3-(156–266), mouse Dok4-(133–242), human Dok4-(133–242), mouse Dok5-(134–242), human Dok5-(129–232), and human IRS1-(160–262) were aligned. Numbers refer to mouse Dok1. The conserving residues were boxed in red and blue. Critical arginines for phosphotyrosine recognition are indicated by green dots. Alignment was generated using CLUSTAL X (1.8). structure of a 1:1 complex of the Dok1 PTB domain (residues all residues of the RET peptide, with the exception of Ser in the 154–256) with an 11-residue peptide derived from the C-ter- Ϫ8 position relative to the phosphotyrosine (pY-8). The pep- minal of RET (residues 1054–1064). The structure of the com- tide-binding site on the Dok1 PTB domain is characterized by plex was determined by molecular replacement using the na- an L-shaped surface groove formed by residues from strand ␤5 tive structure as a search model. The structure of the complex and the C-terminal ␣-helix, ␣2. The peptide forms a ␤-turn to is displayed in Fig. 2a, and statistics for the structure deter- occupy the L-shaped binding site (Figs. 2a and 3). mination are given in Table I. Clear density was observed for Phosphopeptide Recognition—Although it is known that PTB 114 4966 Structural Basis for the Recognition of RET by Dok1

FIG.3. Stereo view of the electron density map covering the RET pep- Ϫ tide. A2|Fo Fc| map is shown at 2.5-Å resolution using phases calculated from the final, refined model and contoured at 1.0␴

FIG.4. The contacts between Dok1 PTB domain and RET peptide side chains that contribute specificity to the interaction. a, molecular surface representation of the Dok1 PTB domain structure calculated and shaded according to electrostatic potential using the program ViewerPro (Accelrys). As shown in b, Arg-208, Tyr-209, Gly-210, Ser-217, and Phe-218 of Dok1 PTB domain form a hydrophobic pocket, which may show a preference for large side chain hydrophobic residues such as Trp, Tyr, Phe, and Met in position pY-6 of the peptide. As shown in c, large hydrophobic side chains are present at pY-5 in the Dok1 PTB domain recognition motifs similar to Shc. As shown in d, Gln-252, Ile-249, and Thr-204 of Dok1 PTB domain form a hydrophobic pocket, which may prefer Leu or Ile in position pY-1 of the peptide. The key residues are shown in ball-and-stick representation.

domains mainly recognize NPXpY motifs, careful analysis of alanine by a glutamate (such as insulin receptor) leads to a binding indicates that these domains have slightly different 30-fold loss of affinity for the IRS1 PTB domain. Studies with a binding specificities (9). Asparagine in position Ϫ3 relative to combinatorial phosphopeptide library have indicated that the phosphotyrosine (pY-3) and the phosphotyrosine group are nec- Dok1 PTB domain recognizes distinct sequences as compared essary for binding to most PTB domains. A hydrophobic residue with the IRS1 and Shc PTB domains. Leu at position Ϫ1 and at position Ϫ5 and a proline at Ϫ2 are crucial for the Shc PTB hydrophobic amino acids Tyr, Met, and Phe at Ϫ6 were domain, but the amino acids from Ϫ6toϪ8 residues N-termi- strongly selected for binding by the Dok1 PTB domain. Similar nal to the phosphotyrosine are important for IRS1 binding to preferences for hydrophobic residues at position Ϫ5toϪ8 have the NPXpY motifs. The proline in the NPXpY motifs also ap- also been reported for other PTB domains. pears to be more important for IRS1 PTB binding than for Shc Our binding studies show that the Dok1 PTB domain can PTB binding. In addition, IRS1 PTB favors a small hydrophobic bind only with the RET peptide and not with the IL-4 receptor amino acid such as alanine at the Ϫ1 position. Substituting this and TrkA peptides (Fig. 1). Previous experiments indicated 115 Structural Basis for the Recognition of RET by Dok1 4967

FIG.5.Stereo view of the interactions between residues at pY-1 of the phosphopeptide, shown in brown, and Dok1 (a) or IRS1 (b) PTB domain. Residues involved in important interactions are shown in ball-and-stick representation. The residues interacting with pY-1 are represented as green; the sulfur atom is represented in yellow. that IRS1 can bind with IL-4 and insulin receptor peptides and with the observation that phosphorylation of the tyrosine is also with the RET peptide but not with the middle T, TrkA, necessary for peptide binding. Replacing Arg-207 with alanine Erb4, or epidermal growth factor receptor peptides that have eliminates the ability of the Dok1 PTB domain to bind phos- Ϫ ␤ ␤ hydrophobic residues at position 5 relative to Tyr(P) (9, 18). phopeptides (6). In addition, integrin 3 and 7 can bind to the The Shc PTB domain can bind with mT, TrkA, Erb4, or epider- Dok1 PTB domain with their tails containing the Dok1 PTB mal growth factor receptor peptides and also with IL-4 and domain recognition motifs (7). The replacement with alanine of ␤ RET peptides (9, 19). The distinct specificities of these PTB the Tyr-747 at pY position of integrin 3 tails or the Tyr-778 at ␤ domains correlate with and may account for some biological pY position of integrin 7 tails also disrupted binding to the differences between these cytoplasmic substrates of tyrosine Dok1 PTB domain (7). kinase-linked receptors. The backbone of N-terminal residues of the RET peptide, Interactions between RET Peptide and the Dok1 PTB Do- including residues pY-7 Thr, pY-6 Trp, pY-5 Ile, pY-4 Glu, pY-3 main—The RET peptide forms a ␤-turn and fills an L-shaped Asn, form a strand that hydrogen-bonds with strand ␤5inan groove on the surface of the PTB domain that is formed by antiparallel orientation. In addition to backbone interactions, residues from the ␤5 strand and the C-terminal ␣ helix. The there are numerous contacts between the domain and peptide estimated surface area of Dok1 PTB buried by the bound pep- side chains that contribute specifically to the interaction. The tide is 761 Å2. The recognition groove is composed of residues indole ring of Trp-6 is bound in a pocket between ␤5 and ␤3 ␤ ␣ from the 5 strand, the C-terminal -helix, and the 310 turn that is composed of Arg-208, Tyr-209, Gly-210, Ser-217, and connecting strands ␤4 and ␤5, including Tyr-203, Thr-204, Phe-218. This large pocket suggests that hydrophobic residues Leu-205, Leu-206, Arg-207, Arg-208, Tyr-209, Arg-211, Ser- with large side chains might be selected here (Fig. 4b). Using a 217, Phe-218, Gly-221, Arg-222, Phe-242, Ile-249, Gln-252, combinatorial peptide library approach, Songyang et al. (10) Lys-253. These residues make extensive contacts with all 10 found that Tyr, Met, and Phe were strongly selected at this site. residues of the RET peptide, through both hydrogen bonds and The side chain of Ile-5 shows numerous contacts with Phe-242 hydrophobic interactions. The phosphotyrosine is coordinated in the C-terminal ␣-helix (Fig. 4c). Large hydrophobic side by Arg-207 and Arg-222, which extend from the ␤5 and ␤6 chains are present at pY-5 in the Dok1 PTB domain recognition ␤ ␤ strands, respectively, and which are conserved in all Dok fam- motifs. Integrin 3 and 7 can bind to the Dok1 PTB domain via ily proteins (Fig. 2b). The pY side chain lies in an open pocket their tails, which contain Dok1 PTB domain recognition motifs ␤ Ϫ ␤ created by the 310 turn and residues at the end of strands 5 (7). Replacement of Asp-773 at the 5 position of integrin 7 and ␤6 (Fig. 2a). An extensive network of hydrogen bonds and tails with more hydrophobic Ala or Phe residues dramatically ionic interactions coordinate the phosphate oxygens, consistent increased Dok1 PTB domain binding to ␤7 tails, and con- 116 4968 Structural Basis for the Recognition of RET by Dok1 versely, a substitution of Ala-742 to Asp at the Ϫ5 position in PH domain-like fold of the PTB domain family (22) (Fig. 6) and ␤ ␤ integrin 3 resulted in reduced binding to Dok1 PTB domain. a common mode of peptide binding, with the same -turn The Asn at pY-3 is similar to that in other PTB domain recog- conformation and orientation of phosphopeptide observed in nition motifs NPXpY and appears to play an important struc- each of the PTB domains. There are further similarities be- tural role in stabilizing the ␤-turn of the peptides formed. The tween IRS1 and the Dok1 PTB domain. Arg-212 and Arg-227, side chains of pY-4 Glu and pY-2 Lys extend away from the which recognize the phosphotyrosine in IRS1, are equivalent to surface of the domain. In Dok1 PTB domain, Leu at the Ϫ1 Arg-207 and Arg-222 in the Dok1 PTB domain. These two position extends into a hydrophobic pocket composed of Gln-252, residues are also conserved throughout the IRS protein family Ile-249, and Thr-204 and was exclusively selected (Fig. 4d). In (Fig. 2b). ϩ addition, pY 1 Gly forms a hydrogen bond with Thr-204, and the Interestingly, the Dok1 PTB domain has a different set of ϩ side chain of pY 2 Met interacts with Lys-253 (Fig. 5a). residues for recognizing the peptide. In IRS1, pY-1 of the pep- Comparison with Other PTB Domains—There is 17% se- tide interacts with a hydrophobic patch composed of Met-209, quence identity between the PTB domains of Dok1 and IRS1, Met-260, Ser-261, and Met-257 (Fig. 5b) (20). Ala was selected whereas there is no significant sequence homology between the in this position, and although pY-1 can be substituted for Glu PTB domains of Dok1 and Shc. Despite the low sequence ho- or Leu, they would result in an unfavorable interaction with mology, the overall structure of the Dok1 PTB domain is sim- this patch. When the pY-1 Ala in IL-4R is substituted by a Glu, ilar to its IRS1 (20) and Shc (21) counterparts. Dok1 shares the as in the case of the insulin receptor, the result is a 30-fold loss in binding to IRS1 (23). In Dok1, pY-1 of the peptide interacts with a hydrophobic pocket composed of Gln-252, Ile-249, and Thr-204, and Leu was exclusively selected in this position (Fig. 5a). The different binding of TrkA and RET phosphopeptides to Dok1 may be due to the replacement of Gln by Leu at the pY-1 position. It is demonstrated that pY-1 Leu is very important to the Dok1 PTB domain binding motif. The proline in position pY-2 is known to be crucial for high affinity binding for Shc and IRS1. Substitution of this residue reduces but does not abolish binding for Shc PTB domain. Meanwhile, substitution of the pY-2 proline with alanine abolishes binding for IRS1 (9). The side chain of pY-2 Lys extends away from the surface of the domain in Dok1 PTB, where it seems that a proline at position pY-2 is not essential. FIG.6. Stereo view of the superposition of Dok1 (red), IRS1 Large hydrophobic side chains are present at pY-5 in the Dok1 (blue), and Shc (green) PTB domains. Dok1, IRS1, and Shc share a common PH domain-like fold. For clarity, selected residues from the PTB domain recognition motifs, similar to Shc. However, there is Shc PTB domain have been omitted. C␣ atoms of core residues of the insufficient space in the IRS1 domain complex to accommodate structures superimpose with an root mean square deviation of Ͻ 1.0Å. large, hydrophobic side chains at peptide position pY-5. As with

FIG.7.The interaction between Dok1 PTB domain and three isoforms of RET. Arg-1064 in RET9 and Ala-1064 in RET 43 were modeled from our structure of the Dok1 PTB domain complexed with the RET51 phosphopeptide. Met-1064 in RET51 (a) and Arg-1064 in RET9 (b) both form an interaction with Lys-253 in the Dok1 PTB domain (3.53 and 3.73 Å, respectively), but Ala-1064 in RET 43 (c) does not. 117 Structural Basis for the Recognition of RET by Dok1 4969 the Shc PTB domain, the Dok1 PTB domain can also recognize Dr. George F. Gao of Oxford University, Oxford, UK, for help with the motifs of growth factor receptors and transforming proteins synthetic peptides. that possess large hydrophobic side chains at pY-5, whereas IRS1 REFERENCES does not bind to growth factor receptors. These differences indi- 1. Carpino, N., Wisniewski, D., Strife, A., Marshak, D., Kobayashi, R., Stillman, cate that Dok1 PTB recognizes distinct sequences (NXLpY) as B., and Clarkson, B. (1997) Cell 88, 197–204 compared with the Shc and IRS1 PTB domain (NPXpY). 2. Yamanashi, Y., and Baltimore, D. (1997) Cell 88, 205–211 Dok1 PTB Domain Binding to RET Isoforms—The RET 3. Shah, K., and Shokat, K. M. (2002) Chem. Biol. 9, 35–47 4. Kato, I., Takai, T., and Kudo, A. (2002) J. Immunol. 168, 629–634 proto-oncogene encodes a tyrosine kinase receptor that is es- 5. Becker, E., Huynh-Do, U., Holland, S., Pawson, T., Daniel, T. O., and Skolnik, sential for the development of the enteric nervous system and E. Y. (2000) Mol. Cell Biol. 20, 1537–1545 6. Murakami, H., Yamamura, Y., Shimono, Y., Kawai, K., Kurokawa, K., and the kidney. Germline mutations of the RET proto-oncogene Takahashi, M. (2002) J. Biol. Chem. 277, 32781–32790 cause multiple endocrine neoplasia (MEN) 2A or 2B (24). RET 7. Calderwood, D. A., Fujioka, Y., de Pereda, J. M., Garcia-Alvarez, B., has three isoforms, RET51, RET9, and RET43, formed by al- Nakamoto, T., Margolis, B., McGlade, C. J., Liddington, R. C., and Gins- berg, M. H. (2003) Proc. Natl. Acad. Sci. U. S. A. 100, 2272–2277 ternative splicing at a site just downstream of tyrosine 1062 8. Dhe-Paganon, S., Ottinger, E. A., Nolte, R. T., Eck, M. J., and Shoelson, S. E. (pY) (25). These isoforms play different roles in tumor develop- (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 8378–8383 ment. RET51-MEN2A and RET51-MEN2B mutant proteins 9. Wolf, G., Trub, T., Ottinger, E., Groninga, L., Lynch, A., White, M. F., Miyazaki, M., Lee, J., and Shoelson, S. E. (1995) J. Biol. Chem. 270, have stronger transforming activity than RET9-MEN2A and 27407–27410 RET9-MEN2B mutant proteins, respectively (26). The activity 10. Songyang, Z., Yamanashi, Y., Liu, D., and Baltimore, D. (2001) J. Biol. Chem. ϩ 276, 2459–2465 of RET43 is very low (27, 28). The Tyr-1604 (pY 2) residue is 11. Esnouf, R. M. (1997) J. Mol. Graphics 15, 132–134 different in each of these RET isoforms. The RET9 isoform has 12. Otwinowski, Z., and Minor, W. (1997) in Macromolecular Crystallography, arginine in the pYϩ2 position, whereas RET43 has alanine and Part A (Carter, C. W., Jr., and Sweet, R. M., eds) Vol. 276, pp. 307–326, Academic Press, Orlando, FL RET51 has methionine in the equivalent position. In our model 13. Terwilliger, T. C., and Berendzen, J. (1999) Acta Crystallogr. Sect. D Biol. of the Dok1 PTB domain-RET peptide complex, the RET pep- Crystallogr. 55, 849–861 tide is derived from RET51, and the Tyr-1604 (pYϩ2) residue is 14. Terwilliger, T. C. (2000) Acta Crystallogr. Sect. D Biol. Crystallogr. 56, 965–972 a methionine that forms a hydrophobic interaction with residue 15. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crys- Lys-253 that extends from the C-terminal ␣-helix (the distance tallogr. Sect. A 47, 110–119 ϩ 16. Bru¨ nger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse- between C⑀ of Met 2toC⑀ of Lys-253 is 3.53Å) (Fig. 7a). When Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, Met in the pYϩ2 position is replaced by Arg, there is still an R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. interaction between Argϩ2 and Lys-253, but it is weakened Sect. D Biol. Crystallogr. 54, 905–921 ϩ 17. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) (the distance between C␨ of Arg 2toC⑀ of Lys-253 is 3.73Å) J. Appl. Cryst. 26, 283–291 (Fig. 7b). However, the substitution of Ala for Met at the pYϩ2 18. Melillo, R. M., Carlomagno, F., De Vita, G., Formisano, P., Vecchio, G., Fusco, position abolishes the hydrophobic interaction altogether (Fig. A., Billaud, M., and Santoro, M. (2000) Oncogene 20, 209–218 19. Asai, N., Murakami, H., Iwashita, T., and Takahasi, M. (1996) J. Biol. Chem. 7c). These findings are consistent with the relative transform- 271, 17644–17649 ing activities of the RET isoforms. 20. Zhou, M. M., Huang, B., Olejniczak, E. T., Meadows, R. P., Shuker, S. B., Miyazaki, M., Trub, T., Shoelson, S. E., and Fesik, S. W. (1996) Nat. Struct. Conclusions—A detailed analysis of the structure of the Dok1 Biol. 3, 388–393 PTB domain and its complex with a RET phosphopeptide has 21. Zhou, M. M., Ravichandran, K. S., Olejniczak, E. F., Petros, A. M., Meadows, revealed the basis for ligand recognition by the Dok1 PTB do- R. P., Sattler, M., Harlan, J. E., Wade, W. S., Burakoff, S. J., and Fesik, S. W. (1995) Nature 378, 584–592 main. We also show that the recognition of peptides by the Dok1 22. Murzin, A. G., Brenner, S. E., Hubbard, T., and Chothia, C. (1995) J. Mol. Biol. PTB domain is specific since Dok1 cannot bind IL-4 receptor and 247, 536–540 TrkA peptides that are recognized by Shc and IRS1 PTB do- 23. He, W., O’Neill, T. J., and Gustafson, T. A. (1995) J. Biol. Chem. 270, 23258–23262 mains, respectively. A structural comparison of the Dok1 PTB 24. Watanabe, T., Ichihara, M., Hashimoto, M., Shimono, K., Shimoyama, Y., domain with other PTB domain structures explains their differ- Nagasaka, T., Murakumo, Y., Murakami, H., Sugiura, H., Iwata, H., Ishiguro, N., and Takahasi, M. (2002) Am. J. Pathol. 2002, 249–256 ent peptide binding specificities. Furthermore, the distinct spec- 25. Ivanchuk, S. M., Myers, S. M., and Mulligan, L. M. (1998) Oncogene 16, ificities of the PTB domains correlate with and should account for 991–996 key biological differences between these cytoplasmic substrates 26. Pasini, A., Geneste, O., Legrand, P., Schlumberger, M., Rossel, M., Fournier, L., Rudkin, B. B., Schuffenecker, I., Lenoir, G. M., and Billaud, M. (1997) of tyrosine kinase-linked receptors. Oncogene 15, 393–402 27. Carter, M. T., Yome, J. L., Marcil, M. N., Martin, C. A., Vanhorne, J. B., and Acknowledgments—We thank Dr. Min Yao for assistance during data Mulligan, L. M. (2001) Cytogenet. Cell Genet. 95, 169–176 collection at beamline 41 XU at SPring-8, Hyogo, Japan. We also thank 28. Lee, D. C., Chan, K. W., and Chan, S. Y. (2002) Oncogene 21, 5582–5592

118 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 5, Issue of January 30, pp. 3361–3369, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Amyloid Nucleation and Hierarchical Assembly of Ure2p Fibrils ROLE OF ASPARAGINE/GLUTAMINE REPEAT AND NONREPEAT REGIONS OF THE PRION DOMAIN*

Received for publication, September 22, 2003, and in revised form, November 4, 2003 Published, JBC Papers in Press, November 10, 2003, DOI 10.1074/jbc.M310494200

Yi Jiang‡, Hui Li§, Li Zhu‡, Jun-Mei Zhou‡¶, and Sarah Perrett‡¶ʈ From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, and the §State Key Laboratory of Magnetism, Center for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, P. O. Box 603, Beijing 100080, China

The yeast prion protein Ure2 forms amyloid-like fila- (ThT)1 (7–9), a dye considered highly specific for amyloid (10, ments in vivo and in vitro. This ability depends on the 11). Amyloids are thought to form by conversion of the native N-terminal prion domain, which contains Asn/Gln re- protein structure to a generic cross-␤ structure, identified by a peats, a motif thought to cause human disease by form- characteristic x-ray diffraction pattern (12). However, an un- ing stable protein aggregates. The Asn/Gln region of the usual property of Ure2 fibrils is their ability to maintain na- Ure2p prion domain extends to residue 89, but residues tive-like ligand binding properties within the fibrillar arrays 15–42 represent an island of “normal” random sequence, (8, 13). Consistent with this, Ure2 fibrils formed by standing at which is highly conserved in related species and is rel- subambient temperatures show a Fourier transform infrared atively hydrophobic. We compare the time course of spectrum consistent with native-like helical content (8), and structural changes monitored by thioflavin T (ThT) the cross-␤ x-ray diffraction band becomes apparent only after binding fluorescence and atomic force microscopy for incubation of the protein close to the Tm (14). Atomic force Ure2 and a series of prion domain mutants under a microscopy (AFM) imaging of these “native-like” fibrils shows range of conditions. Atomic force microscopy height im- them to be homogeneous, with a height of around 12 nm and a ages at successive time points during a single growth periodicity of around 50 nm (8). experiment showed the sequential appearance of at Ure2 prion formation in vivo (2) and fibril formation in vitro least four fibril types that could be readily differenti- (5, 15) are dependent on the presence of the N-terminal ϳ90 ated by height (5, 8, 12, or 9 nm), morphology (twisted or amino acids. The N-terminal prion domain (PrD) is unstruc- smooth), and/or time of appearance (early or late in the tured in the native state (6, 16) and is rich in Asn and Gln ؍ plateau phase of ThT binding). The Ure2 dimer (h residues (see Fig. 1). Deletion of all or parts of the PrD has no nm) and granular particles corresponding to 0.5 ؎ 2.6 discernible effect on the dimeric structure, thermodynamic sta- nm) could also be 12–4 ؍ higher order oligomers (h bility, folding kinetics, or folding pathway of Ure2 under a wide detected. The mutants 15Ure2 and ⌬15–42Ure2 showed range of conditions (9, 15, 16, 20–22). Expansion of Gln (or the same time-dependent variation in fibril types but with an increased lag time detected by ThT binding CAG) repeats is responsible for a number of human neurode- compared with wild-type Ure2. In addition, ⌬15–42Ure2 generative diseases, including Huntington’s disease (23). The showed reduced binding to ThT. The results imply a role ability of poly-Gln or poly-Asn regions to aggregate by forming ␤ of the conserved region in both amyloid nucleation and a hydrogen bonded -sheet structure is thought to cause dis- formation of the binding surface recognized by ThT. ease (24–27), either by direct toxicity (28) or by sequestration of Further, Ure2 amyloid formation is a multistep process other vital cellular proteins (29, 30). There is evidence for via a series of fibrillar intermediates. poly-Gln and other amyloid diseases that the species most damaging to cells are protofibrils, or intermediates formed early in the aggregation process, rather than large fibrillar Ure2p is the protein determinant of the epigenetic factor aggregates (31, 32). [URE3] of Saccharomyces cerevisiae, which has been demon- ThT binding provides a convenient method to measure the strated to represent a prion of yeast (1, 2). Analogous to the effect of different environmental factors on the kinetics of mammalian prion protein (3), Ure2p is aggregated, inactive, amyloid formation (9, 33). The time course of Ure2 amyloid and protease-resistant in prion strains (1, 2). In addition, amy- formation monitored by ThT binding shows a sigmoidal loid-like filaments are observed both in vivo (4) and in vitro (5, curve, representing a lag time, an exponential growth phase, 6). Fibrils formed in vitro show characteristic green birefrin- and a plateau region (7–9). The lag time can be circumvented gence on Congo red binding (5, 7, 8) and also bind thioflavin T by seeding with preformed amyloid-like fibrils (5–7) and is protein concentration-dependent (6, 9). This is consistent with a nucleation-dependent mechanism (34, 35), where the * This work was supported in part by Natural Science Foundation of lag time reflects the kinetic barrier to association of a suffi- China Grant 30070163, 973 Project of the Chinese Ministry of Science cient number of molecules to form a thermodynamically sta- and Technology G1999075608, and State Key Development Plan Pro- ble nucleus or seed. However, once this stable nucleus is ject 199801012. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be formed, exponential growth from the fibril ends is then ob- hereby marked “advertisement” in accordance with 18 U.S.C. Section served, until steady-state conditions are reached. Results 1734 solely to indicate this fact. from a number of laboratories indicate that conditions that ¶ To whom correspondence may be addressed. Tel.: 86-10-6488-8496; produce this characteristic increase in dye binding for Ure2 Fax: 86-10-6484-0672; E-mail: [email protected] or sarah.perrett@ iname.com. ʈ Supported by the Chinese Academy of Sciences, the Royal Commis- 1 The abbreviations used are: ThT, thioflavin T; AFM, atomic force sion for the Exhibition of 1851, and the Royal Society. spectroscopy; EM, electron microscopy; PrD, prion domain; WT, wild-type.

This paper is available on line at http://www.jbc.org 3361 119 3362 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils

also lead to the eventual appearance of well formed amyloid- like fibrils, visualized by EM or AFM (5–9). Oligomeric particles or rods of Ure2 have been observed by EM (6) and AFM (8). However, the relationship between the time course of changes in ThT binding and evolution of amyloid-like structure has not been investigated for Ure2. AFM offers particular advantages over EM, in that hydrated samples can be observed directly, in air, without requirement for staining. In addition, AFM can detect the presence of aggregated species as well as differences in fibril morphology which are not apparent in EM images (8, 36, 37). Here we compare the time course of structural changes monitored by ThT binding and AFM and examine the role of different parts of the Ure2 PrD sequence on the kinetics of fibril formation.

EXPERIMENTAL PROCEDURES Materials—ThT and Tris were from Sigma. Ure2 and N-terminal variants, 15Ure2, ⌬15–42Ure2, 42Ure2, and 90Ure2 (see Fig. 1) were produced in Escherichia coli with a short His tag and purified as described previously (9, 16). 42Ure2 was constructed as described previously for the other mutants (16). Proteins were stored at Ϫ80 °C and FIG.1.Primary structure of the Ure2p N-terminal PrD in the defrosted in a 25 °C water bath immediately prior to use. Samples were WT protein and in the prion domain deletion mutants. Repetitive regions detected by sequence analysis (16) are indicated by diagonal prepared in 50 mM KH PO -Na HPO buffer containing 0.15 M NaCl, or 2 4 2 4 stripes or bold type. Hydrophobic regions of the PrD, identified by in 50 mM Tris-HCl buffer containing 0.2 M NaCl as described (9) and plotting the relative hydrophobicity (17, 18), are underlined. The C- ϫ centrifuged at 18,000 g for 30 min at 4 °C to remove any aggregated terminal region has homology to the glutathione S-transferase protein protein. family (19). Amyloid Formation—The kinetics of amyloid formation of Ure2 proteins was monitored using ThT binding fluorescence as described previously (7, 9, 33, 38). Incubation was at a constant temperature of 25 or RESULTS 37 °C with shaking, as described previously (9). Alternatively, proteins Ure2 Mutants 15Ure2 and ⌬15–42Ure2 Show an Increase in were incubated without shaking at 4 or 25 °C. NaN3 (0.02% w/v) was added to prevent bacterial growth. The pH range of buffers used was the Lag Time Detected by ThT Binding—ThT binding provides 7.5–8.4 (at 25 °C), and the protein concentration range was 15–40 ␮M a convenient method to assay the effect of different factors on for full-length Ure2 and 30–140 ␮M for Ure2 mutants. The pH values the kinetics of amyloid formation (9, 33). We compared the given in the text are correct at the temperature of incubation, allowing ThT-monitored kinetics of amyloid formation for full-length for the temperature dependence of the pH of Tris buffer. At regular time Ure2 and a series of PrD deletion mutants. The mutants ex- ␮ intervals, 10- l aliquots were removed from the reaction mixture and amined were 15Ure2, which lacks the first stretch of repetitive assayed for ThT binding, as described previously (9). Samples were sequence; ⌬15–42Ure2, which retains all the Asn/Gln repeat incubated in parallel whenever possible. When comparing the time course of amyloid formation by ThT binding and AFM, samples were regions, but lacks the island of “normal” random sequence taken simultaneously from the same reaction vessel whenever possible. within the PrD; 42Ure2, which lacks the first 41 residues of the AFM—A 10-␮l drop of the protein sample was deposited on freshly PrD; and 90Ure2, in which the entire Asn/Gln repeat region cleaved mica, allowed to stand for 10 min in air, then washed with three has been deleted (Fig. 1). The WT and mutant Ure2 proteins 200-␮l aliquots of distilled deionized water, before drying for 4 min in a were compared under a range of incubation conditions, includ- stream of nitrogen. Tapping mode AFM was performed using a Nano- ing different temperatures (4, 25, and 37 °C), buffer systems scope IIIa Multimode-AFM instrument (Digital Instruments) under (sodium/potassium phosphate or Tris-HCl), and with or with- ambient conditions. Super-sharp silicon tips (Silicon-MDT Ltd.) with resonance frequency of about 106 kHz were used at a scan rate of 1–2 out agitation. Representative curves for a variety of conditions Hz. Once the tip was engaged, the set point value was adjusted to are shown in Fig. 2. The mutants 42Ure2 and 90Ure2 showed minimize the force exerted on the sample while maintaining the sharp- a negligible increase in ThT binding fluorescence even at max- ness of the image. imal protein concentrations. This is consistent with the re- Height measurements of granular and fibrillar particles were per- quirement of residues 1–65 for induction or maintenance of the formed manually using the software provided with the Nanoscope in- prion state in vivo (2, 40). Interestingly, the mutant 15Ure2 strument. To compare the size distribution of granules over time, the maximal height of every granular particle detected within a represent- consistently showed a sigmoidal time course monitored by ThT ative scan area of fixed size was measured for each time point. To binding, similar to that for WT Ure2, but with a longer lag time determine the distribution of heights of fibrils, the height profiles were (Fig. 2). ⌬15–42Ure2 showed greatly reduced binding to ThT measured perpendicular to the fibril over a region greater than the compared with 15Ure2 or WT. However, under certain condi- periodicity of height variations within an individual fibril. The average tions (particularly in Tris buffer at relatively high protein peak height for each fibril was recorded (maximal variation around 1 concentrations), the limited increase in ThT binding for ⌬15– nm). Mean heights were obtained by fitting to a Gaussian curve. The 42Ure2 could be seen to be sigmoidal, revealing a lag time errors shown are the standard deviation. Scanning different regions of the mica surface confirmed that the slower than for WT Ure2 and similar to 15Ure2 at the same distribution of particles or fibrils was uniform and that the scan areas protein concentration (Fig. 2B). This suggests a role of both sampled were representative, with the exception that protofilaments Asn/Gln repeat (residues 1–14) and nonrepeat (residues 15–42) were deposited preferentially at the edge of the grids, suggesting that regions of the PrD in nucleation of amyloid structure. However, they are more easily dislodged from the mica surface by the washing it also indicates that deletion of either one of these two regions process than mature fibrils. This has important consequences for the does not ablate the ability to form an amyloid-like structure. interpretation of the data because it indicates that although protofila- Characterization of the Ure2 Dimer by AFM—AFM height ment formation clearly precedes fibril formation, protofilaments are present earlier and more abundantly than apparent from the AFM imaging provides a convenient method to characterize the mor- assay procedure. This may explain in part the increased tendency to phology of biological macromolecules at submolecular resolu- observe protofilaments when fibrils are grown in situ on the mica (39). tion without requirement for staining (36, 37, 39, 41–43). Typ- 120 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils 3363

contribute to the height of the Ure2 monomer or dimer as measured by AFM. Comparison of Time Course of Structural Changes Monitored by ThT Binding and AFM—To ascertain the structural basis of the differences in kinetics detected by ThT binding for Ure2 and the PrD mutants described above, we measured the time course of structural changes in parallel by ThT binding and tapping mode AFM. In each case, aliquots were removed from the reaction vessel for assay. Fig. 4 shows a comparison of the time course measured by the two methods for Ure2 incubated in phosphate buffer, pH 8.0, at 37 °C with shaking. Under these conditions, abundant well formed fibrils are formed within 24 h, as detected by EM, and the time course of ThT binding is highly reproducible and relatively rapid (9), so that a plateau is reached within 12 h (Fig. 4A). The initial Ure2 protein solution was found to contain a variety of sizes of granular particles (Fig. 4, B and E, 0h), ranging in height from 1 to 85 nm, although greater than 90% of the particles were less than 20 nm in height. The larger particles appear to be dispersed or precipitated after the onset of shaking and are concluded to represent amorphous aggregates. Occasional fibrillar structures are also detected in the initial sample (Fig. 4E, 0h). FIG.2.Kinetics of formation of amyloid-like structure for Ure2 The presence of a low concentration of preformed fibrils, or and PrD mutants monitored by ThT binding under a range of nuclei for fibril formation, could account for the linear rather conditions. Values of pH are correct at the temperature of incubation. than exponential dependence of the lag time on initial Ure2 A,40␮M Ure2 (●), 15Ure2 (Œ), ⌬15–42Ure2 (f), and 42Ure2 (ࡗ) incubated in Tris-HCl buffer, pH 7.5, 0.2 M NaCl at 25 °C with shaking. concentration, as discussed previously (9). B,30␮M Ure2 (●); 40 ␮M (Œ) and 80 ␮M (‚) 15Ure2; 40 ␮M (f) and 80 Changes in the height distribution of granular particles over ␮M (Ⅺ) ⌬15–42Ure2; and 40 ␮M (ࡗ) and 80 ␮M (छ) 42Ure2 incubated in the time course of the ThT-monitored curve were examined by Tris-HCl buffer, pH 7.2, 0.2 M NaCl at 37 °C with shaking. C,30␮M ● ␮ Œ ␮ ⌬ f recording the heights of all granules within a representative Ure2 ( ), 40 M 15Ure2 ( ), and 80 M 15–42Ure2 ( ) incubated in ␮ sodium/potassium phosphate buffer, pH 8.0, 0.2 M NaCl at 37 °C with 2- m square at hourly time points between the onset of incu- shaking. D,40␮M Ure2 (●), ⌬15–42Ure2 (f), 42Ure2 (ࡗ), and 90Ure2 bation (0 h) and the onset of fibril formation (7 h). Within the (ϩ) incubated in Tris-HCl buffer, pH 9.0, 0.2 M NaCl at 4 °C lag phase region (0–2 h), there was a marked increase in the without shaking. number of particles of height 4–6 nm, which was then followed (2–3 h) by an increase in particles of height 8–12 nm (Fig. 4C), coinciding with an increase in ThT binding fluorescence (Fig. ically, the sample is adsorbed onto mica, and the surface is 4A). Given the height of the Ure2 dimer of 2.6 Ϯ 0.5 nm (Fig. 3), scanned with an oscillating or “tapping” tip on a microcantile- ver. The variations in height can then be represented by a gray this then suggests that the 4–6-nm particles that appear dur- scale, ranging from white (high) to black (low), to form the ing the lag phase are tetramers or hexamers, whereas the image. A characteristic of AFM imaging is that the size of the 8–12-nm particles are likely to represent larger oligomers. scanning tip relative to the size of protein oligomers or fibrils The earliest fibril-like structures appear late in the exponen- results in an overestimation of the width, whereas the height of tial phase of ThT binding (6 h) and have a height of around 5 the sample above the mica surface can be measured with ac- nm, thus resembling the protofilaments observed for other curacy and reproducibility. Nevertheless, the height of biolog- amyloidogenic proteins (28, 31, 36, 37, 39, 42, 43). These are ical molecules measured by AFM tends to be smaller than the succeeded by 8-nm fibrils (7 h) and then 12-nm fibrils (8 h). diameter measured by other structural methods, which may Significant numbers of fibrillar structures are not detected reflect the absence of stain, the degree of hydration, and/or until ThT binding has already reached a plateau (Fig. 4, A, D, compression by the AFM tip. and E). However, the number of protofilaments is underesti- To calibrate the height of the Ure2 dimer by AFM, we pre- mated in the AFM assay (see “Experimental Procedures”). It is pared a series of dilutions of Ure2 and the mutants ⌬15– therefore likely that both protofilaments (5 nm; also 2.5 nm, see 42Ure2 and 90Ure2 in Tris-HCl buffer, pH 8.4, 0.2 M NaCl at below) and larger granules (8–12 nm) contribute to the onset of 25 °C. Under these conditions the protein shows a minimal ThT binding. tendency to aggregate and is expected to be predominantly Continued monitoring of the fibril heights and morphology dimeric at micromolar protein concentrations (16), although reveals further structural changes over time, with little further species with sedimentation values corresponding to monomers variation in the ThT binding fluorescence (Fig. 4). Early in the and tetramers are detected under similar buffer conditions at plateau phase (8 h), the majority of fibrils have a height of 15 °C, depending on the protein concentration (6). After adsorp- around 12 nm and a relatively smooth appearance, although tion of a 1 ␮M protein solution of WT or mutant Ure2 onto mica, the height is observed to vary with a periodicity of 40–70 nm, AFM imaging reveals a homogenous population of spherical similar to the “native-like” fibrils produced after a week of particles (Fig. 3). The predominant species has a height of 2.6 Ϯ standing in Tris buffer at 4 °C (8). Over the course of the 0.5 nm (Fig. 3C, upper panel). The WT sample contained a following hours and days of incubation at 37 °C, there was a minor population (less than 5%) of larger particles (Fig. 3A), gradual decrease in the mean fibril height, until at 7 days the which have heights in the range 4–8 nm (data not shown). At fibril heights resolved into two peaks, indicating the presence lower protein concentrations, an additional peak at 1.3 Ϯ 0.3 of two distinct fibril types (Fig. 4D). (Fitting the combined data nm appears (Fig. 3C, lower panel), consistent with population to a two-peak Gaussian gives a height of 11.8 Ϯ 0.9 nm for the of the monomer. Identical peaks are observed for WT Ure2, fibril type that dominates early in the plateau phase, and a ⌬15–42Ure2, and 90Ure2, indicating that the PrD does not height of 9.0 Ϯ 1.2 nm for the fibril type that dominates at 121 3364 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils

FIG.3.AFM characterization of the Ure2 dimer. AFM height images of Ure2 (A) and ⌬15–42Ure2 (B) in Tris-HCl, pH 8.4, 0.2 M NaCl, room temperature, and 1 ␮M protein concentration. The scale bar represents 200 nm, and the full range of the gray scale corresponding to height was 10 nm. C, height distribution of the particles for Ure2 (black) and ⌬15– 42Ure2 (gray)at1␮M protein concentration (upper panel) or at approximately 0.1 ␮M (lower panel). In each case the scan area was a 2-␮m square or less.

extended incubation times.) The other change that is apparent binding for the mutant proteins (Fig. 2) coincides with forma- over this time period is that most fibrils no longer appear tion of fibrillar structures. However, the mutant fibrils are smooth, but have a clearly distinguishable twisted or zigzag shorter in length than WT and do not elongate further even at morphology (Fig. 5A). Careful inspection reveals that the small extended incubation times (Fig. 5, A–C). This is particularly proportion of “twisted” fibrils present at time points when marked for ⌬15–42Ure2, which shows only rod-like structures 12-nm fibrils dominate (twisted fibrils indicated by arrows in (150–200-nm length). However, the WT and mutant fibrils or Fig. 5A, 8h) consistently have heights of around 8 nm. This rods show a similar pattern of height changes over time, with then indicates that as well as protofilaments, at least two progressive appearance of 5-, 8-, 12-, and 9-nm height proto- additional types of fibril are present, distinguishable by their filaments or fibrils (Fig. 5, D–F). height and morphology, the relative proportions of which Reduced ThT Binding Ability of the ⌬15–42Ure2 Mu- change over time. The preferential loss of the thicker “smooth” tant—On first inspection, the low level of ThT binding for the fibrils over time suggests that the twisted fibrils may be de- ⌬15–42Ure2 mutant, particularly in phosphate buffer, appears rived from the smooth fibrils by conformational conversion or to correlate with the inability of the fibrils to extend beyond separation of the constituent strands. short rods (Fig. 5C). However, when investigating Ure2 and its Comparison of Fibril Morphology for Ure2, 15Ure2, and ⌬15– mutants by AFM under “nonaggregating” conditions (Tris, pH 42Ure2—As described above, a parallel assay by ThT binding 8.4, at 25 °C), we made the unexpected discovery that although and AFM indicates that long fibrils of WT Ure2 are present by WT Ure2 aggregation is strongly reduced under these condi- the end of the exponential growth phase (Fig. 5A, 6h), are tions (16), fibrils of ⌬15–42Ure2 are readily formed on standing abundant by early plateau phase (Fig. 5A, 8h), and persist in this buffer when stored at 4 °C (Fig. 6). WT Ure2 fibrils (Fig. even at very long incubation times (Fig. 5A, 4d). Variations in 6, A and D, insets of E) formed at 4 °C in this buffer, or at morphology over this time course include a change in the dis- slightly lower pH as used to produce “native-like” Ure2 fibrils tribution of fibril heights, indicating the progressive appear- (8, 13), are morphologically indistinguishable from these ⌬15– ance of 5-, 8-, 12-, and 9-nm fibrils (Figs. 4D and 5D). The ThT 42Ure2 fibrils (Fig. 6, B, C, and E). Subpopulations of proto- binding assay (Fig. 2) suggests that 15Ure2, and to a lesser filaments with heights of around 2.5 and 5 nm can be clearly extent ⌬15–42Ure2, are also able to form amyloid-like struc- distinguished (Fig. 6, D and E), and bundling or branching of ture, although with a longer nucleation-dependent lag time. A the filaments can occasionally be observed (Fig. 6C). In the comparison by AFM of WT and mutant fibrils at equivalent high pH buffer, ⌬15–42Ure2 fibrils are far more abundant than stages of the ThT-monitored time course is shown in Fig. 5. WT at all time points (Fig. 6E). In contrast to the phosphate Incubation of the proteins was under identical buffer conditions buffer time course (Fig. 4), few granular particles greater than (phosphate buffer, pH 8.0, 37 °C, with shaking), but with the 4 nm were observed in Tris buffer, suggesting that larger protein concentration of the mutants increased to give a similar granular particles are not obligate intermediates in fibril for- kinetic time course as WT. (At lower protein concentrations, mation and that the ThT binding under these conditions is the similar short fibrils are observed for 15Ure2, but only amor- result of the presence of protofilaments and fibrils. phous structures could be detected for ⌬15–42Ure2, data not The contradiction between the extent of ThT binding (Fig. shown.) The results indicate that the observed increase in ThT 2D) and the abundance of fibrils for Ure2 and ⌬15–42Ure2 122 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils 3365

FIG.4.Comparison of the time course of formation of amyloid-like structure monitored by ThT binding and AFM. 30 ␮M WT Ure2 protein was incubated in sodium/potassium phosphate buffer, pH 8.0, 0.15 M NaCl, and 37 °C with shaking. Structural changes were monitored by ThT binding (A) and AFM (B–E). B, population distribution of heights of granular particles observed in the initial protein sample, derived from analysis of two representative scan areas each of 5 ␮m square. C, population distribution of heights of granular particles observed over different time points, as indicated. All particles detected within a standard, representative scan area of 2 ␮m square for each hourly time point were included. D, population distribution of heights of fibrils observed at different time points, as indicated. A representative 5-␮m square scan area from the center of the mica surface was analyzed in each case (but see “Experimental Procedures” and Fig. 6). E, AFM height images during the course of fibril formation. Samples were removed from a single reaction vessel at the time points indicated. The bars represent 1 ␮m. The full range of the gray scale corresponding to height was 20, 30, or 40 nm for 0–4 h and 50 nm thereafter, except 2d, which was 100 nm. 123 3366 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils

FIG.5.Morphology and height distribution of amyloid-like structures monitored by AFM for WT and mutant Ure2. A and D,30␮M WT Ure2; B and E,80␮M 15Ure2; and C and F,80␮M ⌬15–42Ure2. The incubation conditions were the same as in Fig. 4. For each protein, the samples were removed from a single reaction vessel at the time points indicated. A–C, AFM height images. The bar represents 1 ␮m. The full range of the gray scale corresponding to height was 30 nm (B, 5h) or 50 nm (all other panels, A–C). D–F, population distribution of heights of fibrils or rods at different incubation times as indicated, obtained by measuring the heights of all fibrils within a representative 5-␮m square scan area, which included the scan areas displayed in A–C.

(Fig. 6E) could be the result of a vastly lower affinity of WT and the presence of fibrils for ⌬15–42Ure2 is that the 15–42 Ure2 for the mica surface. However, the lack of WT Ure2 fibrils region is important for binding of the hydrophobic dye ThT. under these conditions is also apparent from EM (9, 15). The Plotting the relative hydrophobicity of the PrD sequence (17, simplest explanation for the discrepancy between ThT binding 18) indicates that the region spanning residues 22–34 is rela- 124 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils 3367

FIG.6.Observation of protofilaments and fibrils of WT Ure2 and ⌬15–42Ure2. Incubation was at 4 °C in Tris-HCl buffer, 0.2 M NaCl, pH 8.6 (A and D)orpH9.0(B, C, and E) for 3 or 7 days, as indicated. (Note: the same buffers have a pH of 8.0 or 8.4, respectively, at 25 °C.) A–C, the bar represents 200 nm, and the full range of the gray scale corresponding to height was 30 nm (A and C)or50nm(B). Fibrils of WT (A)or ⌬15–42Ure2 (B and C) have a twisted or braided appearance with a height of 8 Ϯ 1 nm and a periodicity of 50–70 nm. C, bundling or branching of 5-nm protofilaments into 8-nm fibrils. The height across the junction region (between arrows)is5.0Ϯ 0.5 nm. D and E, population distribution of protofilaments and fibrils within representative 5-␮m scan areas at the center (black) or the edge (gray) of the mica surface for WT (D and insets of E) and ⌬15–42Ure2 (E, main panels). tively hydrophilic. However, two hydrophobic regions consist- (44). Within Saccharomyces species, the highly conserved re- ing of residues 9–21 and 35–43 flank this region (Fig. 1). This gion extends from residue 1 to 43. Overexpression of fragments may then account for the reduced binding of ThT to the mutant spanning this region causes curing of the prion state in prion ⌬15–42Ure2, despite its ability to form fibrillar structures strains and inactivation of the Ure2 protein in non-prion morphologically indistinguishable from those formed by WT strains (44). This suggests that the region spanning residues Ure2. 1–43 is involved in intermolecular interactions important for DISCUSSION formation of the prion state. Our finding that the Ure2 mutants 15Ure2 and ⌬15–42Ure2, which have deletions within this The importance of the Ure2 N-terminal domain in prion crucial region, are nevertheless able to form amyloid-like fibrils induction and propagation has been established by genetic is therefore somewhat surprising. Comparison with the Ure2 studies (2, 40), and the requirement of the PrD to form amyloid- like fibrils in vitro has also been demonstrated (5, 15). The fragments that have been studied in vivo (Table I) would pre- mutants initially used in genetic studies to define the PrD were dict that these two mutants would be unable to induce or cure designed at the DNA level, on the basis of convenient endonu- the prion state. Possible explanations for the curing properties clease restriction sites (2, 40), whereas the mutants used in this of the conserved region when overproduced in vivo include a study were designed at the protein level, based on interesting “crystal poisoning mechanism” caused by the interaction of features of the of the PrD primary structure (Ref. 16 and see heterogenous molecules with the growing prion seed; induction Fig. 1). Protein sequence analysis of Ure2 homologs in different of chaperones, which then cure the prion state; or the require- species of yeast has recently identified a conserved region in ment for a cellular cofactor to maintain the prion state, which the otherwise divergent PrDs, corresponding to residues 10–40 is depleted by the Ure2 fragment (44, 45). Our in vitro results, 125 3368 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils

TABLE I TABLE II Properties of Ure2 mutants and fragments in vivo Properties of Ure2 mutants in vitro Experimental details are given in the references indicated. ϩ, ob- Exact experimental details are given in the references or figure served; Ϫ, not observed (or very low rate of occurrence); ND, not deter- legends indicated. ϩ, observed; Ϫ, not observed; ND, not determined. mined; NA, not applicable. a Rate of ThT Fibril length Protein Solubility b c d a b c d Spontaneous nucleation binding by AFM Protein Curing Inactivation Induction Propagation generatione WT Ure2 Ϫ ϩϩϩ ϩϩϩ ϩϩϩ Ure2 WT Ϫϩ ϩ ϩ ϩ 15Ure2 ϩ ϩ ϩϩ ϩϩ Ure2 ⌬2–20 ϪϪ Ϫ ND ND ⌬15–42Ure2 ϩϩ ϩ ϩ ϩ Ure2 13–65 ϪϪ Ϫ ND NA 42Ure2 ND ϪϪ Ϫ Ure2 9–65 ϩϩ Ϫ ND NA 74Ure2 ϩ ND ND ND Ure2 1–65 ϩ ϩ ϩϩ ϩ NA 90Ure2 ϩϪϪϪ ϩ ϩϩϩ Ure2 1–80 ND ND NA a Ure2 1–44 ϩϩ Ϫ ND NA Solubility in E. coli cell extracts (16) or in pure solution (9) in Ure2 1–35 ϪϪ Ϫ ND NA phosphate buffer, pH 7.5. Note that all constructs can be solubilized Ure2 ⌬1–65 ϩϪ Ϫ Ϫ ND using Tris-HCl buffer, pH 8.4 (16), and that amyloid-like fibrils of Ure2 PrD fusion proteins have been observed in bacterial cell extracts (7). a Curing of the prion state when the gene is expressed in a WT b Relative rate of nucleation of amyloid-like structure, assayed by background in an initially [URE3] prion strain (44, 45). ThT binding (ϩϩϩ, shorter lag time; ϩ, longer lag time; Ϫ, no increase b Inactivation of the Ure2 protein (but not necessarily induction of a in ThT binding observed; see Fig. 2). stable prion [URE3] state) when the gene is expressed in vivo inaWT c Relative ThT binding in plateau phase (Fig. 2). background (44). d Relative lengths of fibrillar structures detected by AFM after incu- c Induction of the [URE3] prion when the gene is expressed in a WT bation in phosphate buffer (ϩϩϩ, long fibrils; ϩϩ, short fibrils; ϩ, rods; background in an initally non-prion strain (2). Ϫ, no fibrils; Figs. 4 and 5). Note that WT and mutant fibrils show the d Ability to propagate the prion state when the gene is expressed in same time-dependent changes in fibril thickness (height) under all vivo in a null (ure2⌬) background (40). conditions and that no differences in fibril length were observed in e Spontaneous generation of the [URE3] prion when the gene is ex- Tris-HCl buffer (Figs. 5 and 6). pressed in vivo in a ure2⌬ background (40). (This is not applicable to N-terminal fragments that lack the Ure2 functional region because they cannot show the heritable loss of Ure2 function which is the signature observed under certain conditions and may also bind ThT. Of of the [URE3] prion.) particular note in the AFM study presented here is the time dependent appearance of a series of Ure2 fibril types, including protofilaments (2–5 nm), intermediate fibrils (8 nm), and two in the absence of cellular cofactors, provide support for a crystal types of mature fibrils (12 and 9 nm), implying a hierarchical poisoning mechanism and demonstrate the importance of se- mechanism of assembly. Consistent with this, some fibrils had quence complementarity during self-association to form amy- a twisted appearance, and bundling or branching of fibrils loid-like structure. could be observed. This is similar to the results obtained for The increased lag time for nucleation-dependent formation of other amyloidogenic proteins (28, 36, 37, 39, 42, 43), including amyloid-like structure for the mutants examined in this study polyglutamine peptides (46). The hierarchical assembly of is consistent with a role of the conserved region of the Ure2 PrD fibrils, by twisting together of protofilaments or protofibrils to in forming inter- or intramolecular interactions that help sta- form a variety of fibril morphologies, is emerging as a common bilize the prion seed. The low level of binding of the amyloid- mechanism of fibril assembly for all amyloidogenic proteins specific dye ThT to ⌬15–42Ure2, independent of fibril morphol- (47, 48). The yeast prion Sup35, like Ure2, has an N-terminal ogy, suggests that the island of normal random sequence PrD containing Asn/Gln repeats (49). Fibrils formed from poly- within the PrD is involved in formation of the structural motif glutamine peptides (46, 50, 51), Sup35 (49–52), or Ure2 (5, 6, or binding surface recognized by ThT. This possibly reflects the 14) share many of the tinctorial, structural and mechanistic relatively hydrophobic nature of this region (Fig. 1), which properties of “typical” amyloids. A striking and unusual prop- could also explain its involvement in curing and inactivation in erty of Ure2, however, is the maintenance of native-like struc- vivo (Table I). The delayed fibril formation kinetics of the tural and functional properties within the amyloid-like fibrillar mutants compared with WT provides an explanation for their arrays (8, 13). Interestingly, fibrils formed by incubation of increased solubility in solution and in E. coli cell extracts native, full-length Sup35 show globular appendages radiating (Table II). The difference in solubility of WT and mutant Ure2 from a central fibrillar core under transmission EM (52), highly in vitro is most marked in phosphate buffer (16), which corre- reminiscent of the “backbone” model proposed for Ure2 fibril lates with destabilization of the native state relative to par- assembly (4, 5, 13, 53). Together, these results are consistent tially folded intermediates, likely to be precursors in amyloid with a model for Ure2 fibril formation, in which the PrDs formation and other aggregation processes (9). In phosphate assemble hierarchically into the protofilaments and fibrils of buffer, some differences in morphology between WT and mu- typical amyloid, while still allowing the globular domains to be tant Ure2 fibrils could be observed, but this was limited to fibril accommodated in a native-like state. length. In Tris buffer, WT and mutant fibrils were indistinguishable in length and morphology. Further, under all condi- CONCLUSIONS tions, the same series of fibrillar intermediates was observed A pure solution of either of the mutants 15Ure2 or ⌬15– for WT and the mutants. This then implies that the mechanism 42Ure2 is able to form amyloid-like fibrils morphologically of assembly of WT and mutant Ure2 fibrils is the same. It will indistinguishable from WT Ure2 but with an increased lag be interesting to test the properties of 15Ure2 and ⌬15–42Ure2 time, whereas 42Ure2 shows no detectable amyloid forming in vivo, particularly to see whether overproduction of these ability. This correlates with the importance of residues 1–43 of mutants in a ure2⌬ background could spontaneously generate the Ure2 N-terminal PrD in mediating prion induction or cur- a heritable prion-like state, as has been demonstrated for the ing in a WT background in vivo (2, 40, 44). The observation of WT protein (40). a series of fibrillar intermediates during assembly of Ure2p Comparison of the time course of structural changes moni- fibrils supports the existence of a common, hierarchical mech- tored by ThT binding and by AFM for Ure2 indicates that anism for fibril assembly in all amyloidogenic proteins, even increased binding of ThT correlates well with appearance of where native-like globular structure is accommodated within fibrillar structures. However, granular aggregates were also the fibrillar arrays. 126 Amyloid Nucleation and Hierarchical Assembly of Ure2 Fibrils 3369

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127 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 33, Issue of August 13, pp. 34983–34990, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits* Received for publication, May 10, 2004 Published, JBC Papers in Press, June 4, 2004, DOI 10.1074/jbc.M405158200

Zhiyi Wei‡§¶, Ping Zhang‡§¶, Zhaocai Zhou‡§, Zhongjun Cheng‡§, Mao Wan‡§, and Weimin Gong‡§ʈ From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China and the §School of Life Sciences, Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, Anhui 230026, People’s Republic of China

eIF3k, the smallest subunit of eukaryotic initiation comprising over 25 polypeptides (2). In contrast, only three to factor 3 (eIF3), interacts with several other subunits of five initiation factors are known in prokaryotes. This difference eIF3 and the 40 S ribosomal subunit. eIF3k is conserved in protein complexity suggests that more protein-RNA and among high eukaryotes, including mammals, insects, protein-protein interactions rather than RNA-RNA interac- and plants, and it is ubiquitously expressed in human tions are required for efficient translation initiation in eukary- tissues. Interestingly, eIF3k does not exist in some spe- otic cells. cies of yeast. Thus, eIF3k may play a unique regulatory In mammalian cells, eIF3 is the largest initiation factor with role in higher organisms. Here we report the crystal an apparent molecular mass of about 600 kDa. It plays a structure of human eIF3k, the first high-resolution central role in steps 1 and 2 of the translation initiation process structure of an eIF3 component. This novel structure (1, 3). For instance, eIF3 can bind to dissociated 40 S subunits contains two distinct domains, a HEAT (named for Hun- and delay the reassociation with the 60 S ribosomal subunit for tington, elongation factor 3, A subunit of protein phos- a long enough time to permit initiation. eIF3 also stabilizes the phatase 2A, target of rapamycin) repeat-like HAM binding of the Met-tRNAMet⅐eIF2⅐GTP ternary complex to the (HEAT analogous motif) domain and a winged-helix-like i WH domain. Through structural comparison and se- 40 S subunits and promotes the formation of a 43 S preinitia- quence conservation analysis, we show that eIF3k has tion complex comprised of the 40 S subunit, the ternary com- three putative protein-binding surfaces and has poten- plex, eIF1, eIF1A, and eIF3. In addition, eIF3 stimulates the 7 tial RNA binding activity. The structure provides key binding of 5Ј-m G-capped mRNA by interaction with the information for understanding the structure and func- mRNA-associated factor eIF4G. tion of the eIF3 complex. eIF3 is a multisubunit protein complex. Various genes encoding eIF3 subunits have been cloned from mammals, plants, and yeasts. Twelve different subunits (eIF3a/p170, b/p116, Translation initiation is a sophisticated cellular process, es- c/p110, d/p66, e/p48, f/p47, g/p44, h/p40, i/p36, j/p45, k/p28, pecially in eukaryotes. In general, translation initiation in l/p69) have been identified in mammals, while in yeast only six eukaryotic organisms involves three steps (1); first, the methio- subunits (eIF3a/TIF32, b/PRT1, c/NIP1, i/TIF34, g/TIF35, Met j/HCR1) have been found and are all homologous to the corre- nyl-initiator tRNA (Met-tRNAi ) binds to the 40 S ribosomal subunit to form a 43 S preinitiation complex; second, the preini- sponding mammalian subunits. The five yeast subunits, eIF3a, tiation complex binds to mRNA and scans to the AUG start eIF3b, eIF3c, eIF3g, and eIF3I, can form a core complex (4). codon in the mRNA; and third, the 60 S ribosomal subunit joins Mammalian and yeast eIF3s differ not only in the number of the mRNA-bound preinitiation complex to form an 80 S initi- subunits but also in the structure of some subunits. For exam- ation complex, ready to commence translation. Each of these ple, mammalian eIF3a contains a repeat region, but this region steps is stimulated by a number of proteins called eukaryotic is absent in the yeast ortholog (2). These differences suggest initiation factors (eIFs).1 At least 11 eIFs have been identified, that mammalian and plant eIF3 have evolved to include additional subunits, which are likely to function as regulatory factors and the extra structural motifs provide the capacity to * This work was supported by the Foundation for Authors of National mediate extra protein-protein or protein-RNA interactions re- Excellent Doctoral Dissertation of the People’s Republic of China (Pro- quired for the tighter regulation in higher eukaryotes. Some ject No. 200128), National Foundation of Talent Youth (Grant No. eIF3 subunits (eIF3a, eIF3c, eIF3e, eIF3f, and eIF3h) may 30225015), the National High Technology Research and Development Program of China (Grant No. 2001AA233021), the 863 Special Program serve as structural scaffolds or to provide docking sites for of China (Grant No. 2002BA711A13), the Key Important Project and other proteins, since they contain PCI or MPN domains, which other projects from the National Natural Science Foundation of China are found in components of large protein complexes and have (Grant Nos. 30121001, 30070170, 30130080, and 30121001), and the been implicated in protein-protein interactions (2, 5). Chinese Academy of Sciences (Grant No. KSCX1-SW-17). The costs of publication of this article were defrayed in part by the payment of page To understand the structure and function of the eIF3 com- charges. This article must therefore be hereby marked “advertisement” plex in eukaryotic translation initiation, we have begun a sys- in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. tematic structural study of the eIF3 components. Here we The atomic coordinates and structure factors (code 1RZ4) have been describe the high-resolution crystal structure of human eIF3k, deposited in the Protein Data Bank, Research Collaboratory for Struc- tural Bioinformatics, Rutgers University, New Brunswick, NJ the smallest non-core subunit of eIF3. Mammalian eIF3k has (http://www.rcsb.org/). recently been characterized (6) to co-express with the five core ¶ These authors contributed equally to this work. subunits of eIF3 and form a stable co-immunoprecipitatable ʈ To whom the correspondence should be addressed. E-mail: complex with the core complex. eIF3k also interacts directly [email protected]. 1 The abbreviations used are: eIF, eukaryotic initiation factor; HTH, helix-turn-helix; HEAT, Huntington, elongation factor 3, A subunit of motif; WH, winged-helix; PHAT, pseudo-HEAT analogous topology; protein phosphatase 2A, target of rapamycin; HAM, HEAT analogous PDB, Protein Data Bank.

This paper is available on line at http://www.jbc.org 34983 128 34984 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits

TABLE I Summary of data collection and processing Numbers in parentheses represent the value for the highest resolution shell. MAD, multiwavelength anomalous dispersion.

MAD data collection Edge Peak Remote Wavelength (Å) 0.97992 0.97969 0.9 Resolution range (Å)30–2.1 30–2.1 30–2.3 (2.15–2.1) (2.15–2.1) (2.35–2.3) No. of total reflections 116,044 218,413 189,782 No. of unique reflections 12,780 (828) 12,597 (822) 9,690 (638) I/␴ 12.0 (3.7) 21.7 (9.5) 16.6 (7.3) Completeness (%) 98.7 (97.6) 100 (100) 100 (99.8)

Rmerge 0.080 (0.300) 0.079 (0.211) 0.108 (0.269)

with eIF3c, eIF3g, and eIF3j. The crystal structure of eIF3k TABLE II reveals a novel ear-like protein structure containing two do- Structural refinement statistics mains. Structural comparisons and sequence conservation Numbers in parentheses represent the value for the highest resolution shell. analysis suggest that eIF3k is likely to act as a structural scaffold for protein-protein and protein-RNA interactions. It Space group P21212 has three putative protein-binding regions and has potential Unit cell dimensions (Å) 83.074 ϫ 44.671 ϫ 55.524 RNA binding activity associated with its HTH (helix-turn-he- Resolution (Å)30–2.1 (2.13–2.1) a Rwork (%) 18.7 (18.7) lix) motif. b Rfree (%) 22.2 (27.3) No. of reflections EXPERIMENTAL PROCEDURES Working set 11,090 Expression and Purification of Human eIF3k—The complete cDNA Test set 1,276 fragment encoding human eIF3k protein was subcloned from a human No. of atoms brain cDNA library into a pET-22b expression vector, and human eIF3k Protein atoms 1,714 (including 6 selenium atoms) was expressed highly as a soluble protein in Escherichia coli strain Water molecules 149 BL21 (DE3) with a 6-residue histidine tag fused to its C terminus. Sulfate ions 5 in 1 sulfate ions Purification of the eIF3k protein was carried out through affinity chro- r.m.s.d. from ideality Bond lengths (Å) 0.005 matography with a Chelating SepharoseTM Fast Flow (Amersham Bio- Bond angles (°) 1.1 sciences). For phase determination, the recombinant plasmid was Average B factor (Å2) transferred into Met-auxotrophic strain B834 to obtain the seleno- Main chain 19.1 methionyl derivative of human eIF3k protein. Side chain 22.8 Crystallization and X-ray Data Collection—Crystals of seleno-methi- Water 29.0 onine-substituted eIF3k protein were grown using the hanging drop Sulfate ion 43.6 vapor diffusion method at 4 °C. The initial crystallization conditions Ramachandran plot (2.0 M ammonium sulfate, 0.1 M Hepes at pH 7.5, 0.1 M NaCl) were Most favored regions (%) 94.9 obtained using Crystal Screen kits I and II from Hampton Research. By Additionally allowed (%) 5.1 optimizing the concentration of ammonium sulfate to 1.6 M, crystals of a ϭ͚͉͉ ͉ Ϫ ͉ ͉͉ ͚͉ ͉ Rwork Fobs Fcalc / Fobs , where Fobs and Fcalc are observed larger size and better quality were obtained. A multiwavelength anom- and calculated structure factors. alous dispersion data set was collected from a single seleno-methionine- b ϭ͚ ͉͉ ͉ Ϫ ͉ ͉͉ ͚ ͉ ͉ Rfree T Fobs Fcalc / T Fobs , where T is a test data set of 10% of substituted eIF3k crystal at 100 K on beamline 3W1A of the Beijing the total reflections randomly chosen and set aside prior to refinement. Synchrotron Radiation Facility at the Institute of High Energy Physics, Chinese Academy of Sciences. The data were collected at three wave- ␭ ϭ ␭ ϭ ␭ ϭ lengths ( edge 0.97992 Å, peak 0.97969 Å, and remote 0.9 Å). All RESULTS data were processed and scaled with the DENZO and SCALEPACK (7), Overall Structure—The human eIF3k structure was deter- respectively. Data collection statistics are presented in Table I. Phasing, Model Building, and Refinement—Six of seven expected mined by multiwavelength anomalous dispersion with seleno- selenium positions were found by SOLVE (8) using the three data sets, methionine substituted protein. The model was refined to 2.1-Å and the initial phase was calculated to 2.5 Å. RESOLVE (9, 10) was resolution with a good agreement with diffraction data and has used for density modification and building of the initial model of human high stereochemical quality (Table II). The final model includes eIF3k. The initial model containing about 75% of the residues was an eIF3k monomer with 213 residues (residue 2–183 and 186– refined against the peak data set in the 30–2.5-Å resolution range with 216), 6 selenium atoms, 1 sulfate ion, and 149 water molecules. maximum-likehood amplitude targets by using the Crystallography The C-terminal 2 residues and the polyhistidine tag are disor- and NMR System (11). Subsequently, the refinement was extended to 184 185 resolution bins of 2.3 Å with iterative manual adjustments and rebuild- dered. No electron density for residues Gly and Ser and Ϫ Ϫ the side chains of Gln119, Asp182, Glu183, and Ser216 was ob- ing of the model using the program O (12) and 2Fo Fc and Fo Fc electron density maps as references. A sulfate ion and water molecules served. In addition, residues Phe56, Glu123, Trp156, Ile196, were added to the model when the resolution extended to 2.1 Å, and the Lys197, and Lys204 have weak electron density. value of Rfree is about 30%. After that, individual atomic B factors were The overall structure of eIF3k has an ear-like shape with refined. Finally, the model was checked for errors with simulated an- dimensions of 35 Å ϫ 35 Å ϫ 60Å. It has 16 helices (14 ␣ helices nealing omit maps covering a 10-residue segment of the structure at a ␤ time. The stereochemical quality of the final model was checked by and two 310 helices) and a three-strand -sheet (Fig. 1). The PROCHECK (13), and the final refinement statistics and geometry are secondary structure elements are indicated in Fig. 2. Although excellent (Table II). sequence analysis did not suggest any known structural motifs, Sequence and Structure Analysis—Seven eIF3k-related sequences a three-dimensional structural comparison of the crystal struc- were identified in the sequence data base using BLAST (14); multiple ture of eIF3k determined here using DALI (17) clearly showed sequences alignment was done with T-coffee (15); the similarity score of that eIF3k consists of two distinct domains. The N-terminal residues were calculated using Blosum62 matrix by ESPript (16); struc- region of eIF3k is a HAM domain, named for HEAT (20) anal- tural similarity searches were performed with DALI (17); and electrostatic surface potentials were calculated with MOLMOL (18). Figs. 1, 3, ogous motifs, in a mostly right-handed superhelical arrange- 4, 5, and 7 were prepared using Ribbons (19); Fig. 2 was prepared with ment, formed by a leading ␣ helix and three HEAT analogous ESPript; and Fig. 6 was prepared using MOLMOL. repeats, H1 (consisting of ␣3 and ␣4), H2 (␣6 and ␣7), and H3 129 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits 34985

FIG.1. The overall structure of human eIF3k. Human eIF3k contains a HAM domain (green) and a WH domain (blue) followed by a ␣ ␣ ␣ C-terminal tail (yellow). The HAM domain consists of eight helices ( ) and two 310 helices (h); the WH domain consists of three helices and three ␤ strands (␤). The disordered region is indicated by a broken line connecting ␤2 and ␤3. The loop between h5 and ␣6 is overlapped by ␣16. The view in B is rotated 90° around a vertical axis from the view in A.

(␣9 and ␣10). All of the repeats and the leading ␣ helix are conserved hydrophobic residues in the HEAT analogous motifs followed by a short helix. The C-terminal half contains a WH of the HAM domain occupy the same positions as the corre- (winged-helix) domain, which is followed by a long C-terminal sponding residues in HEAT repeats (20, 25). However, unlike tail flanked by an ␣ helix at both ends. The WH domain is a most other HEAT repeats, no proline residues are found in the compact ␣/␤ structure containing three ␣ helices (␣12, ␣13, and eIF3k helices (␣3, ␣6, and ␣9) corresponding to the ␣A of HEAT ␣14) and three ␤ strands (␤1, ␤2 and ␤3). Approximately 1500 repeats. As a consequence, the ␣ helices in the HAM domain ⌭2 of solvent-accessible surface area is buried by the HAM-WH are not kinked. These differences between the HAM domain interdomain interactions. The combination of the two domains and other HEAT domains suggest that the HEAT analogous and C-terminal tail results in two distinct faces of the protein motifs in the HAM domain are related but distinct, and they surface: a concave face and a convex face (Fig. 6). may belong to the new subfamily of ADB (named for ␤-adatin; The HAM Domain; Comparison with HEAT-repeat-contain- Ref. 25). The absence of a consensus proline residue in ␣Aisa ing Proteins—HEAT-repeat-containing proteins such as the unique feature of the ADB repeat in the HEAT repeats family. PR65/A subunit of protein phosphatase 2A (21), nuclear trans- This is exemplified by the high similarity (Z score ϭ 6.4 by port protein karyopherin-␤2 (22), and ␣-adaptin C, a subunit of DALI) between the HAM domain and the HEAT motifs (resi- the AP2 complex (23), play important roles in assembling mul- dues Ala340 to Ala434)in␣-adaptin C, an ADB subfamily mem- tiprotein complexes in various cellular life activities (24). The ber. Nevertheless, it is possible that the HAM domain may HEAT repeat motif is formed by two antiparallel ␣ helices belong to a novel class in HEAT repeats as H1, H2, and H3 are (named ␣A and ␣B), and it is usually 37–43 residues long. The structurally different when these three HEAT analogous motifs motif occurs in blocks of at least 3 and up to 22 tandem repeats are compared. The intra-repeat connecting helices in the HAM (20). HEAT repeat family members have similar patterns of domain do not exist in the PR65/A HEAT repeats and most hydrophobic residues, and a highly conserved proline is fre- HEAT repeats of other proteins (Fig. 3). This unusual topology quently found in certain ␣A helices located in the middle of is also found in a few heat-repeat-containing proteins, such as many HEAT repeats to facilitate the kink of the helices (20). the PHAT (pseudo-HEAT analogous topology) domain of The human eIF3k HAM domain (residues 24–121) is gener- Smaug (26) (Fig. 3). The two and a half HEAT analogous ally similar to that in HEAT-repeat-containing proteins, but it repeats of the HAM domain are more similar to the PHAT also shows some unusual features. Its three HEAT analogous domain (r.m.s.d. ϭ 2.7 Å for 84 residues) than to the PR65/A motifs have 21 (H3) to 32 (H1 and H2) residues. Adjacent HEAT repeats (Fig. 3). Another unusual conformation in the

HEAT analogous motifs are connected by a short 310 helix (h5, HAM domain is the packing between H3 and H2, which is between H1 and H2) or a short ␣ helix (␣8, between H2 and almost side-by-side instead of face-to-face, as in normal HEAT H3). Compared with the canonical HEAT-repeat-containing repeats, due to its unusual left-handedness. The unusual H3 protein PR65/A, two and a half HEAT analogous repeats (␣3, turn causes ␣6, ␣9, ␣10, and ␣12 to form a hydrophobic core ␣4, ␣6, ␣7, and ␣9) in the HAM domain resemble the HEAT (Fig. 4). A similar type of conformation also appears in the repeats 13 and 14 and ␣A of repeat 15 of PR65/A, and they can structure of the C-terminal region of the vesicular transport be superimposed with a r.m.s.d. (root mean square deviation) of protein Sec17 (27) (Fig. 3). 3.2 ⌭ for 84 residues in the region (Fig. 3). An analysis of the In addition, the eIF3k HAM domain also shows some simi- protein sequences (data not shown) shows that several highly larity to several other proteins containing antiparallel ␣ helical 130 34986 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits

FIG.2. Sequence alignment of eIF3k homologues. Protein sequences were from Homo sapiens (human), Mus musculus (house mouse), Drosophila melanogaster, Anopheles gambiae, Caenorhabditis elegans, Oryza sativa, and Arabidopsis thaliana. Sequence accession numbers of the Swiss-Prot data base are Q9UBQ5 (for human), Q9DBZ5 (for mouse), Q9W2D9 (for D. melanogaster), Q7QGK4 (for A. gambiae), Q9XUP3 (for C. elegans), Q94HF1 (for O. sativa), and Q9SZA3 (for A. thaiana). The sequence of A. gambiae is derived from an EMBL/GenBankTM/DDBJ whole genome shotgun entry, which should be considered preliminary data. The secondary structure of human eIF3k, which is mainly defined by the analysis of the structure using DSSP program (47), is indicated above the alignment. Residues in the alignment that are identical are shown in red boxes; those that are similar are shown in yellow boxes. The sequences highlighted in a pink box correspond to the disordered regions (Ser184, Gly185, Ser217, and Gln218) missing from the human eIF3k structure. The characters under the alignment denote the predicted function of the conserved residues. The elucidations for these characters are listed as follows: 1, 2, and 3, the residues on the binding surface I, II, and III, respectively (Fig. 6); h, intra-molecular hydrophobic interaction (h colored in red denotes residues that participate in forming the hydrophobic core between the HAM domain and the WH domain shown in Fig. 4); s, the two highly conserved residues that form a salt bridges (Fig. 7); t, the conserved glycines that make turns between the secondary structure elements; orange triangle, the residues that are special in C. elegans compared with other organisms (hydrophobic residues in other organisms were replaced by hydrophilic residues in C. elegans or in reverse). The sequence of C. elegans eIF3k has distinct property in some position. For instance, the residues that are indicated by the orange triangle are very different between C. elegans and other organisms; and an additional sequence in the orange box between ␣10 and ␣11 that belong to the HAM domain and WH domain, respectively, exist in C. elegans only. 131 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits 34987

FIG.3.Comparison of the HAM domain with other HEAT or HEAT-like repeats. The HAM domain, PR65/A HEAT repeats, and the Sec17 C-terminal region all contain three antiparallel ␣-helical repeats, while the PHAT domain of Smaug contains only two and a half antiparallel ␣-helical repeats. A, a top view of four HEAT/HEAT analogous repeats; B, a lateral view. The red arrows denote the places of the locations of the helices connecting HEAT analogous motifs in the HAM domain and in the PHAT domain. The left-handed superhelix at the C termini of the HAM domain and the Sec17 is seen very clearly from the top view (A).

(29). The three short ␤ strands, each containing only 2 residues, form a twisted antiparallel ␤-sheet, with ␤1 bonding to the ␤ hairpin formed between ␤2 and ␤3, which are bonded by exactly two hydrogen bonds. This arrangement of ␤ strands is a common feature of HTH motifs with a ␣/␤ topology (named winged-helix motifs). The hydrophobic residues in the ␣ helices, together with Trp179 and Ile189, interdigitate to form another hydrophobic core stabilizing the architecture of the WH domain. Canonical winged-helix motifs commonly have two large loops or wings (w1 and w2). Wing w1 connects ␤2 and ␤3, and wing w2 extends from strand ␤3 to the C terminus of the winged-helix domain (30). In the WH domain of eIF3k, wing w1 is very short (residues 189–193) (Fig. 5); and two residues, 191 and 192, are disordered in the structure. In addition, wing w2 is replace by the ␣ helix (␣15) of the C-terminal tail. FIG.4. The hydrophobic core between the HAM and WH do- Comparison with Other Winged-helix Motifs—A structural mains. Highly conserved hydrophobic residues in ␣6, ␣9, ␣10, and ␣12 form a main part of the core. The core-forming residues are showed in similarity search in the PDB (Protein Data Bank) with DALI a ball-and-stick models; they include Leu128, Ile131, Leu71, Phe134, using the WH domain (residues 132–191) resulted in a number Leu74, Val138, Leu77, and Phe141 on the left side in an order from the top of matches to proteins containing winged-helix motifs. The down and on the right side are Ile102, Leu121, Leu105, Trp118, Phe117, 109 114 most similar proteins found by DALI are the selenocysteine- Leu , and Phe . All of these residues are highly conserved (Fig. 2) ϭ except Leu77, Leu121, and Leu128 (in ␣11), although the residues corre- specific elongation factor SelB (PDB code: 1LVA; Z score 6.5 sponding to these three are also hydrophobic among eIF3k homologues and r.m.s.d. ϭ 2.4 for 56 residues) (31), the purine operon in other species (Fig. 2). repressor of Bacillus subtilis (PDB code: 1P41; Z score ϭ 6.1 and r.m.s.d. ϭ 1.9 for 54 residues) (32), Rap30 DNA-binding repeats, including tetratricopeptide repeats and armadillo re- domain (PDB code: 2BBY; Z score ϭ 5.4 and r.m.s.d. ϭ 2.4 for peats that are both involved in protein-protein interactions 53 residues) (33), IclR transcriptional factor (PDB code: 1JMR; (24), and to part of the ␣ helix domain (residues 44–164) of Z score ϭ 5.3 and r.m.s.d. ϭ 2.7 for 55 residues) (34), endonu- chondroitin AC lyase (28). clease FokI (PDB code: 2FOK; Z score ϭ 5.2 and r.m.s.d. ϭ 2.4 The WH Domain; Conformation of the WH Domain—The WH for 58 residues) (35), double-stranded RNA-specific adenosine domain has the appearance of an earlobe in an ear-like struc- deaminase (PDB code: 1QBJ; Z score ϭ 5.2 and r.m.s.d. ϭ 2.7 ture (Fig. 1). This domain is stably packed against the HAM for 54 residues) (36), and the Esa1 histone acetyltransferase domain via the hydrophobic core formed mainly by the con- domain (PDB code: 1FY7; Z score ϭ 5.2 and r.m.s.d. ϭ 2.6 for 56 served hydrophobic residues in ␣6, ␣9, ␣10, and ␣12 (Fig. 4). residues) (37). All of winged-helix motifs in these proteins, in- The WH domain comprises three ␣ helices and three ␤ strands cluding the WH domain, differ in the length of the third helix in the order of ␣12-␤1-␣13-␣14-␤2-␤3. ␣12 and ␣13 are antipa- (corresponding to ␣14 in the WH domain) (Fig. 5), which is rallel to each other, while ␣14 is almost perpendicular to ␣13 associated with major-groove DNA binding and is called the (Fig. 5). The latter two helices are connected by a short turn of recognition helix. The ␤ hairpin (the wing w1) is also involved in three amino acids. This architecture belongs to a HTH motif DNA binding via the DNA backbone and/or the minor groove. 132 34988 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits

FIG.5.A comparison of winged-helix domains. The recognition helix in the WH domain is ␣14, and W1 indicates wing w1 in the WH domain. The two winged-helix domains on the upper left side (SelB-C and Esa1) do not have DNA/RNA binding activity, while the two winged-helix domains on upper rightside (FokI-D3 and Rap30) interact weakly with DNA and are also involved in protein-protein interactions. The lower three winged-helix domains (PurR, Z␣ domain, and IclR) are all involved in DNA binding. The disordered region in the WH domain is indicated by a broken line. DISCUSSION interacts with other proteins, we combined the structural The HAM Domain Can Supply Binding Surfaces for Protein- knowledge with sequence conservation to identify potential Protein Interactions—HEAT repeats have been proposed to protein-protein interaction sites on eIF3k. We aligned the se- mediate protein-protein interactions (38, 39), and the internal quences of seven eIF3k homologues from different organisms repetition enlarges the available protein binding surface area. that are available in public protein databases (Fig. 2). And we Another eukaryotic translation initiation factor, eIF4GII, also found that many highly conserved residues are distributed contains a HEAT domain that interacts with eIF4A (40) and throughout the whole protein. The conserved residues can be eIF1 and eIF5 (41). The detailed binding regions in HEAT divided into three classes: hydrophilic amino acids (class I), motifs have not yet been delineated, but the loops connecting hydrophobic amino acids involved in inside hydrophobic inter- ␣A with ␣B (AB loop) may be the binding surface based on actions (class II), and hydrophobic amino acids exposed on the sequence conservation, mutational analysis, and oncogenic mu- surface (class III). The residues in class II are mainly located at tation studies (21). The structure of the tetra-protein complex the interface of ␣ helices that interdigitate to maintain the AP2 (23) provides a model for understanding how proteins bind structure of eIF3k. Most of these three classes of residues are the AB loop. In the HAM domain of human eIF3k, the AB loops marked in Fig. 2 with their predicted function labeled. help the formation of the concave face that might be suitable for Previous experiments indicated that eIF3k could interact protein-protein interactions (see below). It is worth mentioning with several other eIF3 subunits (eIF3c, eIF3g, and eIF3j), as that in the protein PR65/A, the intra-repeat turns of repeats well as the 40 S ribosomal subunit (6). Thus, the aforemen- 13–15, which are similar to that in the HAM domain (Fig. 3), tioned class I and class III residues can serve as potential were found to be the protein-binding site (21, 42). Although the binding sites for the other proteins. Fig. 6 shows the distribu- intra-repeat turns in the HEAT repeats are replaced by ␣ tion of the conserved residues on the solvent-accessible protein helices (h2, h5, and ␣8) in the HAM domain, the location of surface. And a surface representation showing the surface elec- conserved hydrophobic residues on these helices (Fig. 2) sug- tronic potential distribution is display side-by-side for compar- gests that they could still serve as the protein binding surface ison. It is interesting to note that the concave side of the protein in eIF3k. These differences might be helpful to enlarge the could be a putative binding surface, which we call binding protein-binding surface of eIF3k. The presence of HEAT anal- surface I, for other proteins. On the binding surface I, there are ogous motifs in eIF3k strongly suggests that the HAM domain 14 conserved residues, including 6 electronegative residues, is essential for interactions between eIF3k and other proteins, Asp43, Glu45, Asp81, Asp135, Asp136, and Glu203; 2 electropositive especially other eIF3 subunits that have been shown to interact residues, Lys197 and Lys199; 3 class III residues, Tyr42, Pro78, and with eIF3k directly by glutathione S-transferase pull-down Leu84; and some hydrophilic residues (Fig. 6, A and B). Thus, this assays (6). concave face may bind a protein through hydrogen bonds (or salt Conserved Residues in eIF3k Suggest Three Binding Sur- bridges) and hydrophobic interactions. Considering this is the faces—To gain insights into the mechanisms by which eIF3k largest potential binding surface, we propose that this region be 133 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits 34989

FIG.6.Surface distributions of conserved residues and electrostatic potential of eIF3k. A, conserved residues are mapped onto the concave face (colored light green). The conserved residues on the binding surface I are marked by red numbers. The binding surface I was circled in brief, and it appears to be capable of interacting with a rather large protein due to its large area. B, the electrostatic potential surface on the concave face of eIF3k is colored red for electronegative residues and blue for electropositive residues. C, conserved residues are mapped onto the convex face. There are two putative binding surfaces (binding surface II and III) for other proteins on the convex face. D, the electrostatic potential surface on the convex face of eIF3k. The charged residues are fewer in this face than in concave face. Obviously, there are more electronegative residues than electropositive residues on molecular surface. This is the reason why human eIF3k is an acidic protein with pI ϭ 4.8 (6). All the conserved residues located on the surface could be found in Fig. 2 (labeled with numbers 1, 2, and 3).

FIG.7.The cleft in the WH domain. The cleft is composed mainly of ␣12 and ␣14, the first two helices of the WH domain. The salt bridge between the N⑀ of Arg155 and a carboxyl oxygen atom of Asp167 is on the left side of the cleft (shown as a dotted line) with an inter- atomic distance of 2.72 Å. There are two conserved residues, Asp136 and Arg139,at the bottom of the cleft and a sulfate ion at the hatch of the cleft.

involved in the interaction between eIF3k and eIF3c, the biggest tail of eIF3k whose surface connects with the surface of h2 and subunit among eIF3c, eIF3g, and eIF3j. h5 to form a rather large protein-binding surface (binding The other class III residues are located in a bipartite region surface II, Fig. 6C). The distribution of these highly conserved of the convex face (Fig. 6C). The residues in or around h2 and residues on the protein surface is consistent with their poten- h5 connecting ␣1 and H1, H1, and H2, respectively, are rea- tial involvement in protein-protein interactions mainly sonably well conserved (Fig. 2). Among these residues, the through hydrophobic interactions. hydrophobic residues Ile18, Tyr21, Pro23, Phe56 (at the C-termi- The third binding surface (binding surface III) is in the WH nal end of ␣4), and Pro58 belong to class III. The class III domain comprising Thr149, Tyr150, Gln151, and Gln192 (Fig. residues Ile205, Phe207, and Val210 are located in the C-terminal 6C). Binding surface III may be responsible for the protein 134 34990 Crystal Structure of Human eIF3k, the First Structure of eIF3 Subunits binding function of the WH domain. Acknowledgments—We thank Dr. Peng Liu, Dr. Yuhui Dong, and In the human eIF3k structure, there is a salt bridge between Deqiang Yao from the Institute of High Energy Physics, Chinese Acad- ⑀ 155 167 emy of Sciences for their kind help in diffraction data collection. We also the N of Arg and a carboxyl oxygen atom of Asp (Fig. 7), thank Prof. R. Xu and Prof. J. W. B. Hershey for their constructive both of which are highly conserved with basic residues (argi- criticism and suggestions. nine and lysine) and acidic residues (asparagine and glutamic acid) respectively. 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Our work provides a starting point for 287, 1232–1239 44. Chaudhuri, J., Chowdhury, D. & Maitra, U. (1999) J. Biol. Chem. 274, further systematic biochemical, genetic, and structural studies 17975–17980 aimed at understanding the structure and function of eIF3 45. Pestova, T. V., Borukhov, S. I. & Hellen, C. U. T. (1998) Nature 394, 854–859 46. Wah, D. A., Hirsch, J. A., Dorner, L. F., Schildkraut, I. & Aggarwal, A. K. complex and at elucidation of the mechanism of translation (1997) Nature 388, 97–100 initiation. 47. Kabsch, W. & Sander, C. (1983) Biopolymers 22, 2577–2637

135 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 17, Issue of April 23, pp. 17459–17465, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Conformational Changes in the Reaction of Pyridoxal Kinase*

Received for publication, November 12, 2003, and in revised form, February 2, 2004 Published, JBC Papers in Press, February 5, 2004, DOI 10.1074/jbc.M312380200

Ming-hui Li‡, Francis Kwok§, Wen-rui Chang‡, Sheng-quan Liu‡, Samuel C. L. Lo§, Ji-ping Zhang‡, Tao Jiang‡¶, and Dong-cai Liang‡ From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China, §Department of Applied Biology Chemical Technology, Hong Kong, China and Polytechnic University, Hung Hom, Kowloon, Hong Kong, China

To understand the processes involved in the catalytic Recently, the three-dimensional structures of PLK from mechanism of pyridoxal kinase (PLK),1 we determined sheep brain and its complex with ATP were determined (7). the crystal structures of PLK⅐AMP-PCP-pyridoxamine, Although structural analyses have shown that PLK exhibits a PLK⅐ADP⅐PLP, and PLK⅐ADP complexes. Comparisons folding pattern similar to the core structure of enzymes in the of these structures have revealed that PLK exhibits dif- ribokinase superfamily (8–13), low sequence homology be- ferent conformations during its catalytic process. After tween the two types of enzymes has been found. Despite kinetic the binding of AMP-PCP (an analogue that replaced studies that have shown that ribokinase and adenosine kinase ATP) and pyridoxamine to PLK, this enzyme retains a both follow an ordered substrate-binding mechanism, PLK ⅐ conformation similar to that of the PLK ATP complex. binds ATP and pyridoxal randomly (8, 10, 14). During the The distance between the reacting groups of the two binding of ATP, a flexible loop containing 12 amino acid resi- substrates is 5.8 Å apart, indicating that the position of dues in the active site of PLK was responsible for triggering a ATP is not favorable to spontaneous transfer of its phos- major conformational change of the protein structure by inter- phate group. However, the structure of PLK⅐ADP⅐PLP acting with the bound ATP. It has been suggested that the complex exhibited significant changes in both the conformation of the enzyme and the location of the ligands purpose for the inability of ATP to interact with this loop at the active site. Therefore, it appears that after bind- before catalysis is to prevent the nucleotide from hydrolysis, ing of both substrates, the enzyme-substrate complex which is an essential feature in the random substrate binding requires changes in the protein structure to enable the mechanism. Further interest in crystallographic studies of PLK in the transfer of the phosphate group from ATP to vitamin B6. Furthermore, a conformation of the enzyme-substrate presence of substrates has arisen from several considerations. complex before the transition state of the enzymatic First, the structure of PLK complexes in the presence of pyri- reaction was also hypothesized. doxal has never been revealed. Thus, the exact interactions between molecules in the active site of PLK are unknown. Secondly, in the PLK⅐ATP complex, ATP ␥-phosphate group is Pyridoxal kinase (PLK)1 catalyzes the phosphorylation of maintained in a position far away from the catalytic site of the vitamin B6 (including pyridoxal, pyridoxine, and pyridoxam- enzyme. Although this could prevent the nucleotide from hy- ine) in the presence of ATP and Zn2ϩ, which is an essential step drolyzing, the enzyme would need to engineer a dramatic con- in the synthesis of pyridoxal 5Ј-phosphate (PLP), an active formational change of this macromolecule for the transfer proc- form of the vitamin in mammals (1–3). PLK is expressed in all ess. This contradicts the design of other kinases found in mammalian tissues because of the fact that PLP cannot cross nature, indicating that cells may have some regulatory mech- cell membranes, and PLK is required for the activation process anism to control PLK activity. Finally, the catalytic process of inside cells (4). Genes encoding PLK have been cloned from PLK consists of several steps. The structure of PLK in the form both mammalian and plant cells. PLK activity has also been of a complex with different substrates or its analog and prod- detected in bacteria, because PLP can be synthesized through ucts allows the systematic observation of reaction cycles. In the PLP salvage pathway (5, 6). this paper, the crystal structures of the PLK⅐AMP-PCP-pyridoxamine complex, the PLK⅐ADP⅐PLP complex, and the ⅐ * This work was supported by the National Natural Science Founda- PLK ADP complex were determined. These structures have tion of China (Grant 30100026), the Life Science Special Fund of Chi- provided detailed information regarding the interactions be- nese Academy of Services (Grant STZ0017), and the National Key tween PLK and its substrates or products. Comparison of these Research Development Project of China (Grant G1999075601). The structures can lead to a thorough understanding of conforma- costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “adver- tional changes that occur in the enzyme in the presence the tisement” in accordance with 18 U.S.C. Section 1734 solely to indicate ligands in this unique phosphorylation process catalyzed by this fact. PLK. The atomic coordinates and structure factors (code 1RFT for PLK⅐AMP-PCP-pyridoxamine, 1RFU for PLK⅐ADP⅐PLP, and 1RFV for MATERIALS AND METHODS PLK⅐ADP) have been deposited in the Protein Data Bank, Research Crystallization and Data Collection—PLK was purified from sheep Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/). brain as described previously (1). Enzyme crystals were obtained by ¶ To whom correspondence should be addressed: National Laboratory using the hanging drop vapor diffusion method at a constant tempera- of Biomacromolecules, Institute of Biophysics, Chinese Academy of ture of 17 °C. Sciences, 15 Datun Rd., Chaoyang District, Beijing 100101, China. Tel.: An initial attempt to diffuse AMP-PCP and pyridoxamine into the 86-10-64888510; Fax: 86-10-64889867; E-mail: [email protected]. native orthorhombic crystals of the enzyme was not successful. How- 1 The abbreviations used are: PLK, pyridoxal kinase; PLP, pyridoxal ever, co-crystallization of PLK in the presence of AMP-PCP and pyri- 5Ј-phosphate; AMP-PCP, adenosine 5Ј-(␤,␥-methylenetriphosphate); doxamine resulted in the formation of crystals of the enzyme-substrate r.m.s.d., root mean square deviation. complex. A solution was prepared consisting of 10 mg/ml PLK, 1 mM

This paper is available on line at http://www.jbc.org 17459 136 17460 Conformation Change of Pyridoxal Kinase

TABLE I Structure determination and refinement

PLK⅐AMP-PCP-pyridoxamine PLK⅐ADP⅐PLP PLK⅐ADP Data collection statistics

Space group P3121 P43 P212121 Cell dimension a ϭ b ϭ 103.7, c ϭ 58.6 a ϭ b ϭ 109.1, c ϭ 284.3 a ϭ 59.1, b ϭ 93.9, c ϭ 128.7 Resolution (Å) 2.8 2.8 2.8 Measured reflections 48,149 342,212 101,511 Unique reflections 9,133 75,513 18,118 Completeness (%) 99.6 (100) 87.5 (95.2) 99.6 (99.9) a Rmerge 0.110 (0.543) 0.0867 (0.465) 0.136 (0.559) ͗I/␴(I)͘ 15.7 (3.4) 11.4 (2.3) 13.0 (3.0) Refinement statistics b Rwork 0.214 0.229 0.190 c Rfree 0.268 0.281 0.222 Number of protein atoms 2,413 19,512 4,798 Number of ligand atoms 45 344 56 R.m.s.d. bonds (Å) 0.010 0.010 0.007 R.m.s.d. angles (°) 1.5 1.5 1.3 Average B-factor (Å2) Protein atoms 30.2 36.0 30.0 Ligand atoms 29.1 33.1 36.2 Solvent atoms 34.3 41.3 34.8 a ϭ⌺ ⌺ ͉ Ϫ͗ ͉͘ ⌺ ⌺ ͗ ͘ Rmerge h i( Ii(h) I(h) )/ h iIi (h), where Ii (h)istheith integrated intensity of a given reflection and I(h) is the weighted mean of all of the measurements of I(h). b ϭ⌺ʈ ͉ Ϫ ͉ ʈ ⌺ ͉ ͉ Rwork h F(h)o F(h)c / h F(h)o for the 90% of reflection data used in refinement. c ϭ⌺ʈ ͉ Ϫ ͉ ʈ ⌺ ͉ ͉ Rfree h F(h)o F(h)o / h F(h)o for the 10% of reflection data excluded from refinement.

pyridoxamine, 1 mM AMP-PCP, and 0.1 mM zinc acetate with a buffer of Bank code 1LHP) as a model. Rigid body refinement reduced the R-

equal volume consisting of 100 mM KH2PO4-K2HPO4 containing 1.4 M factor from 0.339 to 0.245. The following cycles of xyz refinement, (NH4)2SO4, pH 8.2. The solution was then equilibrated against the B-factor refinement, and model rebuilding including the addition of ϩ buffer containing 1.4 M ammonium sulfate, pH 8.2, for approximately missing residues such as ADP molecules, Zn2 ions, and water mole- one month at 290 K. Similar conditions were used for the crystallization cules resulted in an R-factor of 0.190 and R-free of 0.222. of a PLK⅐AMP-PCP-pyridoxamine complex. When AMP-PCP was re- All of the model rebuilding were performed by program O (22), and placed by ADP and pyridoxamine was replaced by PLP, the the models were evaluated using PROCHECK (23). Computing pro- PLK⅐ADP⅐PLP complex crystals were obtained. Interestingly, the grams including MOLSCRIPT (20), RASTER3D (25), and GRASP (26) PLK⅐AMP-PCP-pyridoxamine complex crystals were trigonal, whereas were utilized to draw figures. the PLK⅐ADP⅐PLP complex crystals were tetragonal. PLK⅐ADP complex crystals were prepared by soaking the orthorhombic crystal of native RESULTS AND DISCUSSION enzyme (15) in 75 mM KH PO -K HPO buffer containing 1 mM ADP, 1 2 4 2 4 Structures of Pyridoxal Kinase in Complexes with Substrates mM ZnAc2, and 30% polyethylene glycol 6000, pH 6.5. Data from PLK⅐AMP-PCP-pyridoxamine and PLK⅐ADP complex and Products—In contrast with the orthorhombic crystals of crystals were collected using the Mar345 image plate in the National native PLK and the PLK⅐ATP complex, the PLK⅐AMP-PCP- Laboratory of Biomacromolecules (Beijing, China) at room tempera- pyridoxamine crystal belongs to the P3 21 space group with the ⅐ ⅐ 1 ture. Data from the PLK ADP PLP complex were collected on a Mar345 complex having one monomer in the asymmetric unit. How- image plate in the Laboratory of Structural Biology, Tsinghua Univer- ever, the two monomers related by the 2-fold crystallographic sity (Beijing, China). Before data collection, the crystals were flash- frozen in liquid nitrogen after short soaking in a solution consisting of axis form a dimeric molecule in a fashion similar to the dimeric 17.5% glycerol, 1.4 M ammonium sulfate, and 100 mM potassium phos- molecules found in the native PLK structure. The overall struc- phate buffer at pH 8.2. All of the data were processed with the HKL ture of the monomeric PLK⅐AMP-PCP-pyridoxamine complex suite of programs (16). Table I shows the data collection statistics. is almost identical to the structures of the enzyme in the Structural Analysis and Refinement—The structure of the ⅐ ⅐ absence of ligands and the PLK ATP complex. Of the 309 res- PLK AMP-PCP-pyridoxamine complex was solved by molecular re- ␣ Ͻ placement using AMORE (17). The solution was obtained using the idues, the C deviations of 287 residues are 1 Å with an unliganded structure (with residues 117–128 omitted) as a search r.m.s.d. of 0.43 Å. In the active site of the enzyme, AMP-PCP model. Because diffraction intensities of this complex crystal were and pyridoxamine were located in substrate binding sites, as slightly dispersed and could affect the measurement of weak reflec- revealed by the electron density map (Fig. 1a). In the pyridoxal tions, the refinement process was carried out using reflections only at binding site, three hydrogen bonds formed between pyridoxam- ␴ above 2 cutoff. After rigid body refinement, the R-factor was dropped ine and its surrounding amino acid residues. One bond formed to 0.293 and then pyridoxamine, AMP-PCP, zinc ions, and the missing water molecules were added. During model rebuilding, xyz and B-factor between the hydroxyl group in the side chain of Ser-12 and N1 refinements were carried out alternately, resulting in an R-free of 0.268 of pyridoxamine. The second bond formed between the hy- in the presence of 22 additional water molecules. droxyl group of Thr-47 and O3, and the third bond formed ⅐ ⅐ The PLK ADP PLP complex crystal was initially indexed as P43212, between the carboxyl group of Asp-235 and O5. Tyr-84 and but was later found to be nearly perfectly twinned with a twinning ratio Val-19 also interacted with the two sides of the pyridine ring of of 0.48 (18). Therefore, data were reprocessed in P4 . The complex 3 pyridoxamine through hydrophobic interactions (Fig. 2). In structure containing eight monomers in an asymmetric unit was solved ⅐ by molecular replacement with the MOLREP (19) program. Refinement contrast to the structure of the PLK ATP complex, which is was performed using the CNS (20) scripts for twinning data, and missing the second substrate bound at the active site, our non-crystallographic symmetry restraint was applied. Initial simulated result showed that the side chain of Tyr-84 in the PLK⅐AMP- annealing (21) changed the R-factor to 0.264, and an electron density PCP-pyridoxamine complex was slightly closer to the nucleo- map was calculated according to the structure to which PLP and ADP tide because of the fact that the position of Tyr was stabilized molecules had been added. After several cycles of xyz refinement, B- by a hydrogen bond between itself and the guanidino group of factor refinement, and model rebuilding, a model with an R-factor of 0.229 and an R-free of 0.281 were obtained. Arg-86. As for the amino acid residue of Phe-43, its phenyl ring The structure of the PLK⅐ADP complex was determined by the dif- rotated at an angle of ϳ80°. In addition, the Thr-47 hydroxyl ference Fourier method using the unliganded structure (Protein Data group moved toward Phe-43, resulting in a shorter hydrogen 137 Conformation Change of Pyridoxal Kinase 17461

FIG.1. Structures of pyridoxal kinase in complexes with substrates or Ϫ products. a, b, and c, the Fo Fc electron density map contoured at 3␴ using the reflection data for the PLK⅐AMP-PCP- pyridoxamine complex, for the PLK⅐ADP⅐ PLP complex, and for the PLK⅐ADP complex, respectively, showing clear density for the ligands bound to the enzyme. d, the superposition of the main chain of the three complexes. The overall structure of the PLK⅐AMP-PCP-pyridoxamine complex (shown in yellow) is similar to that of the PLK⅐ADP complex (shown in blue) and is also similar to the PLK⅐ATP complex structure in which structure has already been solved. However, the PLK⅐ ADP⅐PLP complex (shown in red) is significantly different from them, the peptide chain moves toward to the active center, and the overall structure becomes more compact.

FIG.2. Pyridoxal binding site. The molecule in the center is the pyridoxamine bound in the PLK⅐AMP-PCP-pyridoxamine complex. The surrounding residues are shown in green, and the hydrogen bonds between the pyridoxamine and the residues are shown as purple dashes. The corresponding residues in the PLK⅐ATP complex are in blue. A comparison of these structures reveals local conformational adjustments of the pyridoxal binding site when the substrates binds.

bonding distance between Thr-47 and O3 of pyridoxamine. A were in close proximity to each other. The PLP phosphate conformational change was detected in Trp-52, which is main- group formed hydrogen bonds with the main chain nitrogen tained in a position located adjacent to Phe-43 and Thr-47 with atoms of Gly-232, Thr-233, Gly-234, and Asp-235, as well as its indole ring made at a complete rotation of 180 degrees. with the side chain of Asp-235 and Thr-127 (Fig. 3). Interac- Therefore, the relative side chain orientation between Phe-43 tions between the other portions of the PLP molecule and the and Trp-52 changes from “edge-to-face” to “offset-stacked.” At protein were similar to those in the PLK⅐AMP-PCP-pyridoxam- the nucleotide binding site, both the conformation of AMP-PCP ine complex. PLP bound tightly in an area of the protein, which and its interactions with surrounding amino acid residues were was structurally more compact than the same domain in the similar to those of ATP in the PLK⅐ATP complex. PLK⅐AMP-PCP-pyridoxamine complex (shown in Fig. 4b and Although the conditions for crystallization were similar to discussed under ‘‘Results and Discussion’’). Remarkably, nei- those of the PLK⅐AMP-PCP-pyridoxamine complex, the crys- ther the pyridoxamine 4Ј-amino group in the enzyme-substrate tals of the PLK⅐ADP⅐PLP complex were tetragonal. Monomers complex nor the PLP 4Ј-aldehyde group in the enzyme-product of the two different enzyme-substrate complexes had signifi- complex were found to be covered by any of the amino acid cant conformation differences. Of a total of 309 amino acids, chains of the protein (Fig. 4c). This finding is in agreement with 117 residues in the PLK⅐ADP⅐PLP complex had ␣ carbon atoms previous research that reported that substrate variation within that deviated by Ͼ1 Å compared with the PLK⅐AMP-PCP- this group did not affect the catalytic activity of PLK (3). In pyridoxamine complex. Such a dramatic variation in the con- other words, the fact that the 4Ј-substitution group of the formation of the whole macromolecule could explain the gen- vitamin is exposed to the solvent explains the broad substrate eration of a new protein crystal form in the presence of specificity of PLK. different substrates. In the asymmetric unit of the In the analysis of the structure of the PLK⅐ADP complex, an PLK⅐ADP⅐PLP structure, eight monomers were found, forming ADP molecule and a Zn2ϩ ion were found in the active site of four dimeric molecules in a manner similar to that of the native each monomer. Since this complex could be used as a model to enzyme. An ADP molecule, a PLP molecule, as well as a Zn2ϩ represent the reaction state in which the phosphate transfer ion bound at the active site of each monomer. The phosphate process had been completed, the product, PLP, was released group of PLP and ␤-phosphate of ADP bridged by a Zn2ϩ ion from the enzyme. The overall conformation of the protein in 138 17462 Conformation Change of Pyridoxal Kinase

FIG.3. Pre-reaction state model based on the structure of the PLK⅐ADP⅐PLP complex. In the PLK⅐ADP⅐PLP complex, the PLP phosphate group is located in the catalyzing site and makes hydrogen bonds with both the side chain carboxyl group of Asp-235 and the main chain nitrogen atoms of residue 232–235. These bonds created an anion hole. The distance between the PLP-phosphorus atom and the oxygen atom of the ADP ␤-phosphate is only 2.5 Å. The pre-reaction model can be constructed by moving the PLP-phosphorus atom toward ADP by 0.8 Å (shown in black) and connecting it to the ADP ␤-phosphate without a great adjustment of the other three oxygen atoms. this complex was almost identical to that of the PLK⅐ATP believe that the conformation of the PLK⅐ADP⅐PLP complex is complex (Fig. 1d) with an r.m.s.d. of only 0.25 Å for all of the more similar to the conformation of the transition state (or the residues with the exception of the loop 117–128. Compared pre-reaction state) than to the conformation of the PLK⅐AMP- with the compact structure of the PLK⅐ADP⅐PLP complex, the PCP-pyridoxamine complex. There are several reasons for this. PLK⅐ADP complex has a relatively open conformation because First, the PLP phosphate group, which corresponds to the the active site is exposed to the solvent region. In addition, the ␥-phosphate of ATP before the reaction, is located in the cata- ADP molecule in this complex is significantly different from lytic site of PLK. It forms a hydrogen bond with the side chain both ATP in the PLK⅐ATP complex and ADP in the carboxyl group of Asp-235 as well as with the main chain PLK⅐ADP⅐PLP complex, primarily at the position of the phos- nitrogens of residues 232–235, which are skeletons of a posi- phate groups. Compared with the ADP molecule in the tively charged anion hole. It is strongly believed that this hole PLK⅐ADP⅐PLP complex, ␣-phosphate of ADP in the PLK⅐ADP plays a functional role in the stabilization of the transition complex could move a distance of 1.1 Å, leading to its inability state of the phosphate group (Fig. 3). Furthermore, ␤-phos- to form hydrogen bonds with Thr-186 and Asn-150. Instead, a phate of ADP is close to the PLP phosphate group that corre- new hydrogen bond was formed with Thr-233. Another move- sponds to the original positions of the ␤- and ␥-phosphate of ment of 2.2 Å was observed to have taken place on the ␤-phos- ATP before the reaction. The distance between ADP O1B atom phate, forming a new hydrogen bond with Thr-186 and decreas- and PLP-phosphorus atom was 2.5 Å (Fig. 4a). In the enzy- ing its distance from Asp-118 (Fig. 5). matic reaction during phosphate transfer, the bond between Reaction State before the Phosphate Transfer—In the O1B of ATP and the ␥-phosphorus atom was broken and a new PLK⅐ATP complex, the ␥-phosphate of ATP is far away from the bond was subsequently formed between the phosphorus atom catalytic site. This prevents ATP from being hydrolyzed before of the ␥-phosphate group and the oxygen atom of the 5Ј-hy- pyridoxal is bound (7). Therefore, it was correct to expect that droxyl group of pyridoxal. These three atoms in the the binding of pyridoxamine would induce some form of confor- PLK⅐ADP⅐PLP complex were almost collinear (Fig. 3). The ar- mational changes on both ATP and PLK, causing the ␥-phos- rangement of molecules in this format is consistent with the phate of ATP to be close to the other substrate. In the other SN2 mechanism. location of the catalytic site of PLK, pyridoxamine should have Therefore, a pre-reaction state model just before the forma- also been bound in a position that allowed its 5Ј-hydroxyl group tion of the transition state was constructed based on the struc- to be able to start a nucleophilic attack on ATP. However, in ture of the PLK⅐ADP⅐PLP complex. The model was constructed structural studies, neither AMP-PCP nor the enzyme in the by moving the phosphorus atom of PLP (in the structure of the PLK⅐AMP-PCP-pyridoxamine complex has exhibited any sig- PLK⅐ADP⅐PLP complex) by 0.8 Å along the line linking it to the nificant difference from the structure in the PLK⅐ATP complex O1B of ADP, and thus, a new bond between these two sub- and the ␥-phosphorus atom was unusually far away from the strates was formed. At the same time, the bond between the 5Ј-hydroxyl oxygen atom. At a distance of 5.8 Å, it would be phosphorus atom and oxygen atom within the PLP phosphate impossible for a spontaneous reaction of phosphate transfer to group was broken. The operation mentioned above would lead take place. Based on these findings, it could be hypothesized to the conversion of ADP and PLP to ATP and pyridoxal with- that there is another state of protein conformation known as out requiring movement of other atoms in either ADP and PLP. the “pre-reaction state,” which might take place just before the Indeed, this process was the reverse of the phosphate transfer phosphate transfer so that the two substrates could be brought via the transition state in the reaction catalyzed by PLK. close enough together for the reaction to occur. Although this Conformational Changes before the Reaction—Superposition reaction state was not visible in the crystal structures of the of different ternary complexes of enzyme-substrate in this in- enzyme-substrate complexes in this study, its existence could vestigation revealed unusual changes in both the location and be proven based on the products formed in the reaction. orientation of the two substrates. In contrast to the PLK⅐AMP- Based on what is known regarding protein chemistry, we PCP-pyridoxamine complex, it is assumed that the molecule of 139 Conformation Change of Pyridoxal Kinase 17463

FIG.4.Structural changes before the reaction revealed by the comparison of the PLK⅐AMP-PCP-pyridoxamine structure and the pre-reaction model. a, the substrates in the two structures. The two substrates in the PLK⅐AMP-PCP-pyridoxamine complex are far away from each other. The ␥-phosphate of AMP-PCP is not in the anion hole, and its phosphorus atom is 5.8 Å away from the O5 atom of pyridoxamine. However, in the pre-reaction model, the ␥-phosphate of ATP forms hydrogen bonds with the catalyzing residues and the distance between its phosphorus atom and the O5 atom of pyridoxamine is only 2.5 Å. b, structural changes of residues around the active site. In contrast with the PLK⅐AMP-PCP-pyridoxamine complex, the residues around the active site of the pre-reaction state model move toward the substrate and push them closer to each other. These residues bind the substrates tightly and restrict the reaction group in a suitable position for the phosphate transfer. c, surface presentation of the active site. The left side shows the PLK⅐AMP-PCP-pyridoxamine complex in which the active site is open. The right side shows pre-reaction state model in which the conformational changes cause the active site to move closer each other and the two substrates are almost buried totally. However, in both of these two structures, the 4Ј-substituted group of pyridoxamine or pyridoxal are exposed, which allows variations within this group. pyridoxal in the pre-reaction state was translocated toward whereas conformational changes of the enzyme would take ATP at a distance of 1.4 Å. Similarly, some conformational place to affect the stability of the ATP phosphate groups. As a adjustment should also occur on the pyridoxal 5Ј-hydroxyl result, translocations of 1.5 Å were detected for the ␤-phos- group. Therefore, both the nitrogenous base and the ribose ring phate group and translocations of 1.9 Å were detected for the of ATP would have to maintain their positions in the active site, ␥-phosphate group. These movements would then enable the 140 17464 Conformation Change of Pyridoxal Kinase

FIG.5.The ADP molecule bound in the PLK⅐ADP complex and the residues interacting with it. The hydrogen bonds between them are shown as blue dashes. The molecule shown as a thin black line is the ADP in the PLK⅐ADP⅐PLP complex. A significant conformational change happens between the two ADP molecules. two substrates to be placed in suitable positions for subsequent phosphate transfer. Despite the movement of substrates, significant conformational changes were also observed in the protein structure (Fig. 4b). Unlike the structure of the PLK⅐AMP-PCP-pyridoxamine complex, over one-third of the C␣ atoms in the PLK⅐ADP⅐PLP complex moved 1 Å or more. In addition, all of the atoms in helices ␣4, ␣5, and ␣6 were found to move ϳ1.5 Å. This type of movement enabled peptide chains within the protein to move toward the active site, thus creating a compact structure in the enzyme (Fig. 1d). In the pyridoxal binding site, the loop con- FIG.6.The entire process of pyridoxal kinase catalysis. a, the necting ␤2 and ␣2 moved approximately 2 Å toward the sub- active site of PLK without any substrate bound to it (drawn according strate pyridoxal. This movement enabled residues Val-41, Phe- to the crystal structure of PLK). b, after the binding of ATP, a loop 43, and Thr-47 on this loop to interact with pyridoxal directly undergoes remarkable conformational changes and interacts with the ⅐ and push pyridoxal toward the ATP. At the same time, Tyr-84, ATP (drawn according the crystal structure of the PLK ATP complex). c, when ATP and pyridoxal are both bound in the enzyme, they are far Tyr-127, His-46, Val-231, and Val-115 moved toward the pyri- away from each other and no significant changes occur on the overall dine ring of pyridoxal from two sides, causing immobilization of structure of PLK (drawn according to the crystal structure of the the substrate in the active site (Fig. 4b). Although small PLK⅐AMP-PCP-pyridoxamine complex with AMP-PCP replaced by ATP changes were detected at the ATP adenine ring, Leu-199, Lys- and pyridoxamine replaced by pyridoxal). d, the active site becomes more compact and binds the substrates more tightly. The two sub- 225, and Phe-230 also moved closer to ATP for the purpose of strates move close to each other, and their reaction groups are located immobilization. Amino residues interacted with the ATP phos- in the catalyzing position (drawn according to the proposed pre-reaction phate group either directly or via cations including Thr-186, state model). e, phosphate transfer occurs, resulting in two substrates, Ser-187, Asn-150, Glu-153, Asp-113, Asp-118, Tyr-127, and ADP and PLP (drawn according to the crystal structure of the PLK⅐ADP⅐PLP complex). f, one of the two substrates, PLP, has been Thr-148, which are mainly located on one side of ATP. The released from the enzyme. The active site is open again, and the con- peptide chain consisting of these amino acid residues tends to formation of ADP is different from the conformation of the move against the ATP molecule, pushing the ␥-phosphate PLK⅐ADP⅐PLP complex. The ADP leaves the enzyme after which new group to the anion hole previously formed by the main chain substrates will be bound (drawn according to the crystal structure of the PLK⅐ADP complex). nitrogens of residues 232–235 at the N-terminal end of ␣7. Consequently, the phosphate was able to form new hydrogen bonds with these amino acid residues (Fig. 4b). Tyr-127 and that the hydroxyl oxygen atom can spontaneously attack the Asp-118 in loop 117–128 interacted with the dorsal portion of ␥-phosphate of ATP. This mechanism is carried out primarily ATP. Dramatic conformational changes of this loop would even- by the side chain carboxyl group of Asp-235 in PLK. Another tually shift these two residues to new positions where these mechanism is carried out by other kinases in the ribokinase residues would provide the ATP molecule with increased superfamily. For example, a positively charged residue, such as stabilization. Lys-43 in ribokinase or Arg-136 in adenosine kinase, exerts a Mechanism of Pyridoxal Kinase—Two major catalyzing stabilizing effect on the ␥-phosphate of ATP before transfer of mechanisms have been suggested for enzymes belonging to the the phosphate group. However, this positively charged residue ribokinase superfamily. An anion hole with the ability to sta- was not found in the active site of PLK. Arg-120, the only bilize the transition state of reactants is formed by the main possible residue located near the active site did not interact chain nitrogen atoms of several continuous residues (8, 10, 13). with ATP or ADP phosphate, suggesting that a positively In PLK, such an anion hole is created by residues 232–235 at charged amino acid is not present for the positioning or stabi- the N-terminal end of the ␣7 helix. A base-catalyzing group in lization of the ␥-phosphate. In contrast, the correct positioning the active site is needed to initiate the reaction through de- of the reaction groups of substrates in PLK relies on extensive protonation of the hydroxyl group on the vitamin substrate so interactions between amino acid residues of the enzyme and 141 Conformation Change of Pyridoxal Kinase 17465 substrates. During the time when conformational changes oc- mechanism behind protein-protein interactions between PLK curred in the enzyme-substrate ternary complex, converting and other binding proteins. the complex from its initial state to the pre-reaction state, Later on, further conformational changes cause the structure amino acid residues of PLK would move toward the active site to become more compact and reach the pre-reaction state and and cause movement toward the substrates through several both substrates are pushed by the surrounding amino acid interactions described above. As a result, substrates bound to residues to move to positions where their reaction groups are the protein became more rigid than before (Fig. 4b). A compar- close to each other. This movement causes the ATP ␥-phos- ison of the structures of the PLK⅐AMP-PCP-pyridoxamine com- phate to be stabilized by an anion hole in the active site, and plex and pre-reaction state model showed that the number of the pyridoxal 5Ј-hydroxyl group forms a hydrogen bond with atom pairs with distances Ͻ4 Å between pyridoxal and protein the side chain carboxyl group of Asp-235 (Fig. 6d). Electrons of increased from 29 to 46 and the number of atom pairs with the oxygen atom of the 5Ј-hydroxyl group starts a nucleophilic short distances increased from 70 to 99. A decrease in the attack on the phosphorus atom ␥-phosphate of ATP, forming a distance between atom pairs leads to a further decrease in the new bond. The phosphorus atom in the ␥-position then moves a volume of an active site, leaving limited free space around the distance of 0.8 Å, causing the bond between it and the ␤-phos- substrates inside the site. As a result, both substrates in this phate group to break. Thus, the phosphate transfer is com- pre-reaction state could be completely buried (Fig. 4c)inthe pleted and the two products, ADP and PLP, are generated protein mass. By limiting the substrate in a restricted space, (observed in the structure of PLK⅐ADP⅐PLP complex and shown this phenomenon directed the reaction group, the ␥-phosphate in Fig. 6e). of ATP, and the 5Ј-hydroxyl group of pyridoxal to collide with To release reaction products, the overall conformation of the each other, allowing the reaction to occur. The positioning and enzyme relaxes again. The active site is exposed to the reaction directing of substrates by cooperative conformational changes medium solution, which allows the products to be released as in the overall protein structure of enzymes is unique in the free molecules (observed in the structure of the PLK⅐ADP com- catalytic mechanism of PLK. plex and shown Fig. 6f). For the second catalytic cycle to start, PLK can accept new substrates again for the next cycle of CONCLUSION catalysis. The Overall Catalyzing Process of PLK—Crystallographic studies of PLK with respect to the binary and ternary complex REFERENCES of enzyme in the presence of substrates and products provide 1. Kerry, J. A., Rohde, M., and Kwok, F. (1986) Eur. J. Biochem. 158, 581–585 2. McCormick, D. B., and Snell, E. E. (1959) Proc. Natl. Acad. Sci. U. S. A. 45, information for the elucidation of an integral mechanism in the 1371–1379 catalytic process carried out by PLK. 3. McCormick, D. B., and Snell, E. E. (1961) J. Biol. Chem. 263, 2085–2088 4. Hanna, M. C., Turner, A. J., and Kirkness, E. F. (1997) J. Biol. Chem. 272, Initially, PLK exhibits an open conformation before the bind- 10756–10760 ing of any substrate. This exposes the ATP binding site to the 5. Yang, Y., Zhao, G., and Winkler, M. E. (1996) FEMS Microbiol Lett. 141, 89–95 solution of the reaction medium but does not expose the pyri- 6. Yang, Y., Tsui, H. C., Man, T. K., and Winkler, M. E. (1998) J. Bacteriol. 180, 1814–1821 doxal binding site (observed in the PLK structure and shown in 7. Li, M.-H., Kwok, F., Chang, W.-R., Lau, C.-K., Zhang, J.-P., Lo, S. C. L., Jiang, Fig. 6a). T., and Liang, D.-C. (2002) J. Biol. Chem. 277, 46385–46390 8. Sigrell, J. A., Cameron, A. D., Jones, T. A., and Mowbray, S. L. (1998) Structure After ATP is bound to the enzyme, the overall structure of 6, 183–193 PLK changes little at this stage. The loop over the pyridoxal 9. Mathews, I. I., Erion, M. D., and Ealick, S. E. (1998) Biochemistry 37, binding site then swings onto the ATP binding site and inter- 15607–15620 10. Schumacher, M. A., Scott, D. M., Mathews, I. I., Ealick, S. E., Roos, D. S., acts with the ATP phosphate. At this time, the ATP ␥-phos- Ullman, B., and Brennan, R. G. (2000) J. Mol. Biol. 298, 875–893 phate is far away from the catalytic site of PLK to prevent 11. Campobasso, N., Mathews, I. I., Begley, T. P., and Ealick, S. E. (2000) Bio- ⅐ chemistry 39, 7868–7877 hydrolysis (observed in the structure of PLK ATP complex and 12. Ito, S., Fushinobu, S., Yoshioka, I., Koga, S., Matsuzawa, H., and Wakagi, T. shown in Fig. 6b). These procedural incidents are consistent (2001) Structure 9, 205–214 with the random substrate binding kinetics followed by PLK. 13. Cheng, G., Bennett, E. M., Begley, T. P., and Ealick, S. E. (2002) Structure 10, 225–235 When pyridoxal as a vitamin B6 substrate binds to the en- 14. Sigrell, J. A., Cameron, A. D., and Mowbray, S. L. (1999) J. Mol. Biol. 290, zyme, conformational changes of amino acid residues localized 1009–1018 15. Li, M.-H., Kwok, F., An, X.-M., Chang, W.-R., Lau, C.-K., Zhang, J.-P., Liu, at the pyridoxal binding site cause the protein to become more S.-Q., Leung, Y.-C., Jiang, T., and Liang, D.-C. (2002) Acta Crystallogr. D compact than its normal state, enabling the substrate to be 58, 1479–1481 tightly bound. Interestingly, this conformational change does 16. Otwinowski, Z. (1993) in Proceedings of the CCP4 Study Weekend (Issacs, N., Bailey, S., and Sawyer, L.) pp. 56–62, Daresbury Laboratories, Warrington, not extend to the ATP binding site maintaining the ATP United Kingdom ␥-phosphate far away from the catalytic site (observed in the 17. Navaza, J., and Saludjian, P. (1997) Methods Enzymol. 276, 581–594 ⅐ 18. Yeates, T. O. (1997) Methods Enzymol. 276, 344–358 structure of PLK AMP-PCP-pyridoxamine complex and shown 19. Vagin, A., and Teplyakov, A. (1997) J. Appl. Crystallogr. 30, 1022–1025 in Fig. 6c). The existence of such a stage in the catalytic mech- 20. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse- anism of PLK may be related to the regulation of PLK through Kunstleve, R. W., Jiang, J. S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T., and Warren, G. L. (1998) Acta Crystallogr. other proteins. Previous reports have shown that PLK could D 54, 905–921 form complexes with some PLP-binding enzymes such as as- 21. Brunger, A. T., Krukowski, A., and Erickson, J. W. (1991) Acta Crystallogr. A 46, 585–593 partate aminotransferase and pyridoxine-5-phosphate oxidase 22. Jones, T. A., Zuo, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crys- (24, 27) to restrict the release of free PLP into the cellular tallogr. A 47, 110–119 environment where phosphatases are present. It is possible 23. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283–291 that the binding of these proteins to PLK may accelerate fur- 24. Kwok, F., and Churchich, J. E. (1980) J. Biol. Chem. 255, 882–887 ther conformational changes in the enzyme and lead to spon- 25. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946–950 26. Merritt, E. A., and Bacon, D. J. (1997) Methods Enzymol. 277, 505–524 taneous enzymatic reactions. However, investigation of this 27. Kim, Y. T., Kwok, F., and Churchich, J. E. (1988) J. Biol. Chem. 263, particular aspect is needed for further understanding of the 13712–13717

142 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 37, Issue of September 10, pp. 39132–39138, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Crystal Structure of Human Bisphosphoglycerate Mutase*

Received for publication, May 28, 2004, and in revised form, June 28, 2004 Published, JBC Papers in Press, July 16, 2004, DOI 10.1074/jbc.M405982200

Yanli Wang‡§, Zhiyi Wei‡§, Qian Bian§, Zhongjun Cheng‡§, Mao Wan§, Lin Liu‡§, and Weimin Gong‡§¶ From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China and the §School of Life Sciences, Key Laboratory of Structural Biology, University of Science and Technology of China, Hefei, Anhui 230026, China

Bisphosphoglycerate mutase is a trifunctional enzyme BPG) (1–3) (see Fig. 1A). The second activity is that of a mutase of which the main function is to synthesize 2,3-bisphos- (phosphoglycerate mutase, EC 5.4.2.1) catalyzing the intercon- phoglycerate, the allosteric effector of hemoglobin. The version between 2- and 3-phosphoglycerate (Fig. 1B) (4). The gene coding for bisphosphoglycerate mutase from the third activity, as a phosphatase (S-succinylglutathione hydro- human cDNA library was cloned and expressed in Esch- lase, EC 3.1.3.13), is to catalyze the hydrolysis of 2,3-BPG to 3- erichia coli. The protein crystals were obtained and dif- or 2-phosphoglycerate and a phosphate (Fig. 1C) (1, 2). The fract to 2.5 Å and produced the first crystal structure of phosphatase reaction can be stimulated by a number of anions bisphosphoglycerate mutase. The model was refined to a including chloride, phosphate, and particularly by 2-phospho- crystallographic R-factor of 0.200 and R of 0.266 with free glycolate (5). These three enzymic activities have been found to excellent stereochemistry. The enzyme remains a dimer occur at a unique active site with two different binding sites for in the crystal. The overall structure of the enzyme resembles that of the cofactor-dependent phosphoglycer- the substrates, one for bisphosphoglycerate and another for ate mutase except the regions of 13–21, 98–117, 127–151, monophosphoglycerate (6, 7). and the C-terminal tail. The conformational changes in BPGM regulates the level of 2,3-BPG in human blood cells. the backbone and the side chains of some residues re- In vivo, the concentration of 2,3-BPG is determined by the veal the structural basis for the different activities be- relative activities of the synthase and phosphatase reactions. tween phosphoglycerate mutase and bisphosphoglycer- In red blood cells, 2,3-BPG is the main allosteric effector of ate mutase. The bisphosphoglycerate mutase-specific hemoglobin. It shifts the equilibrium between the oxy and residue Gly-14 may cause the most important conforma- deoxy conformations of hemoglobins by preferentially stabiliz- tional changes, which makes the side chain of Glu-13 ing the unliganded form. Sickle cell anemia is characterized by orient toward the active site. The positions of Glu-13 and polymerization of deoxygenated hemoglobin mutants giving Phe-22 prevent 2,3-bisphosphoglycerate from binding in rise to deformed erythrocytes and vaso-occlusive complications. the way proposed previously. In addition, the side chain 2,3-BPG has been shown to facilitate this polymerization. The of Glu-13 would affect the Glu-89 protonation ability ability to modulate the 2,3-BPG level in vivo would have im- responsible for the low mutase activity. Other structural portant implications in the treatment of ischemia and sick cell variations, which could be connected with functional anemia. One therapeutic approach would be to decrease the differences, are also discussed. intraerythrocytic level of 2,3-BPG by increasing the phosphatase activity of the BPGM. Based on its enzymatic properties and amino acid sequence Bisphosphoglycerate mutase (BPGM)1 is an erythrocyte-spe- homology, BPGM is closely related to the glycolytic housekeep- cific trifunctional enzyme. The main activity is that of synthase ing enzyme, cofactor (2,3-BPG)-dependent phosphoglycerate (BPGM, EC 5.4.2.4), catalyzing the formation of 2,3-bisphos- mutase (dPGM) (8, 9), involved in glycolytic and gluconeogenic phoglycerate (2,3-BPG) from 1,3-bisphosphoglycerate (1,3- pathways with sequence identities in the 40–50% range (6). In the SCOP data base, BPGM and dPGM are grouped into a * This work is supported by Project 200128 from the Foundation for superfamily along with fructose-2,6-bisphosphatases and acid Authors of National Excellent Doctoral Dissertation of China, Grant phosphatase. Sequence and structural comparisons show that 30225015 from the National Foundation of Talent Youth, Grant they share a set of conserved residues forming the catalytic 2001AA233021 from the National High Technology Research and De- core but otherwise exhibit many differences associated with velopment Program of China, Grant 2002BA711A13 from the 863 Spe- cial Program of China, the Key Important Project and other projects substrate specificities and catalytic activities. For example, the from the National Natural Science Foundation of China (Grant No. synthase activity of BPGM is higher than dPGM, but the latter 30121001, No. 30070170, No. 30130080 and No. 30121001), and Grant has stronger mutase activity. KSCX1-SW-17 from the Chinese Academy of Sciences. The costs of A modest resolution structure of dPGM from Saccharomyces publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” cerevisiae was reported in 1974 (10). Recently, the high-resolu- in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. tion structures of dPGMs and the complex with their inhibitors The atomic coordinates and structure factors (code 1T8P) have been were reported (11–17). According to these structural results, deposited in the Protein Data Bank, Research Collaboratory for Struc- the substrate binding sites and the mutase catalytic mecha- tural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/). nisms have been discussed. However, no BPGM three-dimen- ¶ To whom correspondence should be addressed: Institute of Biophys- sional structure information is available, although BPGM has ics, 15 Datun Rd., Chaoyang District, Beijing 100101, China. Tel.: been crystallized (18), Here we report the crystal structure of 86-10-64888467; Fax: 86-551-3607154; E-mail: [email protected]. human BPGM (hBPGM) for the first time. Structural compar- 1 The abbreviations used are: BPGM, bisphosphoglycerate mutase; hBPGM, human BPGM; dPGM, cofactor-dependent phosphoglycerate ison of hBPGM and dPGMs show some significant differences mutase; BPG, bisphosphoglycerate. between the two groups of enzymes.

39132 This paper is available on line at http://www.jbc.org 143 Crystal Structure of Human Bisphosphoglycerate Mutase 39133

EXPERIMENTAL PROCEDURES TABLE I Gene Cloning, Expression, and Protein Purification—The hBPGM Summary of data collection and structure refinement gene was amplified from human brain cDNA library (Clontech) by a Numbers in parentheses represent the value for the highest resolu- PCR using the 5Ј- and 3Ј-end special primers 5Ј CATATGTCCAAGTA- tion shell. Ј Ј Ј CAAACTTATTATG 3 and 5 CTCGAGTTTTTTAGCTTGTTTCAC 3 Unit cell (Å°) a ϭ 38.6 (Sangon) designed based on the mRNA sequence of hBPGM (Gen- b ϭ 61.8 BankTM accession number X04327). Those oligonucleotides were intro- c ϭ 123.3 duced with NdeI and XhoI restriction sites, respectively. Taq polymer- ␤ ϭ 95.0 ase, T-vector, DNA ligase, and the relevant restriction enzymes were Resolution limit (Å)30–2.5 (2.61–2.5) obtained from Takara. The polymerase chain reaction product (ϳ800 Completeness (%) 96.0 (97.2) bases) was purified with the Gel Extraction mini kit (Watson BioTech- Number of reflections 176,376 nologies) and cloned into a T-vector. The positive clones were identified Number of independent reflections 18,907 by restriction digestion. The DNA fragment was ligated into the NdeI/ Rmerge 0.058 (0.183) XhoI-cleaved plasmid pET22b (Novagen) to give the pET22b-hBPGM I/␴ 9.94 (4.14) R-factora 0.200 (0.302) construction that was amplified in E. coli BL21 (DE3). The recombinant b protein contains eight non-native residues at the C terminus. The Rfree 0.266 (0.337) integrity of the gene was confirmed by DNA sequencing. Single colonies Number of non-H atoms 4,221 Protein atoms 3,989 were cultured in Luria-Bertani broth medium with ampicillin (100 ␮g Ϫ Water molecules 232 ml 1) for expression. Cells were induced with 0.5 mM isopropyl-␤-D- Average B-factors (Å2) thiogalactopyranoside after attaining an A600 of 0.4 and grown for an Main chain 36.68 additional4hat310K.Thecells were harvested by centrifugation, Side chain 37.63 resuspended in lysis buffer containing 0.5 M NaCl, 20 mM Tris-HCl (pH Water 39.88 7.5), and lysed by sonication on ice. After centrifugation, the superna- Root mean square distance of 0.007 tant was loaded onto a nickel-nitrilotriacetic acid column (Qiagen) and bond lengths (Å) eluted using a step gradient of 0.05–0.5 M imidazole. The fractions were Root mean square distance of 1.34 tested for purity by SDS-PAGE. The purified human BPGM protein was bond angles (°) desalted and concentrated to 30 mg mlϪ1, determined by a Bio-Rad a R-factor ϭ⌺ʈF ͉ Ϫ ͉F ʈ/⌺͉F ͉, where F and F are observed Protein Assay. Sample purity and molecular weight (ϳ30 kDa) were obs calc obs obs calc and calculated structure factors. verified by SDS-PAGE and mass spectrometry, respectively. b ϭ⌺ ʈ ͉ Ϫ ͉ ʈ ⌺ ͉ ͉ Rfree SUB Fobs Fcalc / T Fobs , where T is a test data set of Crystallization and Data Collection—Crystals were grown by hang- 10% of the total reflections randomly chosen and set aside prior to ing drop vapor diffuse method at 291 K from a protein solution contain- Ϫ refinement. ing hBPGM (30 mg ml 1), 20 mM Tris-HCl (pH 7.5) with 50 mM NaCl and an equal volume reservoir solution comprising 100 mM HEPES- NaOH (pH 7.0) and 20% (w/v) polyethylene glycol 6000. Crystals appeared after 3 days and kept growing for a week. The diffraction data were collected on a Mar-CCD detector at the Beijing Synchrotron Ra- diation Facility (␭ ϭ 0.9 Å) at the Institute of High Energy Physics, Chinese Academy of Science. A total of 200 frames of data to 2.5 Å were collected with oscillation range of 1° at 100 K. Data were processed with Denzo and Scalepack (19). Structure Determination and Refinement—Molecular replacement was performed with program AmoRe (20) using data from 15 to 3.5-Å resolution with S. cerevisiae dPGM (PDB entry: 5PGM) as the searching model. Multiple cycles of refinement were performed with package of CNS (21). The non-crystallography symmetry was applied during all steps of refinement. Water molecules were included near the end of refinement, followed by manual modification in the graphics program O (22). The quality and stereochemistry of the final model was analyzed with PROCHECK (23).

RESULTS AND DISCUSSION Structure Determination Crystals grew with a rod-shaped morphology and belonged to space group P21 based on the systematic absences in the diffraction data. The unit cell dimensions are a ϭ 38.6 Å, b ϭ 61.8 Å, c ϭ 123.3 Å, ␤ ϭ 95.0° with a solvent content of 48% corresponding to two monomers for each asymmetric unit. The final model refined at a 2.5-Å resolution contains residues from Ser-2 to Asp-250 of the total 267 residues (including the His tag) in each monomer with no definite electron density beyond residue 250. The data in Table I show a well refined structure with excellent stereochemistry. In the Ramachandran plot, FIG.1. Reactions catalyzed by BPGM. A, synthase activity; B, 91.4% of the residues are located in the most favored areas, and mutase activity; C, phosphatase activity. 8.1% are located in the additional allowed regions. Only one residue, Ser-24, is located at generously allowed regions (dis- six ␤-strand in the order ␤A, ␤B, ␤C, ␤D, and ␤F in parallel and cussed below). The model fits well with the corresponding elec- strand ␤E in antiparallel conformations. The ␤-sheet is flanked tron density except for the C-terminal residues. by six ␣-helices. The C-terminal tail ends around the active site. Glu-249 and Overall Structure Asp-250 lie on the center of the active cleft mouth with their The hBPGM monomer (Fig. 1)contains two domains includ- side chains oriented from the active cleft. Lys-246 is hydrogen ing six ␤-strands (named ␤A–F) and ten ␣-helices (named ␣1– bonded to OE-1 of Glu-249 via its NZ atom. The OE-1 atom of 10). The ␣/␤-fold of hBPGM resembles that of the dPGMs from Glu-33 interacts with the NZ atom of Lys-247 by a hydrogen S. cerevisiae and E. coli (Fig. 2). The protein core consists of a bond. It is noteworthy that there is always an acidic residue at 144 39134 Crystal Structure of Human Bisphosphoglycerate Mutase

FIG.2.Stereo view of the structural superposition of the hBPGM (green), E. coli dPGM (purple), and S. cerevisiae dPGM (blue). The regions (residue 13–21, 98–117, 127–151, and the C-terminal tail of hBPGM) whose conformations are different from PGM are colored in yellow. This figure was produced using the Lsqman (24) and Ribbons (25) programs. residue 33 in BPGMs. These interactions may make the C- terminal helix (helix 10) more stable and fix it to the active site pocket. The values of the B-factors indicate that the C-terminal region is more flexible compared with the other parts of the molecule. Similarly, in the C-terminal tail, 12 residues cannot be observed in S. cerevisiae dPGM and 9 residues are missing in E. coli dPGM in its unphosphorylated form. The C-terminal residues play an important role in the activities of the enzymes in this family. Removal of the 12 C-terminal residues from S. cerevisiae dPGM is associated with loss of mutase activity but no change in phosphatase activity (26). The deletion of the last seven residues completely abolished the three catalytic activities of the hBPGM (9). The C-terminal residues would be involved in transferring a phosphoryl group to the internal active site (27). Therefore, the disordering of the C-terminal tail appears to be a common feature in both of BPGMs and of dPGMs and could accommodate the access of the substrate to the active FIG.3.The dimer of hBPGM viewed along the non-crystallo- site. graphic 2-fold axis.

Dimer Association root mean square distance between their C␣ atoms is 0.51 Å. hBPGM forms a dimer in the crystal in agreement with those The following discussion is based on the structure of monomer observed in solution (5). The dimer is formed between the A. surface of the ␤C strands and ␣3 helices of the two monomers Comparison with dPGMs with a non-crystallographic 2-fold symmetry (Fig. 3) similar to E. coli dPGM and S. cerevisiae dPGM. The side chains of Ile-64, Sequences Alignment and Backbone Comparison—Similari- Trp-68, Leu-69, Leu-71, and Val-81 form a hydrophobic dimer- ties of the hBPGM structure to some dPGM structures (PDB ization core. Specifically, the side chains of Trp-68 from both codes 5PGM, 1E58, 1E59, 1QHF, and 1FTZ) were analyzed monomers stack with each other across the 2-fold axis. Those using the program DALI (28) and LSQMAN (24). A structure- hydrophobic residues are conserved in all BPGMs and the based sequence alignment of BPGMs and dPGMs is shown in dimerized dPGMs but not in Schizosaccharomyces pombe Fig. 4. The sequence of hBPGM is ϳ50% identical to dPGMs. dPGM, which is a monomer. In addition, the salt bridge be- The catalytic site residues Arg-10, His-11, Arg-62, Glu-89, Arg- tween Lys-29 and Glu-72 and several hydrogen bonds formed 90, Arg-116, Arg-117, and His-188 are conserved in all of them. by Glu-51, Phe-52, Asp-53, His-65, Glu-77, and Arg-140 However, some residues involved in the substrate binding in strengthen the dimer interactions. Arg-140 forms two hydrogen dPGMs have been substituted in BPGMs (discussed below). bonds to the carbonyl oxygen of Phe-52 and to the OD-2 atom of The topology of the ␣/␤ domain of BPGM shows considerable

Asp-53 via its NH2 atom and forms a hydrogen bond to the similarity to dPGMs. A superposition of hBPGM with the struc- OE-1 atom of Glu-51 via its NE atom. His-65 forms a hydrogen ture of S. cerevisiae dPGM and E. coli dPGM yields root mean bond to the side chain of Glu-77 via its NE-2 atom. All of these square distances of 0.69 and 0.74 Å, respectively, for C␣ atoms residues discussed above are conserved in BPGMs. The two in 124 residues in three regions (hBPGM residues 4–11, 25–97, subunits of the dimer show few differences when overlaid. The and 157–199), indicating strong structural homology within 145 Crystal Structure of Human Bisphosphoglycerate Mutase 39135

FIG.4. Structure-based sequence alignment of BPGMs from human (hBPGM), rabbit (rbBPGM), rat (rtBPGM), and mouse (mBPGM) and dPGMs from human brain (hPGM-B), human muscle (hPGM-M), E. coli (ecPGM), S. cerevisiae (scPGM), and S. Pombe (spPGM). The secondary structure elements in the crystal structure of hBPGM are shown above the alignment in blue. Arrows indicate ␤-strands and coils indicate helices. Strictly conserved and conservatively substituted residues are boxed and marked with red and yellow background, respectively. Residues conserved only for BPGMs are colored in purple. The residues in the C-terminal region that are different between BPGMs and dPGMs are colored in red. Cys-23 is present in all BPGMs and human muscle dPGM, resulting in their sensitivity to Hg2ϩ, and marked in green background. Glu-13 and Gly-14 are marked by black stars. Every 10 residues of the hBPGM sequence are marked with dots and the residue numbers in each sequence are showed in the front. The figure was generated using ESPript (29). those regions, consistent with the concept that BPGM and between the two subunits by forming a hydrogen bond with dPGM are structurally homologous enzymes. The most signif- His-65. Ser-63 and Ser-186, in which the equivalent residues icant variations in the backbone occur in the regions 13–21, are both Ala in dPGMs located near the active site, form two 98–117, 127–151, and the C-terminal tail (Fig. 2). With a hydrogen bonds between their main-chain and side-chain oxy- four-residue insertion at residues 136, 137, 143, and 144, an gen atoms. The hydroxyl oxygen of Ser-192 forms three hydro- additional ␣-helix is formed from residue 133 to 138, resulting gen bonds with the carbonyl oxygen atoms of His-188 and in the different conformations at the region of residues 127– Gly-189, and the main-chain nitrogen atom of Arg-193. These 151. This region is far away from the active site, and the additional hydrogen bonds may help stabilize the structure. structural differences would not contribute to the catalytic Gly-14 is a critical BPGM-specific residue. A mutation of activity. The fragments 13–21, 98–117, and the C-terminal Gly-14 of hBPGM to Ser did not modify the synthase activity, fragment surround the active site. These conformational whereas the mutase and phosphatase activities were 2-fold changes may have significant effect on the enzymatic activity. increased or decreased, respectively. However, replacing Residues Specific for BPGMs—There are 24 residues (Fig. 4, Gly-14 with Arg enhanced phosphatase activity by 28.6-fold, pink) that are identical in BPGMs but differ from those in whereas synthase and mutase activities were decreased 10-fold dPGMs. Among them, Glu-77 is involved in the interactions (30). In dPGMs, the equivalent residue Ser interacts with the 146 39136 Crystal Structure of Human Bisphosphoglycerate Mutase

FIG.5.Stereo drawing of the superposition of the active site pocket of hBPGM (green) and S. cerevisiae dPGM (gray). The critical residues in the active site pocket are labeled.

substrate (12). In prostatic acid phosphatase, Arg-15, the Arg-62. The mouth of the cleft is defined by Lys-18, Asn-20, equivalent residue of Gly-14 of BPGM, points toward the active Arg-100, and Arg-116 on one side and Ile-208, Asn-209, and site and is involved in the substrate binding too (31–33). Fig. 5 Thr-211 on the other side (Fig. 5). Residues 246–250 lie on the shows that the conformation around Gly-14 varies signifi- surface of the active site pocket. The general shape of the active cantly. As a consequence, the side chain of Glu-13 in hBPGM cleft looks similar to those of dPGMs, but the details differ points toward the active site, forming a hydrogen bond network resulting from the conformational changes at regions of 13–21, with Arg-10, His-11, Glu-89, and Gly-189 via three water mol- 98–117, and the C termini. The catalytic site cleft contains ecules, whereas the equivalent residue of dPGMs orients away many basic residues resulting in a highly positive electrostatic from the active site. Glu-89 is conserved in all BPGMs and potential accommodating for the negative charged substrates dPGMs. In mutase activity, Glu-89 acts as an acid or a base as dPGMs. during enzyme phosphorylation and dephosphorylation (12). His-11 and His-188 are conserved in BPGMs and dPGMs. In The phosphotransfer step of the mutase reaction requires a the hBPGM structure, their side chains adopt very similar proton to be transferred to or from Glu-89. The hydrogen bond conformations to those in the structure of dPGM (Fig. 5). between Glu-13 and the side chain of Glu-89 would affect the His-11 was proposed to accept a phosphate group during the protonation ability of Glu-89, so that the mutase activity is reactions (6). His-188 was confirmed to be very important for lower in BPGMs. In contrast, the first phosphotransfer of the catalysis, but its precise function is still speculative (34, 35). In synthase reaction involves the transfer of an acyl-phospho the hBPGM structure, the NE-2 atom of His-11 forms a hydro- group and does not require a proton to be transferred (6). gen bond to the ND-1 atom of His-188. The hydroxyl group of Ser-24 is reported to be involved in the binding of both Ser-58 is hydrogen-bonded to atom NE-2 of His-188. This in- monophosphoglycerates and 2-phosphoglycolate (7). This posi- teraction is also conserved in dPGMs in the rat prostatic acid tion is conserved as a Gly in all dPGMs. It was proposed that its phosphatase (between Thr-75 and His-257) and in fructose-2,6- backbone nitrogen atom interacts with the substrate carboxy- bisphosphatase (between Ser-52 and His-141), suggesting they late group (15). Because its dihedral angle is located in a contribute to the correct orientation of the His-188 imidazole general allowed region in the Ramachandran plot, it was pre- ring. dicted that Ser-24 would be the major reason for the different Most of the residues involved in bisphosphoglycerate binding enzymatic activities of BPGMs and dPGMs by adopting a dif- (Arg-10, Asn-17, Arg-62, Glu-89, Arg-90, Tyr-92, Arg-116, Arg- ferent dihedral values and changing the main-chain conforma- 117, and Asn-190) are conserved in BPGMs as in dPGMs. Upon tion (12, 15). In our hBPGM structure, no significant structural a superposition of the structures of hBPGM and dPGMs, Arg- change was observed except the side chain of Ser-24 was added. 10, Arg-62, Glu-89, Arg-90, and Asn-190 fit well; Asn-17, Arg- Although the Ser-24 side chain fits the electron density well, its 116, and Arg-117 shift with the backbone movement. The side conformation is in an unfavorable region of the Ramachandran chains of Arg-116 and Arg-117 are flexible and cannot be ob- plot (Fig. 6). The unfavorable stereochemistry may be compen- served in the electron density map. sated by the formation of a hydrogen bond between its hydroxyl Thr-20 and Lys-97 (numbered as in dPGMs), in which the oxygen and the backbone nitrogen atom of Tyr-92. Its carbonyl side chains were proposed to be involved in 2,3-BPG binding in oxygen maintains contact with the NH2 atom of Arg-62 as in dPGMs, are substituted by Cys-23, and Arg-100, respectively, dPGMs. So it is unlikely that Ser-24 plays an important role in in hBPGM. Cys-23 is conserved in BPGMs and in muscle distinguishing the activities of BPGMs and dPGMs. dPGM leading to a susceptibility to inactivation by Hg2ϩ (6). In Active Site and the Substrate Binding Pocket—The active hBPGM, the guanidinium group of Arg-62, which is necessary site pocket was found at the carboxyl end of the parallel for substrate binding, contacts the SH group of Cys-23 in van ␤-strands of the ␣/␤-domain. His-11 and His-188 are located at der Waals distance. If a positively charged Hg2ϩ bound to the bottom of the active site pocket as well as Arg-10 and Cys-23, it should push away the same positively charged 147 Crystal Structure of Human Bisphosphoglycerate Mutase 39137

؊ ␴ ␾ ␺ FIG.6.The electron density map (2Fo Fc, 1.0 ) of Ser-24. The hydrogen bond between Ser-24 and Arg-90 is labeled. The and angles of this residue are 53.5° and Ϫ125.1°, respectively. These two angles in the equivalent residue Gly in E. coli dPGM are 61.4° and Ϫ130.8°, and in S. cerevisiae dPGM are 67.6° and Ϫ124.9°, respectively.

Arg-62 and prevent the substrate from binding. It also should The narrower active cleft and varieties of residues involved be noted that in dPGMs, the side chain of Lys-97 points toward in substrate binding could be another reason for different phos- the active site pocket. However, in hBPGM, the equivalent phorylation rates of BPGMs and dPGMs by 2,3- and 1,3-BPG, residue Arg-100 turns its side chain away from the active site respectively, which leads to the different mutase and synthase ϳ90°, toward the surface of the active cleft. It was reported that activities. The mutase reaction requires that the 2,3-BPG stay the substrate binding is not the rate-limited step, and the as an intermediate and change its orientation in the active site different catalytic ability of BPGMs and dPGMs is caused during each round of catalysis (6). However, in hBPGM, the mainly by the phosphorylation rates of 1,3-BPG and 2,3-BPG narrower active site pocket would limit the reorientation of (36). Whether the moving away of Arg-100 is necessary for the 2,3-BPG. Although in the synthase reaction, 2,3-BPG should be specificity of phosphorylation needs to be investigated further. released as a product. Compared with dPGMs, the space around the catalytic In conclusion, hBPGM is similar in the folding, dimerization His-11 is more crowded in hBPGM. Several backbone and pattern, and the active site architectures to dPGMs as pre- residue differences contribute to this. First, the backbone of dicted from the sequence homology. The major structural vari- residues 13–21 shifts with a distance of 5.0 Å between Glu-19 ations occur at residues 13–21, 98–117, 127–151, and the C- and its equivalent residue in S. cerevisiae dPGM. Second, the terminal tail. Gly-14 may have caused the most important side chain of Glu-13 points toward the active site, and the side conformational changes where the inside flipping of Glu-13, chain of Phe-22 rotates closer to the catalytic His-11 leading to together with the relocation of Phe-22, resulted in a more the small active site space. As the consequence, the 2,3-BPG crowded substrate binding pocket and could prevent 2,3-BPG binding model of E. coli dPGM (15) cannot be adopted in hB- from binding in the way that was proposed in dPGMs. In PGM without the backbone or side-chain movements, because addition, the side chain of Glu-13 would affect Glu-89 protona- the side chain of Glu-13 leads to the steric clash with the tion ability that is critical for the mutase activity. phospho group near the catalytic site, and the side chains of Tyr-92 and Phe-22 lead to steric clash with the distal phospho Acknowledgments—We thank Prof. Peng Liu and Yuhui Dong for synchrotron data collection. group of 2,3-BPG. Moreover, the binding model of 3-phosphoglycerate to S. cerevisiae dPGM observed experimentally (37) REFERENCES cannot be adopted by hBPGM, in which Glu-13 occupies the 1. Rose, Z. B. (1968) J. Biol. Chem. 243, 4810–4820 position of the ligand, either. If the similar binding mode re- 2. Rose, Z. B. (1970) J. Biol. Chem. 248, 1513–1519 3. Rose, Z. B. (1980) Adv. Enzymol. Relat. Areas Mol. Biol. 51, 211–253 mains in hBPGM, large conformational changes should happen 4. Rosa, R., Gaillardon, J., and Rosa, J. (1973) Biochem. Biophys. Res. Commun. upon the substrate binding. It also should be noted that the 51, 36–542 binding of dPGMs with 2,3-BPG is only a theoretical model 5. Rose, Z. B., and Liebowitz, J. (1970) J. Biol. Chem. 245, 3232–3241 6. Fothergill-Gilmore, L. A., and Watson, H. C. (1989) Adv. Enzymol. Relat. Areas derived from the complex of E. coli dPGM and a liner tetra- Mol. Biol. 62, 227–313 vanadate (15). We are trying to obtain the hBPGM-substrate 7. Ravel, P., Craescu, C. T., Arous, N., Rosa, J., and Carel, M. C. (1997) J. Biol. Chem. 272, 14045–14050 complex crystals, which will provide deeper insight into the 8. Hass, L. F., Kappel, W. K., Miller, K. B., and Engle, R. L. (1978) J. Biol. Chem. binding and catalytic mechanism. 253, 77–81 148 39138 Crystal Structure of Human Bisphosphoglycerate Mutase

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149 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 29, Issue of July 16, pp. 30514–30522, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Structural Basis for Coronavirus-mediated Membrane Fusion CRYSTAL STRUCTURE OF MOUSE HEPATITIS VIRUS SPIKE PROTEIN FUSION CORE*

Received for publication, April 5, 2004, and in revised form, April 22, 2004 Published, JBC Papers in Press, April 27, 2004, DOI 10.1074/jbc.M403760200

Yanhui Xu‡§¶, Yiwei Liu‡§¶, Zhiyong Lou‡§¶, Lan Qin‡§, Xu Li‡§, Zhihong Bai‡§, Hai Pang‡§, Po Tienʈ, George F. Gaoʈ**‡‡, and Zihe Rao‡§ §§ From the ‡Laboratory of Structural Biology, Tsinghua University, Beijing 100084, China, the §National Laboratory of Biomacromolecules, Institute of Biophysics, Beijing 100101, China, the ʈInstitute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China, and the **Nuffield Department of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DU, United Kingdom

The surface transmembrane glycoprotein is responsi- The Coronaviridae exhibit a broad host range, infecting many ble for mediating virion attachment to cell and subse- mammalian and avian species and causing upper respiratory, quent virus-cell membrane fusion. However, the molec- hepatic, gastrointestinal, and central nervous system diseases. ular mechanisms for the viral entry of coronaviruses Coronaviruses in humans and fowl primarily cause upper res- remain poorly understood. The crystal structure of the piratory tract infections, whereas porcine and bovine coronavi- fusion core of mouse hepatitis virus S protein, which rep- ruses establish enteric infections that result in severe economic resents the first fusion core structure of any coronavirus, loss (3). The coronaviruses also include mouse hepatitis virus reveals a central hydrophobic coiled coil trimer sur- (MHV),1 infectious bronchitis virus, feline infectious peritonitis rounded by three helices in an oblique, antiparallel man- virus, and the newly emergent human severe acute respiratory ner. This structure shares significant similarity with both syndrome-associated coronavirus (HcoV-SARS) (4). the low pH-induced conformation of influenza hemagglu- The surface glycoproteins of enveloped viruses play essential tinin and fusion core of HIV gp41, indicating that the roles in viral entry into cells by mediating virion attachment to structure represents a fusion-active state formed after cells and the virus-cell membrane fusion, the initial events of several conformational changes. Our results also indicate that the mechanisms for the viral fusion of coronaviruses the viral infections. The spike (S) protein is the sole viral are similar to those of influenza virus and HIV. The coiled enveloped glycoprotein responsible for cell entry in coronavi- coil structure has unique features, which are different ruses. It binds to the cell surface receptor and mediates subse- from other viral fusion cores. Highly conserved heptad quent fusion of the viral and cellular membranes (5). Under the repeat 1 (HR1) and HR2 regions in coronavirus spike pro- electron microscope, the spike proteins can be clearly seen as teins indicate a similar three-dimensional structure 20-nm-long surface projections on the virion membrane (6). among these fusion cores and common mechanisms for The spike proteins of coronaviruses share several features the viral fusion. We have proposed the binding regions of with other viral glycoproteins mediating viral entry, including HR1 and HR2 of other coronaviruses and a structure the hemagglutinin (HA) protein of influenza virus, gp160 of model of their fusion core based on our mouse hepatitis human immunodeficiency virus (HIV) and simian immunode- virus fusion core structure and sequence alignment. Drug ficiency virus (SIV), GP of Ebola virus, and fusion protein of discovery strategies aimed at inhibiting viral entry by paramyxovirus (7, 8). These glycoproteins are all synthesized blocking hairpin formation may be applied to the inhibi- as single polypeptide precursors that oligomerize in the endo- tion of a number of emerging infectious diseases, includ- plasmic reticulum to form trimers. Most of the enveloped pro- ing severe acute respiratory syndrome. teins with fusion activity contain two noncovalently associated subunits: S1 ϩ S2 in coronaviruses, HA1 ϩ HA2 in influenza viruses, gp120 ϩ gp41 in HIV/SIV, GP1 ϩ GP2 in Ebola virus, Coronaviruses are enveloped viruses with single-stranded, and F1 ϩ F2 in paramyxoviruses, all of which are generated by positive-sense genomic RNA that is 26–31 kb in length (1, 2). proteolytic cleavage. Nevertheless, some enveloped proteins have no cleavage in their precursors and yet still maintain fusion activity, such as the S proteins of some coronaviruses (9) * This work was supported in part by Projects 973 and 863 of the Ministry of Science and Technology of China Grants 200BA711A12, and GP of Ebola virus (10). G199075600, and 2003CB514116, the National Natural Science Foun- A hydrophobic region in the membrane-anchored subunit of dation of China Grant 30221003, and the Key Project of the Knowledge enveloped proteins, termed the fusion peptide in class I fusion Innovation Program of Chinese Academy of Sciences. The costs of proteins, has been shown to insert into the cellular membranes publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” during the fusion process (11, 12). The regions following the in accordance with 18 U.S.C. Section 1734 solely to indicate this fact. fusion peptide have a 4-3 heptad repeat (HR) of hydrophobic The atomic coordinates and structure factors (codes 1WDF and residues, a sequence feature characteristic of coiled coils. The 1WDG) have been deposited in the Protein Data Bank, Research Col- first heptad repeat, termed HR1 (HRA or N peptide), is fol- laboratory for Structural Bioinformatics, Rutgers University, New Bruns- wick, NJ (http://www.rcsb.org/). lowed by a short spacer domain and a second heptad repeat, ¶ These authors contributed equally to this work. termed HR2 (HRB or C-peptide), followed by another short ‡‡ Supported by the Chunhui Project Scheme of Ministry of Education of China. To whom correspondence may be addressed. Tel.: 44-1865-228- 927; Fax: 44-1865-222-901; E-mail: [email protected]. 1 The abbreviations used are: MHV, mouse hepatitis virus; HA, he- §§ To whom correspondence may be addressed: Laboratory of Struc- magglutinin; HIV, human immunodeficiency virus; HR, heptad repeat; tural Biology, Tsinghua University, School of Life Sciences and Engi- MES, 4-morpholineethanesulfonic acid; MMLV, Moloney murine leuke- neering, Beijing 100084, China. Tel.: 86-10-6277-1493; Fax: 86-10-6277- mia virus; S protein, spike protein; SARS, severe acute respiratory 3145; E-mail: [email protected]. syndrome; SIV, simian immunodeficiency virus; TM, transmembrane.

30514 This paper is available on line at http://www.jbc.org 150 Crystal Structure of MHV Spike Protein Fusion Core 30515 spacer and the transmembrane (TM) anchor (13). Biochemical and concentrated to 8 mg mlϪ1. Crystals with good diffracting quality could be obtained in 0.1 M MES, pH 6.5, 10% PEG 4000 (v/v), 8% and structural analyses of HA2 (14), HIV-1/SIV gp41 (15–21), Ebola virus GP2 (22, 23), and SV5F1 (24) indicate that these dimethyl sulfoxide (v/v), 5 mM hexaminecobalt trichloride after 3 days. The expression, purification, and crystallization of nMHV is the same heptad repeat regions form six-helix bundles. The N-terminal as for MHV 2-Helix. Crystals with good diffracting quality could be heptad repeat forms a central coiled coil, which is surrounded obtained in 0.1 M MES, pH 6.5, 13% PEG 4000 (v/v), 5% dimethyl by three HR2 helices in an oblique, antiparallel manner. sulfoxide (v/v). Among all enveloped glycoproteins, the membrane fusion Data Collection and Processing—The MHV 2-Helix crystal was mechanism of the HA of influenza viruses has been studied in mounted on nylon loops and flash-frozen in an Oxford Cryosystems cold greater detail (7, 8, 25). HA is proteolytically cleaved to gener- nitrogen gas stream at 100 K. Multiple wavelength anomalous dispersion data were collected by a rotation method using a MarCCD detector ate a receptor binding subunit (HA1) and an anchored subunit with synchrotron radiation on beamline 3W1A of the Beijing Synchro- (HA2) containing the fusion peptide. Numerous evidences sug- tron Radiation Facility. Data were collected from a single selenomethio- gest that the HA of influenza undergoes a conformational nyl derivative crystal at peak (0.9799 Å), inflection (0.9801 Å), and change, from a native (nonfusogenic) to fusion-active (fuso- remote (0.9000 Å) wavelengths to 2.5 Å. Data collection from the nMHV genic) state during the viral fusion process. In the native HA, 2-Helix crystal was performed in-house on a Rigaku RU2000 rotating ␣ ␭ ϭ part of the heptad repeat region of HA forms a nonhelical loop anode x-ray generator operated at 48 kV and 98 mA (Cu K ; 1.5418 2 Å) with a MAR 345 image plate detector. The crystal was mounted on (26) but converts into a coiled coil when exposed to low pH (14). nylon loops and flash-frozen at 100 K using an Oxford Cryosystems cold The later conformation is generally regarded to be a fusogenic nitrogen gas stream. Data were indexed and scaled using DENZO and state because the low pH also activates influenza membrane SCALEPACK programs (30). Data collection statistics are shown in fusion. This conformation change is also the basis of the Table I. “spring-loaded mechanism” for activation of viral fusion (27). Phase Determination and Model Refinement—For MHV 2-Helix The spike protein of MHV A59 has been identified as a class structural determination, initial multiple wavelength anomalous dispersion phasing steps were performed using SOLVE (31) and followed I fusion protein and shares common features with other viral by density modification by RESOLVE (32). The program O (33) was fusion proteins (28). However, there are several significant used for viewing electron density maps and manual building. The initial differences between the membrane-anchored subunits of coro- structure was subsequently refined to a final R-value of 22.4% and free R-value of 29.1%. The quality of the structure was verified by PRO- navirus spike proteins and HA2, gp41, GP2, and SV5F1. First, the ectodomain is much larger (550 residues versus 120–380 CHECK (34). None of the main chain torsion angles is located in residues) in size in S protein. Second, the HR1 region is pre- disallowed regions of the Ramachandran plot. The statistics for the structure determination and refinement are summarized in Table I. dicted to be much larger (more than 100 residues versus 30–60 The figures were generated with the programs GRASP (35), SPDBView residues) in size by the learn-coil VMF program (29) and also (36), and MOLSCRIPT (37). verified by proteinase K-resistant experiments (28). Third, the putative fusion peptides of all other viral fusion proteins are RESULTS AND DISCUSSION located at the N terminus of the membrane-proximal subunits, Structure Determination—Two peptides (HR1 and HR2, Fig. whereas the S protein features an internal fusion peptide. 1, A and B) encompassing the N-terminal and C-terminal hep- Highly conserved HR1 and HR2 regions in coronavirus spike tad repeats of the MHV spike protein assemble into a stable proteins suggest that they share similar three-dimensional trimer of heterodimers (28). The HR1 and HR2 regions of the fusion core structures and a common mechanism for viral fu- MHV S protein consist of residues 968–1027 and residues sion. The binding region of the HR1⅐HR2 complex of other 1216–1254, respectively (Fig. 1, A and B). The fusion core of the coronaviruses and likely structures of their fusion cores can be MHV spike protein was prepared as a single chain by linking proposed based on MHV fusion core structure and sequence the HR1 and HR2 domains via an eight-amino acid linker alignment. Analogous to HIV C-peptides, HR2 peptides of coro- (GGSGGSGG, single amino acid abbreviation used here). The naviruses are likely to act in a dominant-negative manner to constructs and the encoded proteins were also called MHV inhibit hairpin formation, thereby inhibiting viral entry. Thus, 2-Helix (Fig. 1A). The preparation and characterization of the drug discovery strategies aimed at inhibiting viral entry by 2-Helix proteins will be reported elsewhere.2 The MHV 2-Helix blocking hairpin formation may also be applied to the inhibi- forms crystals that have unit cell parameters a ϭ b ϭ 48.3 Å, tion of emerging infectious diseases such as SARS. c ϭ 199.6Å , ␣ ϭ ␤ ϭ 90°, ␥ ϭ 120° and belong to the space Although previous biochemical and electron microscopic group R3. The crystals contain two MHV 2-Helix molecules/ analyses have shown that the HR1⅐HR2 complex in the S asymmetric unit, and the diffraction pattern extends to 2.5 protein of MHV forms a fusion core (28), the exact binding Å resolution.2 region of the HR1⅐HR2 complex and the detailed structure of The crystal structure of the MHV 2-Helix was solved by the fusion core remain unknown. Here we report the determi- multiple wavelength anomalous dispersion from a single sel- nation of the crystal structure of the fusion core of MHV A59 enomethionyl derivative crystal. Four selenium sites could be spike protein to 2.5 Å resolution by x-ray crystallography and located in one asymmetric unit from Patterson maps calculated discuss the implications of the structure for coronavirus mem- using the program CNS 1.0 (38). The experimental electron brane fusion. density map was easily interpretable in the helical regions. The model was improved further by cycles of manual building and EXPERIMENTAL PROCEDURES refinement using the programs O (33) and CNS (38). The struc- Expression, Purification, and Crystallization—The expression, puri- ture was subsequently refined to a final resolution of 2.5 Å with fication, and preliminary crystallographic studies of the MHV 2-Helix an R-value of 22.4% and free R-value of 29.1%. The final model protein have been described elsewhere.2 The PCR-directed gene was inserted into pET22b (Novagen) vector, and the selenomethionine MHV statistics are summarized in Table I. 2-Helix derivative was expressed in M9 medium containing 60 mg Description of the Structure—In the three-dimensional struc- literϪ1 selenomethionine in Escherichia coli strain BL21 (DE3). The ture of the MHV 2-Helix, the fusion core has a rod-shaped product was purified by nickel-nitrilotriacetic acid affinity chromatog- structure ϳ80 Å in length and a maximum diameter of 28 Å. raphy followed by gel filtration chromatography. The purified MHV The complex is a six-helix bundle comprising a trimer of MHV 2-Helix derivative was dialyzed against 10 mM Tris, pH 8.0, 10 mM NaCl 2-Helix. The center of this bundle consists of a parallel trimeric coiled coil of three HR1 helices that were packed by three 2 Y. Xu, Z. Bai, L. Qin, X. Li, G. F. Gao, and Z. Rao, submitted for antiparallel HR2 helices (Fig. 2, A and B). The N terminus of publication. HR1 and the C terminus of HR2 are located at the same end of 151 30516 Crystal Structure of MHV Spike Protein Fusion Core

TABLE I Data collection and model refinement statistics

Data set statistics

MHV 2-Helix nMHV 2-Helix Peak Edge Remote native Space group R3 R3 R3 R3 Unit cell parameters (Å) 48.4 48.4 200.0 48.47 48.47 200.1 48.3 48.3 199.4 51.6 51.6 198.2 Wavelength (Å) 0.9799 0.9801 0.9000 1.5418 Resolution limit (Å) 2.4 2.4 2.4 2.06 Observed reflections 49,717 50,167 49,352 83,487 Unique reflections 6,842 6,867 6,804 12,068 Completeness (%) 100(100)a 100(100) 100(100) 98.6(100) ͗I/␴(I)͘ 14.3(4.1) 14.6(4.5) 13.7(3.8) 28.7(4.3) b Rmerge (%) 9.4(34.0) 8.4(31.0) 9.3(36.1) 9.4(29.9)

Final refinement statistics MHV 2-Helix nMHV 2-Helix

c Rwork (%) 22.4 26.2 d Rfree (%) 29.1 29.8 Resolution range (Å)35–2.5 50–2.06 Total reflections used 5,833 11,689 No. of reflections in working set 5,501 11,092 No. of reflections in test set 332 597 r.m.s.d.e bonds(Å) 0.012 0.012 r.m.s.d. angles(°) 1.8 1.4 a Numbers in parentheses correspond to the highest resolution shell. b ϭ⌺⌺ Ϫ͗ ͘ ⌺ ⌺ ͗ ͘ ͗ ͘ Rmerge h lIih Ih / h I Ih , where Ih is the mean of the observations Iih of reflection h. c ϭ⌺࿣ Ϫ ࿣ ⌺ Rwork ( Fobs Fcalc )/ Fobs. d Rfree is the R-factor for a subset (5%) of reflections that was selected prior refinement calculations and not included in the refinement. e r.m.s.d., root mean square deviation from ideal geometry. the six-helix bundles, placing the fusion peptide and TM do- the HR1 consists of residues 968–1017, the HR2 consists of mains close together. A region of about 190 amino acids would residues 1216–1254, and the new fusion core was prepared as be located at the other end of the six-helix bundle between HR1 a single chain by linking the HR1 and HR2 domains via a and HR2. The linker and several terminal residues were dis- 22-amino acid linker (LVPRGSGGSGGSGGLEVLFQGP), ordered in both molecules. In one asymmetric unit, one mole- which is flexible and long enough to allow the HR1 and HR2 to cule includes residues 970–1023 in HR1 and 1216–1252 in form a natural interaction (Fig. 1A). The nMHV 2-Helix forms HR2, and the other molecule includes residues 969–1022 in crystals in space group R3 with lattice dimensions of a ϭ b ϭ HR1 and 1216–1254 in HR2. The two trimers are created by 51.6 Å, c ϭ 198.2 Å, ␣ ϭ ␤ ϭ 90°, ␥ ϭ 120°. The crystals contain the same 3-fold axis of the crystallographic unit cells and are two 2-Helix molecules/asymmetric unit and diffract x-rays to a both parallel with the 3-fold axis of the crystallographic unit resolution of at least 2.1 Å. cells, and there is about 30 degrees rotation in the orientation The crystal structure of nMHV 2-Helix was determined by parallel with the 3-fold axis between the two trimers. The root molecular replacement with the MHV 2-Helix structure as a mean square deviation of the two molecules in one asymmetric search model. Rotation and translation function searches were unit is 0.36 Å. There is only one weak hydrogen bond between performed in CNS (38). The model was improved further by the two parallel trimers, from OH (Tyr1233) to O (Glu1254) with cycles of manual building and refinement using the programs O a distance of 3.34 Å. (33) and CNS (38). The final R-value and free R-value for the Residues 969–1022 of HR1 fold into a 15-turn ␣-helix refinement are 26.2 and 29.8%, respectively. The final model stretching the entire length of the coiled coil. As in other statistics are listed in Table I. naturally occurring coiled coils of the fusion core, the residues The nMHV 2-Helix structure is largely similar to the MHV in the a and d positions of HR1 are predominantly hydrophobic 2-Helix structure, with the exception of several residues at the (Fig. 1B). A sequence alignment of MHV with other represent- N terminus of HR2 (Fig. 2C). The overall root mean square ative coronavirus spike proteins shows that the residues at deviation between the two structures is 0.48 Å, which is calcu- these two heptad repeat positions are highly conserved lated using the CCP4 program LSQKAB. The nMHV 2-Helix (Fig. 1B). structure also contains two molecules/asymmetric unit. One Residues 1232–1247 of HR2 form a 5-turn amphipathic ␣-he- molecule includes residues 968–1017 in HR1 and 1224–1254 in lix, whereas residues 1216–1231 and 1248–1254 form two HR2, whereas the other molecule includes residues 970–1017 extended chains at the N and C terminus of HR2, respectively. in HR1 and 1229–1254 in HR2. The linker is also disordered Each HR2 fits into the long grooves formed by the interface of and cannot be traced in the structure. The N terminus of HR2 the three HR1 helices, and no interaction is observed between cannot be seen in the structure because the C terminus of HR1, individual HR2 helices (Fig. 2, A and B). The C terminus of which is important for binding the N terminus of HR2, has HR2 ends with Glu1254, which is aligned with Gln970 of HR1; been discarded in the new construct. The linker is long and Gln970 is also the N terminus of the HR1 domain. The N flexible enough, so we can conclude that both structures surely terminus of HR2 starts with Asp1216, which is aligned with represent the natural structure of the complex of HR1 and HR2 Ile1023 of HR1 (Fig. 2C). because the choice of linker does not affect the real interaction Linker between HR1 and HR2 and nMHV 2-Helix Struc- between the two heptad repeat regions. We will focus our ture—To verify whether the linker (GGSGGSGG) between HR1 following structural analysis on MHV 2-Helix structure. and HR2 affects the natural structure of the MHV 2-Helix, we Interactions between HR1 and HR2—Three HR2 helices pack made a new construct (termed nMHV 2-Helix) that includes a obliquely against the outside of the HR1 coiled coil trimer in an shorter HR1 and longer linker. In the nMHV 2-Helix construct, antiparallel orientation. The HR2 helices interact with HR1 152 Crystal Structure of MHV Spike Protein Fusion Core 30517

FIG.1. Structure determination of the MHV spike protein fusion core trimer. A, schematic representation of coronavirus MHV A59 spike protein and the MHV 2-Helix and nMHV 2-Helix constructs. S1 and S2 are formed after proteolytic cleavage (vertical arrow) and noncovalently linked. The enveloped protein has an N-terminal signal sequence (SS) and a TM domain adjacent to the C terminus. S2 contains two HR regions (hatched bars), termed HR1 and HR2 as indicated. FP (hatched bars) is a putative fusion peptide followed by HR1 region. For the MHV 2-Helix, two HR regions were linked to a single polypeptide with an 8-residue linker (GGSGGSGG). For the nMHV 2-Helix, HR2 and a shortened HR1 were linked with a 22-amino acid linker (LVPRGSGGSGGSGGLEVLFQGP). B, sequence alignment of coronavirus spike protein HR1 and HR2 regions. Letters above the sequence indicate the predicted hydrophobic HR a and d residues, which are highly conserved. C, helical wheel representation of HR1 and HR2. Three HR1 helices and one HR2 helix are represented as helical wheel projections. The view is from the top of the structure. The three central HR1 helices form a central hydrophobic core with the interaction of residues in the a and d positions. The three HR2 helices pack against these hydrophobic surface grooves through interactions with residues in the a and d positions in HR2 and e and g positions in HR1. These residues, mediating the interactions between HR1 and HR2, are always hydrophobic and conserved (see B).

mainly through hydrophobic residues in three grooves on the comparison between MHV and HcoV-OC43 spike proteins surface of the central coiled coil trimer (see Fig. 4A). Sequence shows that no nonconservative changes exist at the e and g comparison between MHV and other coronavirus spike pro- positions of HR1, and only three such changes (L to I, L to F teins shows that residues contributing to the HR1/HR2 inter- and I to L) occur in HR2 at the a and d positions. In contrast, action (e and g positions in HR1, a and d positions in HR2) are 7 of 26 nonconservative changes occur at the outside f, b, and c highly conserved (Fig. 1B). positions in HR1, and 5 of 12 nonconservative changes occur at This pattern of sequence conservation can also be shown by positions other than a and d in the helical region (1232–1248) a helical wheel representation of three HR1 helices and one of HR2 (Fig. 1B). HR2 helix (Fig. 1C). In this diagram, residues in the a and d Comparison with Other Fusion Protein Structures—The positions of HR2 pack against residues in the e and g positions structure of the MHV fusion core was compared with the of HR1, mainly through hydrophobic interactions. Sequence known structures of other viral fusion proteins (Fig. 3A). Al- 153 30518 Crystal Structure of MHV Spike Protein Fusion Core

they are all extended to form a strand-like conformation. In these three parts, there is an interesting O-X-O motif where O represents hydrophobic residues, and X represents any residue but is generally hydrophilic. Part 1 contains the residues LSL, part 3 contains the residues VTL and LDL, and part 5 contains the residues INL. The two hydrophobic residues in these motifs pack against hydrophobic grooves on the surface of the HR1 core, either facing the central core or aligning with the hydrophobic groove. As a result, the O residues form hydrophobic interactions to stabilize the six-helix bundle, leaving the X residue directed into solvent. This pattern, which we think is a major reason why these three parts do not form ␣-helices, is also observed in the structure of SV5F (24), HRSV F (39), MMLV TM (40) and Ebola GP2 (41) (Fig. 4B). In these structures, partial regions in HR2 or C-peptide are extended and strand-like rather than ␣-helical. In the 3-4-3-4-3 pattern in HR2 of these glycoproteins, the presence of an O-X-O motif would result in hydrophobic residues interacting with the hydrophobic grooves on the surface of HR1 core, thus destroying the typical ␣-helix. In these three-dimensional structures, the distance between the two hydrophobic residues in the O-X-O motifs is about 5 Å, which is also the distance between the two adjacent helices. Thus, the two hydrophobic residues could exactly pack against the grooves of the central coiled coil formed by three HR1 helices. This compatibility of HR2 segments makes the fusion core more stable in solvent because FIG.2.Overall views of the fusion core structure and superposition of nMHV (new construct for MHV fusion core) and most of the hydrophobic residues in HR2 are packed against MHV fusion core. A, top view of the MHV fusion core structure the central core, leaving the hydrophilic residues exposed to showing the 3-fold axis of the trimer. B, side view of the MHV fusion solvent. This pattern also explains why not all residues in HR2 core structure showing the six-helix bundle. C, side view showing the of fusion cores from many other viral proteins form ␣-helices superposition of nMHV fusion core (colored in blue) and MHV fusion core (colored in yellow). The columns at both sides of the map represent and why HR1 structures of these fusion cores are highly con- two HR1 and HR2 regions of nMHV and MHV fusion cores. The number served, whereas HR2 regions always differ in their three-di- at the end of these columns represents the end residues in the mensional conformations (Fig. 3A). two structures. Second, a proteinase K-resistant fusion core of MHV A59 spike protein has been reported by Bosch et al. (28). After digestion by proteinase K, the fusion core comprising residues though there are significant differences in the sequences, sizes, and structural properties of these viral fusion proteins, the 958–1040 in HR1 and 1216–1254 in HR2 remains intact. In similarities in their overall structures suggest a common mech- this fusion core, the HR1 region is about 30 residues longer anism for membrane fusion. These fusion core proteins are all than the HR1 region of the fusion core we constructed. Al- trimeric coiled coils with the putative fusion peptides located at though the fusion core structure we determined here is only the N-terminal end of HR1 and the TM domains located at the part of the proteinase K-resistant fusion core, we propose that C-terminal end of HR2 (7). The three HR2 polypeptides that residues 958–967 and 1023–1040 in HR1 would also form form the outer layer of the central core vary in conformation coiled coils in the natural fusion core on the basis of their among these structures, but they always form ␣-helices and resistant capacity and other biochemical analyses (28). In the always pack antiparallel to the interior coiled coil. In this proteinase K-resistant fusion core of MHV spike protein, the pattern, which has been proposed to be a fusogenic conforma- central coiled coil HR1 region has about 80 amino acids, which tion, all of these fusion proteins would have their fusion pep- is considerably longer than HR1 segments in other fusion cores tides and TM anchors aligned at the same end of the coiled coil. such as HIV gp41 and SV5F1. This length is comparable with There are three major differences between the MHV and that of the fusion core in influenza HA, whose mechanisms for other viral fusion core structures and their relevant regions, the membrane fusion have been studied in extensive detail indicating unique features of fusion core structure in coronavi- (25). In addition, the HR1 region of the MHV spike protein is rus S proteins. First, the conformation of HR2 in the fusion core predicted to contain more than 100 amino acids by the learn- structure is different from those of all other fusion core HR2 coil VMF program (29). This long helical coiled coil might be regions (Fig. 3A). In the MHV fusion core structure, a major consistent with the long sequence of S protein, which is more 5-turn ␣-helix and a single-turn ␣-helix could be observed, and than 1200 residues, to form the central skeleton of spikes on the remaining parts are extended segments. We can divide the the surface of coronavirus. HR2 polypeptide into five parts (Fig. 4A, right), parts 1–5. Part Third, although the fusion peptide is not part of the fusion 4 is a typical 3-4-3-4-3 pattern and forms a 5-turn ␣-helix of core, it is also very important for investigating viral fusion which the residues at positions a and d pack against residues mechanism. The putative fusion peptide of the MHV A59 spike at the e and g positions of the HR1. Part 2 is also an ␣-helix that protein is located at the N-terminal end of the HR1 region, and exhibits the 3-4 spacing pattern, although it has only four the cleavage site of the spike protein is about 250 amino acids residues, FEKL. Of these four residues, the residues in the a away from the fusion peptide (28). The cleavage sites of other position (Phe1221) and d position (Leu1224) also pack against class I viral fusion proteins are all typically located adjacent to hydrophobic grooves formed on the surface of the HR1 core. the fusion peptides (13). In the latter pattern, the likely role of Parts 1, 3, and 5 should also be ␣-helical based on prediction by the six-helix bundle structure is to facilitate juxtaposition of the learn-coil VMF program (29). However, the structure shows the viral and cellular membranes by bringing the fusion pep- 154 Crystal Structure of MHV Spike Protein Fusion Core 30519

FIG.3.Viral fusion proteins and models for membrane fusion. A, comparison of MHV fusion core with other viral fusion protein structures. The proteins under comparison include SV5F, Ebola GP2, HIV gp41, MMLV Env-TM, and low pH-induced influenza virus HA, tBHA2. Top and side views are shown for the six fusion core structures. B, model for coronavirus-mediated membrane fusion. The first state is the native conformation of coronavirus spike protein on the surface of viral membrane. It has been reported that the spike protein is trimeric in this conformation and about 200 Å in length (6), but the exact structure of the full-length protein remains unknown. The second state is the prehairpin state of the S2 subunit. After several conformational changes, the fusion peptide inserts into the cellular membrane with the aid of other regions of S protein and possibly including the receptor. Although the internal fusion peptide is not exposed at the N-terminal of S2, it could insert into part of the target membrane by means of some hydrophobic residues. This insertion would be stable enough to drive the membrane motion with the conformational changes of HR1 region, which is adjacent to the fusion peptide. The third state is conformational change and juxtaposition of the target and viral membranes. With the help of other regions of S protein, the HR1 and HR2 regions move together and facilitate juxtaposition of the cellular and viral membrane. The last state is the postfusion conformation. The coiled coil will reorient with its long axis parallel to the membrane surface. The fused cellular and viral membranes make it possible for subsequent viral infections. tide, which inserts into the cellular membrane, close to the stable to both thermal denaturation and proteinase K digestion transmembrane segment, which is anchored in the viral mem- (28). The six-helix bundle has a melting temperature of about brane (7). In the case of the MHV spike protein, the question of 85 °C and could not be separated in general SDS-PAGE unless why the HR1 region and fusion peptide are so far away from boiled at 100 °C with a loading buffer containing a high con- the cleavage site remains unknown. Nevertheless, some vi- centration of SDS (28). These properties indicate that the com- ruses such as coronavirus (9) and Ebola virus (10) do not have plex is very stable and could not be dissociated by any biolog- cleavage sites in fusion proteins but still retain their fusion ically relevant interaction. This form of fusion core must be activity. This indicates that the location of the fusion peptides, present at the later stage of conformational changes for viral whether exposed at the N terminus of the membrane-anchored fusion, although it is not known whether the complex main- polypeptide or not, is not an essential requirement for the viral tains this conformation throughout the entire process. fusion. We will give a possible mechanism in the further Second, virus-cell entry inhibition and cell-cell fusion inhibi- discussion. tion experiments (28) also provide strong evidence that the Evidence for the Conformational Change—Structural studies fusion core is formed after one or more conformational changes. of the influenza virus HA and HIV gp41 have established a HR2 of the MHV 2-Helix could block viral entry and cell-cell paradigm for understanding the mechanisms of viral and cel- fusion in a concentration-dependent manner and appears to be lular membrane fusion (7). For coronaviruses, direct evidence a potent inhibitor (28). In HIV gp41, the C-peptide and its for the conformational change in spike protein is lacking, al- derivatives have been shown to act as dominant-negative in- though the crystal structure of the MHV fusion core bears hibitors by binding to the endogenous N-peptide coiled coil similarity to these fusion-active state molecules. The structure trimer within viral gp41 (19, 42, 43). A reasonable interpreta- of the MHV 2-Helix could correspond to the fusion core of MHV tion of the data for the MHV fusion core is that HR2 functions spike protein in either the fusogenic or the native form of the in a dominant-negative manner similar to the C-peptide in HIV envelope glycoprotein, or both. Several considerations provide gp41 by binding to the transiently exposed coiled coil in the good evidence that the fusion core in the crystal structure prehairpin intermediate and thus preventing the conforma- presented here is the final, stable form of the protein, which is tional changes required for viral fusion. a fusion-active state following one or more conformational Third, mutations in the MHV spike protein that abolish changes. viral-cell fusion activity often map to the HR1 or HR2 residues, First, the fusion core of MHV spike protein is exceedingly which are expected to stabilize the fusion core structure re- 155 30520 Crystal Structure of MHV Spike Protein Fusion Core

FIG.4.O-X-O motifs in HR2 regions of MHV and the comparison with those of other fusion proteins. A. Left and center, surface map showing the hydrophobic grooves on the surface of three central HR1 helices. Three HR2 helices pack against the hydrophobic groove in an antiparallel manner. The helical regions in HR2 extended regions could be observed clearly. The helical region of HR2 just packs against the deep groove, and the extended region packs against the shallow groove. Right, detailed structure of O-X-O motifs in MHV HR2 region. One HR2 helix is divided into five parts based on its secondary structure. The helical regions (parts 2 and 4) HR2 are colored in red, and extended regions (parts 1, 3, and 5) are colored in blue. The essential residues of the three extended regions and O-X-O motifs in these regions are shown; residues colored in green represent the hydrophobic residues in O-X-O motifs. The three panels on the left show the enlarged images of parts 1, 3, and 5. The hydrophobic residues in these motifs are all packed against the hydrophobic grooves on the surface of three HR1 helices. B, detailed structures of O-X-O motifs in other fusion proteins including SV5F, HRSV F, MMLV Env-TM, and Ebola GP2. They all contain similar motifs in HR2 regions. The regions in which O-X-O motifs are located form extended regions but not ␣-helices, in a way similar to the MHV 2-Helix. ported here. These studies show that mutations in some essen- replacement of the same residues with other hydrophobic tial positions in HR regions abolish infectivity and membrane amino acids (F977L, L981I) does not reduce fusion activity fusion (44, 45). The L981K and F977K mutations are particu- (44). L1224A/L1231A, L1224A/I1238A, L1224A/L1245A, and larly noteworthy because cells expressing mutant spike pro- I1231A/L1245A mutations in HR2 also abolish fusion activity teins with one of these mutations are almost completely defec- greatly (45). In these double substitution mutants, the Leu and tive in membrane fusion, although the surface expression level Ile residues are both in d positions in HR2 and are also very of spike proteins remains the same as for the wild type (44). important for the formation of the fusion core (Fig. 1C). These Residue Leu981 is in the a position and Phe977 in the d position double substitution mutants could not maintain a stable coiled of the HR1 peptide, and thus both are essential for the forma- coil structure even though Leu or Ile was changed for Ala, a tion of the central hydrophobic coiled coil (Fig. 1C). The L981K hydrophobic residue. The locations of these particular muta- and F977K mutations in HR1 region substitute hydrophobic tions indicate that the interactions between HR1 and HR2 are residues with hydrophilic residues, destroying the hydrophobic critical for membrane fusion. interaction and the formation of the six-helix bundles and Lastly, the structural similarities between the MHV 2-Helix subsequently abolishing the membrane fusion. In contrast, complex, the fusion core of low pH-induced conformation of 156 Crystal Structure of MHV Spike Protein Fusion Core 30521 influenza HA2 (14), and the structure of HIV gp41 (19), each of and a and d positions of HR2, are all highly conserved. We can which has been proposed to have fusion-active conformations, conclude that coronavirus spike proteins share a similar bind- indicate that the MHV 2-Helix structure studied here repre- ing region of the HR1⅐HR2 complex and three-dimensional sents the core of the fusogenic conformation of spike protein fusion core structure. Analogous to the HIV C-peptides, the after conformational change (Fig. 3A). In all three structures, HR2 region of coronavirus spike proteins most likely functions the putative hydrophobic fusion peptides are located close to in a dominant-negative manner by binding to the transiently the N-terminal end of the HR1 region, which forms a central exposed hydrophobic grooves in the prehairpin intermediate coiled coil. Three strands of HR2 which pack against the coiled and consequently blocking the formation of the fusion-active coil trimer in an antiparallel manner stabilize this hydrophobic hairpin structures (43). These strategies have been used suc- coiled coil. These common features suggest that the MHV spike cessfully in fusion inhibitors design for HIV (7, 42, 49–51). A protein also possesses a conformational change mechanism similar approach may be applied to identify inhibitors of coro- similar to influenza HA and HIV gp41 (7). navirus infection. HR1 and HR2 regions and their derivatives Implications for Models of Membrane Fusion Mechanisms— are all potential inhibitors. Cavities and grooves on the surface Although we have no structures of full-length MHV spike pro- of the central coiled coil are strong potential binding sites for tein either in the prefusion or postfusion state, we can propose small molecule inhibitors. a model for MHV membrane fusion mechanism based on the In conclusion, the crystal structure of MHV fusion core fusion core structure studied here and previous analysis of shows the first fusion core structure of any coronavirus. Al- spike proteins. Current models for the class I viral fusion though the structure shares common features with those of mechanisms suggest that the exposed fusion peptide located at other viral fusion proteins, it has unique characteristics that the N terminus of the membrane-anchored subunit may be distinguish it from other fusion core structures. Sequence important for the juxtaposition of two membranes prior to alignment of HR regions among coronaviruses indicates a sim- fusion (7). For coronaviruses, the S2 fragment contains a pu- ilar structure among coronavirus spike proteins and suggests a tative internal fusion peptide that is not exposed at the N common mechanism for viral fusion. This structure will also terminus (44). This pattern of internal fusion peptide in the open an avenue toward the structure-based fusion inhibitor MHV spike protein is reminiscent of fusion loops in class II design of peptides, or peptide analogs, e.g. small molecules, viral fusion proteins, which are internally located in the fusion targeted against emerging infectious diseases, such as SARS. protein (46, 47). 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158 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 47, Issue of November 19, pp. 49414–49419, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. Crystal Structure of Severe Acute Respiratory Syndrome Coronavirus Spike Protein Fusion Core*

Received for publication, August 2, 2004, and in revised form, August 25, 2004 Published, JBC Papers in Press, September 1, 2004, DOI 10.1074/jbc.M408782200

Yanhui Xu‡, Zhiyong Lou‡, Yiwei Liu‡, Hai Pang‡, Po Tien§, George F. Gao§¶, and Zihe Rao‡ʈ From the ‡Laboratory of Structural Biology, Tsinghua University, Beijing 100084 and National Laboratory of Bio-Macromolecules, Institute of Biophysics, Beijing 100101, China, ¶Nuffield Dept of Clinical Medicine, John Radcliffe Hospital, Oxford University, Oxford OX3 9DU, United Kingdom, and §Institute of Microbiology, Chinese Academy of Sciences, Beijing 100080, China

Severe acute respiratory syndrome coronavirus is a characterized coronaviruses isolated from either humans or newly emergent virus responsible for a recent outbreak animals, and it has therefore been assigned to a new, distinct of an atypical pneumonia. The coronavirus spike pro- group within the genus (4, 5, 9, 10). tein, an enveloped glycoprotein essential for viral entry, Coronaviruses are enveloped, positive-strand RNA viruses belongs to the class I fusion proteins and is character- with the largest genomes of any RNA virus and are characterized by the presence of two heptad repeat (HR) regions, ized by 3–4 envelope proteins embedded on the surface (11, 12). HR1 and HR2. These two regions are understood to form Both the receptor binding and the subsequent membrane fu- a fusion-active conformation similar to those of other sion process of coronaviruses are mediated by the spike mem- typical viral fusion proteins. This hairpin structure brane glycoprotein (S protein) (13). Recent studies show that likely juxtaposes the viral and cellular membranes, thus murine coronavirus (mouse hepatitis virus (MHV)) uses a facilitating membrane fusion and subsequent viral en- spike-mediated membrane fusion mechanism similar to that of try. The fusion core protein of severe acute respiratory so-called class I virus fusion proteins (14, 15). syndrome coronavirus spike protein was crystallized, and the structure was determined at 2.8 Å of resolution. Class I viral fusion proteins, including the hemagglutinin pro- The fusion core is a six-helix bundle with three HR2 tein of influenza virus, gp160 of human immunodeficiency virus helices packed against the hydrophobic grooves on the (HIV-1), glycoprotein of Ebola virus, and fusion protein (F pro- surface of central coiled coil formed by three parallel tein) of paramyxovirus (16, 17), are all type I transmembrane HR1 helices in an oblique antiparallel manner. This glycoproteins that are displayed on the surface of viral mem- structure shares significant similarity with the fusion brane as oligomers. Most of these glycoproteins are synthesized core structure of mouse hepatitis virus spike protein as single chain precursors containing a protease cleavage site, and other viral fusion proteins, suggesting a conserved and these precursors are cleaved into two noncovalently associ- mechanism of membrane fusion. Drug discovery strate- ated subunits: S1 and S2 in coronavirus, hemagglutinin 1 and 2 gies aimed at inhibiting viral entry by blocking hairpin in influenza virus, gp120 ϩ gp41 in HIV/simian immunodefi- formation, which have been successfully used in human ciency virus, glycoprotein-1 and -2 in Ebola virus, and F1 and -2 immunodeficiency virus 1 inhibitor development, may in paramyxovirus. Class I viral fusion proteins also contain a be applicable to the inhibition of severe acute respira- fusion peptide and at least two heptad repeat regions, termed tory syndrome coronavirus on the basis of structural HR1 and HR2. After binding to the receptor or induced by low information provided here. The relatively deep grooves pH, the fusion proteins undergo a series of conformational on the surface of the central coiled coil will be a good changes to mediate membrane fusion. The first step involves target site for the design of viral fusion inhibitors. exposure of the fusion peptide, a hydrophobic region in the membrane-anchored subunit, which then inserts into the cellular lipid bilayer. Subsequently, HR1 and HR2 peptides form a trimer-of- Severe acute respiratory syndrome (SARS)1 is a new life- hairpins-like structure via a transient pre-hairpin intermediate threatening form of atypical pneumonia (1, 2) caused by a novel to facilitate juxtaposition of the viral and cellular membranes coronavirus, SARS-CoV (3–10). Phylogenetic analysis of SARS- followed by virus-cell membrane fusion and viral entry. Biochem- CoV shows that it is not closely related to any of the previously ical and structural analysis of these fusion cores from class I viral fusion proteins shows that these complexes of two heptad repeat * This work was supported by Projects 973 and 863 of the Ministry of regions form a stable six-helix bundle, which is designated as a Science and Technology of China (Grants 200BA711A12, G199075600, fusion core in which three HR1 helices form a central coiled coil GZ236(202/9), and 2003CB514103. The costs of publication of this ar- surrounded by three HR2 helices in an oblique, antiparallel man- ticle were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 ner (18–26). U.S.C. Section 1734 solely to indicate this fact. The coronavirus spike protein shares many features with other The atomic coordinates and structure factors (code 1WNC ) have been class I viral fusion proteins. It is a type I membrane protein that deposited in the Protein Data Bank, Research Collaboratory for Struc- associates into trimers on the surface of coronavirus membrane tural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/). (27). The distal subunit (S1) of the spike protein contains the ʈ To whom correspondence and reprint requests should be addressed. receptor binding domain (28, 29), and the membrane-anchored Tel.: 86-10-62771493; Fax: 86-10-62773145; E-mail: raozh@xtal. subunit (S2) contains a putative internal fusion peptide and two tsinghua.edu.cn. heptad repeat regions (HR1 and HR2) (14, 15). 1 The abbreviations used are: SARS, severe acute respiratory syn- Agents that prevent conformational changes in the fusion drome; HIV, human immunodeficiency virus; HR, heptad repeat; SARS-CoV, severe acute respiratory syndrome coronavirus; MHV, protein by stabilizing the intermediate state are expected to mouse hepatitis virus. prevent fusion activation and, thus, inhibit viral entry. In the

49414 This paper is available on line at http://www.jbc.org 159 Crystal Structure of SARS Spike Protein Fusion Core 49415

FIG.1. Structure determination of the MHV spike protein fusion core trimer. A, schematic diagram of SARS-CoV spike protein indicating the location of structurally significant domains. S1 and S2 are formed after proteolytic cleavage (vertical arrow) and noncovalently linked. The enveloped protein has an N-terminal signal sequence (SS) and a transmembrane domain (TM) adjacent to the C terminus. S2 contains two HR (heptad repeat) regions (hatched bars), HR1 and HR2 as indicated. The HR1 (898–1005) and HR2 (1145–1184) used in this study were derived from the LearnCoil-VMF prediction program (37). The 2-Helix protein construct consists of HR2 and part of HR1, which is the major region binding HR2, connected by a 22-amino acid linker (LVPRGSGGSGGSGGLEVLFQGP) as indicated. B, sequence alignment of coronavirus spike protein HR1 and HR2 regions. Letters above the sequence indicate the predicted hydrophobic residues at the a and d positions in two heptad repeat regions, which are highly conserved. FP, feline panleukopenia; IBV, infectious bronchitis virus; FIPV, feline infectious peritonitis virus. case of HIV-1 gp41, peptides derived from C peptides can core, suggesting that a similar approach might be used in iden- effectively inhibit infection in a dominant-negative manner by tifying inhibitors of SARS-CoV infection effectively. This struc- binding to the transiently exposed hydrophobic grooves of cen- ture also provides important detailed structural information and tral coiled coil in the intermediate state and consequently target site for structure based drug design. blocking the formation of the fusion-active six-helix bundle structure (30). EXPERIMENTAL PROCEDURES We have recently determined the three-dimensional struc- Construction, Expression, and Purification—The SARS spike gene TM ture of murine coronavirus MHV spike protein fusion core and was cloned from SARS coronavirus GZ02 (GenBank accession number AY390556). Two peptides (HR1 and HR2 regions of SARS-CoV proposed a model for coronavirus-mediated membrane fusion spike protein) interact, and their binding regions were characterized by in which the S protein undergoes a series of conformational recent biochemical studies and sequence alignment with MHV fusion changes similar to those of influenza virus and HIV-1 (14). core complex.2 The HR1 and HR2 regions of SARS-CoV spike protein Recent studies show that HR1 and HR2 of SARS-CoV spike consist of residues 900–948 and residues 1145–1184, respectively, cor- protein form a stable six-helix bundle, and synthesized pep- responding to the HR1 and HR2 regions in new MHV structure (14). tides corresponding to the HR2 region have inhibitory activity The fusion core of SARS-CoV spike protein was prepared as a single 2 chain (termed SARS 2-Helix) by linking the HR1 and HR2 domains via for viral fusion (31–36). These studies also propose the binding a 22-amino acid linker (LVPRGSGGSGGSGGLEVLFQGP), which is regions between HR1 and HR2 and identify the inhibition flexible and long enough to facilitate a natural interaction between the efficiency of peptides derived from the HR2 region. However, HR1 and HR2 peptides and allows for easy expression and purification the detailed three-dimensional structure of the HR1/HR2 com- of the fusion core complex (Fig. 1A). The PCR-directed gene was in- plex remains unknown. serted into pET22b (Novagen) vector, and the SARS 2-Helix protein was To verify that the SARS-CoV spike protein indeed forms a expressed in LB culture medium in Escherichia coli strain BL21(DE3). The product was purified by nickel nitrilotriacetic acid affinity chroma- trimer-of-hairpins structure and to provide a structural basis for tography and was further purified by gel filtration chromatography the design of viral fusion inhibitors, we characterized the binding (Superdex 75™, Amersham Biosciences). of the two HR regions of the SARS-CoV spike protein and solved Crystallization and Structure Determination—The purified protein the crystal structure of this fusion core complex to 2.8 Å of was dialyzed against 10 mM Tris-HCl, pH 8.0, 10 mM NaCl and then Ϫ1 resolution. The structure shows a similar conformation to other concentrated to 15 mg ml . Crystals with good diffracting quality could class I viral fusion proteins, especially MHV spike protein fusion be obtained after 2 weeks by using the hanging drop method by equilibrating a 2-␮l drop (protein solution mixed 1:1 with reservoir solution) against a reservoir containing 0.1 M citric acid, pH 2.5, 10–15% poly- 2 Y. Xu, J. Zhu, Y. Liu, Z. Lou, F. Yuan, Y. Liu, D. K. Cole, L. Ni, N. ethylene glycol 4000, 0.02 M spermidine tetra-HCl. The SARS 2-Helix Su, L. Qin, X. Li, Z. Bai, J. I. Bell, H. Pang, P. Tien, Z. Rao, and G. F. crystal was mounted on nylon loops and flash-frozen in cold nitrogen- Gao, submitted for publication. gas stream at 100 K using an Oxford Cryosystems coldstream with 0.1 160 49416 Crystal Structure of SARS Spike Protein Fusion Core

TABLE I Data collection and final refinement statistics Numbers in parentheses correspond to the highest resolution shell. ϭ⌺⌺ ͉ Ϫ͗ ͉͘ ⌺ ⌺ ͗ ͘ ͗ ͘ Rmerge h I Iih Ih / h I Ih , where Ih is the mean of the ϭ⌺ ʈ ͉ Ϫ ͉ ʈ ⌺͉ ͉ observations Iih of reflection h. Rwork ( Fobs Fcalc )/ Fobs ; Rfree is the R factor for a subset (5%) of reflections that was selected before refinement calculations and not included in the refinement. r.m.s.d., root mean square deviation from ideal geometry. Data collection statistics Space group C2 Unit cell parameters a ϭ 121.2 Å, b ϭ 66.3 Å, c ϭ 70.0 Å, ␤ ϭ 107.4° Wavelength (Å) 1.5418 Resolution limit (Å) 2.8 Observed reflections 27,312 Unique reflections 11,974 Completeness (%) 91.4 (80.8) ͓I/␴(I)͔ 5.7 (1.2)

Rmerge (%) 13.9 (51.1) Final refinement statistics

Rwork (%) 23.3 Rfree (%) 27.3 Resolution range (Å) 50–2.8 Total reflections used 10,718 Number of reflections in 10,166 working set Number of reflections in 552 test set Average B (Å2) 42.7 r.m.s.d. bonds (Å) 0.013 r.m.s.d. angles(°) 1.8

M citric acid, pH 2.5, 25% polyethylene glycol 4000 as the cryoprotectant. The crystals have unit-cell parameters a ϭ 121.2 Å, b ϭ 66.3 Å, c ϭ 70.0 Å, ␣ ϭ ␥ ϭ 90°, ␤ ϭ 107.4° and belong to space group C2. The crystals contain 6 SARS 2-Helix molecules in one asymmetric unit, and the diffraction pattern extends to 2.8 Å of resolution. Data collection was performed in-house on a Rigaku RU2000 rotating copper-anode x-ray generator operated at 48 kV and 98 mA (Cu K␣; ␭ ϭ 1.5418 Å) with a MAR 345 image-plate detector. Data were indexed, integrated, and scaled using DENZO and SCALEPACK programs (38). The structure of SARS 2-Helix was determined by molecular replacement with the MHV 2-Helix structure (PDB code 1WDF) as a search model. Rotation and translation function searches were performed in the program CNS (39). The model was improved further by cycles of manual building and refinement using the programs O (40) and CNS (39). The quality of coordinates was examined by PROCHECK (41). The figures were generated with the programs GRASP (42), SPDBView (43), and MOLSCRIPT (44). FIG.2.Overall views of the fusion core structure. A, top view of the SARS-CoV spike protein fusion core structure showing the 3-fold RESULTS AND DISCUSSION axis of the trimer. B, side view of the SARS-CoV spike protein fusion core structure showing the six-helix bundle. Structure Determination—The crystal structure of SARS 2-Helix was solved by molecular replacement using the program CNS (39) with the MHV 2-Helix structure (PDB code Here, we chose A, B, and C molecules as the SARS spike 1WDF) employed as a search model. Six molecules (two trimers protein fusion core for the following structure description. In of SARS 2-Helix) per asymmetric unit were located from cross- the SARS 2-Helix three-dimensional structure, the fusion core rotation and translation function searches. The model was has a rod-shaped structure with a length of ϳ70 Å and a improved further by cycles of manual building and refinement diameter of ϳ28 Å. Similar to MHV 2-Helix and other class I using the programs O (40) and CNS (39). The structure was viral fusion proteins, the SARS spike protein fusion core is a subsequently refined to a final resolution of 2.8 Å with an R six-helix bundle comprising a trimer of 2-Helix molecules. The value of 23.3% and Rfree value of 27.3%. No residue was in center of the fusion core consists of a parallel trimeric coiled coil disallowed regions of the Ramachandran plot. The statistics for of three HR1 helices surrounded by three HR2 helices in an the data collection, structure determination, and refinement oblique, antiparallel manner (Fig. 2, A and B). Residues 902– are summarized in Table I. 947 in HR1 fold into a 12-turn ␣-helix stretching the entire Description of the Structure—One asymmetric unit contains length of the fusion core. As in MHV 2-Helix and other class I six SARS 2-Helix molecules, including residues 902–947 in viral fusion proteins, the residues in positions a and d of HR1 HR1 and 1153–1175 in HR2 (A molecule), residues 902–947 in are predominantly hydrophobic (Fig. 1B). Residues 1160–1177 HR1 and 1150–1184 in HR2 (B molecule), residues 902–947 in in HR2 form a 5-turn ␣-helix, whereas residues 1150–1159 at HR1 and 1153–1184 in HR2 (C molecule), residues 901–947 in the N terminus and residues 1178–1184 at the C terminus of HR1 and 1152–1181 in HR2 (D molecule), residues 901–948 in HR2 form two extended conformations, respectively. Three HR1 and 1153–1178 in HR2 (E molecule), and residues 901–947 HR2 helices pack against the grooves formed by the interface of in HR1 and 1154–1181 in HR2 (F molecule), respectively. The the central three HR1 helices, and no interaction was observed linker and several terminal residues could not be traced in the between individual HR2 regions. The N terminus of HR2 starts electron density map due to their disordered nature. with Ile1150, which is aligned with Gln947 of HR1. The C ter- 161 Crystal Structure of SARS Spike Protein Fusion Core 49417

FIG.3. Detailed structure of the SARS-CoV spike protein fusion core and OXO motifs in HR2 regions. A, surface map showing the hydrophobic grooves on the surface of the central coiled coil (right side). Three HR2 helices pack against the hydrophobic grooves in an oblique antiparallel manner (left side). The helical regions and extended regions in HR2 helices could be observed clearly, and the boundaries of these regions are marked. B,OXO motifs in HR2 regions of SARS-CoV spike protein fusion core structure. The enlarged images show two regions containing OXO motifs. The hydrophobic residues in these motifs all pack against the hydrophobic grooves on the surface of three HR1 helices.

minus of HR2 ends with Leu1184, which is aligned with Gln902 ical regions of SARS-CoV HR2 segment (residues 1161–1184) of HR1 (see Fig. 4). pack exactly against the relatively deep grooves of the central Interactions between HR1 and HR2—Three HR2 helices in- coiled coil and the extended regions (residues 1150–1160) pack teract with HR1 helices mainly through hydrophobic interac- against the relatively shallow grooves. Based on our previous tion between hydrophobic residues in HR2 regions and the biochemical analysis and the crystal structure, we propose that grooves on the surface of the central coiled coil. Similar to those the deep groove is an important target site for the design of in MHV 2-Helix, HR2 helices in SARS 2-Helix also contain viral fusion inhibitors (16, 30, 34, 45–48). OXO motifs, in which O represents a hydrophobic residue, and Conformational Change and Membrane Fusion Mecha- X represents any residue but is generally hydrophobic. 1153IN- nisms—Our previous structural study of the MHV spike pro- ASVVNI1160 and 1178LIDL1181 in HR2 regions are both com- tein fusion core led us to propose a model for coronavirus- posed of OXO motifs; the side chains of the O residues inset into mediated membrane fusion mechanism (14). The remarkable or align with the hydrophobic grooves of the central coiled coil, similarity between SARS-CoV and MHV spike protein fusion whereas the side chains of the X residues are directed into core structures as well as similar HR2 peptide inhibition phe- solvent (Fig. 3B). As described in our previous paper (14), the nomena and remarkable stability to both thermal denaturation OXO motifs are responsible for the partially extended confor- and proteinase K digestion (31–36) suggest a conserved mech- mation of HR2, and this pattern also makes the fusion core anism of membrane fusion mediated by the spike protein. Sim- stable in solvent, as most of the hydrophobic residues in HR2 ilar to the MHV spike protein and HIV gp41, the SARS-CoV helices are packed against the central coiled coil, leaving the spike protein likely undergoes a series of conformational hydrophilic residues exposed to solvent. changes to become fusion-active. The fusion loop but not fusion Comparison with MHV 2-Helix Structure—Among coronavi- peptide, which will insert into the cellular membrane, and rus spike proteins, only the structure of the MHV spike protein distinct conformational states proposed for the MHV spike fusion core has been determined (14). In general, the fusion protein fusion core, including the native state, the pre-hairpin core from SARS-CoV and MHV adopt a similar fold, consistent intermediate, and fusion-active hairpin state, may also apply to with their high sequence identity and similarity between the SARS-CoV spike protein. The existence of the pre-hairpin in- two proteins. The structure of SARS spike protein fusion core termediate conformation of the SARS-CoV spike protein is was compared with that of MHV spike protein (Fig. 4). These strongly supported by the viral inhibition assay, in which the structures can be superimposed with a root mean square dif- peptides corresponding to the HR2 regions can inhibit viral ference of 0.91 Å for all C␣ atoms. Alignments of the peptides fusion in a dominant-negative manner (32, 34). A reasonable derived from HR1 and HR2 regions of SARS-CoV spike protein interpretation of these phenomena is that the HR2 peptide and those of other coronaviruses reveal high sequence identity functions by binding to the transiently exposed hydrophobic and similarity, suggesting that structures of spike protein fu- groove on the surface of central coiled coil, thus blocking the sion cores from other coronavirus might share significant sim- conformational transition to the fusion active form and subse- ilarity with those of MHV and SARS-CoV (Fig. 1B). quent membrane fusion and viral entry. Although the main chains of the MHV 2-Helix and SARS- Binding Regions of SARS-CoV Spike Protein Fusion Core— CoV 2-Helix structures can be superposed closely, the two Recent studies on the fusion-active complex of SARS-CoV have complexes have significant differences in their hydrophobic confirmed that HR1 and HR2 associate into an antiparallel grooves on the surface of the central coiled coil (Fig. 4B). As six-helix bundle, with structural features of other typical class discussed in our previous paper detailing our SARS-CoV fusion I viral fusion proteins by means of CD, native PAGE, proteo- core model, the central coiled coil had relatively deep grooves lysis protection analysis, and size-exclusion chromatography. and relatively shallow grooves.2 The deep grooves, consisting of In their biochemical analysis, Ingallinella et al. (31) mapped three hydrophobic deep pockets or cavities, were clearly deeper the specific boundaries of the key region of interaction between than the corresponding grooves on the surface of MHV 2-Helix HR1 and HR2 peptides as residues 914 and 949 in HR1 region control coiled coil. From the structure presented here, the hel- and residues 1148 and 1185 in HR2 region (31). The exact 162 49418 Crystal Structure of SARS Spike Protein Fusion Core

FIG.4. Comparison between fusion core structure of SARS-CoV and MHV. A, side view showing a structural comparison between SARS-CoV spike protein fusion core (colored in green) and MHV spike protein fusion core (colored in purple). The columns at both sides of the map represent two HR1 and HR2 regions of MHV and SARS fusion cores. The numbers at the end of these columns represent the specific boundaries of the HR1-HR2 interaction region in the two structures. B, surface map showing the comparison between hydrophobic grooves on the surface of three central HR1 regions of MHV (left side) and SARS-CoV (right side). The figure on the right side shows the deep and relatively shallow grooves on the surface of central HR1 coiled coil of SARS-CoV. Three numbers, 1–3, in circles represent three deep cavities, composing the deep grooves. The residues represent the boundaries of the grooves and cavities. TABLE II

Amino acid sequences and EC50 values of inhibitory peptides

Peptide EC50 Sequence

␮M NP-1 (892–931)a Marginal GVTQNVLYENQKQIANQFNKAISQIQESLTTTSTALGKLQ CP-1 (1153–1189)a 19 GINASVVNTQKEIDRLNEVAKNLNESLIDLQELGKYE HR1 (889–926)b 3.68 NGIGVTQNVLYENQKQIANQFNKAISQIQESLTTTSTA HR2 (1161–1187)b 5.22 IQKEIDRLNEVAKNLNESLIDLQELGK HR2-1 (1126–1189)c 43 Ϯ 6.4 ELDSPKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE HR2-2 (1130–1189)c 24 Ϯ 2.8 PKHELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE HR2-8 (1126–1193)c 17 Ϯ 3.0 ELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYEQYIK HR2-9 (1126–1184)c 34 Ϯ 4.0 ELDSFKEELDKYFKNHTSPDVDLGDISGINASVVNIQKEIDRLNEVAKNLNESLIDLQEL HR2-6 (1150–1189)c Ͼ50 DISGINASVVNIQKEIDRLNEVAKNLNESLIDLQELGKYE a Data are from the paper by Liu et al. (35). b Data are from the paper by Yuan et al. (33). c Data are from the paper by Bosch et al. (32). boundaries, residues 902 and 947 in HR1 region and residues identified, they may serve as useful drugs against SARS-CoV 1150 and 1184 in HR2 region, can be observed from the crystal infection. In the case of HIV-1, several strategies to block structure of SARS-CoV spike protein fusion core with a slight hairpin formation have been successfully developed to identify difference from previous results. The N terminus of the HR1 viral entry inhibitors that bind to the hydrophobic pocket and region (Gln902) aligns with the C terminus of the HR2 region grooves on the surface of the central coiled coil consisting of (Leu1184), and the C terminus of the HR1 region (Gln947) aligns HIV-1 gp41 N peptides. These useful viral entry inhibitors with the N terminus of the HR2 region (Ile1150). Although the include D peptides, 5-Helix, and synthetic peptides derived residue numbers of the HR1 and HR2 regions are different (46 from N or C peptides (45–47). Successful viral entry inhibitors in HR1 and 35 in HR2), the two peptides are equivalent in have also been identified for other viruses, such as T20 for length in the three-dimensional structure since HR1 forms a HIV-1 (49, 50) and GP610 for Ebola virus (51). These strategies typical ␣-helix, whereas HR2 forms a partial helical conforma- could also be used for the design of SARS fusion inhibitors. The tion (Fig. 3A). This pattern of HR2 helices is also strongly well defined hydrophobic grooves on the surface of the central supported by proteolysis protection experiments (31). The real coiled coil of the SARS-CoV spike protein fusion core identified boundaries of the fusion core might extend beyond those found here may be a significant target for drug design. in the structure studied here, whereas the major binding re- Several peptides derived from the HR1 and HR2 regions of gions and the interactions between HR1 and HR2 peptides can SARS-CoV spike proteins have been found to have inhibitory be identified clearly from the SARS-CoV spike protein fusion activity in recent studies (32, 33, 35) (Table II). Analogous to core structure. the HIV-1 C peptides and MHV HR2 peptides, the HR2 pep- Inhibitory Molecules for SARS-CoV Infection—If small, bio- tides of SARS-CoV spike protein likely function in a dominant- available molecules that prevent hairpin formation can be negative manner by binding to the transiently exposed hydro- 163 Crystal Structure of SARS Spike Protein Fusion Core 49419 phobic grooves in the pre-hairpin intermediate, thus, blocking A., Lowe, L., Frace, M., DeRisi, J. L., Chen, Q., Wang, D., Erdman, D. D., Peret, T. C., Burns, C., Ksiazek, T. G., Rollin, P. E., Sanchez, A., Liffick, S., viral entry. The efficacy of HR2 peptides of SARS-CoV spike Holloway, B., Limor, J., McCaustland, K., Olsen-Rasmussen, M., Fouchier, protein is, however, significantly lower than corresponding R., Gunther, S., Osterhaus, A. D., Drosten, C., Pallansch, M. A., Anderson, HR2 peptides of murine coronavirus mouse hepatitis virus in L. J., and Bellini, W. J. (2003) Science 300, 1394–1399 11. Siddell, S., Wege, H., and Ter Meulen, V. (1983) J. Gen. Virol. 64, 761–776 inhibiting MHV infection (32). Synthetic peptides with the 12. Cavanagh, D. (1983) J. Gen. Virol. 64, 2577–2583 highest inhibitory efficacy encompass residues 1161–1187, de- 13. Gallagher, T. M., and Buchmeier, M. J. (2001) Virology 279, 371–374 14. Xu, Y., Liu, Y., Lou, Z., Qin, L., Li, X., Bai, Z., Pang, H., Tien, P., Gao, G. F., rived from the HR2 region (33). This peptide is just the corre- and Rao, Z. (2004) J. Biol. Chem. 279, 30514–30522 sponding region that binds to the relatively deep grooves on the 15. Bosch, B. J., van der Zee, R., de Haan, C. A., and Rottier, P. J. (2003) J. Virol. surface of central coiled coil. It is not clear why HR2 peptides of 77, 8801–8811 16. Eckert, D. M., and Kim, P. S. (2001) Annu. Rev. Biochem. 70, 777–810 SARS-CoV have lower inhibitory efficacy. However, the struc- 17. Hernandez, L. D., Hoffman, L. R., Wolfsberg, T. G., and White, J. M. (1996) tural information provided here will be useful for the design of Annu. Rev. Cell Dev. Biol. 12, 627–661 18. Bullough, P. A., Hughson, F. M., Skehel, J. J., and Wiley, D. C. (1994) Nature antiviral compounds such as D peptides, 5-Helix, and some 371, 37–43 peptides (or mutants) derived from HR1 or HR2 peptides based 19. Lu, M., Blacklow, S. C., and Kim, P. S. (1995) Nat. Struct. Biol. 2, 1075–1082 on the crystal structure of SARS-CoV spike protein fusion core. 20. Weissenhorn, W., Dessen, A., Harrison, S. C., Skehel, J. J., and Wiley, D. C. (1997) Nature 387, 426–430 The peptides encompassing residues 1161–1187 will be good 21. Chan, D. C., Fass, D., Berger, J. M., and Kim, P. S. (1997) Cell 89, 263–273 targets for mutagenesis in the search for peptides with higher 22. Tan, K., Liu, J., Wang, J., Shen, S., and Lu, M. (1997) Proc. Natl. Acad. Sci. inhibitory efficacy. The exposed hydrophobic grooves in the U. S. A. 94, 12303–12308 23. Caffrey, M., Cai, M., Kaufman, J., Stahl, S. 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164 THE JOURNAL OF BIOLOGICAL CHEMISTRY Vol. 279, No. 48, Issue of November 26, pp. 50025–50030, 2004 © 2004 by The American Society for Biochemistry and Molecular Biology, Inc. Printed in U.S.A. The Yeast Prion Protein Ure2 Shows Glutathione Peroxidase Activity in Both Native and Fibrillar Forms*

Received for publication, June 14, 2004, and in revised form, September 10, 2004 Published, JBC Papers in Press, September 15, 2004, DOI 10.1074/jbc.M406612200

Ming Bai‡§, Jun-Mei Zhou‡¶, and Sarah Perrett‡¶ From the ‡National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, Beijing 100101, China and §Graduate School of the Chinese Academy of Sciences, 19 Yuquan Road, Fengtai District, Beijing 100039, China

Ure2p is the precursor protein of the Saccharomyces protective role against a range of diseases including cancer. cerevisiae prion [URE3]. Ure2p shows homology to glu- GSTs are dimeric proteins with a relatively conserved N-ter- tathione transferases but lacks typical glutathione minal thioredoxin-like domain and a more variable C-domain. transferase activity. A recent study found that deletion GST activity is typically tested using the “universal” GST sub- of the Ure2 gene causes increased sensitivity to heavy strate, 1-chloro-2,4-dinitrobenzene (CDNB). However, a num- metal ions and oxidants, whereas prion strains show ber of GSTs identified by structural criteria have failed to show normal sensitivity. To demonstrate that protection activity toward CDNB (5). Some GSTs have been shown to have against oxidant toxicity is an inherent property of na- overlapping functions with other glutathione-binding enzymes tive and prion Ure2p requires biochemical characteriza- such as glutathione peroxidases (GPxs) and glutaredoxins (1– tion of the purified protein. Here we use steady-state 3). These enzyme families share the GSH-binding thioredoxin kinetic methods to characterize the multisubstrate per- domain but are otherwise structurally and mechanistically dis- oxidase activity of Ure2p using GSH with cumene hy- similar (7–10). Characterization of the GSTs, glutaredoxins, droperoxide, hydrogen peroxide, or tert-butyl hydroperoxide as substrates. Glutathione-dependent peroxidase and phospholipid hydroperoxide glutathione peroxidases pres- activity was proportional to the Ure2p concentration ent in Saccharomyces cerevisiae reveals some redundancy of and showed optima at pH 8 and 40 °C. Michaelis-Menten function between the different classes of enzyme (11–13). The behavior with convergent straight lines in double recip- versatility of the glutathione-binding enzymes and their tend- rocal plots was observed. This excludes a ping-pong ency to show overlapping functions may contribute signifi- mechanism and implies either a rapid-equilibrium ran- cantly to the ability of the host organism to adapt to change. dom or a steady-state ordered sequential mechanism for Ure2p is the protein determinant of the S. cerevisiae prion Ure2p, consistent with its classification as a glutathione [URE3] (14). Analogous to the mammalian prion (15), the her- transferase. The mutant 90Ure2, which lacks the unstruc- itable [URE3] prion phenotype is conveyed by a structural tured N-terminal prion domain, showed kinetic para- change in Ure2 to an aggregated form (16). It has recently been meters identical to wild type. Fibrillar aggregates showed demonstrated that drugs isolated using a yeast prion cell- the same level of activity as native protein. Demonstra- screening assay are also active against mammalian prions, tion of peroxidase activity for Ure2 represents important suggesting that there may be features of the cellular mecha- progress in elucidation of its role in vivo. Further, estab- nism of prion formation and/or maintenance that are common lishment of an in vitro activity assay provides a valuable to yeast and mammalian prions despite the diversity of the tool for the study of structure-function relationships of proteins involved (17). Conversion of Ure2 to the prion form the Ure2 protein as both a prion and an enzyme. depends on the N-terminal ϳ90 amino acids (18). This N- terminal prion domain also directs the formation of amyloid- like fibrils in vitro (19, 20) and is predominantly unstructured The glutathione S-transferases (GSTs)1 are a multifunc- in the native dimeric state (21, 22). Ure2 is involved in the tional family of enzymes broadly distributed in nature that regulation of nitrogen metabolism in vivo. This function is play a critical role in the cellular detoxification process (re- carried out by the C-terminal region of the protein and is lost viewed in Refs. 1–6). GSTs have the general function of conju- on conversion to the prion form (16, 23). The crystal structure gating GSH to electrophilic substances to reduce their toxicity. of the C-terminal region has been solved in both apo (24, 25) As a consequence, GSTs are involved in development of resist- and glutathione-bound (26) forms, confirming the classification ance toward drugs, insecticides, and herbicides and have a of Ure2 as a glutathione transferase (6, 23). However, attempts to demonstrate typical GST activity for Ure2, such as using * This work was supported by the Natural Science Foundation of China CDNB, have so far proved unsuccessful (11, 21, 23, 27). A Ure2 (30070163, 30470363), the 973 Project of the Chinese Ministry of Science and Technology (G1999075608), and the Chinese Academy of Sciences homologue in Aspergillus nidulans was found to lack the nitro- Knowledge Innovation Project (KSCX2-SW214-3). The costs of publication of gen metabolite repression activity of Ure2 but contributed to this article were defrayed in part by the payment of page charges. This heavy metal and xenobiotic resistance, including resistance to article must therefore be hereby marked “advertisement” in accordance with oxidative stress (28). Further, it was recently found that the 18 U.S.C. Section 1734 solely to indicate this fact. ¶ Recipient of a special grant from the Chinese Academy of Sciences deletion of the S. cerevisiae Ure2 gene increases the sensitivity and research fellowships from the Royal Commission for the Exhibition of the cell to metals and cellular oxidants such as hydrogen of 1851 and the Royal Society. To whom correspondence may be ad- peroxide (27, 29), raising the possibility that Ure2 possesses dressed. Tel.: 86-10-64888496; Fax: 86-10-64840672; E-mail: sarah. GPx activity. This has implications for the role of Ure2 in vivo. [email protected] or [email protected]. In addition, it implies the potential to establish an in vitro 1 The abbreviations used are: GST, glutathione S-transferase; CDNB, 1-chloro-2,4-dinitrobenzene; GPx, glutathione peroxidase; CHP, cu- activity assay for Ure2, which would serve as an invaluable tool mene hydroperoxide; t-BH, tert-butyl hydroperoxide; ThT, thioflavin T. in structure-function analysis.

This paper is available on line at http://www.jbc.org 50025 165 50026 The Yeast Prion Ure2p Has Glutathione Peroxidase Activity

In this study, we tested the activity of Ure2 toward a number of oxidant substrates in vitro to establish whether the peroxidase activity related to the Ure2 gene is an inherent property of the Ure2 protein. Having detected GPx activity for Ure2, we employed steady-state kinetic techniques to characterize the kinetic parameters for the substrates cumene hydroperoxide

(CHP), tert-butyl hydroperoxide (t-BH), and H2O2 and to investigate the reaction mechanism. Further, we compared the activity of wild type Ure2 with that of a Ure2 deletion mutant, 90Ure2, which lacks the prion domain. Finally, we compared the activity of the native dimeric protein with that of fibrillar aggregates.

EXPERIMENTAL PROCEDURES Materials—GSH, ␤-NADPH, CHP, t-BH, and glutathione reductase

were from Sigma. Ure2 and 90Ure2 were produced in Escherichia coli FIG.1.Glutathione-dependent reduction of CHP catalyzed by with an N-terminal His6 tag and purified by nickel affinity chromatog- Ure2p. The initial velocity of the Ure2-catalyzed reaction is plotted as raphy or produced without a tag and purified by a series of ionic a function of the Ure2 concentration. The reaction conditions were 100 exchange and gel filtration chromatographic steps, as described previ- mM sodium phosphate buffer, pH 7.5, 1 mM GSH, and 1.2 mM CHP at ously (21). Proteins were stored at Ϫ80 °C in 50 mM Tris-HCl buffer, pH 25 °C. Other details are as described under “Experimental Procedures.” 8.4, containing 0.2 M NaCl and defrosted in a 25 °C water bath imme- Inset, the non-enzymatic rate (solid line) was measured and subtracted diately prior to use. The protein concentration in terms of monomers from the reaction rate measured in the presence of Ure2 (1 ␮M (dashed- was measured by absorbance at 280 nm using an extinction coefficient dotted line); 2.5 ␮M (dashed line)) in each case. In the absence of GSH, Ϫ Ϫ of 40,700 M 1 cm 1 (21) unless otherwise stated. no reaction was observed. Enzyme Assays and Steady-state Kinetic Analysis—The GPx activity of Ure2 was determined using GSH with one of the hydroperoxides, 240 ␮l of sample, a 50-␮l aliquot of the resulting supernatant was CHP, H O ,ort-BH, as substrates using a coupled spectrophotometric 2 2 assayed for GPx activity. A further 10-␮l aliquot of supernatant was assay as described previously (30) with slight modifications. Unless used for protein concentration determination using the method of Brad- otherwise indicated, the assay was carried out at 25 °C in a 1-ml ford (38). The precipitate was resuspended in 240 ␮l of the same buffer, reaction volume containing 100 mM sodium phosphate buffer, pH 7.5, 4 and then a 50-␮l aliquot of the resuspended mixture was assayed for mM sodium azide, 0.5–5.0 mM GSH, 0.15 mM ␤-NADPH, 0.24 units of GPx activity. Thus, the final protein concentration in the GPx assays glutathione reductase, and 0.3–3.0 ␮M Ure2. The reaction mixture was was 1.5 ␮M for the total reaction mixture and a maximum of 1.5 ␮M in preincubated at 25 °C for 6 min, after which the reaction was started by either the supernatant or the pellet fraction, depending on the relative the addition of the hydroperoxide substrate to a final concentration of distribution of protein between the fractions during the course of fibril 0.5–5.0 mM to both cuvettes. The progress of reactions was monitored formation. The pattern of change observed was highly reproducible in continuously by following the decrease in NADPH absorbance at 340 independent experiments. nm on a Shimadzu UV2501PC14 spectrophotometer. Initial rates were determined from the linear slope of progress curves obtained with an Ϫ Ϫ RESULTS extinction coefficient for NADPH of 6220 M 1 cm 1 after subtracting the non-enzymatic velocities due to the auto-oxidation of GSH by the hy- Ure2 Shows Glutathione Peroxidase Activity—The ability of droperoxide determined from the corresponding blank. When bovine Ure2 to reduce hydroperoxides was tested in vitro using puri- serum albumin was used in place of Ure2, no increase over the base-line fied Ure2 with the oxidant substrate CHP and the reducing rate was observed. The presence or absence of 4 mM sodium azide had agent GSH. Reactions were followed by the oxidation of no affect on the Ure2 activity. When GSH was omitted from the reaction NADPH, which is coupled to the reduction of GSSG to GSH by mixture, no Ure2 activity was observed. Steady-state kinetic analysis was carried out by obtaining sets of glutathione reductase. The rate of non-enzymatic oxidation of initial velocities over a wide range of concentrations of one substrate NADPH in the absence of Ure2 was subtracted in each case. while the concentration of the other substrate was kept constant (31, When Ure2 was added in the presence of all of the other 32). The data were fitted to the Michaelis-Menten equation or the components of the assay, a significant increase in the oxidation Lineweaver-Burk equation. The values obtained from these plots, and rate of NADPH was observed (Fig. 1, inset) and the initial Eadie-Hofstee plots were the same within error. Single or global fitting velocity of the Ure2-catalyzed reaction was found to be propor- was carried out using the regression wizard of SigmaPlot. The errors shown are the S.E. of the fit, or the mean Ϯ S.E. obtained from inde- tional to the Ure2 concentration (Fig. 1, main panel). As is pendent measurements, as appropriate. characteristic of an enzyme-catalyzed reaction (32), the enzy- Determination of true kinetic parameters and investigation of the matic activity of Ure2 toward CHP showed pH and tempera- reaction mechanism were performed by obtaining Michaelis-Menten ture optima, in this case at around pH 8.0 and 40 °C (Fig. 2). In curves at a series of concentrations of the second substrate and then contrast, the uncatalyzed rate was observed to increase steeply fitting the data globally to the Michaelis-Menten model describing above pH 8 or above 30 °C (data not shown). Therefore, we two-substrate sequential binding (32–34). The values obtained by linear extrapolation using secondary plots or by global fitting were the same adopted pH 7.5 and 25 °C as the standard conditions for the within error. Ure2 GPx activity assay. A control using bovine serum albumin Assay of Ure2 GPx Activity during the Time Course of Amyloid-like in place of Ure2 over the same protein concentration range Fibril Formation—The initial sample was centrifuged at 18,000 ϫ g for showed no detectable GPx activity (data not shown). The pres- ␮ 30 min at 4 °C to remove any preexisting aggregates, and 300 lofthe ence or absence of 4 mM sodium azide had no effect on the Ure2 supernatant was transferred into each of a series of tubes, one for each GPx activity, ruling out the possibility that the observed activ- time point. The reaction mixture contained 30 ␮M full-length Ure2 in 50 mM sodium phosphate buffer, pH 7.5, containing 0.2 M NaCl. The ity is due to contamination with a heme-containing peroxidase samples were incubated in parallel at a constant temperature of 37 °C such as catalase or myeloperoxidase. Ure2 showed no peroxi- with shaking as described previously (35, 36). Under these conditions, dase activity in the absence of GSH. This then demonstrates the increase in fluorescence due to ThT binding correlates directly with that Ure2 has GSH-dependent peroxidase activity. the appearance of fibrillar aggregates of Ure2 (36). At each time point, Comparison of Different Hydroperoxide Substrates—To fur- ␮ one of the samples was placed on ice. A 50- l aliquot of the complete ther characterize the GPx activity of Ure2, we employed reaction mixture was removed and assayed for GPx activity using 1 mM GSH and 1.2 mM CHP as substrates, as described above. A further 10-␮l steady-state methods to obtain the apparent kinetic parame- aliquot of the reaction mixture was removed to assay for ThT binding, ters for the enzymatic reaction. The results of steady-state as described previously (35–37). After centrifugation of the remaining kinetic analysis of Ure2 GPx activity toward the substrates 166 The Yeast Prion Ure2p Has Glutathione Peroxidase Activity 50027

FIG.3. GPx activity of Ure2p with different hydroperoxide FIG.2.Optima of Ure2 catalyzed glutathione peroxidase activ- substrates measured under steady-state conditions. The fit to the ity toward CHP. A, pH dependence of activity measured at 25 °C. B, Michaelis-Menten equation is shown. The Ure2 concentration was 0.6– temperature dependence of activity measured at pH 7.5. The Ure2 1.3 ␮M. A, varying concentrations of GSH with a fixed hydroperoxide ␮ ● E concentration was 1.2 M. Other details are as in Fig. 1. substrate concentration of 1.2 mM for CHP ( )orH2O2 ( )and5mM for t-BH (). B, varying concentrations of hydroperoxide substrates with a fixed GSH concentration of 1 mM. Symbols are as in A. CHP, hydrogen peroxide, and t-BH are shown in Fig. 3 and Table I. When the concentration of one substrate was fixed and and, under certain conditions, the rate equations can be re- the concentration of the other substrate was varied, the GPx duced to simple forms (31–34). Fig. 4 shows double-reciprocal activity was hyperbolic with respect to substrate concentration plots of the initial velocity versus one substrate concentration, (Fig. 3) and double-reciprocal Lineweaver-Burk plots were lin- obtained for a range of concentrations of the second substrate. ear (Fig. 4), as is typical of adherence to Michaelis-Menten The slope of the lines was observed to decrease with increasing kinetics (31). Ure2 showed activity toward all three substrates concentration of the second substrate, and the lines intersected Ն Ͼ at a common point. This rules out a ping-pong mechanism with an apparent preference in the order H2O2 CHP t-BH. This indicates that Ure2 has GPx activity toward hydrogen (which is characterized by parallel double-reciprocal plots). The peroxide as well as typical organic hydroperoxide substrates. pattern observed is consistent with a sequential mechanism, The Prion Domain Does Not Contribute to Peroxidase Activ- and the data can be fitted to Equation 1 (32–34), ity—The apparent kinetic parameters obtained for wild type V [A][B] ϭ max Ure2 (with and without a His6 tag) and for the prion domain v (Eq. 1) KiAKmB ϩ KmB[A] ϩ KmA[B] ϩ [A][B] deletion mutant 90Ure2 are shown in Table II. The results show that not only does the presence of a His6 tag have no effect where KmA and KmB are the Michaelis constants for substrates on the enzymatic activity of Ure2 but also that the detected A and B, respectively, and KiA is the inhibition constant for activity cannot be attributed to contamination with a similar substrate A (which under certain circumstances is equal to the enzyme, given the radically different purification methods for dissociation constant for A binding to the enzyme). It has been tagged and non-tagged protein (see “Experimental Proce- demonstrated there are two situations where the form of the dures”). The parameters obtained for 90Ure2 are the same equation simplifies in this way (32, 33), namely, a rapid-equi- within error as those obtained for wild type Ure2, indicating librium random mechanism or a compulsorily ordered mecha- that the prion domain does not contribute to the GPx activity. nism (Fig. 5). Because of the equivalent form of the rate equa- This result is consistent with the finding that the Ure2 prion tions, it cannot be distinguished from the current data whether domain is essentially unstructured in the native dimer (21, 22) binding is random or ordered. However, if binding is ordered, and has no affect on the stability or folding of Ure2 (21, 39). given that GSH binds to Ure2 in the absence of a second Investigation of the Reaction Mechanism and Determination substrate (26), GSH must bind first. The true kinetic parame- of True Kinetic Parameters—To further investigate the mech- ters obtained by fitting of the data shown in Fig. 4 to Equation anism of Ure2 GPx activity, we obtained a data set of initial 1 are shown in Table III. velocities over a wide range of GSH and CHP concentrations. Ure2 Fibrillar Aggregates Show Peroxidase Activity—Ure2 The exact steady-state solutions of the mechanisms for two- was incubated under conditions that have been thoroughly substrate reactions are extremely complicated. However, in characterized by electron microscopy and atomic force micros- practice, only a limited number of mechanisms are observed copy and that promote rapid and abundant fibril formation (35, 167 50028 The Yeast Prion Ure2p Has Glutathione Peroxidase Activity

TABLE I Apparent steady-state kinetic constants for Ure2 activity toward different hydroperoxide substrates The apparent kinetic constants were determined from Michaelis-Menten plots of initial velocities versus varying concentrations of one substrate with a fixed concentration of the other substrate under standard assay conditions as described under “Experimental Procedures” and shown in Fig. ͓ ͔ ␮ Ϯ 3. The Ure2 concentration, E 0, was 0.6–1.3 M. The values shown are the mean S.E. of repeated measurements. a Fixed ͓hydroperoxide substrate͔ Fixed ͓GSH͔ at1mM Substrate ͓ ͔ ͓ ͔ Km(GSH)(app) Vmax(app)/ E 0 Km(app) Vmax(app)/ E 0 Ϫ1 Ϫ1 mM s mM s CHP 2.6 Ϯ 0.1 0.12 Ϯ 0.02 7.8 Ϯ 0.2 0.37 Ϯ 0.02 Ϯ Ϯ Ϯ Ϯ H2O2 2.1 0.4 0.36 0.05 4.3 0.9 0.36 0.06 t-BH 5.5 Ϯ 1.0 0.16 Ϯ 0.04 7.9 Ϯ 2.9 0.07 Ϯ 0.02 a ͓ ͔ ͓ ͔ ͓ ͔ Fixed CHP or H2O2 at 1.2 mM; fixed t-BH at5mM.

the sum of the pellet and supernatant fractions, remained almost constant throughout the course of the experiment (Fig. 6B). This then indicates that Ure2 GPx activity is maintained within ordered aggregates and suggests that the level of activity is essentially unaffected by fibril formation, at least under the conditions used here.

DISCUSSION The bovine spongiform encephalopathy epidemic (40) and the subsequent emergence of a new variant of the equivalent human disease (41) has prompted a massive worldwide effort to understand the prion phenomenon (15). The finding that prions also exist in fungi (14) has contributed significantly to establishing the viability of the prion concept (42). To understand the molecular mechanism of prion formation requires characterization of the structural and folding properties of the prion proteins. The natural tendency of prion proteins to aggregate makes this a difficult task. Nevertheless, significant progress has been made in recent years. High resolution structures are available for the mammalian prion protein, PrP (43, 44), and for Ure2 (24–26). In addition, the stability and kinetics of folding have been studied by a number of spectroscopic methods for PrP (45–47) and Ure2 (20, 21, 35, 39, 48, 49). The disadvantage of purely spectroscopic methods for folding studies is that it is often difficult to separate the native-structure signal from those of native-like or partially folded states. Therefore, the availability of an assay for native activity is an extremely important tool in structure-function analysis (31). In the case of Ure2, it was found that the native state could be distinguished from a spectroscopically identical misfolded na- FIG.4. Double-reciprocal plots of Ure2p activity at a fixed concentration of one substrate versus varying concentrations of tive-like state by the difference in their unfolding kinetics (39). the second substrate for GSH and CHP. The concentration of Ure2p However, this unfolding assay requires the addition of high in the reactions was 0.6 ␮M. The observed pattern of intersecting concentrations of chemical denaturant and is not readily appli- straight lines excludes a ping-pong reaction mechanism and is consistent with either a steady-state ordered sequential mechanism or a rapid- cable to fibrillar aggregates. Thus, the establishment of an in equilibrium random sequential mechanism. The parameters obtained vitro activity assay for Ure2, as described here, not only ad- by global fitting of the data to Equation 1 are shown in Table III. dresses questions regarding the physiological structure and function of Ure2 but also provides an important tool for further 36). Under these conditions, it was found that the increase in mechanistic analysis of Ure2 as both an enzyme and a prion. the binding fluorescence of the amyloid-specific dye ThT corre- Ure2 showed glutathione-dependent peroxidase activity to- lates directly with the time dependent appearance of fibrillar ward both hydrogen peroxide and standard organic hydroper- aggregates of Ure2, providing a convenient method to quantify oxide substrates (Fig. 3 and Table I). This finding indicates the extent of fibril formation (36). Aliquots were removed at that Ure2, while lacking typical GST activity (23), nevertheless regular time intervals for analysis (see “Experimental Proce- belongs to the subset of GST proteins that are active against dures”). The course of fibril formation was monitored by assay- oxidant substrates (1, 5). Most GPxs contain a selenocysteine, ing the ThT binding of the incubation mixture and by meas- which reacts covalently with GSH, generally via a ping-pong uring the decrease in the protein concentration in the enzyme reaction mechanism (7). In contrast, GSTs use a con- supernatant fraction subsequent to sedimentation of the aggre- served tyrosine, serine, or cysteine residue to interact with the gates (Fig. 6A). In parallel, the GPx activity was assayed for the thiol group of GSH, thus increasing the reactivity of GSH, complete reaction mixture, and for the supernatant and pellet typically via a sequential mechanism (8–10). Thus, the obser- fractions (Fig. 6B). Concomitant with the formation of fibrillar vation of a sequential mechanism for Ure2 peroxidase activity aggregates and the loss of protein from the supernatant frac- (Figs. 4 and 5) is in agreement with the designation of Ure2 as tion, the GPx activity of the solution was lost from the super- a GST. The residue Asn124 has been suggested as a candidate natant fraction and instead was found in the pellet fraction. for the catalytically essential residue in the Ure2 GSH-binding The level of activity of the complete incubation mixture, or of domain (26), although this remains in question, particularly 168 The Yeast Prion Ure2p Has Glutathione Peroxidase Activity 50029

TABLE II Apparent steady-state kinetic constants for Ure2 and 90Ure2 Details are as for Table I.

Fixed ͓CHP͔ at 1.2 mM Fixed ͓GSH͔ at1mM Protein ͓ ͔ ͓ ͔ Km(GSH)(app) Vmax(app)/ E 0 Km(CHP)(app) Vmax(app)/ E 0 Ϫ1 Ϫ1 mM s mM s Ure2 (no tag) 2.6 Ϯ 0.4 0.14 Ϯ 0.02 7.1 Ϯ 0.6 0.39 Ϯ 0.04 Ure2 2.6 Ϯ 0.1 0.12 Ϯ 0.02 7.8 Ϯ 0.2 0.37 Ϯ 0.02 90Ure2 2.4 Ϯ 0.1 0.14 Ϯ 0.02 7.7 Ϯ 0.5 0.42 Ϯ 0.03

FIG.5. Minimal scheme for a sequential enzyme reaction mechanism. The enzyme, E, binds to two substrates, A and B, to give products, P and Q. In a rapid-equilibrium situation, the binding of the substrates is rapid compared with the rate of the reaction. The reaction may be ordered with a particular substrate always binding first, or the sequence of substrate binding may be random.

TABLE III True kinetic constants for Ure2 derived from steady-state kinetic analysis The kinetic parameters were measured using the coupled enzyme assay with ͓Ure2͔ϭ0.6 ␮M, ͓GSH͔ϭ0.7 Ϫ 4.0 mM, and ͓CHP͔ϭ1.0 Ϫ 4.0 mM to obtain a series of sets of data as shown in Fig. 4. The parameters were obtained by global fitting of the data to Equation 1. The errors shown are the S.E. of the fit. FIG.6.Relationship between peroxidase activity and the time course of fibril formation. Incubation was in 50 mM sodium phos- Kinetic parameter Value Method of determination phate buffer, pH 7.5, 0.2 M NaCl at 37 °C with shaking, conditions that Ϯ Ϫ1 ͓ ͔ strongly favor fibril formation (35, 36). A, fibril formation was moni- kcat 1.9 0.3 s Vmax/ E 0 Ϯ tored by assaying changes in ThT binding (●) and by measuring the Km(GSH) 4.8 0.6 mM Measured Ϯ protein concentration in the supernatant fraction after centrifugation Km(CHP) 7.4 1.4 mM Measured Ϯ (E). B, in parallel, the GPx activity in the resuspended pellet fraction KI(GSH) 3.2 0.5 mM Measured Ϯ (●), supernatant fraction (E), and total reaction mixture (‚) was as- Km(CHP) 4.9 1.3 mM KI(GSH)Km(CHP)/Km(GSH) Ϯ ϫ 2 Ϫ1 Ϫ1 sayed. The initial velocities are shown for a final protein concentration kcat/Km(GSH) 4.0 0.8 10 M s kcat/Km(GSH) Ϯ ϫ 2 Ϫ1 Ϫ1 in the GPx assay of 1.5 ␮M for the total reaction mixture and a maxi- kcat/Km(CHP) 2.6 0.7 10 M s kcat/Km(CHP) mum of 1.5 ␮M in either the pellet or the supernatant fraction, depending on the distribution of the protein between the fractions over time. because enzymatic activity had not been demonstrated until now (25). The establishment of an assay for Ure2 activity paves fully dispersed soluble protein (Fig. 6). This finding is consist- the way for mutagenesis studies to define the residues required ent with the observation that fibrillar aggregates of Ure2 main- for Ure2 catalytic activity. tain the ability to bind GSH (50) and fibrils formed from other

The kinetic parameters measured for Ure2, namely Km val- enzymes linked to the Ure2 prion domain can still react with 2 3 ues in the millimolar range and kcat/Km values in the 10 –10 their specific substrates, provided that the substrate is small range (Table III), are consistent with the values observed for enough to diffuse into the fibrillar arrays (51). In principle, the related enzymes. For example, the S. cerevisiae GSTs (which kinetics of an immobilized enzyme may be different from the react with CDNB but not with hydroperoxides) also showed kinetics of the enzyme free in solution because of one or more of apparent Km(GSH) values in the millimolar range (11). The the following factors: 1) a change in conformation; 2) a change S. cerevisiae glutaredoxins showed apparent kcat/Km values of in environment; 3) a change in the effective concentration of the around 103 for CDNB and 104 for CHP with apparent substrate substrate; or 4) diffusional effects (52). Diffusional effects will

Km values in the millimolar range (12). The apparent specific- be negligible if the substrate can easily reach the enzyme, or if ity constant for the bacterial GST from Proteus mirabilis re- catalysis is slow with respect to diffusion (i.e. kcat/Km is low) as 3 Ϫ1 Ϫ1 acting with CDNB is around 10 M s with an apparent is the case for Ure2. The results presented here provide direct

Km(GSH) of 0.34 mM and an apparent Km(CDNB) of 2.5 mM (10). support for the suggestion that formation of fibrillar aggregates The observation of oxidant sensitivity for Ure2 mutants (27), of Ure2 does not involve significant structural change within combined with demonstration here that peroxidase activity is the C-terminal globular region but rather that the native-like an inherent property of the Ure2 protein, indicates that Ure2 is structure and activity are preserved. This finding then sup- functional in S. cerevisiae cells as a peroxidase. ports the hypothesis that a loss of nitrogen metabolite repres- A particularly interesting and controversial aspect of the sion in the [URE3] prion state is due to a steric blocking Ure2 prion protein is its ability to assemble into amyloid-like mechanism, rather than to a loss of native-like Ure2 structure fibrils (19, 22, 36) while still retaining native-like structural (51). Furthermore, these results are consistent with the obser- properties (50, 51). We observed the same level of GPx activity vation that prion strains show normal sensitivity to oxidant in fibrillar aggregates of Ure2 as for the same concentration of stress (27), indicating that the Ure2 fibril formation assay is an 169 50030 The Yeast Prion Ure2p Has Glutathione Peroxidase Activity excellent model for the structural changes accompanied by 23. Coshigano, P. W., and Magasanik, B. (1991) Mol. Cell. Biol. 11, 822–832 24. Bousset, L., Berlhali, H., Janin, J., Melki, R., and Morera, S. (2001) Structure prion formation in yeast cells. The availability of a convenient 9, 39–46 and relevant in vitro assay system to conduct structure-func- 25. Umlaud, T. C., Taylor, K. L., Rhee, S., Wickner, R. B., and Davis, D. R. (2001) tion analysis will allow further investigation of the interplay of Proc. Natl. Acad. Sci. U. S. A. 98, 1459–1464 26. Bousset, L., Berlhali, H., Melki, R., and Morera, S. 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Mark Bartlam,1,3 Ganggang Wang,1,3 Haitao Yang,1,3 ␣-melanocyte-stimulating hormone, suggesting a possi- Renjun Gao,2 Xiaodong Zhao,1 Guiqiu Xie,2 ble biological role in controlling the concentration of Shuigui Cao,2 Yan Feng,2 and Zihe Rao1,* these factors (Jones and Manning, 1988). Sequence 1Laboratory of Structural Biology analysis indicates that acylpeptide hydrolases share a Tsinghua University and strong resemblance in their C-terminal domains, which National Laboratory of Biomacromolecules is thought to reflect their peptidase activity (Barrett and Institute of Biophysics Rawlings, 1992; Rawlings et al., 1991). Chinese Academy of Science To date, human, porcine, and rat acylpeptide hy- Beijing 100084 drolases from various tissues have been characterized China (Kobayashi et al., 1989; Mitta et al., 1996; Miyagi et al., 2 Key Laboratory for Molecular Enzymology 1995). All are 732 amino acids in length, share more than and Engineering of Ministry of Education 90% sequence identity with each other, and are reported Jilin University to form homotetramers. The catalytic residues in human Changchun 130023 and porcine enzymes have been identified by chemical China modification and site-directed mutagenesis experiments (Mitta et al., 1998; Scaloni et al., 1992). A deficiency in the expression of human APH has been linked Summary with small cell lung carcinomas and renal carcinomas (Erlandsson et al., 1991; Naylor et al., 1989), while APH Acylpeptide hydrolases (APH; also known as acylam- in porcine brain has been identified as a sensitive site ino acid releasing enzyme) catalyze the removal of an for reaction with organophosphorus compounds and is N-acylated amino acid from blocked peptides. The a potential target for cognitive enhancing drugs (Rich- crystal structure of an APH from the thermophilic arch- ards et al., 2000). Further evidence suggests that APH ˚ aeon Aeropyrum pernix K1 to 2.1 A resolution confirms may be a more sensitive target for cognitive-enhancing it to be a member of the prolyl oligopeptidase family organophosphorus compounds than acetylcholinester- of serine proteases. The structure of apAPH is a sym- ase (AChE) (Duysen et al., 2001; Richards et al., 2000). metric homodimer with each subunit comprised of two As such, the acylpeptide hydrolases have a high poten- domains. The N-terminal domain is a regular seven- tial for drug discovery. An acylpeptide hydrolase from ␤ bladed -propeller, while the C-terminal domain has the thermophilic archaeon Pyrococcus horikoshii has ␣ ␤ a canonical / hydrolase fold and includes the active also been characterized, but is 100 residues shorter than site and a conserved Ser445-Asp524-His556 catalytic its mammalian counterparts and forms a homodimer triad. The complex structure of apAPH with an organo- (Ishikawa et al., 1998). phosphorus substrate, p-nitrophenyl phosphate, has Despite advances in understanding the biological also been determined. The complex structure unam- functions of acylpeptide hydrolases, little is known of biguously maps out the substrate binding pocket and the structural basis for the sequential deacetylation of provides a basis for substrate recognition by apAPH. N-terminally acetylated proteins. Human APH has been A conserved mechanism for protein degradation from crystallized, but the structure is still unavailable today archaea to mammals is suggested by the structural (Freese et al., 1993). Recently, suitable crystals of an features of apAPH. APH from the thermophilic archaeon Aeropyrum pernix K1 (apAPH) were obtained for structure determination Introduction (Wang et al., 2002, 2003). Aeropyrum pernix K1 is an aerobic strain classified as crenarchaeota in archaeon Acylpeptide hydrolases (APH; also known as acylamino (Sako et al., 1996); the complete genome of A. pernix acid releasing enzyme or acylaminoacyl peptidase K1 has been sequenced, and four genes (Ape1547, [EC3.4.19.1]) catalyze the removal of an N-acylated amino acid from blocked peptides (Tsunasawa et al., Ape1832, Ape2290, and Ape2441) have been desig- 1975). Peptide substrates of various sizes and with dif- nated as encoding acylpeptide hydrolases. This paper ferent acyl groups at the N terminus (acetyl, formyl, and describes the structure of apAPH, the gene product of ˚ chloroacetyl) can be hydrolyzed by APH to generate an Ape1547, to 2.1 A resolution. Although apAPH shares acyl amino acid and a peptide with a free N terminus only 27% sequence identity with human acylpeptide that is shortened by one amino acid. Acetylation occurs hydrolase, there is a surprising conservation of second- during or following the biosynthesis of the polypeptide ary structure between eukaryotic APH proteins and chains, suggesting that this process protects the intra- apAPH. We have also determined the structure of cellular proteins from proteolysis (Hershko et al., 1984). apAPH in complex with an organophosphorus (OP) sub- Acylpeptide hydrolases are also active on small acet- strate, p-nitrophenyl phosphate (pNP). Serine proteases ylated bioactive peptides, such as ␤-endorphin and share common inhibitors and have the potential to react with OP compounds, and so the complex of apAPH with *Correspondence: [email protected] pNP should provide a structural basis for the design of 3 These authors contributed equally to this work. specific inhibitors for acylpeptide hydrolases.

171 Structure 1482

Table 1. Data Collection and Refinement Statistics

Data Collection Statistics

MAD Peak MAD Edge MAD Remote apAPH-pNP Complex

Wavelength (A˚ ) 0.9795 0.9799 0.9800 1.5418

Space group P212121 P212121 Unit cell (A˚ , Њ)aϭ 63.88 A˚ ,bϭ 104.62 A˚ ,aϭ 63.88 A˚ ,bϭ 104.62 A˚ ,cϭ c ϭ 168.00 A˚ , ␣ϭ␤ϭ 168.00 A˚ , ␣ϭ␤ϭ␥ϭ90Њ ␥ϭ90Њ Resolution limit (A˚ ) 50.0–2.1 (2.18–2.1) 50.0–2.2 (2.28–2.2) 50.0–2.2 (2.28–2.2) 50.0–2.7 (2.85–2.7) Total reflections 427,387 379,459 392,979 215,959 Unique reflections 67,958 59,504 59,604 31,768 Completeness 99.2 (97.5) 99.5 (98.2) 99.6 (98.5) 100 (100) a Rmerge 7.9 (21.2) 6.3 (17.7) 12.4 (37.9) 10.0 (37.7) ϽI/␴(I)Ͼ 16.6 (6.1) 18.4 (7.5) 9.7 (3.8) 6.9 (2.0) Redundancy 7.4 (7.2) 7.4 (7.2) 7.5 (7.0) 6.8 (7.0)

Refinement Statistics

apAPH apAPH-pNP Complex

Resolution range (A˚ ) 30.0–2.1 30.0–2.7 b Rwork 19.3 20.8 b Rfree 23.0 26.9 Rms deviation bonds (A˚ ) 0.010 0.010 angles (Њ) 1.59 1.64 Average B factors (A˚ 2) Protein (chain A/B) 19.4/22.9 31.0/34.4 Water 27.3 34.8 Ramachandran plot Favored (%) 90.1 85.0 Allowed (%) 9.5 14.3 Generously allowed (%) 0.4 0.6 Disallowed (%) 0 0.1

Numbers in parentheses correspond to the highest resolution shell. a Rmerge ϭ⌺h⌺i|Iih ϪϽIhϾ|/⌺h⌺iϽIhϾ, where ϽIhϾ is the mean of the observations Iih of reflection h. b Rwork ϭ⌺(||Fp(obs)| Ϫ |Fp(calc)||)/⌺|Fp(obs)|;Rfree ϭ R factor for a selected subset (5%) of the reflections that was not included in prior refinement calculations.

Results and Discussion and 2A). The N-terminal domain (residues 24–324) is a ␤-propeller with seven blades; each blade consists of Structure Determination a four-stranded antiparallel ␤ sheet. The C-terminal do- The structure of apAPH was determined by MAD phas- main (residues 325–581) has a canonical ␣/␤ hydrolase ing from a selenomethionyl derivative. Data sets were fold, with a central eight-strand mixed ␤ sheet flanked collected at peak, edge, and remote wavelengths on by five helices on one side and six helices on the other. beamline BL41XU of SPring-8 (Hyogo, Japan). The crys- This central ␤ sheet is all parallel with the exception of tal contained two molecules in the asymmetric unit. The the second ␤ strand. A short ␣ helix at the N-terminal quality of the experimental electron density map was (residues 8–23) extends from the ␤-propeller domain good such that residues 8–581 of chain A and residues and forms part of the hydrolase domain. Between the 8–581 of chain B could be traced continuously. No den- domains is a large cavity approximately 45 A˚ in width, sity was observed for residues 1–7 and 582. The final which is accessible via a tunnel in the ␤-propeller do- model consists of 1148 residues, 580 water molecules, main. Three prolines—Pro312, Pro359, and Pro370—in 2 ␤-octyl glucoside molecules, and 2 glycerol molecules. each protomer are in the cis conformation. Data collection and refinement statistics are summa- Interestingly, the structure includes a detergent mole- rized in Table 1. cule, ␤-octyl glucoside, bound within the central cavity The structure of the apAPH-pNP complex was deter- of each subunit. The detergent molecule, added during mined from a single crystal by molecular replacement, crystallization, does not bind to the active Ser445 but using data collected in-house to 2.7 A˚ resolution. Clear instead forms a single hydrogen bond with the O␥ atom electron density for the substrate was observed from of Ser26. Further hydrophobic contacts are made with an |Fo| Ϫ |Fc| difference map in the binding pocket of residues Phe41, Val46, Phe381, Ile558, Ala564, and each subunit. Continuous electron density was ob- Leu568. A glycerol molecule is also found within the served for residues 9–581 of chain A and 9–581 of chain central channel of the ␤-propeller in each subunit. Coor- B. The final model consists of 1146 residues, 181 water dination of the glycerol occurs via hydrogen bonds with molecules, and 2 pNP molecules. Ser157 and Leu251 and hydrophobic contacts with Ser199, Ala200 and Trp250. Structural Overview A DALI (Holm and Sander, 1998) search for structural The structure of apAPH is a symmetric homodimer, and similarity confirms that the overall architecture of apAPH each subunit is comprised of two domains (Figures 1 most resembles prolyl oligopeptidase (POP; PDB ID 172 Crystal Structure of apAPH 1483

Hydrophobic interactions are mediated by residues positioned on helices ␣1, ␣11, and ␣12. In contrast to acylpeptide hydrolases from A. pernix K1 and P. horikoshii, which form homodimers, their mammalian counterparts have been reported to form homotetramers. A multiple sequence alignment shows that the residues in the dimer interface are conserved in mammalian enzymes, suggesting a common mode of dimer formation. Unlike the archaeal enzymes, however, the mammalian enzymes all possess a large hydrophobic insertion near the N-terminal, which may be involved in higher oligomer formation similar to DPP-IV (Engel et al., 2003). Lack of this N-terminal insertion may explain why apAPH forms a dimer rather than a tetramer.

␤-Propeller Domain The N-terminal domain (residues 24–324) is a regular ␤-propeller consisting of seven blades, each of which is made up of four antiparallel strands (Figure 2C). Blade III is the single exception since it has an additional fifth ␤ strand due to crosslinking from blade II. The sheets are twisted and radially arranged around a pseudo 7-fold axis such that they pack face to face. The central tunnel of the ␤-propeller is lined with hydrogen donors and acceptors, which are water solvated. The ␤-propeller is connected to the catalytic domain via two polypeptide Figure 1. Topology of the apAPH Structure main chains. The two domains are stabilized by 29 hy- A topology diagram showing the domain structure of apAPH. The drogen bonds and salt bridges, with additional stability ␣ helices are shown as yellow cylinders, ␤ strands in the N-terminal provided by hydrophobic forces. domain are shown in blue, and ␤ strands in the C-terminal domain Internal structural stability is provided predominantly are shown in red. Two cysteine residues (Cys416 and Cys453) lo- by hydrophobic interactions. There is also a high fre- cated in the C-terminal domain form a disulfide bridge between helices ␣6 and ␣7 and are shown as green circles. quency of charged residues (Arg and Glu) located on the end of strands in the ␤-propeller domain, resulting in the formation of 12 ion pairs between neighboring 1QFM) (Fulop et al., 1998) and dipeptidyl peptidase IV/ blades. These ion pairs may be a contributory factor to CD26 (DPP-IV; PDB ID 1ORV) (Engel et al., 2003), both the high thermostability of apAPH. It is worth noting of which are members of the prolyl oligopeptidase family that five of the seven blades have an aspartate residue of serine proteases. As with apAPH, both structures (Asp52, Asp119, Asp140, Asp224, and Asp274) located possess an N-terminal ␤-propeller domain and a C-ter- on the end of the third strand. A similar motif is found ␤ minal ␣/␤ hydrolase domain. The ␤-propeller domain of in the -propeller domain of POP (Fulop et al., 1998). POP features seven blades, whereas the corresponding The significance of this aspartate motif is not clear, but in domain of DPP-IV has eight blades. Unsurprisingly, simi- both structures, the aspartates are directed into solvent. larities were also found between the C-terminal domain While the primary sequence similarity between ␤ of apAPH and other esterase structures sharing the -propeller domains is generally low, their three-dimen- same hydrolase fold, including bacterial cocaine ester- sional structures can be closely superimposed. The ␤ ase (Larsen et al., 2002). apAPH -propeller domain is more regular and compact than the POP propeller, with an rmsd between them of 2.7 A˚ . It more closely resembles the seven-bladed Dimerization propellers of Integrin ␣V␤3 (PDB ID 1JV2) or G protein The structure of apAPH is a symmetric dimer in which (PDB ID 1TBG), with respective rmsds of 1.9 A˚ and 2.1 A˚ . the two subunits are related by a 2-fold rotation axis A number of ␤-propeller domain structures have evolved (Figure 2B). Protomers A and B are essentially similar, ways to close the circle between the first and last blades, with an rmsd between them of 0.4 A˚ for all C␣ atoms. The including covalent bonds between the first and last dimer interface is located exclusively in the C-terminal blades, or by strand exchange between the first and last hydrolase domain, and the total surface area buried by blades. The apAPH ␤-propeller is not stabilized in this the dimer is 2060 A˚ 2. The subunits are arranged such way, and only hydrophobic interactions exist between that the central hydrolase ␤ sheet of one subunit forms the first and last blades. an extension of the central hydrolase ␤ sheet of the second subunit. Hydrogen bonds are formed between strand ␤37 of each subunit by the residues Lys544, Catalytic Domain Thr545, Phe546, Ala548, His549, Ile550, and Asp553. The catalytic domain has a canonical ␣/␤-hydrolase fold Additional hydrogen bonds are formed between resi- and spans residues 8–23 and 325–581 (Figure 2D). The dues located on the N-terminal ␣1 helix (Ser10, Glu17) of central eight-stranded ␤ sheet is all parallel, with the one subunit and helix ␣11 (Gln522) of its partner subunit. exception of the second strand, and is twisted by more 173 Structure 1484

Figure 2. The Structure of apAPH (A) A ribbon diagram showing the structure of apAPH. The coloring is from blue at the N terminus to red at the C terminus. The N- and C termini are labeled. (B) The apAPH dimer structure. Each subunit is colored from blue at the N terminus to red at the C terminus. (C) The ␤-propeller domain viewed down the pseudo 7-fold axis. (D) A view of the ␣/␤-hydrolase domain showing the twisted central ␤ sheet. than 90Њ in line with other serine proteases (Figure 2D). Characteristic of ␣/␤ hydrolases, the active serine is The central ␤ sheet is flanked by six ␣ helices on one located on a sharp turn known as a nucleophile elbow. side and five ␣ helices on the other. The primary se- The sequence surrounding the active serine is Gly-Tyr- quence of apAPH contains only two cysteines (Cys416 Ser-Tyr-Gly, which is consistent with the Gly-X-Ser-X- and Cys453), which are located in the catalytic domain Gly consensus sequence observed in the ␣/␤ hydrolase and form a disulfide bond linking helices ␣6 and ␣7. folds of the lipase, esterase, and serine protease superfamily. The main chain conformation of Ser445 is Active Site strained, with (φ, ␸) ϭ (61.3Њ, Ϫ125.1Њ). This is an ener- The serine proteases are known to possess a conserved getically unfavorable conformation also observed in Ser-Asp-His catalytic triad. The three-dimensional ar- other ␣/␤ hydrolases and is believed to provide an en- rangement of Ser445, Asp524, and His556 in apAPH ergy reservoir for catalysis. The location of several gly- matches with other hydrolase structures. This triad is cine residues (Gly443, Gly447, and Gly448) in very close located in the C-terminal hydrolase domain where it is proximity to the catalytic Ser445 allows the avoidance of covered by the tunnel formed by the N-terminal any steric hindrance in the sharp turn of the nucleophile ␤-propeller domain. Ser445 is located on the turn be- elbow. The net result is that Ser445 is well exposed and tween ␤34 and ␣7; Asp524 is located on the loop be- readily accessible to both the catalytic His556 imidazole tween ␤36 and ␣11; and His556 is located on the loop group and the substrate. between ␤36 and ␣12. The main entrance to the active site is via a tunnel in

174 Crystal Structure of apAPH 1485

the ␤-propeller domain, whose diameter is approxi- and Ala-Asp. It is likely that Phe485 and Phe488, which mately 7 A˚ ; this is large enough for small peptides to serve as anchors for the pNP substrate, influence the enter but would clearly prevent larger peptides and pro- recognition of Phe and Leu in the P1 position. Further teins from accessing the central cavity and undergoing study of the substrate specificity using p-nitrophenyl accidental hydrolysis. A second, smaller side opening alkanoate esters (C2-C18 acyl groups) shows that also provides access to the active site and is located apAPH has optimal activity for substrates with an acyl .(6A˚ wide opening is lined chain length of C8 (Y.F., unpublished dataف between blades 1 and 2. The by the residues Asn65, Arg81, Asp82, Glu88, Asp553, The S2 pocket is not mapped by the pNP substrate, Ala557, Ile558, Asn559, and Asn563. As with the main but its location can be inferred through a detailed com- propeller entrance, the side entrance is also water sol- parison with POP and DPP-IV. The putative S2 pocket vated. Assuming the reaction proceeds via a general is also a hydrophobic environment and is particularly serine protease mechanism, this side opening may pro- rich in phenylalanines (Phe153, Phe155, Phe163, and vide an exit for the reaction product following nucleo- Phe371). The S2 pocket of DPP-IV features a dual Glu- philic attack and formation of an acyl-enzyme interme- Glu recognition motif (Glu205-Glu206), which binds the diate. free amino terminus of the P2 residue and is essential for enzyme activity. While apAPH does not have this Glu-Glu motif, it does have an equivalent binding site Substrate Recognition and Catalytic Mechanism formed by Phe153 and Phe155. The S2 site is also lined Acylpeptide hydrolases are unique among the prolyl oli- by Arg526, which is structurally equivalent to Arg125 gopeptidase family for their substrate preference, which in DPP-IV and Arg643 in POP. This arginine has been is a short peptide blocked at the N terminus. In order confirmed in both DPP-IV and POP to stabilize and acti- to understand more about the substrate specificity of vate the P2 residue carbonyl oxygen. Arg526 is also apAPH, we determined the structure of a complex with found to be conserved in all other APH sequences. Fur- p-nitrophenyl phosphate, a small organophosphorus ther work is required to confirm the specific role of this compound known to be a nonspecific inhibitor of ester- residue. ases. As with many serine proteases, apAPH is a bifunc- The oxyanion binding site is an essential feature for tional enzyme, possessing both acylpeptide hydrolase serine protease catalysis. The negatively charged oxy- and esterase activity (Y.F., unpublished data). This simi- anion is generated from the carbonyl of the scissile bond larity between esterases and acylpeptide hydrolases and stabilized by two hydrogen bonds. In apAPH, a means that they share common inhibitors (Scaloni et hydrogen bond is made by the main chain nitrogen of al., 1994). Gly369 to the O2P atom of the phosphate group of pNP. The complex structure unambiguously maps out the The second hydrogen bond is most likely provided by ˚4Aف S1 substrate binding pocket located in close proximity the main chain amide of Tyr446, which is located to the active site (Figures 3A and 3B). The pocket pro- from the O2P atom of the phosphate group of pNP. This vides a hydrophobic environment for the substrate and arrangement, in which one of the bonds is formed by is lined by the residues Met477, Phe485, Phe488, Ile489, the main chain amide group adjacent to the catalytic Leu492, Trp474, Tyr446, and Val471. Of these, only serine, is typical of the ␣/␤ hydrolase fold family. A differ- Met477 is conserved in human, porcine, and rat APH. ent hydrogen bonding pattern is observed in POP, It is surprising to note that the phosphate group of pNP wherein the equivalent to the Gly369 main chain hydro- is not covalently attached to the catalytic serine. Instead, gen bond is provided by the hydroxyl group of Tyr473 in protomer B the O3P atom of the phosphate group is and not by the main chain amide group. However, super- hydrogen bonded to the O␥ atom of Ser445 with a dis- position of their active sites shows that the OH group tance of 2.8 A˚ (Figure 3C). The O2P atom forms a hydro- of Tyr473 in POP is in a structurally equivalent position gen bond with the main chain amide of Gly369 (2.9 A˚ ), to the amide nitrogen of Gly369 in apAPH. indicating the location of the oxyanion binding site. Fi- nally, a water molecule is hydrogen bonded to the O4P atom (2.4 A˚ ). The phenyl ring is stabilized by hydropho- Conclusions bic interactions with two phenylalanines, Phe485 and In summary, we have successfully determined the struc- Phe488, as well as with Thr527. A similar orientation of ture of an acylpeptide hydrolase from the thermophilic the substrate is observed in the pocket of protomer A, archaeon Aeropyrum pernix K1. To the best of our but with the lack of the water molecule hydrogen bonded knowledge, this is the first structure of an acylpeptide to O4P. Consequently, the hydrogen bond distance be- hydrolase to be determined. The structure confirms that tween O3P and Ser445 O␥ is reduced to 2.3 A˚ , and the acylpeptide hydrolases are members of the prolyl oligo- hydrogen bond distance between O2P and the Gly369 peptidase family of serine proteases. The apAPH struc- main chain amide is also reduced to 2.3 A˚ . ture shares the catalytic ␣/␤ hydrolase domain of other Previous studies of apAPH have indicated that the serine proteases, as well as the ␤-propeller domain substrate recognition is not specific. Of a series of Ac- found in prolyl oligopeptidase family structures for the amino acid-pNAs tested, apAPH shows the highest ac- specific recognition of small peptides. The apAPH struc- tivity for Ac-Phe and Ac-Leu substrates, while the lowest ture also includes many features known to be important activity is for Ac-Ala and Ac-Lys (Y.F., unpublished data). for serine protease catalysis, such as the Ser-Asp-His Conversely, the human and rat forms of APH show high- catalytic triad, Gly-X-Ser-X-Gly sequence motif, and est activity for Ac-Ala, Ac-Met, and Ac-Ser. In addition, oxyanion binding site. Despite the relatively low se- apAPH also has high activity for the dipeptides Ala-Phe quence similarity among acylpeptide hydrolases, the

175 Structure 1486

Figure 3. The Active Site of apAPH (A) Cross-sections through the surface of apAPH showing the central cavity and the bound pNP molecule near the active site. The pNP molecule is shown in cyan, and the location of the active Ser445 is marked in yellow on the molecular surface. The apAPH structure is shown in ribbon form with the same coloring as in Figure 2. (B) A stereo diagram showing the active site and S1 pocket of apAPH in the complex structure. Active site residues are shown in green, and the bound pNP substrate is shown in yellow. An omit map contoured at 1 ␴ is shown covering the pNP substrate. (C) A schematic showing the pNP substrate and active site residues. Ser445, Asp524, and His556 form the catalytic triad, while Gly369 and Tyr446 form the oxyanion binding site. The gray circle represents a water molecule. Hydrogen bonds are shown as dotted lines, and hydrogen bond distances are given. Res- idues Phe485, Phe488, and Thr527 form hydrophobic contacts with pNP.

structural features of apAPH suggest a general serine acylpeptide hydrolases will be important for further protease mechanism for protein degradation from arch- study of this important family of enzymes. aea to mammals. We have also determined the structure of a complex with a small OP substrate, p-nitrophenyl Experimental Procedures phosphate. The complex structure reveals the basis for Cloning, Expression, Purification, and Crystallization substrate recognition by apAPH and maps out the active apAPH site residues important for catalysis, including the oxya- The cloning, expression, purification, and crystallization of apAPH nion binding site. The design of specific inhibitors for have been described previously (Chen et al., 2002; Wang et al.,

176 Crystal Structure of apAPH 1487

2003). Briefly, the purified protein was concentrated to 10 mg/ml References and transferred into a buffer containing 20 mmol/l Tris-HCl (pH 8.0). For preparation of the Se-Met protein derivative, 5 mM DTT was Barrett, A.J., and Rawlings, N.D. (1992). Oligopeptidases, and the used for antioxidation during the purification procedure. Crystalliza- emergence of the prolyl oligopeptidase family. Biol. Chem. Hoppe tion trials were conducted at 291 K in 16-well plates using the hang- Seyler 373, 353–360. ing-drop vapor-diffusion method. The best crystals were obtained Brunger, A.T., Adams, P.D., Clore, G.M., DeLano, W.L., Gros, P., from reservoir of 6% PEG4000, 50 mM/l NaAC (pH 4.6), 15 mM/l Grosse-Kunstleve, R.W., Jiang, J.S., Kuszewski, J., Nilges, M., DTT, 0.2 mM/l EDTA. Pannu, N.S., et al. (1998). Crystallography & NMR system: a new pNP inhibitor complex software suite for macromolecular structure determination. Acta apAPH crystals were soaked with 20 mM p-nitrophenyl phosphate Crystallogr. D Biol. Crystallogr. 54, 905–921. dissolved in the buffer containing 6% PEG 4000, 25 mM NaAC (pH Chen, Y., Zhang, X., Liu, H., Wang, Y., and Xia, X. (2002). Study 4.6). A 5 ␮l aliquot of such solution was added to the drop, and the on Pseudomonas sp. WBC-3 capable of complete degradation of crystals were soaked overnight. All of the crystals were cryopro- methylparathion. Wei Sheng Wu Xue Bao 42, 490–497. tected in 30% glycerol prior to freezing in a cryostream. Duysen, E.G., Li, B., Xie, W., Schopfer, L.M., Anderson, R.S., Broom- field, C.A., and Lockridge, O. (2001). Evidence for nonacetylcholines- Data Collection terase targets of organophosphorus nerve agent: supersensitivity of ␭ϭ ˚ ␭ϭ Three data sets were collected at peak ( 0.9795 A), edge ( acetylcholinesterase knockout mouse to VX lethality. J. Pharmacol. ˚ ␭ϭ ˚ 0.9798 A), and remote ( 0.9800 A) wavelengths from a single Exp. Ther. 299, 528–535. selenomethionyl derivative crystal on beamline BL14XU of SPring-8 Engel, M., Hoffmann, T., Wagner, L., Wermann, M., Heiser, U., Kiefer- (Hyogo, Japan). Data were processed and scaled using HKL 2000 sauer, R., Huber, R., Bode, W., Demuth, H.U., and Brandstetter, H. (Otwinowski and Minor, 1997) to a maximum resolution of 2.1 A˚ . (2003). The crystal structure of dipeptidyl peptidase IV (CD26) re- Data from a single crystal of apAPH in complex with p-nitrophenyl veals its functional regulation and enzymatic mechanism. Proc. Natl. phosphate were collected in-house on a Rigaku RAXIS-IVϩϩ detec- Acad. Sci. USA 100, 5063–5068. tor at wavelength 1.5418 A˚ and 100 K. All data were processed with MOSFLM (Leslie, 1992) to 2.7 A˚ resolution, and scaled and merged Erlandsson, R., Boldog, F., Persson, B., Zabarovsky, E.R., Allikmets, with SCALA (Evans, 1997). R.L., Sumegi, J., Klein, G., and Jornvall, H. (1991). The gene from the short arm of chromosome 3, at D3F15S2, frequently deleted in renal cell carcinoma, encodes acylpeptide hydrolase. Oncogene 6, Structure Determination and Refinement 1293–1295. The structure of apAPH was determined to 2.1 A˚ resolution by the ϩ multiwavelength anomalous dispersion (MAD) method. CNS Evans, P.R. (1997). SCALA. In Joint CCP4 ESF-EACBM Newslet- (Brunger et al., 1998) was used to locate 20 selenium atoms and ter, pp. 22–24. calculate initial phases to 3.0 A˚ . The initial phases and heavy-atom Freese, M., Scaloni, A., Jones, W.M., Manning, J.M., and Remington, sites were then input into RESOLVE (Terwilliger, 2000) for phase S.J. (1993). Crystallization and preliminary X-ray studies of human extension and density modification. Noncrystallographic symmetry erythrocyte acylpeptide hydrolase. J. Mol. Biol. 233, 546–549. (NCS) consistent with point group (rotation) symmetry was found Fulop, V., Bocskei, Z., and Polgar, L. (1998). Prolyl oligopeptidase: among 18 of the 20 heavy-atom sites, and NCS averaging was an unusual beta-propeller domain regulates proteolysis. Cell 94, consequently used by RESOLVE to improve the quality of the elec- 161–170. tron density map. A total of 980 residues were traced automatically Hershko, A., Heller, H., Eytan, E., Kaklij, G., and Rose, I.A. (1984). Role in two molecules, and the remainder of the structure was built into of the alpha-amino group of protein in ubiquitin-mediated protein the experimental electron density map using O (Jones et al., 1991) breakdown. Proc. Natl. Acad. Sci. USA 81, 7021–7025. and ARP/wARP (Perrakis et al., 1999). Refinement of the model was Holm, L., and Sander, C. (1998). Protein folds and families: sequence performed using CNS with alternate cycles of manual rebuilding in and structure alignments. Nucleic Acids Res. 26, 316–319. O. NCS restraints were applied in the early stages of refinement and were released in later stages. The current model has working Ishikawa, K., Ishida, H., Koyama, Y., Kawarabaysi, Y., Kawahara, J., and free R factors of 19.3% and 23.0%, respectively. The model Matsui, E., and Matsui, I. (1998). Acylamino acid-releasing enzyme has good stereochemistry, with 90.1% of residues in the most fa- from the thermophilic archaeon Pyrococcus horikoshii. J. Biol. vored region of the Ramachandran plot generated by PROCHECK Chem. 273, 17726–17731. (Laskowski et al., 1993) and none in disallowed regions. Jones, W.M., and Manning, J.M. (1988). Substrate specificity of an The structure of the apAPH-pNP complex was refined to 2.7 A˚ acylaminopeptidase that catalyzes the cleavage of the blocked resolution using the native wild-type structure as a starting point. amino termini of peptides. Biochim. Biophys. Acta 953, 357–360. Manual adjustments were made to the model in O, and refinement Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. (1991). | | Ϫ | | was performed in CNS. From an Fo Fc difference map, a Improved methods for building protein models in electron density p-nitrophenyl phosphate inhibitor molecule was located near the maps and the location of errors in these models. Acta Crystallogr. active site of each subunit. The current model has working and free A 47, 110–119. R factors of 20.8% and 26.9%, respectively. Stereochemistry of the Kobayashi, K., Lin, L.W., and Yeadon, J.E. (1989). Cloning and se- structure is good, with 85.0% of residues in the most favored region quence analysis of a rat liver cDNA encoding acyl-peptide hydrolase. of the Ramachandran plot generated by PROCHECK. J. Biol. Chem. 264, 8892–8899. Larsen, N.A., Turner, J.M., and Stevens, J. (2002). Crystal structure Acknowledgments of a bacterial cocaine esterase. Nat. Struct. Biol. 9, 17–21.

We thank Min Yao for assistance during data collection at SPring-8, Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M. Japan. We are also grateful to Kazuhiko Ishikawa, Hiroyasu Ishida, (1993). PROCHECK: a program to check the stereochemical quality Susumu Ando, and Yoshitsugu Kosugi. Z.R. was supported by of protein structures. J. Appl. Crystallogr. 26, 283–291. grants from Projects “863” (no. 2002BA711A12) and “973” (no. Leslie, A.G.W. (1992). Recent changes to the MOSFLM package for G1999075602) of the Ministry of Science and Technology, China. processing film and image plate data. In Joint CCP4 ϩ ESF-EAMCB Y.F. was supported by the EYTP (the Excellent Young Teachers Newsletter on Protein Crystallography 26. Program of MOE, China). Mitta, M., Ohnogi, H., and Mizutani, S. (1996). The nucleotide sequence of human acylamino acid-releasing enzyme. DNA Res. 3, Received: April 1, 2004 31–35. Revised: May 16, 2004 Mitta, M., Miyagi, M., and Kato, I. (1998). Identification of the catalytic Accepted: May 25, 2004 triad residues of porcine liver acylamino acid-releasing enzyme. J. Published: August 10, 2004 Biochem. (Tokyo) 123, 924–931.

177 Structure 1488

Miyagi, M., Sakiyama, F., and Kato, I. (1995). Complete covalent structure of porcine liver acylamino acid-releasing enzyme and identification of its active serine residue. J. Biochem. (Tokyo) 118, 771–779. Naylor, S.L., Marshall, A., Hensel, C., Martinez, P.F., Holley, B., and Sakaguchi, A.Y. (1989). The DNF15S2 locus at 3p21 is transcribed in normal lung and small cell lung cancer. Genomics 4, 355–361. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. In Macromolecular Crystallogra- phy, Part A, C.W. Carter, Jr., and R.M. Sweet, eds. (New York: Academic Press), pp. 307–326. Perrakis, A., Morris, R., and Lamzin, V.S. (1999). Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463. Rawlings, N.D., Polgar, L., and Barrett, A.J. (1991). A new family of serine-type peptidases related to prolyl oligopeptidase. Biochem. J. 279, 907–908. Richards, P.G., Johnson, M.K., and Ray, D.E. (2000). Identification of acylpeptide hydrolase as a sensitive site for reaction with organophosphorus compounds and a potential target for cognitive enhancing drugs. Mol. Pharmacol. 58, 577–583. Sako, Y., Nomura, N., and Uchida, A. (1996). A novel aerobic hyperthermophilic archaeon growing at temperature up to 100 degrees C. Int. J. Syst. Bacteriol. 46, 1070–1077. Scaloni, A., Jones, W.M., and Barra, D. (1992). Acylpeptide hydrolase: inhibitors and some active residues of the human enzyme. J. Biol. Chem. 267, 3811–3818. Scaloni, A., Barra, D., Jones, W.M., and Manning, J.M. (1994). Human acylpeptide hydrolase: studies on its thiol groups and mechanism of action. J. Biol. Chem. 269, 15076–15084. Terwilliger, T.C. (2000). Maximum-likelihood density modification. Acta Crystallogr. D Biol. Crystallogr. 56, 965–972. Tsunasawa, S., Narita, K., and Ogata, K. (1975). Purification and properties of acylamino acid-releasing enzyme from rat liver. J. Bio- chem. (Tokyo) 77, 89–102. Wang, G.G., Gao, R.J., Ding, Y., Yang, H., Cao, S., Feng, Y., and Rao, Z. (2002). Crystallization and preliminary crystallographic analysis of acylamino acid releasing enzyme from hyperthermophilic archaeon Aeropyrum pernix. Acta Crystallogr. D Biol. Crystallogr. 58, 1054– 1055. Wang, G.G., Gao, R.J., Yang, H.T., Cao, S.G., Feng, Y., and Rao, Z. (2003). Archaeal acylamino acid releasing enzyme/lipase: crystallization and preliminary crystallographic analysis in a new crystal form. Chin. Sci. Bull. 48, 154–156.

Accession Numbers

The coordinates and structure factors for apAPH have been deposited in the Protein Data Bank with PDB accession code 1VE6. The coordinates and structure factors for the apAPH-pNP complex have been deposited in the Protein Data Bank with PDB accession code 1VE7.

178 Antiviral Therapy 9:x-xx Short communication Probing the structure of the SARS coronavirus using scanning electron microscopy Yun Lin1,2, Xiyun Yan1*, Wuchun Cao3, Chaoying Wang4, Jing Feng1,2 , Jinzhu Duan1,2 and Sishen Xie4

1National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences (CAS), Beijing, China 2State Key Laboratory of Microbial Resources, Institute of Microbiology, CAS, Beijing, China 3Department of Epidemiology, Institute of Microbiology and Epidemiology, Beijing, China 4Center for Condensed Matter Physics, Institute of Physics, CAS, Beijing, China

*Corresponding author: Tel: +86 10 64888583; Fax: +86 10 64888584; E-mail: [email protected]

A novel coronavirus, SARS-CoV, has been confirmed to be electron microscopy (SEM) to image the virus particles. We the aetiological agent of SARS. Transmission electron show here the three-dimensional appearance of SARS-CoV. microscope (TEM) images played an important role in Enhanced detail of the ultrastructure reveals the trimeric initial identification of the pathogen. In order to obtain structure of the 10–20 nm spikes on the virion surface. greater morphological detail of SARS-CoV than could be These results contribute to characterization of the SARS obtained by TEM, we used ultra-high resolution scanning agent and development of new antiviral strategies.

Introduction

It has been confirmed by several research groups [1–4] Enzyme-linked immunosorbent assay that the worldwide outbreak of severe acute respira- Inactivated virions were coated onto 96-well plates and tory syndrome (SARS) is caused by a novel incubated with either normal sera or convalescent sera coronavirus, named SARS coronavirus (SARS-CoV). from SARS patients, and then detected by HRP conju- The ultrastructural features of coronaviruses, including gated anti-human IgG. Positive and negative controls SARS-CoV, have been established by transmission elec- were from a diagnostic kit of antibodies for SARS virus tron microscope (TEM) imaging [2]. However, little is (BGI-GBI Biotechnology Ltd, Beijing, China) and were known about the appearance of a complete virus independent of the sera we used. The cut off value was particle and the ultrastructure of the virus surface. determined by the equation: cut off

Here we provide the first observation of SARS-CoV value=0.13+Valuenegative control (OD450 nm). If the colour particles by means of a dedicated ultra-high resolution reaction represented a higher value than the cut off scanning electron microscope (SEM) (HITACHI S- value, it was judged as positive. 5200, Japan). These data contribute to a more comprehensive understanding of SARS-CoV. Sample preparation for scanning electron microscopy The purified viruses were submitted to the fixation and Materials and methods sputter coating procedure before viewing by SEM. Briefly, 3×5 mm cover slides or 200 mesh copper grids Preparation of purified SARS virus were coated with 1% poly-L-lysine (87 000) and then Given the serious nature of SARS, all clinical specimens rinse with phosphate-buffered saline (PBS, pH 7.2) to were handled in a biosafety level 3 laboratory. Serum remove excessive poly-lysine. Viruses with different specimens were inactivated by β-lactone before outside dilution in TNE were dripped on cover slides or copper serological testing. SARS virus strain BJ01 [5] was grids and let adhere for about 30 min. Excessive obtained from a patient with SARS and established in samples were sucked up and rinsed with PBS. After the Vero E6 cell line. Culture supernatant was collected fixation in 2.5% glutaraldehyde for 30 min and a and centrifuged at low-speed to remove cells frag- further 30 min in 1% osmium tetroxide, samples were ments. After sucrose-gradient ultracentrifugation, the dehydrated through an ethanol series in buffer: 50% – purified virus pellet was resuspended in TNE (0.25 M 70% – 90% – 100% – 100% for 5 min each and crit- NaCl, 0.02 M Tris-Cl pH 7.5, 0.001 M EDTA) buffer. ically point dried from ethanol. Samples were mounted

179 Y Lin et al.

Figure 1. Specific binding of the purified SARS-CoV BJ01 to in agreement with the reported diameter of the SARS convalescent sera from SARS patients virus spike. With further magnification of this part (Figure 2D, arrowheads), we observed the projections with a regular structure composed of three subunits, 2.0 1.8 like a flower with three petals. 1.6 1.4 Conclusion 1.2 1.0 In this study, we provide the first three-dimensional 0.8 OD450 nm 0.6 structure of the causative agent in SARS infection and 0.4 the detailed information about the ultrastructural 0.2 surface of SARS-CoV by using SEM, which offers 0.0 advantages over TEM for the study of biological mole- 1:10 1:100 1:1000 Positive controlNegative control cules such as viruses, nucleic acid and proteins, due to its higher resolution and less disruptive nature of the Sample dilution technique. We observed all the surfaces of SARS virions bear flower-shaped projections that contain three S protein subunits. The S glycoprotein is known on specimen stubs with conductive paint and coated to as a major immunogenic determinant of pathogenesis, a thickness of 10 nm with Au in a sputter coater. binds to specific receptors and then undergo a temper- Samples were viewed in lens on the Hitachi S-5200 ature-dependent, receptor- mediated conformational SEM with slow scan mode, 10 kV accelerating voltage change that leads to fusion of the viral envelope with and 0–0.3mm working distance. host membranes to initiate infection. Delmas et al. demonstrated by in vitro experiment that coronavirus Results S protein tends to oligomerize into a trimer and the trimerization was a rate-limiting step after polypeptide In order to identify the biological characteristics of synthesis [6]. Together with our structural observations the purified virus, we first tested the reactivity of the of trimeric S protein on the surface of virion, we virus with convalescent sera from SARS patients hypothesize that the identification of the receptor using an enzyme-linked immunosorbent assay binding sites and the conformational change after S (ELISA). Comparing with positive and negative protein activation, as well as molecular interpretation controls, the purified SARS-CoV showed very strong of trimerization, may give rise to new strategies for binding to the convalescent sera but not to normal development of novel antiviral drugs. sera (Figure 1). This specific reaction indicated that It has been accepted that the size of coronaviruses the virus we purified from the culture supernatant of are about 80–200 nm observed by TEM. However, we Vero E6 cells was SARS-CoV. found in the SEM images that the size of the SARS To better understand the morphological detail of CoV BJ01 varied, most of them were about 150–200 SARS-CoV, we used ultra-high resolution scanning nm, a few up to 400 nm in diameter, which is signifi- electron microscopy to image the virus particles. Under cantly larger than the known 80–220 nm size of the SEM, we observed large numbers of virus particles SARS-CoV, even if the thickness of Au coating (20 nm) with predominantly 150–200 nm in diameter either was added. We noticed that the larger virions had the isolated or in aggregates (Figure 2). These SARS-CoV same flower-shaped projections as those with normal particles with a typical crown structure were further size, and both particles in different sizes were seen in confirmed by using TEM (data not shown). the same view. Although we are not able to prove these Incidentally, we found a few virus particles as large as variations by further experiments at the moment 400 nm in diameter, which had identical shape and because of the lack of SARS-CoV material, it remains surface substructure as the 200 nm particles and an interesting question to be addressed in future. presented in a single field (Figure 2C). Taken together, our data vividly revealed the three- The virus particles appear round and full, with dimensional appearance of SARS-CoV as well as their numerous tiny surface projections. Some are tightly ultrastructural surfaces with three subunits-based adhered with their projections sticking into each other, projections. These results would enrich the morpho- forming a mosaic patch and leading to the compression logical studies of the SARS-CoV and contribute to of the virions. These flower-shaped projections corre- better understanding of SARS-CoV, with application to sponding to the spike, the main constituent of which both basic virology and clinical practice. was S protein, have a size ranging from 10 to 20 nm,

180 SARS-CoV SEM

Figure 2. SARS-CoV observed under scanning electron microscope

A B

C D

(A) Virions with diameter of 200 nm. (B) Virions with sizes of 100 and 200 nm. (C) Virions of 400 nm in diameter. (D) The ultrastructure of the surface projections. Two typical spikes are magnified to show the trimer structure (insets).

Acknowledgements 3. Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Penaranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, We acknowledge Jinzhu Zhang for advice on virus Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, identification, Lixin Liu and Guangxia Gao for sugges- Gunther S, Osterhaus AD, Drosten C, Pallansch MA, tions on virus purification, and Sarah Perrett for Anderson LJ & Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory editing the manuscript. This work is supported by the syndrome. Science 2003; 300:1394–1399. National 973 grant specific for SARS prevention and 4. Drosten C, Gunther S, Preiser W, van der Werf S, Brodt HR, therapy. Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RA, Berger A, Burguiere AM, Cinatl J, Eickmann M, Escriou N, Grywna K, Kramme S, Manuguerra JC, Muller References S, Rickerts V, Sturmer M, Vieth S, Klenk HD, Osterhaus AD, Schmitz H & Doerr HW. Identification of a novel coro- 1. Nicholls JM, Poon LL, Lee KC, Ng WF, Lai ST, Leung CY, navirus in patients with severe acute respiratory syndrome. Chu CM, Hui PK, Mak KL, Lim W, Yan KW, Chan KH, New England Journal of Medicine 2003; 348:1967–1976. Tsang NC, Guan Y, Yuen KY & Peiris JS. Lung pathology 5. Qin Ede, Zhu Qingyu, Yu Man et al. A complete sequence of fatal severe acute respiratory syndrome. Lancet 2003; and comparative analysis of a SARS-associated virus 361:1773–1778. (Isolate BJ01). Chinese Science Bulletin. 2003; 48:941–948. 2. Ksiazek TG, Erdman D & Goldsmith CSA. Novel coron- 6. Delmas B & Laude H. Assembly of coronavirus spike avirus associated with severe acute respiratory syndrome. protein into trimers and its role in epitope expression. New England Journal of Medicine 2003; 348:1953–1966. Journal of Virology 1990; 64:5367–5375.

Received 14 August 2003, accepted 25 November 2003

Antiviral Therapy 9:2 171

181 doi:10.1016/j.jmb.2004.03.045 J. Mol. Biol. (2004) 339, 207–215

Unique Structural Characteristics of Peptide Deformylase from Pathogenic Bacterium Leptospira interrogans

Zhaocai Zhou1,2, Xiaomin Song1,2, Yikun Li1,2 and Weimin Gong1,2*

1National Laboratory of Peptide deformylase (PDF), which is essential for normal growth of Biomacromolecules, Institute of bacteria but not for higher organisms, is explored as an attractive target Biophysics, Chinese Academy of for developing novel antibiotics. Here, we present the crystal structure of Sciences, Beijing, 100101 Leptospira interrogans PDF (Li PDF) at 2.2 A˚ resolution. To our knowledge, People’s Republic of China this is the ﬁrst crystal structure of PDF associating in a stable dimer. The key loop (named the CD-loop: amino acid residues 66–76) near the 2School of Life Sciences, Key active-site pocket adopts “closed” or “open” conformations in the two Laboratory of Structural monomers forming the dimer. In the closed subunit, the CD-loop and Biology, University of Science residue Arg109 block the entry of the substrate-binding pocket, while the and Technology of China, Hefei active-site pocket of the open subunit is occupied by the C-terminal tail Anhui, 230026, People’s from the neighbouring molecule. Moreover, a formate group, as one Republic of China product of deformylisation, is observed bound with the active-site zinc ion. Li PDF displays signiﬁcant structural differences in the C-terminal region compared to both type-I and type-II PDFs, suggesting a new family of PDFs. q 2004 Elsevier Ltd. All rights reserved. Keywords: peptide deformylase; dimerization; active-site pocket; *Corresponding author conformational change; formate group

Introduction biosynthesis.2 Thus, inhibition of PDF would halt bacterial growth and spare host cell function. In Bacterial protein synthesis begins with a formyl- fact, as an attractive target for the development of ated methionine residue.1,2 Following translation novel antibiotics, the peptide deformylase is initiation, peptide deformylase (PDF) catalyzes the currently studied extensively, not only regarding hydrolytic removal of the N-terminal fMet residue catalytic properties, but also from a three-dimen- of most nascent polypeptides in eubacteria and sional structure perspective. It was long believed the organelles of certain eukaryotes.3–9 Although that Escherichia coli PDF was a zinc enzyme until it N-formylation is not essential for the survival of was characterized as a ferrous native enzyme with all bacterial species, it can stimulate protein extraordinary lability caused by oxygen-mediated synthesis by facilitating the participation of Met- inactivation.20 – 22 The ferrous can be replaced by a tRNA fMet in translation initiation and by prevent- nickel ion without significant loss of catalytic ing its recognition by the elongation apparatus.10,11 efficiency, whereas the zinc form, prepared from However, the first step in N-terminal processing the apo-enzyme or by displacement of ferrous or by PDF is essential for the bacterial survival, nickel ion, proved to be virtually inactive.23 – 26 because mature proteins do not retain N-formyl- However, an eukaryotic PDF from Arabidopsis methionine and all known N-terminal peptidases thaliana seedlings (AtPDF1A) was recently charac- cannot utilize formylated peptides as terized by Serero et al.27 to be a zinc enzyme with substrates.12 – 19 This formylation/deformylisation full activity. To date, attempts to explain the enor- cycle is apparently unique to eubacteria and is not mous activity difference between ferrous PDF and utilized in eukaryotic cytosolic protein zinc PDF from a structure analysis of a metal centre have not been successful.23 Phylogenetic tree anal- Abbreviations used: PDF, peptide deformylase; Li, ysis and systematic sequence alignment classify Leptospira interrogans; Ec, Escherichia coli. available PDF structures into type-I and type- 25,28 E-mail address of the corresponding author: II. Most of type-I PDFs, represented by E. coli [email protected] deformylase, belong to Gram-negative organisms

0022-2836/$ - see front matter q 2004 Elsevier Ltd. All rights reserved. 182 208 Unique Structural Characteristics of Zinc LiPDF and have ,30% sequence identity with each other; three other key residues Gly49, Gln54 and Glu145 whereas type-II PDFs, represented by Staphylococcus within the active centre remains conserved. aureus deformylase, come from a distinct group of Consistent with the result of size exclusion Gram-positive organisms. Compared to type-I column chromatography experiments,29 the asym- PDFs, type-II PDFs are characterized by three metric unit of Li PDF crystals consist of two sub- sequence insertions and a hydrophobic C terminus.28 units (named A and B) forming a dimer, related As a ubiquitous environmental bacterium, by a non-crystallographic 2-fold axis. To our Leptospira can cause strong leptospirosis infection knowledge, this is the first crystal structure of a of animal and human by entering the host through dimerized PDF (although P. falciparum PDF mucosa and broken skin. The resultant bacteria is exhibited a tendency to form dimers; Kumar frequently found as the complication after et al.26). Each of the dimers is part of a tetramer operation. Most of the related pathogens show drug sitting on a crystallographic 2-fold axis. Detailed tolerance to conventional antibiotics, making it an examinations of the four monomers (monomer A, urgent need to develop effective and novel drugs. B, A0 and B0;A0 and B0 are symmetry related Here we analysed the crystal structure of pep- molecules of A and B, respectively) in the tetramer tide deformylase from Gram-negative bacterium definitely revealed that electrostatic interactions pathogen Leptospira interrogans (Li PDF) in the zinc predominate on the interface between the crystallo- bound form. Interestingly, Li PDF was observed to graphic 2-fold related subunits (A–A0 or B–B0, be a dimer in crystals although Kumar et al.26 have buried surface ,800 A˚ 2). Contrarily, quite a few seen complex oligomers in crystals of Pseudomonas hydrophobic residues contribute to the interactions falciparum PDF,26 consistent with its stable bio- between the non-crystallographic symmetry logical association in solution.29 Such a dimer has related subunits (A–B or A0 –B0) and they are most not been reported in other PDF structures. likely to compose the biological dimer (Figure 2). Unexpectedly, unique “closed” and “open” sub- The dimeric association is primarily mediated by strate-binding pockets were formed, respectively, the hydrophobic interactions of strands bE, bHof in the two monomers. More importantly, the one subunit and their counterparts of the other sub- active-site zinc ion was observed to coordinate unit, mostly contributed by Phe164, Phe166, Met108 with one of its catalytic reaction products, a formate and Met9. The solvent-accessible surface area buried group, instead of a water molecule as in other PDF between the subunits is approximately 10% of the structures. Besides, the key loop around the active surface area of one subunit. Whether such dimerisa- cleft (CD-loop) and the C terminus exhibit great tion is of any significance to the catalysis mechanism differences compared with other PDFs, suggesting remains to be elucidated. that Li PDF belongs to a new PDF family. The unique C terminus

With five X-ray structures of PDFs from different Results and Discussion origins currently available,23,25,26,28,30,31 we have performed a detailed comparison of Li PDF with Overall structure and dimer association of type-I and type-II deformylases. Some important Li PDF structural differences have been revealed ranging from topology to the substrate-binding pocket. Similar to other PDF structures, the core struc- Although the overall structure of Li PDF is similar ture of Li PDF contains two a-helices, seven b- to other PDFs, sequence alignments (Figure 1) and strands and three 310 helices (Figure 1). As highly structural comparison clearly distinguished Li PDF conserved structural elements, these three 310 from either type-I or type-II PDFs. Li PDF helices comprise the bottom of the active-site apparently belongs to the type-I family based on hydrophobic pocket and help to build the internal its N-terminal character. However, the C-terminal microenvironment required for catalysis. The first part shows little sequence or structural homology conserved 310 helix, which plays a role in sealing to either type-I or type-II PDFs and is even much up the back of the active-site pocket, is embedded more hydrophobic than type-II PDFs. Type-I PDFs in the middle of the coil preceding the N-terminal possess a long C-terminal a-helix, which is parallel aA helix. Located on the BC loop, that is flanked to bF.16,18,19 In contrast, the C terminus of type-II with the first and the second strands of the PDF turns back to form a mixed b-sheet with bE N-terminal three-stranded antiparallel b-sheet, is and bF. 14 However, the C terminus of Li PDF, con- the second 310 helix, which provides Gln54 as a sisting of a short b-strand (bJ) and an a-helix key residue from the first conserved box for the (aK), heads to the direction between type-I and indirect coordination of the zinc ion (Figure 1). type-II PDFs (Figure 3). bJ joins the C-terminal The central aI helix forms the core of the PDF antiparallel b-sheet, interacting with bF, instead of structure and provides two residues, His144 and bE as in type-II PDFs. His148, for the coordination of the active-site Both molecules in the asymmetric unit have the metal ion. Residue Leu103, acting as a Lewis acid same C-terminal conformation. But their last four for the polarisation of the formyl carbonyl group tail residues go in different directions mostly due in the process of substrate cleavage, together with to different packing environments. PDF was

183 Unique Structural Characteristics of Zinc LiPDF 209

Figure 1. Structure based sequence alignment of Li PDF with type-I and type-II PDFs. This alignment was basically performed with program CLUSTALW39 and redressed according to the result of structure overlapping by LSQMAN.† The sequence labels are shown on the left in each block. Type-I (E. coli, P. aeruginosa, P. falciparum) and type-II (S. aureus, Bacillus stearothermophilus) peptide deformylases are indicated in green and orange, respectively, while Li PDF is highlighted in blue. Three identiﬁed motifs have been boxed with strictly conserved residues in dark blue. Striking sequence variations are observed in a loop region near the active pocket (namely CD-loop in Li PDF). The secondary structural elements of Li PDF determined by PROMOTIF‡ are drawn above the sequences and labelled as for Figure 4 The lines connecting to the small ball in purple indicate those residues coordinating with the zinc ion in Li PDF. Note: (*) identity; (:) strongly similar; (.) weakly similar. Three conserved 310 helices are presented in pentagons. thought to act while bound to the ribosome3,32,33 Two conformations of the CD loop and its C-terminal part was proposed to serve to anchor the enzyme to the ribonucleoproteic Besides a unique C terminus, a striking confor- complex for the proximity of substrate.34 This is mational change of the CD-loop (from Ser66 to consistent with the variable conformations Pro76 between bC and bD) adjacent to the active observed in PDF’s C terminus. centre was observed. Compared to type-I and type-II PDFs, Li PDF has the longest CD-loop (Figure 1). The structures of the two subunits are essentially identical with the r.m.s. deviation † Kleywegt, G. J.; LSQMAN v 020925 Department of between the corresponding Ca atoms to be 0.34 A˚ Cell and Molecular Biology, Uppsala University, except for the CD-loop and the last four C-terminal Biomedical Centre, Box 596, SE-75124 Uppsala, Sweden. ‡ Hutchinson, E. G. & Thornton, J. M.; PROMOTIF residues. The CD-loops of type-I and type-II PDFs, v2.0; Biomolecular Structure and Modelling Unit, although adopting different conformations due to Department of Biochemistry and Molecular Biology, different lengths, are both positioned to make the University College, Gower Street, London WC1E 6BT, active-site pocket open for substrate binding UK. (Figure 4(a) and (b)). Nevertheless, utterly different

184 210 Unique Structural Characteristics of Zinc LiPDF

Figure 2. Dimerization of Li PDF. Interactions between NCS related molecules in the asymmetric unit that form a stable dimer. Different conformations (open and closed) of the substrate-binding pocket were observed in these two subunits, which result in the non-symmetric appearance of the dimer. The C terminus is also related with a different packing environment and is in keeping with the case of the substrate-binding pocket. Residues forming the hydrophobic core (Phe164, Phe166, Met108 and Met9) are rendered in ball-and-stick format. The active-site zinc ion is highlighted with a purple ball. This Figure and Figures 3, 4, 5 and 6 were generated by MOLSCRIPT40 and rendered by Raster3D.41 Figure 4. Comparison of CD-loop conformations. Green, CD-loop; brown, C-terminal tail; white, the additional part. EcPDF and SaPDF represent type-I and from them, the corresponding CD-loop of Li PDF type-II peptide deformylase, respectively. a, Ec PDF; b, was observed to have two distinct conformations Sa PDF; c, open form of Li PDF; d, closed form of Li PDF. in the two subunits. In one subunit, the CD-loop is located with the active-site pocket open similar to other PDFs (this subunit is named as the open (Figure 5(a)). The side-chain of Arg109 shifts form; Figure 4(c)). In the other subunit, surpris- inside, forming a hydrogen bridge with Arg71(O), ingly, the CD-loop markedly turns towards the modifying the electrostatic and hydrophobic active-site crevice as a closing cover (this subunit nature of the substrate-binding cleft. Thus, the is therefore named as the closed form; Figure 4(d)). CD-loop, together with Arg109, blocks the active- The side-chains of Arg71 and Tyr72 (on the tip of site entrance, which is critical for substrate/ CD-loop), which are hydrogen bonded with each inhibitor binding. If the natural inhibitor of PDF, other, protrude deeply into the active-site cleft actinonin, is modeled into this closed form, serious collisions are observed between the Tyr72 side- chain and the side-chains at P20 and P30 of the inhibitor, suggesting that the CD-loop “lid” must be opened before substrate molecules access the catalytic site. No structural equivalents of Arg71 and Tyr72 were observed in other PDFs structures. The fact that the CD-loop in the closed subunit is completely solvent-exposed and not involved in crystal packing, indicates that the closed form would exist naturally, whereas, in the open form, a neighbouring molecule related by a crystallographic 2-fold axis protrudes its C-terminal tail into the open active pocket (Figure 5(b)).

Metal binding site

Li PDF, which was puriﬁed and crystallized with

a no extra metal ions added, was determined by Figure 3. Overlaping of C atoms of Li PDF with type-I atomic absorption spectroscopy to contain one (E. coli) and type-II (S. aureus) PDFs. White, E. coli PDF 29 (Ec PDF); green, S. aureus PDF (Sa PDF); yellow, Li PDF. zinc atom per monomer. The activity of Li PDF is 24 This Figure was calculated by Lsqman and checked by much higher than that of E. coli zinc-PDF but program O. The sequence alignment in Figure 1 is much lower than that of E. coli Fe(II)-PDF.20 It is referred to as such a kind of structure overlapping. still unclear whether such differences are related

185 Unique Structural Characteristics of Zinc LiPDF 211

Figure 5. Stereo view of closed and open subunits of Li PDF. The protein skeleton is shown using a coil model with the active-site pocket in green and the CD-loop in black. The small purple sphere represents the active-site zinc ion. (a) The closed subunit: CD-loop residues Arg71 and Tyr72 protrude into the pocket. These two residues, together with Arg109, block the entry of the pocket. The glycine residue in the S0 pocket is represented in a bond model. (b) The open subunit: the CD-loop and Arg109 withdraw from the closed position. The symmetry related neighbouring tail is highlighted in pink. Asterisks represent residues on this neighbouring tail. The simulated product MAS was modelled by superimposing E. coli PDF (PDB entry ID 1BS8) to Li PDF. to the special dimer association of Li PDF. Com- replaced with a well-deﬁned formate group (from parison of the metal coordination with available crystallization solution) in the structure of Li PDF, structures reveals a perfectly conserved catalytic leading to the ﬁve-coordination of the zinc ion. core, supporting the view that all PDFs adopt the This formate group, one of the products of the same mechanism. Three residues, His144, His148, deformylisation reaction, provides two formate Cys102, are absolutely conserved and involved in oxygen atoms as coordinating ligands with one of the coordination with the metal ion. A water them binding to the zinc ion weakly (2.8 A˚ ) molecule is generally present as the fourth ligand. (Figure 6). Besides, one oxygen atom of the formate However, the metal-coordinating water molecule group also hydrogen bonds to the “proton shuttle” universally observed in other PDF structures is residue Glu145 and the other oxygen atom to the

186 212 Unique Structural Characteristics of Zinc LiPDF

Figure 6. Electron map of the metal binding site. (a) If one water molecule was filled; (b) if two water molecules were filled; (c) if none was filled, the formate group is present here for the purpose of comparison; (d) a formate group was filled. Notes: green: 2Fo 2 Fc map; red: Fo 2 Fc map with a 3 sigma cut-off. The electron density of this local area is essentially identical for the two subunits in the asymmetric unit. main-chain nitrogen atom of Leu103 and Gln54 active-site metal ion, forming an intermediate NE2. Consistent with previous reports,30,31 the complex during the last two steps. Our structure side-chain of Gln54 is not only hydrogen bonded essentially supports such a catalytic model. Super- with the ligand water molecule at ground state, imposing of the Li PDF structure with E. coli but also involved in binding the formyl group of deformylase (Ec PDF) complexed with its natural the substrate during the catalytic process. inhibitor actinonin (PDB entry: 1LRU) reveals that At the opposite side of the formate group, a the formate group of Li PDF assumes almost the highly conserved three-molecule water chain is same spatial position as the pseudo-formyl end of observed, contributing to the stabilization of the the actinonin (r.m.s.d.: 1.2 A˚ ). In fact, our obser- active centre. The first water molecule (nearest to vation corresponds to the enzyme–formate the active-site zinc ion) interacts with Gln154 with complex, providing the first direct evidence for a hydrogen bond. The middle water molecule the states in the last two steps. Although one coor- hydrogen bonds to the carbonyl oxygen atom of dinating water molecule (W1) is surely necessary His144. The third water molecule hydrogen bonds for the ground state of PDF, detailed checking of to the side-chains of Arg114 and Asp147. These models available revealed some spatial variations conserved residues and water molecules, together of this water molecule. It appears that the second with Glu100 and Arg157, create an extensive water molecule (W2) is not always present. hydrogen bond network, which maybe partially contributes to the stability of catalytic Substrate binding pocket intermediates. Concerning the catalytic cycle, Becker et al.23 pro- Residues Ile86 and Leu125 in Ec PDF are posed a five-step mechanism in which the cleaved replaced with Phe98 and Tyr137 in Li PDF, respect- formate group from the substrate binds to the ively, with their bigger side-chains contributing to

187 Unique Structural Characteristics of Zinc LiPDF 213 a narrower substrate entrance. The resultant con- the crystallizing sample. Crystals were grown by vergence effect to the pocket has serious conse- vapour-diffusion at 277 K by the hanging-drop method. quences for substrate/inhibitor binding, which is Good crystals were obtained within four days under the a possible factor for the relative low catalytic effi- condition of 4 M sodium formate, Gly–HCl buffer ciency of Li PDF compared with nickel-containing (pH 3.0). Interestingly, the optimized crystal is very small but possesses excellent diffraction quality. Ec PDF.17 However, Li PDF exhibits much higher activity compared with zinc bound Ec PDF.29 No Data collection and processing direct explanation for the fact that PDF activity is depending on the bound metal has been obtained Data were collected on a MAR Research image-plate from the present structure. system with a local X-ray source at 100 K. The wave- In addition, a glycine molecule from the crystal- length was 1.5418 A˚ and the exposure time was five min- lization buffer solution is observed in the bottom utes per image. The oscillation step for each image was 0 of the S1 pocket of Li PDF, along the direction of 18 The crystal-to-detector distance was set to 150 mm. P10 side-chain. This indicates that the S10 pocket of The data were processed with DENZO and SCALE- 27 Li PDF is, at least, not strictly hydrophobic, in line PACK. The space group was determined to be P3121 with the fact that Tyr137 projects its side-chain with which the correct molecular replacement solution hydroxyl group to form the bottom of S10. was obtained. Details of data collection and processing In the crystal packing of Li PDF, the C-terminal statistics are shown in Table 1. tail of one neighbouring molecule is docked snugly into the active-site pocket of the open form, Structure determination and refinement reminding us that an active site is occupied by the Phases were obtained by molecular replacement with simulated product Met-Ala-Ser in the complex 35 structure (PDB entry: 1BS8) (Figure 5(b)). The the AMoRe package. The structure of P. aeruginosa PDF (PDB code: 1LRY) was taken as an initial search model second rearmost residue Leu177* (the asterisks over the resolution range 15–4.0 A˚ . A weak solution represent residues on this neighbouring C-terminal with two molecules in one asymmetric unit was obtained tail) extends its side-chain into the S10 hydrophobic in space group P3121. Remarkably, the C-terminal pep- pocket with the side-chain of Asp178* directing to tides of the two subunits in this solution were found to 0 the position of P3 . It seems that such a C-terminal seriously involve each other when checked with tail mimics a real substrate peptide normally program O.36 Then the C terminus was cut and non- much longer than the simulated three amino acid conserved amino acid residues except glycine were set residue product. Interestingly, the part of the to alanine. The subsequent refinement was performed 37 C-terminal tail outside the pocket is braced by a with CNS, using standard protocols and solvent correc- CD-loop (through interactions between Leu163* tion. After rigid body and energy minimization refinements, manual rebuilding of the model including the and Pro73, His174* and Tyr72 in Li PDF), C-terminal peptide was carried out with program apparently facilitating the proper anchoring of the O. Twofold NCS redundancy was exploited with about substrate to the active-site. To date, no description 90% atomic coordinates being restrained to obey non- on the full-length substrate binding has been crystallographic symmetry. After several cycles of local reported and our observations provide a possible rebuilding and refinement the electron density appeared model for the naturally occurred enzyme– to be quite good. The zinc atom and the coordinating for- substrate interactions. mate group, as well as the glycine molecule in the S10 To conclude, this study shows the first structure pocket were incorporated into the refined model by of a dimerized peptide deformylase and reveals direct examination of Fo 2 Fc map. The R-factor of the ð ¼ Þ some unique characters of Li PDF distinct from final model is 0.187 Rfree 0:236 (Table 1). Statistics type-I and type-II PDFs, suggesting a novel family of PDFs. Instead of the well-accepted open sub- Table 1. Statistics of data collection and refinement strate-binding cleft, a striking closed pocket is observed. Besides, important differences are Space group P3121 revealed regarding the catalytic site. For the first Unit cell parameters a ¼ b ¼ 91.03 A˚ , ˚ time, a formate group as one of the reaction c ¼ 86.38 A Resolution range (A˚ ) (last shell) 100–2.15 (2.20–2.15) products is directly observed to coordinate with No. total reflections 178,754 the metal ion. Moreover, the C-terminal tail of a No. independent reflections 22,512 neighbouring molecule is observed to occupy the Completness (%) 98.1(99.6) active-site pocket of the open form subunit. Rmerge 0.103(0.514) I/s (I) 14.49(3.0) Percentage of reflections used for 8 R-free No. protein atoms 2807 Materials and Methods (occupancy . 0) No. ligand atoms 6 Purification and crystallization No. metal atoms 2 No. solvent molecules 521 Isolation and purification were carried out basically R-value (last shell) 0.187(0.288) 29 R-free (last shell) 0.236(0.417) following the protocol described. Additional steps ˚ were mainly towards the application of FPLC S-100 and r.m.s.d. of bond length (A) 0.0078 r.m.s.d. of bond angle (deg.) 1.3880 Mono-Q columns, which greatly improved the purity of

188 214 Unique Structural Characteristics of Zinc LiPDF generated by PROCHECK38 showed that the model ties of Escherichia coli peptide deformylase. quality is beyond the normal standard. J. Bacteriol. 177, 1883–1887. 12. Schmitt, E., Guillon, J. M., Meinnel, T., Mechulam, Y., Protein Data Bank accession code Dardel, F. & Blanquet, S. (1996). Molecular recognition governing the initiation of translation in Escherichia coli. Biochimie (Paris), 78, 543–554. The atomic coordinates of the reﬁned model of Li PDF 13. Hirel, P. H., Schmitter, M. J., Dessen, P., Fayat, G. & have been deposited in RCSB Protein Data Bank under the accession number 1RN5. Blanquet, S. (1989). Extent of N-terminal methionine excision from Escherichia coli proteins is governed by the side-chain length of the penultimate amino acid. Proc. Natl Acad. Sci. USA, 86, 8247–8251. 14. Dalboge, H., Bayne, S. & Pedersen, J. (1990). In vivo processing of N-terminal methionine in E. coli. 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Edited by I. Wilson

(Received 29 December 2003; received in revised form 16 March 2004; accepted 16 March 2004)

190 doi:10.1016/j.jmb.2004.09.036 J. Mol. Biol. (2004) 344, 317–323

COMMUNICATION Crystal Structure of Human Coactosin-like Protein

Lin Liu1,2†, Zhiyi Wei1,2†, Yanli Wang1,2, Mao Wan2, Zhongjun Cheng1,2 and Weimin Gong1,2*

1National Laboratory of Human coactosin-like protein is an actin filament binding protein but does Biomacromolecules, Institute of not bind to globular actin. It associates with 5-Lipoxygenase both in vivo Biophysics, Chinese Academy of and in vitro, playing important roles in modulating the activities of actin Sciences, Beijing 100101 and 5-Lipoxygenase. Coactosin counteracts the capping activity of capping People’s Republic of China protein which inhibits the actin polymerization. We determined the crystal structures of human coactosin-like protein by multi-wavelength anom- 2School of Life Sciences, Key alous dispersion method. The structure showed a high level of similarity to Laboratory of Structural ADF-H domain, although their amino acid sequences share low degree of Biology, University of Science homology. A few conserved hydrophobic residues that may contribute to and Technology of China the folding were identified. This structure suggests coactosin-like protein Hefei, Anhui 230026, People’s bind to F-actin in a different way from ADF/Cofilin family. Combined Republic of China with the information from previous mutagenesis studies, the binding sites for F-actin and 5-Lipoxygenase were analyzed, respectively. These two sites are quite close, which might prevent F-actin and 5-Lipoxygenase from binding to coactosin simultaneously. q 2004 Elsevier Ltd. All rights reserved. Keywords: human coactosin-like protein; crystal structure; F-actin; *Corresponding author 5-Lipoxygenase; capping protein

Actin plays important roles in cell architecture, sequence was initially found as a sequence flanking motility, phagocytosis, endocytosis and cytoplasmic a deletion on chromosome 17 characterizing the streaming.1 Its functions are modulated by a large Smith–Magenis syndrome (SMS). The SMS critical number of actin-binding proteins (ABPs). The region overlaps with a breakpoint cluster region structures of actin and many of its binding proteins associated with primitive neuro-ectodermal have been determined to high resolution using tumors, suggesting that the CLP gene is involved X-ray crystallography and NMR spectroscopy, in DNA rearrangements of somatic cells.5 CLP is whereas electron microscopy and image processing also reported as a human pancreatic cancer antigen have established the interaction sites on F-actin for by SEREX method.6 myosin and a range of actin-binding proteins.2 CLP binds directly to filamentous-actin (F-actin) Coactosin is a 17 kDa actin-binding protein but does not form a stable complex with globular originally isolated from Dictyostelium discoideum.3 actin (G-actin). CLP binds to actin filaments with a It is revealed that coactosin is able to counteract the stoichiometry of 1 : 2 (CLP: actin subunits), but activity of capping proteins that retard actin could be cross-linked to only one subunit of actin.7 polymerization, while coactosin itself has no effect Human CLP was first obtained in a yeast two- on actin polymerization.4 hybrid screen using 5-Lipoxygenase (5LO), also an The human version of coactosin named coacto- actin-binding protein, as a bait.8 5LO is a 78 kDa sin-like protein (CLP) shows a significant homology enzyme, the first enzyme in cellular leukotriene to coactosin with 33.3% identity and 75% homology biosynthesis. 5LO catalyzes two-step conversion of in amino acid sequence. Human CLP nucleotide arachidonic acids to leukotrienes, which are potent mediator of inflammation of allergy disorders including arthritis, asthma, and allergic reactions. † L.L. & Z.W. contributed equally to this work. In resting cells, 5LO is localized in soluble Abbreviations used: ABPs, actin-binding proteins; CLP, coactosin-like protein; SMS, Smith–Magenis syndrome; compartments, in the cytosol and/or within the MAD, multi-wavelength anomalous dispersion; PDB, nucleus. Upon activation, 5LO becomes associated Protein Data Bank; rmsd, root-mean-square deviation. with the nuclear membrane. The migration of 5LO E-mail address of the corresponding author: is probably of the most importance for regulation [email protected] of the cellular 5LO activity.9 Modulation of

0022-2836/$ - see front matter q 2004 Elsevier Ltd. All rights reserved. 191 318 Crystal Structure of Human Coactosin-like Protein translocation and activation of 5LO may involve six His residues in the C-terminal end) per selenium interactions with other proteins. atom. The final models contain two monomers in the asymmetric unit. The C-terminal region seems very disordered, with no electron density fitting for Structure overview residues 138–148 in chain A, and residues 132–148 The crystal structure of human CLP is the first in chain B, respectively. structure of coactosin/CLP family. The structure The monomer structure consists of a six-stranded was solved by multi-wavelength anomalous dis- mixed b-sheet in which the four central strands persion (MAD) method using a seleno-methionine (b2-b5) are anti-parallel and the two edge strands substituted protein crystal, and refined at 2.8 A˚ (b1 and b6) run parallel with the neighboring resolution (Table 1). There is only one methionine strands. The sheet is surrounded by two a-helices (Met70) in the recombinant human CLP protein. on each side (Figure 1). Such a structure is a typical Mass spectroscopy experiment proved that the first ADF-H domain,10 which is the core structure of Met was removed when expressed in Escherichia coli many actin-binding proteins. The two monomers (data not shown). To our knowledge, this is one of are almost structurally identical with an root-mean- the structures solved using MAD method with the square deviation (rmsd) of 0.65 A˚ for 130 residues most number of residues (148 residues tagged with (Figure 2(B)), related by a non-crystallographic

Table 1. Data collection, MAD phasing and refinement statistics Data collection Space group C2 Unit cell parameters aZ124.0 A˚ , bZ37.0 A˚ , cZ60.3 A˚ , bZ106.88 Data sets Edge (0.9816 A˚ ) Peak (0.9813 A˚ ) Remote (0.9000 A˚ ) Resolution range (A˚ ) 50–2.8 (2.87–2.8) 50–2.8 (2.87–2.8) 50–2.8 (2.87–2.8) No. of total reflections 52027 77113 92275 No. of unique reflections 5856 (387) 5756 (377) 6039 (403) I/s 17.7 (5.9) 22.6 (9.2) 25.0 (9.8) Completeness (%) 88.8 (88.6) 87.4 (85.7) 91.5 (91.6) a Rmerge (%) 5.6 (13.5) 5.0 (11.5) 4.9 (13.1) MAD phasing (20–3A˚ ) Mean FOMb 0.44 Mean FOMb after density modification 0.70 Structure refinement Resolution (A˚ ) 50–2.8 (2.98–2.8) c Rcryst/Rfree (%) 19.8 (29.8)/26.7 (37.5) No. of reflections Working set 5382 Test set 657 Average B-factor (A˚ 2) Main-chain 34.4/37.3d Side-chain 33.5/37.2d Water 31.0 No. of atoms Protein atoms 2051 Water molecules 33 Selenium atoms 2 rmsd Bond distances (A˚ ) 0.008 Bond angles (deg.) 2.1 The recombined human CLP was expressed in E. coli bacterial strain BL21(DE3) using expression vector pET22b(C) (Novagen), and was purified using affinity chromatography as a standard procedure. For phase determination, the recombinant plasmid was transferred into Met-auxotrophic strain B834(DE3) to obtain the seleno-methionyl derivative of human CLP protein. Crystals of CLP were obtained at 277 K by the hanging-drop vapor diffusion method from the protein sample (20 mg/ml protein in 50 mM Tris–HCl (pH 8.0), 5 mM NaCl, 2 mM imidazole) combined in a 1 : 1 ratio with a reservoir solution consisting of 30% (w/v) PEG2K, and 0.1 M Hepes (pH 7.0). A MAD data set was collected from a single seleno-methionine substituted CLP crystal at 100 K on Beijing Synchrotron Radiation Facility (BSRF) beamline 3W1A at the Institute of High Energy Physics, Chinese Academy of Sciences. All data were processed and scaled with the DENZO and SCALEPACK.21 Two expected selenium positions were found in an asymmetric unit by SOLVE.22 RESOLVE23,24 also built a fragmented model of modest quality containing backbone atoms for about 50% of all residues. The program O25 was used to rebuild and connect the fragments manually for the initial model. The model was refined against the high- energy remote data set in 50–2.8 A˚ resolution range by using CNS.26 NCS restraints were applied through all stages of refinement aside from last cycle. The stereochemical quality of the final model was checked by PROCHECK.27 a Z K = Rmerge SjIi Imj SIi, where Ii is the intensity of the measured reflection and Im is the mean intensity of all symmetry-related reflections. b Mean FOM ðfigure of meritÞZ!jSPðaÞeia a=SPðaÞj:, where a is the phase and P(a) is the phase probability distribution. Numbers in parentheses represent the value for the highest resolution shell. c Z K = Z K = Rcryst SjjFobsj jFcalcjj SjFobsj, where Fobs and Fcalc are observed and calculated structure factors. Rfree STjjFobsj jFcalcjj STjFobsj, where T is a test data set of about 10% of the total reflections randomly chosen and set aside prior to refinement. d Values for the two different monomers (A and B) respectively in an asymmetric unit. Numbers in parentheses represent the value for the highest resolution shell.

192 Crystal Structure of Human Coactosin-like Protein 319

Figure 1. The stereo view of ribbon diagram of human CLP. The six-stranded mixed b-sheet is in purple; the helices are in light- green; and the connecting loops are in gray. Structural elements are labeled in the left diagram. Figures 1–3(B) were prepared using Ribbons.17 2-fold screw axis with a 32 A˚ translation along the family shows some conserved hydrophobic axis (Figure 2(A)). Recently, the secondary structure residues throughout the amino acid sequence of CLP determined by NMR has been reported.11 (Figure 3(A)). These conserved hydrophobic NMR structures of human CLP (PDB code: 1WNJ) residues interdigitate to form two hydrophobic and mouse CLP (PDB code: 1UDM) were released cores (Phe29, Tyr31, Phe59, Phe61, Val101 and in PDB. Superposition of these two solution Val105 forming the first hydrophobic core, and structures and our crystal structure in backbone Cys53, Trp81 and Leu120 forming the second (Figure 2(B)) shows that the loop between b4 and b5 hydrophobic core, Figure 3(B)), which are essential are obviously flexible, while the other regions keep for stabilizing the similar folds of CLP, cofilin and highly similar. It has been reported that human CLP gelsolin. This result provides key information to 7 could exist both as a monomer and a dimer. During explain why CLP and ADF-H domains have low the purification, we also observed human CLP similarity in sequence but are highly conserved in always showed two bands with the molecular three-dimensional structure. masses corresponding to the monomer and the Although CLP is similar to ADF-H domains in dimer on SDS-PAGE, but gave a sharp single peak folding, the actin-binding models revealed by the in mass spectroscopy with the monomer mass. The putative cofilin-actin complex UNC-60B13 could not interactions between the two monomers in the be simply applied to CLP. Cofilin binds to both crystal are only two hydrogen bonds, (carbonyl 3 G-actin and F-actin, while CLP binds to F-actin only. oxygen of Gly67-A to nitrogen of Gly33-B, and N of Systematic mutagenesis studies suggest that the Lys126-A to carbonyl oxygen of Asp32-B,) the residues (except Lys75) whose counterparts biological significance of this packing needs further involved in cofilin–actin binding have no effects investigation. on CLP–F-actin interactions. Our CLP structure may provide explanation on why CLP does not bind to G-actin. Compared with yeast cofilin, the 1 5 Comparison with ADF-H proteins delegate of AC family, the N terminus MSRSG of which Ser4 and Gly5 are highly conserved for both A structural similarity search in the Protein Data G-actin and F-actin binding is not at all conserved in Bank (PDB) with program DALI12 indicates that human CLP with the N-terminal sequence 1 5 human CLP shares highly homology with ADF/ MATKI. Another important residue for G-actin cofilin family (A/Cs) in secondary structures binding to cofilin, Arg96 located in the “kinked arrangement and peptide folding, with the confor- helix”, is replaced with Leu89 in human CLP. mational variations most occurring in the loops The “kinked” a-helix (a3 in CLP), which is (Figure 3(B)), although the amino acid sequence considered to be the F-actin-binding region in identity between human CLP and A/Cs is as low as both cofilin and gelsolin, is also kinked in CLP as less than 15%. Another group of actin-binding in cofilin. Although residue G95 is in the middle of proteins structurally similar to human CLP is a3 in CLP, it would not be the fact causing the bend gelsolin/villin family, which contains a common because it is not conserved in coactosin and AC b-sheet and a long helix as CLP (Figure 3(B)). family, and its dihedral angles are in the most Sequence alignment of human CLP with other favored regions in Ramachandran plot. In order to CLP or coactosin, A/C family and gelsolin/villin characterize the geometry of the “kinked” a-helices

193 Figure 2. The two monomers of human CLP. (A) The ribbons diagram of two human CLP monomers packing in an asymmetric unit. The two monomers are related by a non- crystallographic 2-fold screw axis. (B) The stereo view of the superposition of the two monomers (green and red), NMR structure of human CLP (blue), and NMR structure of mouse CLP (yellow). The structural difference of these four structures, the loop connecting b4 and b5, are shadowed. Actin-binding site Lys75 and 5LO binding site Lys131 are showed in stick and ball model (purple). The each model of the two NMR structures used for superposition is the ﬁrst model of 20 models. The N termini (residues before initial Met) and the C termini (residues after Ala132) of the selected models are cut before superposition, because the N termini do not exist in nature structure and the N- and C termini are highly disordered in the two NMR structures.

194 Crystal Structure of Human Coactosin-like Protein 321

Figure 3. (A) Sequence alignment of human CLP and the proteins in ADF-H and gelsolin/villin families. The sequences of CLP from Homo sapiens (Human), CLP from Mus musculus (House Mouse), and coactosin from D. discoideum were aligned using ClustalW. The sequence of human CLP is aligned with AC family members: yeast coﬁlin (PDB code: 1COF), Acanthamoeba actophorin (PDB code: 1CNU), Arabidopsis thaliana ADF1 (PDB code: 1F7S), human destrin (PDB code: 1AK6), mouse ADF-H domain (PDB code: 1M4J), and gesolin family members: human gelsolin (PDB code: 1H1V) domain G4, human Cap-G (PDB code: 1J72) domain1, chicken villin (PDB code: 2VIK) mainly based on the structural element alignment gave by DALI. The secondary structure of human CLP, which is deﬁned by the analysis of the structure using DSSP program, is indicated above the alignment. The conserved hydrophobic residues forming the two hydrophobic cores are boxed in blue, and red respectively. The essential actin and 5LO-binding sites are

195 322 Crystal Structure of Human Coactosin-like Protein in human CLP and AC family members, program second is the region of subdomain 1, which is HELANAL16 was used to calculate the bending consisted of 361EYED364. To be consistent, the angle. The results show that the maximum bending biochemical studies on Lys75 also suggested the angle of the “kinked” a-helix in human CLP (21.38) N-terminal peptide of actin subdomain 1 could act is smaller than those in AC family members as a “fishing rod” to attracting the positive charged (w40–508). A critical role of maize ADF residues surfaces of actin-binding proteins.7 Tyr67 (strictly conserved in AC family) in proper Lys131 lies on the surface of helix 4. The distance protein folding has been demonstrated by mutating between the NZ atom of Lys75 to the Ca atom of Tyr67 (equivalent to yeast cofilin Tyr64) to phenyl- Lys131 is 7.0 A˚ only. Since F-actin is an elongated alanine, which implicates that the strong hydrogen structure and 5LO is a 78kD large protein, Lys75 bond between the hydroxyl of Tyr64 (in yeast and Lys131 are so spatially close that the steric cofilin) and the carbonyl oxygen of Tyr101 (in hindrance could make the CLP–5LO–F-actin tern- yeast cofilin) is necessary for F-actin binding. The ary complex impossible. The current structure gives strong hydrogen bond would be helpful for support to the experimental result that the 5LO– stabilizing the kinked a-helix of AC family CLP and CLP–F-actin interactions are mutually members. However, the corresponding position to exclusive, suggesting amodulationinactin yeast cofilin Tyr64 is Phe59 in human CLP dynamics. This is also consistent with the fact that (Figure 3(A)), which indicates that the smaller no F-actin–CLP–5LO ternary complex has ever been bending angle of human CLP is properly caused observed experimentally. by missing the strong hydrogen bond conserved in Interestingly, these two critical binding residues AC family. In addition, the “kinked” a-helix of are both close to the C-terminal region in structure human CLP is shorter (14 residues) than that of and the C-terminal structure is quite disordered, structures of AC family and gelsolin/villin family suggesting the flexibility of the C-terminal region of (18–19 residues). Arg96 and Lys98 of yeast cofilin in CLP is important for actin and 5LO binding. this helix are involved in cofilin–actin interactions,14 In addition, actin-binding proteins compose a but the corresponding residues in human CLP are complexsystemofdifferentkindsofproteins, Leu89 and Arg91. There is no evidence indicating regulating in different ways and competing with they are related to actin binding. These structural each other in binding with monomeric or polymeric variations imply the actin-binding mode of human actin. Coactosin interferes with the activity of CLP is different from that in AC family. capping proteins in this complicated system. The hydrophobic region of subdomains 1 and 3 are supposed to be the binding surfaces for capping F-actin and 5LO binding sites in CLP proteins.15 According to the F-actin–CLP models suggested by us, these surfaces would not be Polar residues cover most area of the CLP surface, exposed when human CLP binds to F-actin, so that with few hydrophobic residues exposed, CLP could efficiently counteract capping proteins suggesting that CLP binds to other proteins with association with F-actin. But because human CLP hydrogen bonds and/or salt bridges. The critical only binds to the “outer side” of F-actin, it would not binding residues for F-actin and 5LO are Lys75 and have any effect on actin polymerization. Lys131, respectively.7,8 Mutation of Arg73 also affects CLP binding to b-actin.8 In the current structure, Lys75 is located in the bottom of a cleft Coordinates formed by b5 and the C-terminal helix (a4) (Figure 2(B)). The C-terminal residues 133–137 of The atomic coordinates for human CLP have chain A, which could not be seen in chain B, cover been deposited with the Protein Data Bank (PDB the cleft and bury Lys75. If Lys75 interacts with accession code: 1T2L). F-actin directly, the relocation of the C-terminal peptide should be necessary. Besides Lys75 in the bottom of the cleft, Arg73 and Lys130 are on each side of the cleft. Based on this basic cleft, F-actin should interact with CLP with an acidic protrusion. Acknowledgements By searching the Holmes–Lorenz model of F-actin,19,20 two potential CLP binding regions, This work is supported by the Foundation for with their negative charged surface and protruding Authors of National Excellent Doctoral Dissertation shape, were found in the F-actin molecule. The first of People’s Republic of China (Project No. 200128), is the N terminus of actin subdomain 1, which is a National Foundation of Talent Youth (Grant No. stretched peptide with the sequence of 1DEDE.4 The 30225015), the National High Technology Research boxed in cyan and yellow, which conserved in CLPs and coactosin. This figure was prepared using ESPript.18 (B) The ribbon representation of human CLP, AC family (rendering with yeast cofilin) and gelsolin/villin family (rendering with human gelsolin) structures. Residues showed with ball-stick correspond to the ones explained above with the same color. The C terminus of human CLP are colored in purple, which buries the actin-binding site Lys75. The black arrow denotes the “long helix” that interacts with G-actin directly in gelsolin domain G4.15

196 Crystal Structure of Human Coactosin-like Protein 323 and Development Program of China (Grant No. 13. Ono, S., McGough, A., Pope, B. J., Tolbert, V. T., Bui, 2001AA233021), the 863 Special Program of China A., Pohl, J. et al. (2001). The C-terminal tail of UNC- (Grant No. 2002BA711A13), the Key Important 60B (actin depolymerizing factor/cofilin) is critical for Project and other projects from the National Natural maintaining its stable association with F-actin and is Science Foundation of China (Grant Nos. 30121001, implicated in the second actin-binding site. J. Biol. 30070170, 30130080 and 30121001) and Chinese Chem. 276, 5952–5958. Academy of Sciences (Grant No. KSCX1-SW-17). 15. McLaughlin, P. J., Gooch, J. T., Mannherz, H. G. & We thank Prof. Peng Liu and Yuhui Dong for Weeds, A. G. (1993). Structure of gelsolin segment diffraction data collection. 1-actin complex and the mechanism of filament severing. Nature, 364, 685–692. 14. Lappalainen, P., Fedorov, E. V., Fedorov, A. A., Almo, References S. C. & Drubin, D. G. (1997). Essential functions and actin-binding surfaces of yeast cofilin revealed by 1. Alberts, B., Bray, D., Lewis, J., Raff, M., Roberts, K. & systematic mutagenesis. EMBO J. 16, 5520–5530. Watson, J. D. (1994). The Molecular Biology of the Cell 16. Bansal, M., Kumar, S. & Velavan, R. (2000). (3rd edit.). Garland Press, New York. HELANAL: a program to characterize helix geometry 2. McGough, A. (1998). F-actin binding proteins. Curr. in proteins. J. Biomol. Struct. Dynam. 17, 811–819. Opin. Struct. Biol. 8, 166–176. 17. Carson, M. (1997). Ribbons. Methods Enzymol. 277, 3. de Hostos, E. L., Bradtke, B., Lottspeich, F. & 493–505. Gerisch, G. (1993). Coactosin, a 17 kDa F-actin 18. Gouet, P., Courcelle, E., Stuart, D. I. & Metoz, F. (1999). binding protein from Dictyostelium discoideum. Cell ESPript: multiple sequence alignments in PostScript. Motil. Cytoskeleton, 26, 181–191. Bioinformatics, 15, 305–308. 4. Rohrig, U., Gerisch, G., Morozova, L., Schleicher, M. & 19. Lorenz, M., Popp, D. & Holmes, K. C. (1993). Wegner, A. (1995). Coactosin interferes with the Refinement of the F-actin model against X-ray fiber capping of actin filaments. FEBS Letters, 374, 284–286. diffraction data by the use of a directed mutation 5. Chen, K. S., Manian, P., Koeuth, T., Potocki, L., algorithm. J. Mol. Biol. 234, 826–836. Zhao, Q., Chinault, A. C. et al. (1997). Homologous 20. Holmes, K. C., Popp, D., Gebhard, W. & Kabsch, W. recombination of a flanking repeat gene cluster is a (1990). Atomic model of the actin filament. Nature, mechanism for a common contiguous gene deletion 347, 44–49. 17 syndrome. Nature Genet. , 154–163. 21. Otwinowski, Z. & Minor, W. (1997). Processing of 6. Nakatsura, T., Senju, S., Ito, M., Nishimura, Y. & Itoh, X-ray diffraction data collected in oscillation mode. In K. (2002). Cellular and humoral immune responses to Macromolecular Crystallography (Carter, C.W.a.S.R.M., a human pancreatic cancer antigen, coactosin-like protein, originally defined by the SEREX method. Eur ed) Methods in Enzymology, vol. 276. J Immunol. 32, 826–836. 22. Terwilliger, T. C. & Berendzen, J. (1999). Automated 7. Provost, P., Doucet, J., Stock, A., Gerisch, G., MAD and MIR structure solution. Acta Crystallog. sect. Samuelsson, B. & Radmark, O. (2001). Coactosin-like D, 55, 849–861. protein, a human F-actin-bining protein: critical role 23. Terwilliger, T. C. (2000). Maximum likelihood density of lysine-75. Biochem. J. 359, 255–263. modification. Acta Crystallog. sect. D, 56, 965–972. 8. Provost, P., Doucet, J., Hammarberg, T., Gerisch, G., 24. Terwilliger, T. C. (2002). Automated main-chain Samuelsson, B. & Radmark, O. (2001). 5-Lipoxygen- model-building by template-matching and iterative ase interacts with coactosin-like protein. J. Biol. Chem. fragment extension. Acta Crystallog. sect. D, 59, 34–44. 276, 16520–16527. 25. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. 9. Peters-Golden, M. & Brock, T. G. (2000). Intracellular (1991). Improved methods for building protein compartmentalization of leukotriene biosynthesis. models in electron density maps and the location Am. J. Respir. Crit. Care Med. 161, S36–S40. of error in these models. Acta Crystallog. sect. A, 47, 10. Lappalainen, P., Kessels, M. M., Cope, M. J. & Drubin, 110–119. D. G. (1998). The ADF homology (ADF-H) domain: a 26. Brunger, A. T., Adams, P. D., Clore, G. M., DeLano, highly exploited actin-binding module. Mol. Biol. Cell, W. L., Gros, P., Grosse-Kunstleve, R. W. et al. (1998). 9, 1951–1959. Crystallography & NMR system (CNS): a new 11. Dai, H., Wu, J., Xu, Y., Tang, Y., Ding, H. & Shi, Y. 1 13 15 software suite for macromolecular structure determi- (2004). H, C and N resonance assignments and nation. Acta Crystallog. sect. D, 54, 905–921. the secondary structures of human coactosin like 27. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & protein (hCLP) D123N. J. Biomol. NMR, 29, 455–456. Thornton, J. M. (1993). PROCHECK: a program to 12. Holm, L. & Sander, C. (1993). Protein structure check the stereochemical quality of protein structures. comparison by alignment of distance matrices. J. Mol. Biol. 233, 123–138. J. Appl. Crystallog. 26, 283–291.

Edited by R. Huber

(Received 25 June 2004; received in revised form 14 September 2004; accepted 16 September 2004)

197

The Journal of General Physiology

is notwellunderstood.Inadditiontomodulatingcell in producingacontrolledinsulinresponse participate the controlofinsulinsecretion,preciselyhowthey cellular cAMP(Sharp,1996). tor agonistsinhibitadenylatecyclaseandreduceintra- sequently activatePKC(V carinic nutrient secretagogues.Forexample,cholinergicmus- mitters, throughthesameintracellularregulatorsas awidevarietyofhormonesandneurotrans- including be radicallymodiﬁedbynonnutrientsecretagogues, other hand,nutrient-inducedinsulinresponsescan such asPKCandPKA(Nesheretal.,2002).Onthe pathways thatleadtotheactivationofproteinkinases gogues, nutrientsalsoactivateintracellularsignaling by metabolismofglucoseandothernutrientsecreta- well-known depolarization–secretioncouplinginitiated andnonnutrientsecretagogues.Despitethe nutrient Insulin secretionissubjecttopreciseregulationby 86-27-87792024; email:[email protected] University ofScienceandTechnology, Wuhan430074,China.Fax: Bioc Address correspondencetoTao Xu,InstituteofBiophysicsand whereas somatostatin,galanin,orthe tide glucagon andglucose-dependentinsulinotropicpolypep- INTRODUCTION toCa Machinery Secretory Protein KinaseActivationIncreasesInsulinSecretionbySensitizingthe

Although proteinkinaseshavebeenimplicatedin

hemistry, SchoolofLifeScience andTechnology,Huazhong

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increasing thenumberofvesiclesthatarehighlysensitivetoCa membrane depolarizationiscombinedwithphotoreleaseofCa and PKA is blockedbyvariousPKCorPKAinhibitors,indicatingtheinvolvementofthesekinases.Theeffects and forskolinalsoincreasethesizeofRRPtoalesserextent.Theaugmentingeffectphorbolestersor resting conditions,butisdramaticallyincreasedbyapplicationofeitherphorbolestersorforskolin.Phorbol sensitive pool(HCSP),areadilyreleasable(RRP),andreserve pool.ThesizeoftheHCSPis Ca secretion. Byusinghightimeresolutionmeasurementsofmembranecapacitanceandﬂash photolysisofcaged designed tounravelthesitesofactionproteinkinaseA(PKA)andC(PKC)inmodulatinginsulin key words: abstract 2 1 Qun-Fang Wan, of vesiclesfromthosecolocalizedwithCa agonists generatediacylgycerol(DAG)andsub- National Laboratory ofBiomacromolecules,InstituteBiophysics,ChineseAcademySciences,Beijing100101,China National Laboratory Institute ofBiophysicsandBiochemistry, SchoolofLifeScience,HuazhongUniversityScienceandTechnology,

Wuhan 430074,China

, wecharacterizethreekineticallydifferentpoolsofvesiclesinratpancreatic

on thesizeofHCSParenotadditive,suggestingaconvergentmechanism.Usingprotocolwhere

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oue14Dcme 04653–662 December 2004 Volume 124 http://www.jgp.org/cgi/doi/10.1085/jgp.200409082 J. Gen.Physiol. Wienecke, 1998), 2-adrenorecep- 2 ©TheRockefellerUniversityPress 2 1 HuaYang, channels.We proposethatPKAandPKCpromoteinsulinsecretionby 198 secretory machinery.secretory Inpancreatic dence alsosuggeststhatPKAorPKCactdirectlyon zem et excitability, calciuminflux,andgeneexpression tion hasalsobeenlinkedtoprimingofCa strom et number ofvesiclesthatareavailableforrelease(Ren- potentiates insulinsecretionbyincreasingthetotal form secretion isregulatedbyPKAandPKCinratpancreatic al., 2002;Zhuet2002). strated inchromaffincellsandgonadotropes(Yang et releasable pool. calcium-sensitive pool;IRP,immediately releasablepool;RRP,readily Abbreviations usedinthispaper: Ca Sullivan, 1998).Recently, adirectmodulationofthe and plenishment isincreased(Smithetal.,1998;Stevens neurons, wherethesizeofRRPanditsrate re- cell types,suchaschromaffincellsandhippocampal hasalsobeensuggestedinother machinery secretory et al.,1997).DirectinteractionsofPKAorPKCwiththe Ca ated insulinsecretionaswellenhancementofnon- tance (C to Ca 1 -cells. We responsedistal focusedonthesecretory XuelinLou, This studyinvestigatesthemechanismswherebyinsulin 2 2 –mediated exocytosis(Eliassonetal.,1996;Efanov sensitivityoffusionbyPKChasbeendemon- 2 manipulation of[Ca signalingbyusingwholecellmembranecapaci- al., 1987;LiuandHeckman,1998),recentevi- 2 2 m al., 1997;Rorsmanet2000).PKCactiva- . ) measurementsanddirectspatiallyuni- , wefindthattheHCSPisadistinctpopulation • 0022-1295 1 JiupingDing, /2004/12/653/10 $8.00 DAG,diacylgycerol;HCSP,highly -cells, namely, ahighlycalcium- 2 ] i withcagedCa 1

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(Bo-

Downloaded from from Downloaded on November 30, 2004 2004 30, November on www.jgp.org

have identified a small, highly calcium-sensitive pool experiments, exocytosis was elicited by photorelease of caged (HCSP) in addition to the previously reported RRP and Ca2 preloaded into the cell via the patch pipette. Flashes of UV light were generated by a flash lamp (Rapp Optoelektronik). the reserve pool. The size of the HCSP dramatically in- 2 2 [Ca ]i was measured with the Ca indicator dyes fura-2, fura-6F, creased after treatment with PMA or forskolin, which or furaptra. The dyes were excited with light alternating between also increased the size of the RRP, albeit to a lesser ex- 340 and 385 nm from a monochromator-based system (TILL tent. To better characterize the specific isoforms of photonics). The resulting fluorescence signal was measured by a 2 PKC involved in the modulation of secretory vesicles, photomultiplier. [Ca ]i was determined from the ratio (R) of the fluorescence signals excited at the two wavelengths, following we tested the effects of various PKC inhibitors on secre- 2 the equation [Ca ]i Keff * (R Rmin)/(Rmax R), where tory responses. Furthermore, we evaluated whether the Keff, Rmin, and Rmax are constants obtained from intracellular actions of PKC and PKA converge to influence the calibration as previously described (Xu et al., 1997). In brief, 2 secretory process. four solutions with [Ca ]i of nominal zero (10 mM EGTA with 2 no added Ca ), 20 M (20 mM DPTA with 4 mM CaCl2), 80 M MATERIALS AND METHODS (20 mM DPTA with 10 mM CaCl2), and 10 mM (10 mM CaCl2 with no added buffer) were dialyzed against the cytosol in the Cell Culture and Solutions whole-cell patch clamp recording. Three to five recordings were made for each calibration solution to estimate the calibration All experiments were performed on isolated rat pancreatic -cells constants. at 30–32C. Pancreatic -cells from adult male Wistar rats were prepared as described previously (Ashcroft et al., 1984). In brief, rats Data Analysis were killed by cervical dislocation, and the islets were collected from the pancreas after collagenase digestion. The islets were fur- Data analysis was performed using IGOR Pro software (Wavemet- ther digested by dispase II to dissociate single -cells. Dispersed rics), and results were presented as mean SEM with the indi- Downloaded from cells were kept in DMEM supplemented with 25 mM HEPES, 2 g/L cated number of experiments. Statistical significance was evalu- NaHCO3, 100 IU/ml penicillin, 100 g/ml streptomycin, and ated using Student’s t test. P 0.05 was considered to be statisti- 10% FCS. Cells cultured for 3–5 d were used in the experiments. cally significant. Standard bath solution for the experiments contained (in mM) 138 NaCl, 5.6 KCl, 1.2 MgCl2, 2.6 CaCl2, 3 glucose, 5 HEPES RESULTS

(pH 7.2, 310 mosm). For pipette solutions, we generally pre- www.jgp.org pared 2 concentrated buffers, which contained 250 mM Cs- Characteristics of Secretory Response in Rat Pancreatic -cells glutamate and 80 mM HEPES (pH 7.2). We added to the 2 2 2 buffer CaCl2, ATP, GTP, caged Ca , and Ca indicators. Stan- We first characterized the secretory response to differ- 2 dard internal solution consisted of (in mM) 110 Cs-glutamate, 2 ent [Ca ]i levels in single rat pancreatic -cells. Exo- MgATP, 0.3 GTP, and 35 HEPES with different loaded caged cytosis was elicited by flash photorelease of Ca2 in on November 30, 2004 Ca2 of either NP-EGTA or DM-nitrophen, and 0.2 mM various 2 2 the whole-cell patch-clamp configuration. Following a Ca indicators, such as fura-6F or furaptra. The basal [Ca ]i was 2 measured to be around 200 nM by fura-2. For experiments with flash, [Ca ]i was uniformly elevated to the M range depolarization, the bath solution contained 10 mM CaCl2.The pi- within few milliseconds. Thus, the sizes of distinct vesi- 2 pette solution was adjusted to pH 7.2 with either HCl or CsOH. cle pools and their secretory kinetics at a given [Ca ]i The osmolarity was adjusted to around 300 mosm. could be studied directly without the complications of Stock solutions of forskolin, PMA, Gö6976, and Gö6983 were [Ca2] microdomains or modulation of Ca2 influx. prepared in DMSO. Stock solutions of PKC19-31 were made in 5% i acetic acid. The final concentration of DMSO or acetic acid in di- Fig. 1 A displays a typical Cm response to a step-like 2 luted solutions was 0.02%. DMEM, Dispase-II, FBS, and BSA [Ca ]i elevation. The Cm trace clearly displayed multi- were from GIBCO BRL; PKC19-31, Gö6976, and Gö6983 were purple kinetic components of exocytosis, indicating the chased from Calbiochem; NP-EGTA, DM-nitrophen, fura-2, fura- presence of different vesicle pools as has been sug- 6F, and furaptra were from Molecular Probes; forskolin, Rp-cAMP, gested for other cell types (Neher, 1993; Heinemann et PMA, and all other chemicals were purchased from Sigma-Aldrich. al., 1994; Xu et al., 1998; Voets, 2000). Each exponen-

Membrane Capacitance (Cm) Measurement tial component of the Cm trace is usually interpreted as release of a discrete vesicle pool, whereas the sustained We selected cells with diameters 11 m for study, so that 90% linear increase is thought to reflect refilling from a re- of the cells were expected to be -cells (Rorsman and Trube, 1986). Conventional whole-cell recordings were conducted using serve pool of vesicles (Sorensen et al., 2002). When we Sylgard-coated pipettes with series resistance ranging from 4 to looked into the detailed kinetics of the initial exocy- 12 M. An EPC-9 patch-clamp amplifier was used together with totic burst at an expanded time scale (Fig. 1 B), we ob- PULSELOCK-IN software (Heka Elektronics). A 1042-Hz, 20- served a small but very fast component of exocytosis at mV peak-to-peak sinusoidal voltage stimulus was superimposed 2 low M [Ca ]i. The amplitude of this fast component on a holding potential of 70 mV. Currents were filtered at 2.9 kHz and sampled at 15 kHz. The capacitance traces were im- reflects release of 6–12 vesicles ( 20 fF) if we assume ported to IGOR Pro (WaveMetrics) for further analysis. that one insulin-containing granule contributes 1.7–3.4 fF of membrane as determined in pancreatic -cells Flash Photolysis (Ammala et al., 1993; Braun et al., 2004). This compo- Flashes of ultraviolet light and fluorescence–excitation light were nent was readily identifiable in 50% of the cells (n generated as described previously (Xu et al., 1997). In the flash 93) studied. This variability likely results from the rela-

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199

Figure 1. The kinetics of exocytosis in pancreatic 2 -cells at different [Ca ]i levels. (A) Example trace of a secretory response following ﬂash photolysis that exhibited two distinct phases. Superimposed is the double exponential ﬁt (solid line) with the rate constants and amplitudes indicated. The exocytotic burst is ex-

panded in the inset. (B and C) Expanded exocytotic Downloaded from 2 bursts in response to different post-ﬂash [Ca ]i levels with superimposed double exponential ﬁts (solid lines). 2 (B) At lower [Ca ]i levels, a small-amplitude exponential component with a relatively fast rate constant was followed by a slower, but larger amplitude second expo- 2 nential component. (C) At higher [Ca ]i levels, the slower but larger phase of exocytosis dominated the www.jgp.org exocytotic burst.

2 on November 30, 2004 tively small size of this pool and considerable cell-to-cell similar post-flash [Ca ]i levels were compared, PMA variation of secretory competence. The most rapid clearly increased the burst component of exocytosis as component of exocytosis had a relatively fast time con- well as the sustained component (Fig. 2 C). To investi- 2 2 stant of 20 ms at a [Ca ]i level of 3.1 M. In contrast, gate the Ca dependence of secretion, the exocytotic recent studies in -cells report exocytosis from a readily bursts were further fitted by a double exponential to releasable pool (RRP) with an amplitude of 200 fF obtain the rate constants and amplitudes of the HCSP and time constants of 1 s or longer upon photoeleva- and RRP. Fig. 3 compared the sizes and the rate con- 2 tion of [Ca ]i to 3 M (Takahashi et al., 1997; Barg stants of the HCSP and RRP from control (n 93) and 2 et al., 2001). Thus, this small, fast component in the PMA-treated (n 117) cells between [Ca ]i levels of 2 exocytotic burst at low [Ca ]i is kinetically distinguish- 0.7 and 30 M. Despite the comparable rate constants, able from the previously described RRP but is similar to the amplitudes of the HCSP were much greater in what has recently been described as a highly Ca2-sensi- PMA-treated cells, as shown in the upper part of Fig. 3. tive pool (HCSP) in chromaffin cells (Yang et al., 2002) We did not observe a clear dependence of the ampli- 2 and rat insulinoma INS-1 cells (Yang and Gillis, 2004). tude on [Ca ]i. 2 As we elevated [Ca ]i to higher values, a slower but The rate constant of release from the HCSP was de- 2 larger phase of exocytosis became dominant (Fig. 1 C). pendent on [Ca ]i between 0.8 and 3 M and 2 This slower phase had an amplitude ( 200 fF) and ki- saturated at [Ca ]i above 3 M. We fitted the HCSP netics comparable to the previously reported RRP (Ta- rate constant to the equation Rate Rmax/(1 (Kd/ 2 n kahashi et al., 1997; Barg et al., 2001; Olofsson et al., [Ca ]i) ), and obtained an estimated Kd of 2.5 0.5 2002). M. The best-fit Hill coefficient (n) was 1.9, suggesting a less cooperativity in the Ca2-dependent fusion of PMA Significantly Increased the Size of the HCSP HCSP compared with the RRP. A shallow dependence 2 Next, we tested the effect of PMA, a PKC activator, on of the rate of exocytosis of the HCSP on [Ca ]i is also exocytosis in pancreatic -cells. A prominent HCSP suggested in pituitary gonadotropes (Zhu et al., 2002), component with much larger size than in control cells chromaffin cells (Yang et al., 2002), and in INS-1 cells is evident after PMA treatment (Fig. 2, A and B). When (Yang and Gillis, 2004). The results reveal a novel 2 the averaged time courses of Cm increase in response to mechanism to increase the apparent Ca dependence

655 Wan et al.

200 Figure 2. PMA increases the size of the HCSP. (A and B) Downloaded from Examples of the kinetics of exocytosis from PMA-treated (100 nM for 2–3 min) cells at two different post-ﬂash 2 [Ca ]i levels. Superimposed solid curves are exponential 2 ﬁts. (C) Averaged [Ca ]i (upper traces) and Cm responses (lower traces) from control (circles, n 14) and PMA- treated (triangles, n 16) cells. www.jgp.org

of insulin release by recruiting more vesicles into a for 3 min after establishing the whole-cell configura- on November 30, 2004 highly calcium-sensitive state. tion before flash. As shown in Fig. 4 A, PKC19-31 abolished the stimulatory effect of PMA on the HCSP. Specificity of PMA Action in Regulating Insulin Secretion At least five PKC isoenzymes (, , , , and ) have PMA activates PKC due to its structural similarity to the been found in rat pancreatic -cells (Kaneto et al., endogenous activator, DAG, by binding to the C1 do- 2002). PMA activates the Ca2-dependent isoforms main of PKC. The specificity of PMA activation of PKC PKC and PKCII, and the Ca2-independent isoforms has been questioned because PMA also activates pro- PKC and PKC (Csukai and Mochly-Rosen, 1999). tein kinase D, RasGRPs, and diacylglycerol kinase Here, we tried to better define the relevant PKC iso- with equal potency (Kazanietz, 2002). Munc13, a fam- forms that are involved in regulating insulin secretion ily of proteins that prime exocytosis, also possess a by comparing the differential effects of Gö6976 and PMA-binding (C1) domain and are translocated to Gö6983. Gö6976 selectively inhibits Ca2-dependent the plasma membrane upon bath application of PMA PKC (IC50 2.3 nM) and PKC I (IC50 6.2 nM), (Rhee et al., 2002). Moreover, a recent report demon- whereas it does not affect the kinase activity of the strates that Munc13-1 functions in regulating insulin se- Ca2-independent PKC isozymes even in the micromo- cretion (Sheu et al., 2003). Thus, we applied a number lar range (Gschwendt et al., 1996). Gö6983 selectively of specific PKC inhibitors to determine whether PKC is inhibits several PKC isozymes but does not discriminate involved in the effect of PMA, and which PKC isoform between them. As shown in Fig. 4 A, Gö6976 (100 nM) might be involved in regulating secretion. Fig. 4 sum- and Gö6983 (100 nM) were equally potent in blocking marizes the averaged amplitudes of the HCSP and the the stimulatory effect of PMA. RRP from control cells and cells treated with PMA and PMA enhanced the size of the RRP and the sustained various PKC inhibitors. A specific pharmacological tool component to a much lesser extent than its effect on to test the involvement of PKC is the inhibitory pep- the HCSP. This effect was also blocked by various PKC tide, PKC19-31, a pseudosubstrate sequence that inter- inhibitors (Fig. 4 A). Furthermore, we tested whether acts with the PKC substrate binding site in the C4 re- the PKC inhibitors used in this study could exert any ef- gion of the catalytic domain. We included 1 M PKC19- fect on exocytosis in the absence of PMA. Fig. 4 B re- 31 (IC50 100 nM) in the pipette solution and waited veals that PKC19-31, Gö6976, and Gö6983 did not in-

656 Sensitization of Insulin Secretion

201 Figure 3. The rate constants and amplitudes of exponential fits Downloaded from 2 to Cm responses with similar post-flash [Ca ]i levels are averaged 2 and plotted versus [Ca ]i. Circles and triangles represent the fast Figure 4. The effect of PMA is mediated by PKC activation. (A) 2 and slow components of double exponential fits. For [Ca ]i Averaged amplitudes of different kinetic components for control 10 M, it is hard to distinguish the HCSP from RRP, therefore we cells and cells with various treatments. The Cm response was fitted only fit a single exponential to the Cm traces and the rate constants by triple exponentials and the amplitudes of the three components are denoted as squares. The open and filled symbols represent were taken as the size of the HCSP, the RRP, and the sustained data from control and PMA-treated cells, respectively. The Ca2 component. PKC19-31 (1 M, n 19), Gö6976 (100 nM, n 22), www.jgp.org dependence of the rate of exocytosis from the HCSP was fitted by or Gö6983 (100 nM, n 14) were included in the pipette solution 2 n the equation (dashed line) Rate Rmax/(1 (Kd/[Ca ]i) ), during perfusion with PMA in the external solution. (B) The effect 1 where Rmax, Kd, and n were 69.4 8.8 s , 2.5 0.5 M, and 1.9 of PKC19-31 (n 21), Gö6976 (n 12), or Gö6983 (n 19) alone on the three kinetic components of exocytosis. Values 0.7, respectively. The dotted lines in the upper panel mark the on November 30, 2004 averaged HCSP sizes for control and PMA-treated cells. represent the mean SEM. Asterisks denote significant differences (t-test, *P 0.05, **P 0.01). The sizes of the HCSP, RRP, and sustained components were normalized to their control values fluence the different components of secretion signifi- from paired experiments, respectively, to guard against day-to-day cantly, suggesting little tonic activity of PKC. variation. The Effect of PKA on Different Exocytotic Components in -cells Convergent Effects of PKA and PKC on Exocytosis To investigate the role of PKA in insulin secretion, we studied the effects of forskolin, an activator of aden- To test whether PKC and PKA act on the same targets ylate cyclase, on the different secretory components in in enhancing exocytosis, we challenged pancreatic pancreatic -cells. After application of 10 M forskolin -cells with combined application of 100 nM PMA and for 2–3 min, the amplitude of the HCSP was greatly en- 10 M forskolin in the bath solution and compared hanced (Fig. 5, A and B, see Fig. 1 for comparison). their effect with that of PMA or forskolin applied alone. 2 As shown in Fig. 7, the cocktail of PMA plus forskolin The averaged Cm response to similar [Ca ]i levels showed a pronounced increase in amplitude over that exerted no greater effect than each compound alone. from control cells (Fig. 5 A). As with PMA, forskolin Thus, the effects of PKC and PKA are not additive, sug- did not change the kinetics of the secretory response, gesting that activation of either one may converge on whereas it increased the size of the HCSP (Fig. 6 A). the same secretory pathway in the regulation of insulin The Ca2 dependence of the release rate from the secretion. HCSP and RRP was fitted to the same equation as in The Relationship between the HCSP and Rapid Fig. 3. As summarized in Fig. 6 (B and C), forskolin dra- Depolarization-evoked Exocytosis matically increased the size of HCSP as well as RRP. The stimulatory effect of forskolin was blocked by a PKA an- A subset of vesicles has been postulated to colocalize tagonist, Rp-cAMP (10 M), demonstrating the involve- with Ca2 channels and is often termed the immedi- ment of PKA activation. Control experiments showed ately releasable pool (IRP) of vesicles (Horrigan and that Rp-cAMP had no effect on exocytosis in the ab- Bookman, 1994). The size of the IRP in pancreatic sence of forskolin. -cells has been estimated to be around 30 fF (Barg et al.,

657 Wan et al.

202 Figure 5. Forskolin significantly increases the size of the HCSP. (A and B) Examples of the kinetics of Downloaded from exocytosis from forskolin-treated cells (10 M for 2–3 2 min) at two different post-flash [Ca ]i levels. Superim- posed solid curves are exponential fits. (C) Averaged 2 [Ca ]i (upper traces) and Cm responses (lower traces) from control and forskolin-treated cells, from experi- 2 ments that had similar post-flash [Ca ]i values (n 14

for control, circles; n 13 for forskolin, triangles). www.jgp.org

2001), which is similar to the basal size of the HCSP in in mouse -cells in addition to the previously described

-cells. To clarify the relationship between the HCSP RRP and reserve pool of vesicles. We have shown that on November 30, 2004 and the IRP, we have designed a cross-depletion experi- application of either PMA or forskolin dramatically in- ment by combining brief membrane depolarization creases the size of the HCSP by a factor of approxi- and flash photolysis of caged Ca2. We employed a mately four, an effect involving activation of PKC or dual-pulse protocol (two successive 30 ms depolarizing PKA as testified by the effectiveness of specific protein pulses separated by 100 ms at holding potential) to esti- kinase inhibitors. The effects of PKC and PKA were not mate the size of the IRP as previously described (Gillis additive, suggesting that a convergent mechanism is et al., 1996), then a subsequent flash uncaging to elicit used to modulate the secretory machinery in pancre- release from the HCSP. One example response in the atic -cells. presence of forskolin is depicted in Fig. 8 A, where ele- 2 2 vation [Ca ]i to 4.3 M is still capable of eliciting ro- [Ca ]i Dependence of Exocytosis in Pancreatic -cells bust exocytosis from the HCSP after the depletion of The Ca2 dependence of insulin secretion is controver- IRP. Next, we repeated the cross-depletion protocol in sial. It has been reported that little exocytosis is evoked the presence or absence of forskolin to determine in pancreatic -cells upon photolysis of caged Ca2 to whether the IRP and HCSP are differentially regulated. levels 3 M (Takahashi et al., 1997; Barg et al., Fig. 8 B summarizes the results from 35 cells. The size 2001), yet we detect robust exocytosis at [Ca2 ] 1 of the IRP has not been significantly enhanced upon i M. It is quite possible that the HCSP we report here treatment of forskolin; however, the size of the HCSP has been overlooked in previous studies on -cells be- following the depletion of the IRP was increased from cause of its small and variable amplitude, yet we also 19.3 4.5 to 78.4 18.0 fF. This result further suggests see robust release from the larger RRP at 1 M. Our re- that granules in the HCSP are distinct from those in sults are consistent with a number of studies that have the IRP. 2 demonstrated insulin secretion at [Ca ]i levels of 1 M (e.g., Bergsten, 1995; Bokvist et al., 1995; Proks et DISCUSSION al., 1996; Lang et al., 1997). One possible reason for We have characterized in detail the secretory response the discrepancy between our results and other caged 2 2 2 in single rat pancreatic -cells to different [Ca ]i lev- Ca studies are differences in the [Ca ]i level before els. We find a highly Ca2-sensitive phase of exocytosis the flash and/or the presence of ATP in the pipette so-

658 Sensitization of Insulin Secretion

203 Figure 7. The effects of PMA and forskolin on exocytosis are not additive. Application of forskolin and PMA produced a fourfold increase in the size of the HCSP. PMA and forskolin also increased the size of RRP and the sustained component; however, the augmentation was not as dramatic as that of the HCSP. The sizes of the HCSP, RRP, and sustained components were normalized to their control values from paired experiments.

ATP are important for the priming and maintenance of the docked RRP (von Ruden and Neher, 1993; Parsons Downloaded from et al., 1995; Eliasson et al., 1997; Xu et al., 1998; Smith et al., 1998; Takahashi et al., 1999). Thus, our results supported the notion that pancreatic -cells possess a high affinity Ca2 sensor for exocytosis. www.jgp.org PKC Isoforms Involved in Insulin Regulation PMA has been employed to investigate the role of PKC in the regulation of insulin secretion. However, be- on November 30, 2004 cause of the ubiquitous expression of many PKC isoforms and the large number of PKC regulators and substrates, the precise role of PKC activity and the identity of the relevant PKC isoforms have often remained elusive. Recently, Munc13s have been suggested as alternative DAG and Ca2 receptors that function in regulating vesicle priming (Rhee et al., 2002). Thus, we used Figure 6. Summary of the effects of forskolin on different various specific PKC inhibitors including PKC19-31, components of exocytosis. (A) The rate constants and amplitudes 2 Gö6976, and Gö6983 to demonstrate that PKC was of exponential fits to Cm responses plotted versus [Ca ]i. Circles and triangles represent the fast and slow components of double indeed involved in the enhancement of exocytosis in exponential fits. The open and filled symbols represent data from -cells. Among multiple PKC isoforms, only classical control and forskolin-treated (10 M) cells, respectively. Squares PKCs (, I, , and ) and atypical PKCs (, /, and denote the rate constants of single exponential fit to the Cm traces ) can be activated by PMA. BIS and the BIS-derived 2 for [Ca ]i 10 M. The dashed line is reproduced from Fig. 3. PKC inhibitor, Gö6983, inhibit several PKC isoforms The lines in the upper panel mark the averaged HCSP size for control and forskolin-treated cells. (B) Comparison of the ampli- ( , , , , and ) without discriminating between tude of the HCSP between control cells and those treated with them. Gö6976 selectively inhibits Ca2 -dependent PKC forskolin, Rp-cAMP (10 M) alone, or Rp-cAMP plus forskolin. (IC50 2.3 nM) and PKC I (IC50 6.2 nM), whereas it (C) Application of forskolin significantly increased the amplitude 2 does not affect the kinase activity of the Ca -indepen- of the RRP. Data are displayed as mean SEM. **P 0.01. dent PKC isoforms (, , and ) even in the micromolar range (Gschwendt et al., 1996). The fact that Gö6976 lution. For example, in the study by Takahashi et al. and Gö6983 were equally effective in blocking the stim- (1999), the pipette solution contained 10 mM DM- ulatory effect of PMA on the HCSP suggested the in- nitrophen together with 0.5–4 mM CaCl 2 and no ATP. volvement of classical PKCs. Among all PKC isoforms, 2 The basal [Ca ]i was estimated to be 5 nM. In the PKC , , , , , and are reported to be expressed in 2 present study we have determined the basal [Ca ]i to rat pancreatic islets. This narrows the PKC isoforms to be 200 nM and we included 2 mM ATP in the pipette PKC and PKC. PKC has been proposed in the solution. It should be noted that both basal Ca2 and priming of synaptic vesicles in the Calyx of Held (Wu

659 Wan et al.

204 clamped -cells and intracellular Ca2 photorelease techniques. We found that activation of either PKA or PKC might act on a common site for changing the Ca2 sensitivity of the primed vesicles. Despite a common effect on the HCSP, stimulation of PKA by 10 M forskolin gives a greater enhancement of the RRP than stimulation of PKC by 100 nM PMA in our hand. Considering synaptotagmin and the soluble N-ethyl- maleimide–sensitive fusion attachment protein receptor (SNARE) complex as an integrated calcium sensor for fusion (Xu et al., 1998), one could envision that phosphorylation of synaptotagmin or SNARE proteins, or other SNARE-interacting proteins, might ﬁnely adjust the Ca2 sensing of exocytosis. The reﬁlling and priming of vesicles involves multiple possible downstream effectors of protein kinases including SNARE proteins, SNAP, and Rab proteins, etc. Overexpression of phosphomimetic and phosphorylation-defective mutant variants of SNAP-25 has recently dissected the role

of PKC-mediated phosphorylation of SNAP-25 during Downloaded from vesicle recruitment in chromafﬁn cells (Nagy et al., 2002). Similar methods can be employed to investigate the substrates of protein kinases in -cells. Alterna- tively, a more systematic proteomic approach will help

Figure 8. The HCSP is distinct from the IRP. (A) Sample response to elucidate the kinase targets that are important in the www.jgp.org to two successive brief depolarizing pulses (30 ms in duration) to regulation of insulin secretion. 10 mV followed by flash photolysis of caged Ca2. Note that the Cm response to the second pulse is substantially smaller than the Model of Insulin Secretion Control by Protein Kinases response to the first pulse, demonstrating the depletion of the IRP. At the time indicated by the arrow, a UV flash was given to elevate Our study has revealed a novel, small HCSP with high on November 30, 2004 2 2 [Ca ]i to 4.3 M. The dashed line is single-exponential fit with Ca sensitivity in rat pancreatic -cells. The origin of the fastest time constant indicated. The experiment is performed this HCSP remains to be revealed since small GABA- in the presence of 10 M forskolin. (B) Summary of the estimated containing synaptic-like vesicles have been suggested in size of IRP and HCSP in the absence (open bars, n 8) and presence of forskolin (filled bars, n 27). The size of the HCSP is pancreatic -cells in addition to dense-core insulin-con- significantly increased by forskolin application (t test, P 0.05), taining granules (Thomas-Reetz and De Camilli, 1994; whereas the size of the IRP remains unchanged. Takahashi et al., 1997). However, recently the release of GABA-containing synaptic-like vesicles has been estimated to contribute only 1% of the capacitance sig- and Wu, 2001), whereas PKC is thought to induce nal in -cells (Braun et al., 2004). In an accompanying c-myc expression and suppress insulin gene transcrip- report, Yang and Gillis (2004) have shown that quantal tion (Kaneto et al., 2002). Recent experiments also 5-HT release correlates well with the exocytosis HCSP have suggested that PMA-stimulated insulin secretion in insulin-secreting INS-1 cell line. Simultaneous mea- involved activation of PKC but not PKC (Carpenter surement of insulin and 5-HT release with modified et al., 2004). Thus, we suspect that PKC is involved in carbon fiber electrodes demonstrates that 5-HT is re- the enhancement of the HCSP in rat pancreatic -cells. leased exclusively from insulin-containing granules (As- pinwall et al., 1999). Thus, it is possible that the HCSP Substrates of Protein Kinases is composed of the same type of insulin-containing Identification of kinase substrates and of their cellular granules as the “conventional” RRP. functions is crucial to a full understanding of the regu- We have shown that PKC and PKA activation can dra- latory roles of protein kinases in insulin secretion. A matically increase the size of the HCSP. Similar effects number of unidentified kinase substrates have been lo- have also been reported in the rat insulinoma INS-1 calized to -cell secretory vesicles or membrane frac- cells (Yang and Gillis, 2004), albeit augmentation of tions, which might be involved in vesicle trafficking, the fraction of granules in the HCSP was less promi- priming, and fusion. In this study, we have restricted nent in this study. The preferential augmentation of the kinase substrates to those that are important for the HCSP has been also reported in chromaffin cells regulating vesicle priming and fusion by using patch- (Yang et al., 2002) and possibly in INS-1 cells when

660 Sensitization of Insulin Secretion

205 stimulated with glucose (Yang and Gillis, 2004). We ogy. 121:1025–1033. have found that the bulk of the HCSP is not released in Braun, M., A. Wendt, B. Birnir, J. Broman, L. Eliasson, J. Gal- response to brief depolarization sufficient to deplete vanovskis, J. Gromada, H. Mulder, and P. Rorsman. 2004. Regu- lated exocytosis of GABA-containing synaptic-like microvesicles the IRP, suggesting that most of the granules in the in pancreatic -cells. J. Gen. Physiol. 123:191–204. 2 HCSP do not colocalize with Ca channels. The same Carpenter, L., C.J. Mitchell, Z.Z. Xu, P. Poronnik, G.W. Both, and conclusion has been drawn from studies in pituitary go- T.J. Biden. 2004. PKC is activated but not required during glu- nadotropes (Zhu et al., 2002), chromaffin cells (Yang cose-induced insulin secretion from rat pancreatic islets. Diabetes. et al., 2002), and INS-1 cells (Yang and Gillis, 2004). 53:53–60. Thus, the HCSP is likely to respond to global elevation Csukai, M., and D. Mochly-Rosen. 1999. Pharmacologic modula- 2 2 tion of protein kinase C isozymes: the role of RACKs and subcel- of [Ca ]i rather than localized Ca microdomains. A lular localisation. Pharmacol. Res. 39:253–259. preferential enhancement of the HCSP would mean Efanov, A.M., S.V. Zaitsev, and P.O. Berggren. 1997. Inositol hexa- that insulin secretion can be potentiated at substimula- kisphosphate stimulates non-Ca2-mediated and primes Ca2- 2 tory [Ca ]i values upon activation of intracellular pro- mediated exocytosis of insulin by activation of protein kinase C. tein kinases (Jones et al., 1985, 1986) This mechanism Proc. Natl. Acad. Sci. USA. 94:4435–4439. may also explain how PMA can give rise to a slowly de- Eliasson, L., E. Renstrom, C. Ammala, P.O. Berggren, A.M. Ber- torello, K. Bokvist, A. Chibalin, J.T. Deeney, P.R. Flatt, J. Gabel, et veloping component of insulin secretion even at a sub- al. 1996. PKC-dependent stimulation of exocytosis by sulfo- threshold glucose concentration (Bozem et al., 1987). nylureas in pancreatic cells. Science. 271:813–815. It is plausible that both nutrient and nonnutrient secre- Eliasson, L., E. Renstrom, W.G. Ding, P. Proks, and P. Rorsman. tagogues might modulate insulin secretion by recruit- 1997. Rapid ATP-dependent priming of secretory granules pre- 2 ing more granules into the HCSP through activation of cedes Ca -induced exocytosis in mouse pancreatic -cells. J. Downloaded from Physiol. 503(Pt 2):399–412. PKA and PKC. Gillis, K.D., R. Mossner, and E. Neher. 1996. Protein kinase C enhances exocytosis from chromaffin cells by increasing the size of We would like to thank Dr. Kevin Gillis for helpful suggestions to the readily releasable pool of secretory granules. Neuron. 16: the manuscript and Mrs. X.P. Xu for cell preparation. 1209–1220. This work was supported by National Science Foundation of Gschwendt, M., S. Dieterich, J. Rennecke, W. 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207 420 Biophysical Journal Volume 86 January 2004 420–427

Crystal Structure of the Hyperthermophilic Inorganic Pyrophosphatase from the Archaeon Pyrococcus horikoshii

Binbin Liu,*z Mark Bartlam,*z Renjun Gao,y Weihong Zhou,* Hai Pang,* Yiwei Liu,* Yan Feng,y and Zihe Rao*z *Laboratory of Structural Biology, Tsinghua University and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; yKey Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130023, China; and zNational Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Science, Beijing 100101, China

ABSTRACT A homolog to the eubacteria inorganic pyrophosphatase (PPase, EC 3.6.1.1) was found in the genome of the hyperthermophilic archaeon Pyrococcus horikoshii. This inorganic pyrophosphatase (Pho-PPase) grows optimally at 888C. To understand the structural basis for the thermostability of Pho-PPase, we have determined the crystal structure to 2.66 A˚ resolution. The crystallographic asymmetric unit contains three monomers related by approximate threefold symmetry, and a hexamer is built up by twofold crystallographic symmetry. The main-chain fold of Pho-PPase is almost identical to that of the known crystal structure of the model from Sulfolobus acidocaldarius. A detailed comparison of the crystal structure of Pho- PPase with related structures from S. acidocaldarius, Thermus thermophilus, and Escherichia coli shows signiﬁcant differences that may account for the difference in their thermostabilities. A reduction in thermolabile residues, additional aromatic residues, and more intimate association between subunits all contribute to the larger thermophilicity of Pho-PPase. In particular, deletions in two loops surrounding the active site help to stabilize its conformation, while ion-pair networks unique to Pho-PPase are located in the active site and near the C-terminus. The identiﬁcation of structural features that make PPases more adaptable to extreme temperature should prove helpful for future biotechnology applications.

INTRODUCTION Inorganic pyrophosphatase (PPase, EC 3.6.1.1) is an resolution crystal structures of enzymes with the same fold essential enzyme that specifically catalyzes the hydrolysis and function in mesophiles, thermophiles and hyperthermo- of the phosphoanhydride bond in inorganic phosphate (PPi) philes have revealed a number of potentially stabilizing (Chen et al., 1990; Lahti, 1983). PPi is a central phosphorus features. A proper understanding of the molecular basis of metabolite and is a by-product of various reversible thermal stability in proteins could have important conse- nucleoside 58-triphosphate–dependent reactions including quences for their application in a range of biotechnological tRNA charging and DNA and protein synthesis that utilize processes. For example, thermostable pyrophosphatases have ATP in vivo. PPases from a wide variety of sources have common uses in cycle sequencing methods using thermo- been studied, but those from Saccharomyces cerevisiae and stable DNA polymerases (Vander Horn et al., 1997). The Escherichia coli are the most highly characterized, both crystal structures of PPases from thermophilic bacterium biochemically and structurally. E. coli pyrophosphatase is Thermus thermophilus (T-PPase; PDB ID 2PRD) (Teplyakov a homohexamer with 175 amino acids per monomer (Avaeva et al., 1994), thermophilic archaebacterium Sulfolobus acid- etal., 1997),whereasS.cerevisiaepyrophosphataseisahomo- ocaldarius (S-PPase; PDB ID 1QEZ) (Leppanen et al., 1999), dimer with 286 amino acids per monomer (Heikinheimo et al., and mesophile E. coli (E-PPase; PDB ID 1JFD) (Avaeva et al., 2001). 1997) have provided basic clues for the PPase catalytic PPases from archaebacterium exhibit different structural mechanism and thermostability, but many important aspects and catalytic properties (Hansen et al., 1999; Richter and remain to be resolved. Schafer, 1992). The archaeal PPases so far reported are Microorganisms can be classified according to their opti- relatively thermostable, especially in the presence of divalent mal growth temperature, T , into four groups: psychro- metal cations (Ichiba et al., 1998). Understanding the opt philic (0 \ T \ 208C), mesophilic (20 \ T \ 508C), structural basis for the enhanced stability of proteins from opt opt hyperthermophilic organisms relative to their mesophilic and thermophilic (50 \ Topt \ 808C), and hyperthermophilic thermophilic counterparts is a highly relevant but complex (80 \ Topt \ 1208C). Considerable efforts have been made and challenging problem. Previous comparisons of high- during recent years to analyze the structural features that determine the extraordinary thermal stability of proteins from hyperthermophiles. Here we have isolated an inorganic Submitted June 12, 2003, and accepted for publication August 27, 2003. pyrophosphatase (Pho-PPase) from the hyperthermophilic Binbin Liu and Mark Bartlam contributed equally to this work. archaeon Pyrococcus horikoshii OT3, whose optimum Address reprint requests to Zihe Rao, Laboratory of Structural Biology, growth temperature (958C) is significantly higher than those Dept. of Biological Science and Biotechnology, Tsinghua University, Beijing 100084, P. R. China. Tel.: 86-10-6277-1493; Fax: 86-10-6277- of S. acidocaldarius (75–808C), T. thermophilus (75–808C) 3145; E-mail: [email protected]. and E. coli (378C). Pho-PPase showed a higher optimal Ó 2004 by the Biophysical Society activity at 888C and an alkaline optimal pH of 10.3 (at 888C). 0006-3495/04/01/420/08 $2.00 The enzyme has extreme thermostability and does not lose

208 Crystal Structure of Pho-PPase 421 activity at 1008C. In addition, Pho-PPase is stable against TABLE 1 Data collection, refinement, and model statistics various denaturants. All of these properties are different from Data collection those of other archaeal PPases: full details of the character- Space group P21212 ization of inorganic Pho-PPase will be reported elsewhere Unit cell parameters a ¼ 71.8, b ¼ 86.7, c ¼ 92.8 A˚ (Feng et al., unpublished results). To gain a more penetrating a ¼ b ¼ g ¼ 908 insight into its function, here we describe the structure Matthews coefficient (A˚ 3 Da1) 1.93 determination of Pho-PPase and a comparison of the Solvent content (%) 35.65 ˚ structure with its mesophilic and thermophilic counterparts Resolution (A) 50-2.66 Total observations 118041 in an attempt to understand the structural basis for thermal Unique reflections 17030 stability. Redundancy 6.93 Average I/s(I) 12.1 (4.3)

Rmerge (%) 7.5 (13.9) MATERIALS AND METHODS Completeness (%) 99.8 (98.0) Refinement Crystallization and x-ray data collection Reflections The preparation and preliminary characterization of Pho-PPase crystals have (observed) 117986 been described elsewhere (B. Liu X. Li, R. Gao, W. Zhou, G. Xie, M. (test) 1687 Bartlam, H. Pang, Y. Feng, and Z. Rao, submitted). Briefly, the gene en- Resolution range (A˚ ) 50-2.66 coding inorganic pyrophosphatase from the archaea P. horikoshii was Protein atoms 4148 cloned into pET15b (Novagen) and expressed in E. coli strain BL21. After Solvent atoms 93 purification, the purified protein was concentrated to 20 mg/ml. Crystalli- Rwork (%) 23.24 zation trials were set up using the hanging drop/vapor diffusion method with Rfree (%) 27.65 Crystal Screen reagent kits I and II (Hampton Research). Crystals suitable Average B value (A˚ 2) 38.19 for diffraction were obtained after two weeks from the condition 3.8% PEG RMSD bonds (A˚ ) 0.009 4000, 0.1 M Na acetate, pH 5.0–5.2, 0.02 M MgCl2. A set of data at 2.66 A˚ RMSD angles (8) 1.6 resolution were collected in house. All data were integrated using DENZO/ Ramachandran plot (%) HKL and scaled and merged with SCALEPACK (Otwinowski and Minor, Most favored regions 76.9% 1997). Crystal lattice properties and data-collection statistics are listed in Additionally allowed regions 19.6% Table 1. Generously allowed regions 3.3% Disallowed regions 0.2% Structure determination and refinement

The structure of Pho-PPase was solved by the molecular-replacement (MR) Pho-PPase shares 47% sequence identity with S-PPase method using the protein S-PPase (PDB ID 1QEZ) (Leppanen et al., 1999) (Fig. 2 A), and the two proteins have a similar core structure. as the starting model. The initial R value for the MR solution obtained from Indeed, superposition of the Pho-PPase structure with the cross-rotation and translation search in CNS (Brunger et al., 1998) was S-PPase, T-PPase, and E-PPase shows that the four PPases 48.4%, using 15171 reflections in the 50-2.66 A˚ resolution range. This R value is ;10% lower than those of the other possible solutions. After rigid- are spatially homologous (Fig. 2 B). The RMSD between ˚ body refinement, the R value decreased to 46.8, and side-chain atoms were Ca atoms of the four PPases range from 0.83 to 1.14 A. fitted into the 2|Fo|-|Fc| electron-density map. The structure was further The mutual positions of the central b-barrel structure and refined to 26.5% (using reflections in the resolution range 50-2.66 A˚ ) a-helices are similar. However, the structure-based sequence following cycles of simulated-annealing refinement using CNS and manual alignment (Fig. 2 A) shows that Pho-PPase contains a single rebuilding in O (Jones et al., 1991). After the placement and refinement of 93 water molecules and individual B factor refinement, the R factor was reduced residue deletion in the loop formed by residues 25–30, two to 23.2%. A Ramachandran plot generated by PROCHECK (Laskowski residues deleted in the loop formed by residues 111–114, and et al., 1993) shows that the structure has reasonable stereochemistry with no three residues deleted in the loop formed by residues residues in disallowed regions. Refinement statistics are summarized in 144–148. Table 1. Coordinates for this structure have been deposited in the Protein Data Bank with PDB ID 1UDE. Oligomeric structure RESULTS AND DISCUSSION The Pho-PPase structure consists of three molecules in the asymmetric unit. The first subunit contains residues 4–171 Monomeric structure out of a total of 178 residues; the second subunit contains The current model of P. horikoshii inorganic pyrophos- residues 4–170; and the third subunit contains residues phatase includes residues 4–171 in chain A, 4–170 in chain 4–170 with a Y170A substitution. Subunits 2 and 3 can B, 4–170 in chain C, and 93 water molecules. Pho-PPase is be superimposed onto the first subunit with RMSDs of 0.61 arranged in a globular form and belongs to the a1b class of A˚ and 0.65 A˚ , respectively. The three Pho-PPase monomers protein folds. The Pho-PPase monomer structure is com- are related by a noncrystallographic threefold axis to form posed of nine b-strands and two a-helices arranged in a a tight trimer with an extensive subunit interface. As can b1-b2-b3-b4-b5-b6-b7-b8-a1-b9-a2 topology (Fig. 1). been seen in Fig. 1 B, the main contact region concerns

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209 422 Liu et al.

active site is very similar to those of E. coli and yeast PPases (Avaeva et al., 1997). It has been previously suggested that 17 residues might be involved in Mg21 and PPi binding, 15 of which appear to be conserved in all sequences of soluble PPases known to date. Accordingly, all 15 of these conserved residues (E23, K31, E33, R44, Y52, Y56, D66, D68, D71, D98, D103, K105, Y140, K141, K146) also reside in the active-site cavity of Pho-PPase (Fig. 2). This implies that Pho-PPase will share the general catalytic mechanism of the PPase family in vivo, although the maximal enzyme activity of Pho-PPase is gained under a strong alkaline environment in vitro. Although Pho-PPase includes the conserved residues involved in Mg21 binding, no Mg ion was observed in the Pho-PPase structure despite the addition of MgCl2 during crystallization. Many crystals soaked in MgCl2 were found to crack, which suggests that conformational changes may occur to prevent Mg21 binding. A similar observation was made in the structure of E-PPase (Kankare et al., 1994). The crystal structure of Pho-PPase reveals that K102, equivalent to residue E101 in E-PPase, is important for the active-site cavity and is located in the highly conserved region including the essential catalytic residues (numbered E97, D102, and K104 in E-PPase). Mutagenesis studies of E-PPase have shown that the enzyme activity of mutants E99D, D102E, and K104E almost disappeared or decreased FIGURE 1 (A) A ribbon representation of the Pho-PPase monomer structure. The structure is colored from blue at the N-terminal to red at the rapidly (Hyytia et al., 2001). However, when E101 is C-terminus. Secondary structure elements have been labeled. (B) Top and replaced by a more negative aspartic acid residue, the en- side views of the Pho-PPase hexamer. Three subunits are related by zyme activity of the mutant was increased by 10%. Align- a noncrystallographic threefold axis to form a trimer. Two trimers are related ment with other PPases shows that the residue located in the by a crystallographic twofold axis to form a tightly packed hexamer. site is conserved as either an acidic or neutral residue. We propose that K102 is related to the alkaline optimal pH (10.3) of Pho-PPase, since only in such an alkaline environment strands b2andb3 of the b-barrel of one subunit and a would K102 not be positive. Further site-directed mutagen- b-hairpin (residues 78–85) of another subunit. There are esis studies are in progress to investigate the role of K102. many hydrophobic and hydrophilic interactions between subunits to enhance the enzyme stability, which will be discussed in further detail below. From the crystallographic symmetry, the trimers are Structural basis of thermostability in Pho-PPase packed such as to form a tightly packed hexamer with The free energy of stabilization of globular proteins is rather twofold crystallographic symmetry. The intertrimer inter- small. It lies in the range from 30 to 65 kJ/mol (Pfeil et al., actions in Pho-PPase are listed in Table 2. There are no large- 1986), which is equivalent to the energy contributed by a scale distortions in monomeric structure, and the increased few hydrogen bonds, ion pairs, or hydrophobic interactions. thermostability of Pho-PPase likely results from an increase The increase in free energy of stabilization observed for in both hydrophilic and hydrophobic interactions. Intertrimer thermophilic proteins is of the same order of magnitude interactions are concentrated in strand b3, helix a1, and the (Harris et al., 1980; Nojima et al., 1978). Recent structural loop between b8 and a1. The overall surface area buried in studies also have identiﬁed several factors which are more ˚ 2 ˚ 2 the hexamer is 2342 A , which is comparable to the 2430 A often observed among thermophilic proteins and may ˚ 2 buried by the T-PPase hexamer and higher than the 2090 A account for their stability. These include an increased buried by the E-PPase hexamer (Salminen et al., 1996). number of salt bridges or hydrogen bonds; optimized stability of helices, loops, and N- and C-termini; decreased solvent-exposed surface area; stronger interactions between Active center the subunits in oligomers; and even an increased number of The active site cavity of Pho-PPase is formed between the buried solvent molecules in hydrophilic cavities. We b-barrel and helix a1. The overall shape and size of the compare the present 2.66 A˚ resolution structure with three

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210 Crystal Structure of Pho-PPase 423

FIGURE 2 (A) A structure-based sequence alignment between Pho-PPase and three related PPase structures from T. thermophilus (T-PPase; PDB ID 2PRD) (Teplyakov et al., 1994), S. acidocaldarius (S-PPase; PDB ID 1QEZ) (Leppanen et al., 1999) and E. coli (E-PPase; PDB ID 1JFD) (Avaeva et al., 1997). Secondary structure elements are shown for Pho-PPase. (B) A stereodia- gram showing the superposition of the four PPase structures. Structures are

represented as Ca backbone traces. The coloring is as follows: red, Pho- PPase; blue, S-PPase; green, T-PPase;

magenta, E-PPase. RMSD between Ca atoms of the four PPases range from 0.83 to 1.14 A˚ .

other PPases, to identify which factors may be important in mostability. Such stabilization by the introduction of proline stabilizing Pho-PPase. residues into loop regions is a well-documented phenomenon (Matthews et al., 1987). A recent study of inorganic pyrophosphatase from thermophilic bacterium PS-3 was Amino acid composition and thermostability carried out in which proline residues were systematically The amino acid composition of a protein has long been replaced by alanines (Masuda et al., 2002). The authors thought to be correlated with its thermostability. Compared found that most of the proline residues in PS-3 PPase play with related PPase structures, the unusual amino acid very important roles, and many of them are critical for the composition of Pho-PPase would account for its extreme structural integrity of the protein. They also concluded that thermostability. The structure-based sequence alignment the thermostability of PS-3 PPase is profoundly related with (Fig. 2) shows the amino acid sequences of the four PPases its subunit structure. compared in this study. More charged residues were found in The total number of hydrophobic residues (Gly, Ala, Val, Pho-PPase, which is consistent with the idea that the number Leu, Ile, Met, Phe, Trp, and Pro) is also highest in Pho- of ion pairs is an important determinant of protein PPase. Compositional differences between the PPases are thermostability. For instance, Pho-PPase contains a total more pronounced among exposed sites. Pho-PPase has an number of eight arginine residues, which have a tendency to increased number of exposed hydrophobic residues, which form multiple ion-pairs and H-bonds. Pho-PPase also are presumably involved in oligomer formation and stability. contains 14 proline residues, which is the largest proportion Interestingly, previous site-directed mutagenesis of in the four PPases studied here. Since proline residues affect E-PPase has shown that aromatic residues play a very local mobility of the chain by decreasing the conformational important role for the thermostability (Hyytia et al., 2001). entropy of the unfolded state, the increased rigidity of the There are an increased number of aromatic residues found in structure would be expected to increase the overall ther- Pho-PPase compared to three other PPases. In particular,

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211 424 Liu et al.

TABLE 2 Oligomeric interactions in E-PPase, T-PPase, S-PPase, and Pho-PPase E-PPase a distance T-PPase a distance S-PPase b distance Pho-PPase distance

From To (A˚ ) From To (A˚ ) From To (A˚ ) From To (A˚ ) Intratrimeric A-B hydrophilic contacts S1 S36 2.79 N27 Y77 3.59 N16 K40 3.41 R28 E78 2.87 Y30 Q80 3.32 I39 V84 2.93 Y30 Y80 3.48 N29 E29 2.98 L39 V84 2.86 L41 V84 2.83 I39 V84 3.09 N29 E78 3.44 V41 V84 2.85 V44 E111 3.23 V41 V84 2.90 N29 P79 3.21 F44 L113 2.96 L45 R116 2.86 D42 T113 3.52 L40 I85 2.76 L45 R116 2.93 V44 T113 2.78 K41 E87 3.39 Q115 L144 3.56 Y46 K112 2.49 L42 I85 2.86 R44 E112 2.82 V45 G112 2.67 Intertrimeric A-D hydrophilic contacts S46 Q133 2.89 A48 F50 3.54 S48 N50 3.13 R28 E132 3.00 A48 F50 3.01 Q132 K148 3.00 S48 Og N50 2.57 T48 H135 3.58 H136 D143 2.76 H136 T140 3.21 H136 H140 3.45 P49 H51 2.64 H136 E143 2.66 H135 E142 2.48 R139 E142 3.01 R138 E142 3.16 Intertrimeric A-E hydrophilic contacts N24 Y77 3.35 R116 E133 3.33 R77 E132 2.74 R116 E133 3.27 R116 E133 2.82 Q115 Q132 3.33 Intratrimeric A-B hydrophobic contacts L2 A28 3.92 P6 L36 3.91 L5 E36 4.03 F4 L39 4.07 D26 Y77 3.58 Y30 V83 3.98 L5 V38 4.05 R28 E78 3.84 P27 Y77 2.89 I39 V83 3.77 I28 Y77 3.78 N29 E78 4.10 I28 Y77 3.76 L41 V109 3.81 I28 L79 4.10 L39 L20 3.85 Y30 S83 3.99 R43 E111 3.98 Y30 Y80 3.51 L40 T84 3.91 L39 S83 3.94 V44 Y77 3.60 K40 V84 4.02 K41 E87 3.79 F40 V84 3.67 V44 V109 3.99 V41 L79 3.95 L42 M76 3.39 V41 L79 3.80 V44 D114 3.81 V41 T113 4.01 L42 I86 3.90 V41 L113 3.73 L80 P81 3.49 V44 Y77 3.72 K44 E112 3.78 F44 T75 3.40 Y46 P115 3.40 V45 M76 4.02 F44 P76 3.69 Y80 P81 3.63 V45 D113 3.53 F44 S114 3.99 Y47 P114 3.89 P82 Y81 3.60

Intertrimeric A-D hydrophobic contacts P27 F50 3.99 A48 F50 3.79 T47 K133 3.38 R28 E132 3.87 S46 L129 3.86 A48 P52 4.00 S48 P52 4.09 T48 H135 3.62 T47 H136 3.57 A48 E133 3.80 S48 K133 4.02 T48 F50 3.24 A48 F50 3.73 Q49 H136 3.91 M49 M49 3.38 P49 F50 3.83 M49 M49 3.88 F50 F50 3.56 H136 L144 3.99 P49 E132 3.38 H136 L144 3.96 Q132 L144 3.98 H140 H140 3.25 P49 P53 4.05 H136 D143 3.37 T140 T140 3.76 F50 F50 4.06 H140 H140 3.61 H51 H51 3.47 H135 L143 3.94 R139 R139 3.51

Intertrimeric A-E hydrophobic contacts R116 E133 4.00 N76 N76 3.81–4.00 P114 A128 3.58 H119 P127 3.41 P115 A129 3.88–4.18 P114 A128 3.58 Y115 P126 3.69 Y115 A128 3.82

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212 Crystal Structure of Pho-PPase 425

TABLE 3 Ionic interactions within a monomer E-PPase distance T-PPase distance S-PPase distance Pho-PPase distance

From To (A˚ ) From To (A˚ ) From To (A˚ ) From To (A˚ ) E13 K162 3.66 K10 E86 3.69 D13 K162 2.64 E15 K161 3.16 D14 R86 2.79 E13 R166 4.12 K29 E31 2.81–3.93 K30 D43 3.12–3.76 D14 H110 3.66 K29 E31 3.86 D33 K40 2.57–5.60 K41 E87 3.96 K29 D42 2.7 D42 R43 2.11 E36 K40 3.20–5.99 R44 E144 3.12 R43 E154 2.71 R43 E145 4.02 R43 E145 2.43–3.20 R44 K112 2.82 D70 K104 2.87 E64 R171 2.89 R43 D42 2.85 D71 K105 3.72 K94 E101 3.47 D70 K104 3.03 E63 R164 2.83 R77 D113 3.26–3.72 D97 K142 3.55 E98 K99 4.5 E63 R171 3.90 K95 E154 4.00 D102 K104 3.07 E98 K142 2.58 E64 R171 3.88 K95 E155 3.16 H140 E139 3.43 D102 K104 3.02 D70 K104 2.94 D98 K141 3.98 H140 D143 2.93 D114 R116 3.13 E86 K110 3.22 D103 K105 3.76 E159 K162 3.76 D122 R158 3.84 R88 D111 3.11 K117 D118 3.15 E98 K142 3.15 E145 K148 3.65 D118 K120 3.54 E98 K148 3.50 E163 R166 4.04 K127 D131 3.16 4.09 D102 K104 2.91 E132 H135 3.73 H140 E143 3.04 R139 E142 3.26 E145 K148 2.46–4.06 R139 K138 3.46 E144 K146 3.56 E157 K160 3.24 E157 K160 3.58 E162 R165 2.22 E169 K171 3.17 there is an increased frequency of phenylalanine and tyrosine mesophilic counterparts (DeDecker et al., 1996; Hennig residues in Pho-PPase, which are liable to form hydrophobic et al., 1995; Yip et al., 1995). A total of 12 ionic interactions and aromatic interactions. Many of these aromatic residues are formed per monomer in the E-PPase short c-axis crystal are observed to form a cluster located at the bottom of the form, which is equivalent to the number in T-PPase and active site, and it is possible that stacking interactions lower than S-PPase (17 ionic pairs). In contrast, there are 28 involving the aromatic residues may contribute to enhanced ionic interactions scattered throughout the Pho-PPase mono- thermostability of Pho-PPase. mer (Table 3). It appears that Pho-PPase is more stabilized The frequency of Asn (2) and Gln (0), which can be by ion-pairs than T-PPase, E-PPase, and S-PPase. Although classed as thermolabile due to their tendency to undergo the number of ion-pairs is increased, the multicenter ion deamidation at high temperatures and therefore may be interactions are decreased. Interestingly, two long ion-pair naturally discriminated against in thermostable proteins, is networks are observed in Pho-PPase. The first ion-pair substantially reduced in Pho-PPase. Cysteine was also network is located in the C-terminus a2 helix, which may completely absent in Pho-PPase, which is easy to interpret stabilize the C-terminus against thermal denaturation. The since cysteine is highly sensitive to oxidation at high second ion network is located in the active center and temperature. The frequency of glycine was not decreased, involves residues 112–120 and 127–139. There is also an but changed in location. Interestingly, residue L83 of Pho- increase in the number of intrasubunit ion-pairs in Pho- PPase is strictly conserved as a glycine in other PPases and is PPase, and their involvement in complex networks mirrors located in the short loop connecting b-strands 5 and 6, thus that observed in the structure of the hyperthermophilic increasing the rigidity of the Pho-PPase structure. Pyrococcus furiosus glutamate dehydrogenase (Yip et al., 1995). The presence of ion-pair networks has also been observed in Sulfolobus solfataricus indole-3-glycerol phos- Ionic interactions and thermostability phate synthase (Hennig et al., 1995) and the TATA-box The importance of ion-pairs as determinants of protein binding protein from P. furiosus (DeDecker et al., 1996). thermostability was first highlighted by Perutz and Raidt The presence of ion-pair networks may be energetically (Perutz and Raidt, 1975) while comparing ferredoxin and favorable due to the shared entropic cost upon ion-pair hemoglobin structures, and ion-pairs were subsequently pro- formation (Nakamura, 1996). posed to be important for the stability of a number of other The positioning of ion-pairs is also crucial (Daggett and thermostable proteins (Korndorfer et al., 1995; Walker et al., Levitt, 1993). Loop or random coil regions of a protein tend 1980). Indeed, several reports of high resolution structures of to be the most flexible areas and are the most likely to deform hyperthermophilic proteins show the number of ion-pairs in at high temperatures. Compared with the three other PPases most of the hyperthermophilic proteins is higher than in their used in this study, Pho-PPase has three shorter loops, of

Biophysical Journal 86(1) 420–427

213 426 Liu et al. which two lie in the active site and the third sits at the increase in the number of charged residues compared with molecular surface. In contrast, the loops found in E-PPase the other PPases (Fig. 2 A). These residues—E157, R161, are longest of the four PPase structures. This observation, E162, R165, E168, K171—are ideally distributed in the that the higher the growth temperature of the organism the sequence to allow the formation of intrahelix ion-pairs. The shorter the protein loops, is consistent with high temperature structure of Pho-PPase shows three intrahelical ion-pairs molecular dynamic simulations on bovine pancreatic trypsin formed between residues E157-R161, E162-R165, and inhibitor, which revealed that loop and turn regions are likely E169-K172 (Table 3), which are not conserved in other to be the parts of the structure that unfold first during thermal PPase structures. These additional ion-pairs may be re- denaturation. The structure of thermostable endocellulase sponsible for the increased thermostability of Pho-PPase by (Sakon et al., 1996) also showed a reduced size of loop stabilizing the C-terminus and increasing its resistance to regions, and a similar strengthening of loop regions was also denaturation. observed in S. solfataricus indole-3-glycerol phosphate synthase (Hennig et al., 1995). CONCLUSIONS Oligomerization and thermostability Comparison of the structure of Pho-PPase with T-PPase, In the PPase family, the oligomerization state stabilizes the S-PPase, and E-PPase has identified a number of determining conformation of the enzyme that binds substrate and vice factors for the thermostability of PPase enzymes. Pho-PPase versa (Baykov et al., 1995). The oligomeric packing appears is the most thermostable of the four structures, and this is to provide a general strategy for enhancing the thermosta- reflected by the following factors. First, shorter and more bility of the PPase family. Pho-PPase seems to be a more convergent loops in the active site imply that the two loops tightly packed hexamer. The total number of oligomeric are important for enzyme-substrate or ion binding under high hydrophilic contacts is listed in Table 2. There are notably temperature, and this is consistent with the idea that shorter more intermonomer hydrophilic interactions in Pho-PPase loops are more helpful for thermostable PPases to stabilize compared with the three other PPases, resulting in tighter the conformation of the enzyme-substrate complex. Second, twofold A-E and threefold A-B interfaces. This effect can be the basis of thermostability in PPases is generally believed to measured by the accessible surface area (ASA) buried per be related to the oligomer structure; Pho-PPase has an monomer on oligomerization, which is 13.6% higher than for increase in the number of both intermonomer and intertrimer S-PPase and 12.1% higher than for E-PPase. These increased interactions, and this results in tighter packing of the hexamer. hydrophilic interactions may provide the extra energy Third, an increase in the number of ion-pairs—in particular, necessary for stabilization. Similar observations are found two ion-pair networks—helps to stabilize the structure. One in several thermophilic protein structures. For example, ion-pair network in the loop connecting strand b8 and helix thermostability was attributed to improved subunit interfaces a1 may help to stabilize the conformation of the active site, in L-lactate dehydrogenase from Bacillus stearothermophilus while another network in helix a2 may stabilize the (Kallwass et al., 1992), malate dehydrogenase from Thermus C-terminus and increase its resistance to thermal denatur- flavus (Kelly et al., 1993), and ornithine carbamoyltransfer- ation. The structure of Pho-PPase and the comparison be- ase from P. furiosus (Villeret et al., 1998). Other studies also tween PPase structures should stimulate further kinetic and indicate that multimer formation and subunit interactions are structural studies of enzymes adapted to extreme temperature critical for thermal stability of, for example, hemocyanin and prove helpful for future biotechnology applications. from the ancient tarantula Eurypelma californicum (Sterner et al., 1995), phosphoribosyl anthranilate isomerase from the We are grateful to Feng Gao for help with data collection. hyperthermophile Thermotoga maritima (Hennig et al., This research was supported by the following grants: Project ‘‘973’’ 1997), GluDH from the hyperthermophile P. furiosus G1999075602; Ministry of Science and Technology (MOST) (Vetriani et al., 1998), and chorismate mutase from the ther- 2002BA711A12. mophilic archaeon Methanococcus jannaschii (MacBeath et al., 1998). REFERENCES

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214 Crystal Structure of Pho-PPase 427

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215 Biophysical Journal Volume 87 September 2004 1991–2001 1991

Three-Dimensional Tracking of Single Secretory Granules in Live PC12 Cells

Dongdong Li,* Jun Xiong,* Anlian Qu,* and Tao Xu*y *Institute of Biophysics and Biochemistry, School of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, People’s Republic of China; and yNational Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China

ABSTRACT Deconvolution wide-field fluorescence microscopy and single-particle tracking were used to study the three- dimensional mobility of single secretory granules in live PC12 cells. Acridine orange-labeled granules were found to travel primarily in random and caged diffusion, whereas only a small fraction of granules traveled in directed fashion. High K1 stimulation increased significantly the percentage of granules traveling in directed fashion. By dividing granules into the near- membrane group (within 1 mm from the plasma membrane) and cytosolic group, we have revealed significant differences between these two groups of granules in their mobility. The mobility of these two groups of granules is also differentially affected by disruption of F-actin, suggesting different mechanisms are involved in the motion of the two groups of granules. Our results demonstrate that combined deconvolution and single-particle tracking may find its application in three-dimensional tracking of long-term motion of granules and elucidating the underlying mechanisms.

INTRODUCTION Vesicular trafficking constitutes a major means for intracel- depth of the evanescent field is limited to several hundreds of lular and transmembrane cargo transportation. For example, nanometers, TIRFM can only be employed to study granules hormones and neurotransmitters are stored in vesicles and are right underneath the plasma membrane close to the cover- released upon fusion with the plasma membrane. Before a glass-solution interface, whereas granules residing deeper vesicle can fuse with the plasma membrane, it has to undergo inside the cytosol are invisible under TIRFM. It is unclear a series of steps such as budding, translocation, tethering, whether the ‘‘unphysiological’’ adhesion of cell membrane docking, and priming (Pfeffer, 1999; Toonen and Verhage, to the coverglass will have an impact on the mobility and 2003; Jahn et al., 2003). To better understand the mechanisms function of secretory granules. On the other hand, although of different steps in vesicular trafficking, it is desirable to TIRFM is generally used for 2-D tracking, z-mobility can be directly visualize the movement of vesicles inside living indirectly inferred from the changes in the intensity of cells. fluorescence (O¨ lveczky et al., 1997; Johns et al., 2001). Two-dimensional (2-D) confocal microscopy has been However, since TIRFM is extremely sensitive to the objects’ used to explore granule movement in single optical section vertical movement, fluctuation in fluorescence unrelated to (Pouli et al., 1998; Levitan, 1998). The contribution from the changes in axial position (such as variation in excitation missing z direction is ignored by assuming that observed power, quenching, or dequenching of fluorescence due to granules move within the observation plane during the pH change, etc.) will result in misinterpretation of the experimental time. Three-dimensional (3-D) single-particle z-position. tracking (SPT) in living cells has been difficult for confocal To avoid the restriction of TIRFM in observing only the fluorescence microscopy. This probably is due to low time cell-glass interface and to expand our knowledge on 3-D resolution inherited with the laser scanning, high photo- movement of granules throughout living cells, we have bleaching, and toxicity at the expense of low light collection constructed a system to combine deconvolution wide-field efficiency. Recently developed total internal reflection fluo- fluorescence microscopy (WFFM) and 3-D single-particle rescence microscope (TIRFM) has proved very successful in tracking technique. We have employed this method to study studying the movement of single granules. The advantages the 3-D mobility of single granules in living PC12 cells. of low background, high temporal resolution, minimal Indeed, 3-D mobility of granules distant from the plasma photobleaching, and phototoxicity have made TIRFM very membrane has yet to be demonstrated. We have compared popular in tracking the docking and fusion of granules the mobility of granules that are either close to the plasma (Steyer and Almers, 1999; Oheim and Stu¨hmer, 2000; membrane (GP) or located deep inside the cytosol (GC). Our Ohara-Imaizumi et al., 2002). However, as the penetration data illustrated that the mobility of internal granules is greater than those near the plasma membrane. Whereas the majority of granules wander in random and caged fashion, stimulation increases significantly the percentage of granules Submitted March 19, 2004, and accepted for publication May 25, 2004. that travel in a directed fashion. We also found that the Address reprint requests to Tao Xu, E-mail: [email protected]; or mobility of GP is more prone to the disruption of F-actin, Anlian Qu, E-mail: [email protected]. 2004 by the Biophysical Society 0006-3495/04/09/1991/11 $2.00 doi: 10.1529/biophysj.104.043281

216 1992 Li et al. whereas that of GC is less affected. Our results demonstrate Image collection that combining deconvolution and 3-D SPT is useful in Cells were grown on high refractive-index glass coverslips and viewed under following the long-term 3-D movement of single granules an inverted microscope (IX70; Olympus America, Melville, NY) with a 1.65 within living cells. numerical-aperture (NA) objective (APO 3100 O HR, Olympus). Excitation light from a ﬁber optical-coupled monochromator (Polychrome IV; TILL Photonics, Bayern, Germany) was passed through a shutter that opened only MATERIALS AND METHODS during camera exposure. The wavelength selection and shutter were con- Cells, labeling, and solutions trolled by the image acquiring software (TILL vision 4.0, Till Photonics). Images were acquired with a cooled charge-coupled device (PCO SensiCam, PC12 cells were cultured as described (Lang et al., 1997). Cells were used Kelheim, Germany) with pixel size of 0.067 mm at the specimen plane. shortly after being transferred to homemade coverslip chambers. Granules Appropriate dichroic mirror (505 DCLP from Chroma Technology, Brattle- were labeled by incubating the cells in a buffer containing 3 mM acridine boro, VT) and emission ﬁlter (535LP from Chroma) were used for imaging. A orange (AO) (Molecular Probes, Eugene, OR) for 15 min at 21C. Then the series of 2-D images were collected via moving the focal plane through a cell cells were washed twice in dye-free buffer, which contained (in mM): 150 with the piezoelectric z axis controller (E-662. LR, Physik Instrumente,

NaCl, 5.4 KCl, 2 MgCl2, 1.8 CaCl2, and 10 HEPES (pH 7.4). Cells were Karlsruhe, Germany). The focal plane advanced ;75% of the distance moved viewed ;60 min later. To verify our determination of the membrane by the objective due to the discrepancy in refractive index between the contour, cells were first incubated in normal external solution containing immersion oil and cytosol. Accordingly, we reconstructed 3-D images of cells 4 mM FM1-43 (Molecular Probes, Eugene, OR) for 5–10 min until we saw with those stacks of 2-D sections. For obtaining successive a stable fluorescence staining that was uniformly distributed along the 3-D images of a cell, we selected the plane where the outmost edge of the plasma membrane. After locating the plasma membrane, FM1-43 was cell appeared sharpest as the reference plane. Starting from the reference washed out from the membrane in dye-free buffer, which resulted in a rapid plane, we sampled sixteen 2-D sections with 0.2 mm stepping size to generate disappearing of the staining. Then, for the same cell we labeled its granules one 3-D image. An illustration of the imaged region is shown in Fig. 1 D with AO as described above. To avoid unnecessary photobleaching, between the dashed lines. As to the same imaged region, we successively fluorescence excitation was turned on only during image acquisition. recorded its 3-D images every 5 s for 70 s to generate a stack including fifteen 1 [K ]o was raised by local perfusion with a multi-channel perfusion system 3-D images. In our imaging protocol, exposure time for each optical section (MPS-1, YiBo Life Science Instrument, Wuhan, China). The stimulation was 5 ms, and the waiting interval for the next section was 170 ms. buffer contained (in mM): 90.4 NaCl, 65 KCl, 2 MgCl2, 1.8 CaCl2, and 10 Occasionally, more sections were sampled to include the whole cell. HEPES (pH 7.4). Sometimes, dense-core granules were labeled by transient transfection with human pro-neuropeptide Y (NPY) (plasmid kindly provided by W. Almers, Vollum Institute, Oregon Health and Science Point spread function and deconvolution University, Portland, OR) fused to the N-terminal of DsRed, which would be used to compare with AO-labeled granules in size, but not used for Knowing the point spread function (PSF) of the imaging system is the successive 3-D imaging due to the longer exposure time required for prerequirement for deconvolution. For our 1.65-NA objective, we de- imaging DsRed labeled granules. Actin cytoskeletons were disrupted by termined the 3-D PSF through either experimental or theoretical method. In incubating the cells with 5 mM latrunculin B (ICN Biomedicals, Aurora, experimental measurement, we dried subresolution fluorescent beads (PS- Ohio) for 2 min. Speck; diameter, 0.175 mm; Molecular Probes) on the coverslip (refractive

FIGURE 1 Point spread function and deconvolution. (A) Comparison of jOTF (u, v)j distribution of corresponding equal-defocus (0.4 mm) optical sections between experimental and theoretical PSF. Experimental PSF was averaged from eight measurements, which gave quite similar OTF as that of theoretical PSF (P ¼ 0.98, KS test). (B) OTF distribution of the point light source from different defocus sections on the focal plane. (C) Eval- uation of deconvolution result using different iterations and high-pass filtering; 15-mm beads with a spherical shell of fluorescence ;0.5–0.7 mm thick were used for the evaluation. Equato- rial sections were used to measure the width of the shell (n ¼ 7 beads). Deconvolution removes the out-of- focus blur and gives better estimates of the width. DC stands for deconvolution, and HP for high-pass filtering at a spatial frequency of 1/mm. (D) Selected deconvolved 3-D images of a PC-12 cell from stacks of images, wherein secretory granules were labeled by AO. Left panel, lateral sections with a distance of 1 mminz direction. Right panel, axial sections with a distance of 3 mminy direction. Dashed lines depict the 3-D region we sampled for analysis at a z-step interval of 0.2 mm. Scale bars, 1 mm.

Biophysical Journal 87(3) 1991–2001

217 Three-Dimensional Mobility of Granules 1993 index, 1.78; thickness, 0.15 mm; Olympus) and then collected its 3-D images at different focal distances. According to the parameters of our imaging system, the theoretical PSF was derived from the mathematic model described in Gibson and Lanni, 1991. The iterative expectation-maximum algorithm based on a maximum- likelihood approach (Conchello and McNally, 1996) was used to deconvolve every recorded 3-D fluorescence image. The deconvolution algorithm used in our study was regularized with intensity regularization that can avoid the appearance of some artificial bright spots in deconvolved images (Conchello and McNally, 1996; Markham and Conchello, 1997). To verify the result of deconvolution, we employed a well-defined 3-D specimen, FocalCheck Fluorescent Microsphere from Molecular Probes. The bead is a spherical shell of fluorescence with a thickness of 0.5–0.7 mm as provided by Molecular Probes.

Evaluation of 3-D SPT with simulation

2-D SPT has been widely applied to monitor subpixel displacements of individual fluorescence particles between successive images, and some evaluation frameworks have been performed (Gosh and Webb, 1994; Kues et al., 2001; Cheezum et al., 2001; Thompson et al., 2002). The rationale of subpixel displacement detection is that fluorescence of single particles spreads over more than one pixel in recorded images, so the subpixel displacement can be tracked by weighting the fluorescence distribution from FIGURE 2 SNR and threshold selection are critical for the performance of multiple pixels between successive time-lapse images. Here, we calculated SPT. (A) Simulated granule (with SNR ¼ 9) trajectories based on measured centroids of successive images to estimate subpixel displacements in three parameters were used to evaluate the influence of different threshold levels dimensions. The centroid of a single axis is (labeled in figure) on the estimation of MSD. The resemblance between SPT-estimated MSD and the actual one was assessed by the P-values given in the Kolmogorov-Smirnov (KS) test, with a maximum P-value indicating m n t . m n t the best resemblance. (B) Assessing mean P-values and bias between Cx ¼ + + + ðxi 3 IijkÞ + + + Iijk; (1) i¼1 j¼1 k¼1 i¼1 j¼1 k¼1 estimated and actual MSD under different threshold levels for SNR ¼ 9 (n ¼ 7 simulated trajectories). Dashed line indicates a P-value of 0.1. The maximum P-value is attained at a threshold of 0.62. (C) Threshold selection in which x is the coordinates of a pixel on the x axis, and I denotes the i ijk is dependent on the SNR of each granule. For every given SNR, the fluorescence intensity of the corresponding pixel. A threshold was defined as optimized threshold for each simulated granule tracking was determined by the fraction of the maximum fluorescence intensity, and those normalized maximizing the P-values. Averaged maximal P-values and the correspond- pixels below the threshold were appointed zero. We applied computer- ing biases are displayed against different SNRs. Larger SNRs give better generated granule trajectories and movement, based on the measured SPT performance with larger P-values and less biases. parameters, to assess the influences of different signal/noise ratios (SNRs) and thresholds on SPT performance. The simulated granule, with similar size with actual granules (120 nm in diameter, Tooze et al., 1991), was Error for the bias was given with STD for a given threshold. Both SPT and initially created in one high-resolution matrix whose cell size was 0.01 mm simulation program were written in MATLAB 6.1. 3 0.01 mm 3 0.03 mm(x, y, z), which was then convolved with the 3-D PSF mentioned above. The simulated CCD image was acquired by covering the same physical extent of the PSF-convolved high-resolution matrix with Mobility analysis of granules residing in different a low-resolution matrix whose cell size was set to 0.07 mm 3 0.07 mm 3 subcellular regions 0.15 mm(x, y, z), which approximates the real sampling size used in our For comparing the mobility of granules residing close to the plasma experiments. Subsequently, shot noise after a Poisson distribution was added membrane and the ones that are deep inside the cytosol, we divided the total for every pixel. For a particular SNR, several stacks, each of which population of granules into two groups according to their relative distances contained sequential 3-D images of the simulated granule, were generated from the plasma membrane. One group included granules localized ,1 mm with computer. Subpixel displacements of the simulated granule between from the contour of the plasma membrane, termed GP. The rest of granules successive 3-D images were achieved through randomly moving granule inside the cytosol were termed GC. The edge-detecting algorithm (first along three dimensions in high-resolution matrix. described by Canny, 1986) implemented in MATLAB 6.1 software was The mean-square displacement (MSD) is of critical importance for employed to detect the membrane contour from the deconvolved image of assessing the parameters of granule’s 3-D mobility, so we evaluated the AO-loaded cells (see Results section for more details). performance of our SPT algorithm for estimating the MSD of the simulated The mobility of each granule can be analyzed by determining its MSD as granule at different SNR levels. The resemblance between SPT-estimated a function of time interval nDt. MSD in three dimensions can be calculated MSD and the actual one was assessed by the P-values given in the as follows: Kolmogorov-Smirnov (KS) test. For every given SNR, the optimized threshold for each simulated granule tracking was determined by maximizing the P-values (see Fig. 2). In addition, the bias and standard 1 Nn MSDðnDtÞ¼ + f½xð jDt 1 nDtÞxð jDtÞ2 deviation (STD) was calculated and used as another indication of tracking N n accuracy for the selection of appropriate threshold: j¼1 1 ½yð jDt 1 nDtÞyð jDtÞ2 1=2 2 bias ¼ Æa aˆæ STD ¼ Æða ÆaæÞ2æ : (2) 1 ½zð jDt 1 nDtÞzð jDtÞ g; (3)

Biophysical Journal 87(3) 1991–2001

218 1994 Li et al. where n ¼ 1,2...... (N 1), N is the total number of images in the recorded confirmed by Fisher equation (Becherer et al., 2003). The median and sequence, Dt is the time interval between two successive 3-D images in median standard error (MSE) was used to describe skewed distributed data. a stack, x(jDt), y(jDt) and z(jDt) are the coordinates of the granule at time jDt, Statistical significance of the difference between two skewed distributions and x(jDt 1 nDt), y(jDt 1 nDt), and z(jDt 1 nDt) are the coordinates of the was assessed with KS test, x2 value, or both. P , 0.05 and P , 0.01 were granule in another image taken nDt later. denoted as * and **, respectively. For random diffusion, granules move with a single 3-D diffusion coefficient (D(3)): RESULTS MSD nDt 6Dð3Þ nDt : (4) ð Þ¼ ð Þ Deconvolution reduces out-of-focus fluorescence

2 2 2 2 in WFFM images In directed diffusion, a drift velocity V ¼ vx 1 vy 1 vz is superimposed on random diffusion: We first determined the experimental and theoretical PSF of our 1.65-NA objective as described in the Materials and 3 2 2 MSDðnDtÞ¼6Dð ÞðnDtÞ 1 V ðnDtÞ : (5) Methods section. For quantitative comparison of the experimental and theoretical PSF, we calculated and compared the The feature of diffusion limited in a cage, termed caged diffusion, can be optical transfer function (OTF) of each section planes based characterized by the following approximate equation (Saxton and Jacobson, on the respective PSFs. We found that the OTF of ex- 1997): j j perimental PSF at given section planes agreed quite well with that of theoretical PSF. As shown in Fig. 1 A, the jOTFjs MSD nDt R2 1 A exp 6A Dð3ÞnDt=R2 ; (6) ð Þ¼ ½ 1 ð 2 Þ at defocus of 0.4 mm for the two PSFs were quite similar (P ¼ 0.98, KS test). Similar analyses were done for sections where A1 ¼ 0.99 and A2 ¼ 0.85, and R is the radius of the spherical cage in which the particle is free to diffuse with D(3). To distinguish the proportion with defocus ,1 mm. We have further confirmed that MSD of granules diffusing with different fashions, we analyzed granules by fitting plots calculated from images processed with either experi- their MSDs with Eqs. 4–6 and then selected the best fits by KS test, and mental or theoretical PSF are quite similar (data not shown). 2 sometimes with the assistant of x value. The scope of movement of Thus, for simplicity, we employed theoretical PSF for a granule is defined as the mean value of its displacements in three subsequent deconvolution calculation. Next, we evaluate dimensions during the observation period. how point light sources at different axial planes influence the image of focal plane. As depicted in Fig. 1 B, when a point Statistics light source is relatively far from the focal plane (open For normally distributed data, population averages were expressed as mean circle), it contributes mainly to the low spatial frequency 6 SE unless otherwise stated, and statistic significance was assessed by the signals at the focal plane; whereas high spatial frequency Student’s t-test. STD was used in Fig. 3 C. Skewed distribution was fluorescence comes mainly from light sources at adjacent

FIGURE 3 Selection of fluorescence spots. (A) Left, examples of AO-labeled particles after different image processing. Right, axial and lateral line profile across the centroid of selected fluorescence spot (marked by the white arrow in the left panel) is plotted against corresponding distance. Each line profile was fitted with single Gaussian distribution. The spot size was determined as the FWHM of the Gaussian fit (marked with the dashed lines). Scale bars, 1 mm. (B) Size distribution of 188 AO-labeled fluorescent spots from images processed by the deconvolution 1 high-pass filtering method. Only fluorescent spots with SNR $ 6 were selected for analysis. (C) Com- parison of the size of AO-labeled spots and NPY-DsRed labeled large dense- core granules. NY-DsRed transfected cells were imaged with 100 ms exposure time, which gave equivalent SNR to that of AO-labeled particles with only 5 ms exposure time (right panel). Error bars represent STD.

Biophysical Journal 87(3) 1991–2001

219 Three-Dimensional Mobility of Granules 1995 optical sections. Thus, applying high-pass filtering to the corresponding P-values, and biases versus SNRs is revealed images could help to remove out-of-focus fluorescence. in Fig. 2 C. We notice that higher SNRs give better accuracy Before applying deconvolution to live cell images, we in SPT. This emphasizes the necessity to choose fluores- assessed the algorithm using well-defined 15-mm diameter cence spots with SNR equal to or above 6 for mobility beads with a thin fluorescent shell of 0.5–0.7 mm in width. tracking. Based on the SNR of each granule, we selected As would be expected, sections in unprocessed 3-D images corresponding thresholds according to Fig. 2 C. For in- of the bead were seriously blurred by out-of-focus light (inset termediate SNRs not simulated, thresholds were chosen by in Fig. 1 C), and the width of shell was much larger than its interpolation between the neighboring integer SNRs. actual size. Deconvolution computationally reduced the out- of-focus blurring, and gradually gave better estimates of the width of the shell with increasing iteration times (Fig. 1 C). Identification of fluorescence spots Since low spatial frequency signal (,1/mm) contributes little Most near-membrane fluorescence spots in PC12 cells labeled to the analysis of the mobility of granules that are generally with AO have been identified as single large dense-core ,1 mm in size (Steyer and Almers, 1999; Oheim and granules (Avery et al., 2000). However, as AO tends to Stu¨hmer, 2000), we first deconvolved time-lapse images accumulate in acidic compartments, it is important to verify with a small number of iterations (100 for this study), and that the cytosolic fluorescence spots that we selected for then high-pass filtered them at a spatial frequency of 1/mm. analysis are actually granules. After deconvolving and high- As depicted in Fig. 1 C, deconvolution with 100 iterations pass filtering the images, we identified fluorescence spots with followed by high-pass filtering at a spatial frequency of 1/mm an SNR equal to or .6 (marked with arrows in Fig. 3 A) for gave similar estimate of the width of the shell as that of further analysis. The lateral and axial fluorescence profiles of simple deconvolution with 1000 iterations. Thus, for the rest each selected AO spot were fitted with Gaussian functions, of the image processing, we routinely employed the 100- and the full width at half-maximum (FWHM) of the fitted iteration deconvolution together with high-pass filtering at Gaussian function was taken as a measure of the size of a spatial frequency of 1/mm. The recorded and processed particles (one example is shown in Fig. 3 A, right). Fig. 3 B images from an AO-loaded PC12 cell are displayed in Fig. displays the size distributions of 188 fluorescent spots with 1 D for comparison. the peak lateral and axial size at 0.35 6 0.02 mm and 0.92 6 0.05 mm (mean 6 STD), respectively. The larger axial size is caused by the relatively lower axial resolution inherited in Accuracy of SPT depends on the SNR and WFFM. We then compared the averaged size of these threshold level fluorescence spots with that of NPY-DsRed labeled large dense-core secretory granules (Lang et al., 2000; Holroyd Both the SNR of the object and the threshold level applied to et al., 2002) with similar SNR and found their sizes were the image are critical for the performance of centroid- nearly equivalent (Fig. 3 C). In fact, the lateral size of our dependent SPT. In this study, simulated granule trajectories selected fluorescent spots is close to the TIRFM observation and movement reconstructions, based on measured param- of dense-core granules in PC12 cells (Lang et al., 2000). Thus, eters, were used to evaluate the performance of SPT. We we verified that the selection criteria seem to restrict most of have generated sequential stacks of 3-D images containing the remaining fluorescence spots to large dense-core granules. single simulated granules at different SNR. Then, we used We further selected those fluorescence spots with both lateral different SNRs as a parameter and identified the optimized and axial size within the mean 6 2s of the Gaussian size threshold for each granule tracking according to its SNR. For distribution for further mobility analysis. Compared with a particular SNR, different threshold selection exerts NPY-DsRed labeled granules, larger SNR could be obtained significant impact on the SPT-estimated MSD as shown in for AO-loaded granules during much shorter exposure time Fig. 2 A. The reason is that as lower threshold is applied, too (Fig. 3 C), so the employment of AO would provide us the many background fluorescence remains around tracked ease of labeling, rapid sampling, and less photodamage for granules, making the centroid-based SPT insensitive to imaging live cells. granule movement and underestimate MSD throughout; whereas high threshold excludes too many pixels critical for the calculation of centroid and induces unexpected variabil- 3-D tracking of single granules in resting cells ity in the tracking as well as overestimation of MSD. Hence, we have examined the influence of different thresholds on Previous studies have suggested that granules diminished in the significance of difference (assayed by the P-value in KS their mobility as they approached the plasma membrane test) and the bias between the real MSD and the one (Steyer et al., 1997; Johns et al., 2001). Also, the dense estimated from SPT (Fig. 2 B). Thus, appropriate threshold cortical actin network underneath the plasma membrane should be chosen to maximize the P-value and minimize the might influence the mobility of granules (Oheim and bias at given SNR. The relationship of optimized thresholds, Stu¨hmer, 2000; Lang et al., 2000). To confirm the usefulness

Biophysical Journal 87(3) 1991–2001

220 1996 Li et al. of our 3-D SPT in studying the mobility of granules at averaged 3-D volume of granules and found little variation different locations inside the cell, we have separated total between successive images, as demonstrated in Fig. 4 D. granules into two groups, GPs and GCs, according to their relative distances from the detected contour of plasma Different motion types of granules membrane. The membrane contour was detected using the edge-detecting algorithm of Canny (1986). Briefly, it Next we studied the mobility of single granules by 3-D SPT. calculates the intensity gradient of images with the derivative Only AO-loaded granules present for the entire imaging time of a Gaussian filter and locates the edge by looking for local were chosen for tracking analysis. Occasionally, we observed maximum of the gradient. This method is robust to noise and disappearance of granules in the middle of the image likely to detect even weak edges. We compared the contour sampling, which might be due to either the ‘‘explosions’’ of detected from deconvolved AO-stained images with that AO-loaded granules or exocytosis when the granule is close to obtained from FM1-43 staining in the same cell. FM1-43 is the plasma membrane. These granules were not included in not fluorescent in solution, and becomes fluorescent when subsequent analysis. We found that fluorescence decayed incorporated into the membrane lipids (Leung et al., 2002; with an averaged time constant of 142.8 s due to photo- Angleson et al., 1999). As shown in Fig. 4 A, the membrane bleaching. Thus the images were corrected for photobleach- contours recognized from AO- and FM1-43-stained images ing before analysis. By fitting the MSD plot with appropriate were quantitatively comparable. The mean absolute differ- equations, we have identified three types of motion among ence between the two contours was 0.29 6 0.02 mm 246 total granules from 17 cells. A straight line fit to the MSD (estimated from four cells) with a maximum and minimum is indicative of random diffusion, which was generally value of 0.42 mm and 0.1 mm, respectively. The same section observed for both GPs and GCs at similar frequency (Fig. 5 as in Fig. 4 A was high-pass filtered and displayed in high A). The major portion of the granules seems to move in magnification in Fig. 4 B. Granules that meet our selection a confined compartment and exhibit a negative curvature in criteria are marked with circles. One granule identified as GP the MSD plots (Fig. 5 B), which manifests a caged diffusion as is indicated with an arrow in Fig. 4 B. The time-lapse images if the granule is confined in a cage constructed by some of this GP in the x, y and x, z plane are displayed in Fig. 4 C.As neighboring obstruction. The averaged MSD of GC was much shown in Fig. 4 C, the granule seems quite consistent in its size larger than that of GP, reflecting that cytosolic and near- and shape. However, sometimes the rotation of the non- membrane granules are probably restricted by different spherical granule may change its projection in the 2-D section. structures. Functional studies have proposed that granules Thus, as further evidence that the deconvolution did not might be transported along some cytoskeletal tracks powered introduce severe artifacts in our study, we have calculated the by motor proteins (Kamal and Goldstein, 2000; Rogers and

FIGURE 4 3-D tracking of near- membrane granules. (A) Membrane position was defined by the edge- detecting algorithm explained in the Materials and Methods section. Mem- brane contours, detected under AO staining and FM1-43 staining from the same cell, are displayed for comparison. The mean absolute difference between them is 0.29 6 0.02 mm (data analyzed from four cells). (B) The same section as in panel A was high-pass filtered and displayed in high magnification. Granules meeting our selection criteria were marked with circles, which were subsequently included in the SPT analysis. (C) Sequential images of a granule marked by an arrow in B. The radial distance between the centroid of the granule and the membrane is 0.53 mm. Thus, the granule should be considered as a GP according to our definition. Scale bars for panels A, B, and C,1mm. (D) The averaged volumes from 25 granules calculated from the pixels that exceed the half- maximum fluorescence are displayed as a function of time.

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221 Three-Dimensional Mobility of Granules 1997

FIGURE 6 Comparison of the mobility between GP and GC. (A) D(3) histograms of GP (n ¼ 119) and GC (n ¼ 127) display a markedly skewed distribution. Inset, cumulative histogram reveals significant difference (P , 0.01, KS test). (B) D(3) distribution in semilogarithmic presentation. (C) Left, distribution of the radius of cage for GPs (n ¼ 69) and GCs (n ¼ 61) that move in caged diffusion. Right, cumulative histograms reveal significant difference (P , 0.05, KS test). (D) Scope of movement also displays FIGURE 5 Three types of motion exist for both GPs and GCs. Example significant difference (P , 0.05, KS test) between GP and GC. For this trajectories (left) and averaged MSDs (right) of granules that travel in figure, wave symbols are defined in A. random diffusion (A), caged diffusion (B), or directed diffusion (C) are depicted, respectively. The numbers of granules analyzed are indicated in the graph. For comparison, averaged MSD of six immobilized 175-nm diameter beads imaged under SNR ¼ 6 condition is also displayed. Open of difference with KS test. It is noticed that GC moves with circle, solid circle, and open triangle symbolize the GC, GP, and a significant higher D(3) than that of GP (P , 0.01). Under immobilized beads, respectively. * and ** mark the points from which on resting conditions, 71% of GPs moved with a D(3) ,3.2 3 significant difference exists between the two MSD plots. 104 mm2/s, whereas only 23.7% of GCs traveled within that D(3) scope. The median of D(3) for GPs was 2.95 6 0.3 3 104 Gelfand, 2000). In our experiments, we have also observed mm2/s (n ¼ 127), which approximates the value measured for a small portion of both GPs and GCs (;10%) moving along membrane-proximal granules by TIRFM (2.0 3 104 mm2/s, a fixed direction as if transported by some already constructed Steyer and Almers, 1999), but much lower than that of GCs tracks (Fig. 5 C). Their MSD plots resulted in a positive (9.5 6 0.9 3 104 mm2/s, n ¼ 119). The D(3) histograms of curvature because the V2 term of Eq. 5 would dominate the GP and GC differ significantly from a simple broad Gaussian MSD for longer time (Fig. 5 C). Interestingly, the directed distribution, instead featuring a markedly skewed distribution velocity of granule transportation for GC (15.4 6 0.8 3 103 and large variation among granules. To check whether there mm/s, median 6 MSE, n ¼ 15) is also larger than that of GP exist distinct groups for GP and GC, we calculated the (8.5 6 0.39 3 103 mm/s, median 6 MSE, n ¼ 13) (P , 0.05, logarithmic D(3) distributions and displayed them in semi- KS test). For comparison, we recorded sequential 3-D images logarithmic presentation (Fig. 6 B). Two separate peaks are of immobilized 0.175-mm diameter beads under various obvious for GP and GC, suggesting they are indeed seg- imaging conditions. As an example, the averaged MSD plot regated into two distinct pools based on their mobility, from six beads under SNR ¼ 6 is displayed in Fig. 5 A, whereas no distinct subgroups are observed within either GP wherein a D(3) of 0.087 3 104 mm2/s is calculated. This or GC (Fig. 6 B). Next, we compared the histograms of the probably reflects our lower limit of detection under this radius of cage for caged diffusion between GP and GC (Fig. 6 imaging condition. C). The histogram of the radius of cage for GC extends broader to the right, and the difference in cumulative Comparing the mobility between GP and GC histogram comparison is significant by KS test (P , 0.05). In the preceding analysis, we have identified various motion GCs moved in significant larger cages with a median of 0.34 types for granules according to MSD analysis, whereas 6 0.01 mm(n ¼ 61) in comparison with GP with a median of detailed comparison of the 3-D mobility between GP and GC 0.22 6 0.01 mm(n ¼ 69). Finally, we found that GCs traveled has not been made. In Fig. 6 A, D(3) distributions of 127 GPs a larger mean distance (scope of movement) (0.37 6 0.04 mm, and 119 GCs from 17 cells were compared. Because of the median 6 MSE, n ¼ 127) in three dimensions than GPs over markedly skewed distribution, we have plotted the cumula- the same observation period (0.27 6 0.02 mm, median 6 tive histogram of D(3) in the inset and checked the significance MSE, n ¼ 119) (P , 0.05), as depicted in Fig. 6 D.

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222 1998 Li et al.

Stimulation increases the percentage of granules actin cytoskeleton has been explored with TIRFM, whereas traveling in directed fashion whether granules located inside the cell are affected by actin cytoskeleton remains less studied. Here we have employed Most granules wandered around their residing positions in latrunculin B (LB) to disrupt F-actin formation in PC12 cells, random or caged diffusion under resting condition, and only and performed 3-D SPT to evaluate the mobility of granules. a small fraction traveled in directed fashion. We found that As shown in Fig. 7 B, LB significantly decreased the D(3) of high K1 (HK) stimulation significantly increased the number GP (P , 0.05, KS test) but left that of GC unaltered, of granules that traveled in directed fashion for both GP and suggesting actin cortex facilitates the movement of near- GC (Fig. 7 A), suggesting an up-regulated active transporta- membrane granules rather than blocks it, which is consistent tion of granules. HK stimulation leads to the influx of Ca21. with the previous observation made by TIRFM (Lang et al., Ca21 has been suggested to play an important role in 2000). Although LB itself did not change the distribution of accelerating the recruitment of secretory granules (von GPs and GCs in different motion types, the stimulatory effect Ru¨den and Neher, 1993; Heinemann et al., 1993; Smith of HK on the number of directed diffusion for GP was et al., 1998). Presumably, active transportation is involved in blocked by LB, an effect not seen for GC (Fig. 7 A). the recruitment of granules. Under stimulation, the median of Similarly, LB blocked HK-induced increase in the scope of D(3) was 3.6 6 0.5 3 104 mm2/s (n ¼ 113) and 10.3 6 1.3 movement for GP but not for GC (Fig. 7 C). Our results 3 104 mm2/s (n ¼ 97) for GP and GC, respectively, which suggest that although actin cytoskeleton participates actively were slightly higher than those of resting cells, but the in the movement of near-membrane granules, the trafficking differences were not statistically significant (P . 0.35, KS of granules deep inside the cytosol is less affected by actin test). In contrast, the scopes of movement of GP and GC cytoskeleton. were significantly increased by HK stimulation (P , 0.05, Fig. 7 C). DISCUSSION The influence of actin cytoskeleton on the mobility Three-dimensional granule tracking of granules To characterize the 3-D mobility of secretory granules Cortical actin cytoskeleton is localized subjacent to the throughout a whole cell, we have combined deconvolution plasma membrane with a thickness of ;0.4 mm (Lang et al., WFFM and centroid-based 3-D SPT method to study granule 2000). The mobility of granules going through the cortical trafficking in live PC12 cells. Although confocal microscopy has proved effective in removing the out-of-focus fluorescence, which improves the resolution for SPT, the inherited low time resolution limits its application in time-resolved 3-D particle tracking. Besides, confocal microscopy suffers from higher photobleaching and photodamage. In contrast, WFFM has the merit of less photobleaching and photodamage due to relatively higher light collection efficiency, especially with the highest NA (1.65) objective used in this study. The out-of-focus fluorescence in 3-D images recorded by WFFM can be computationally removed using deconvolution. In fact, WFFM combined with deconvolution has demonstrated the advantage over confocal microscopy for quantitatively studies of weakly fluorescent organelles in living cells (Swedlow and Platani, 2002). In classical 2-D time-resolved particle tracking, the contribution from the missing axial direction is usually ignored. TIRFM-based tracking attempts to resolve the 1 FIGURE 7 Effects of high K stimulation and latrunculin-B on granule z-mobility from the fluctuation in granule’s fluorescence that mobility. (A) Percentages of granules that fall into different types of motion for GP and GC. ‘‘C’’ is abbreviation for control condition, ‘‘HK’’ for high is exponentially related to the change in axial position. How- K1 stimulation, ‘‘LB’’ for latrunculin B treatment, and ‘‘LB 1 HK’’ for ever, small changes in the axial position will result in large pretreatment with LB followed by high K1 stimulation (n ¼ 8–11 cells for changes in fluorescence measured with TIRFM. Also, fluc- each condition mentioned above). (B) LB decreases the D(3) of GP tuation in fluorescence unrelated to axial position will result (3) significantly (P , 0.05, KS test) but does not change the D of GC. (C) in misinterpretation of the z-position. Moreover, TIRFM can Comparison of the scope of movement for GP and GC under different conditions. For B and C, data are presented as median 6 MSE, and the only be employed to study vesicles right underneath the numbers of granules selected for analysis under various conditions are from plasma membrane, whereas vesicles residing deeper inside 77 to 127 granules. the cytosol are invisible under TIRFM. Despite the recent

Biophysical Journal 87(3) 1991–2001

223 Three-Dimensional Mobility of Granules 1999 development in 3-D tracking of single particles (Kao and that of NPY-DsRed labeled granules with 100 ms exposure Verkman, 1994; Speidel et al., 2003; Levi et al., 2003), the time (Fig. 3 C). Thus, the advantage of AO is not only its ease 3-D mobility of granules within living cells has not been of use, but also the less exposure time and hence less demonstrated. In this study, we have employed a centroid- photodamage. PC12 cells are densely packed with secretory based 3-D SPT from time-resolved stacks of 3-D images, and granules. Our selection criteria might exclude most of the the displacements of single granules in three dimensions weakly stained spots (i.e., small synaptic like vesicles) and could be directly obtained. We found that granules can be large spots for analysis; however, ;65% of the observed assumed to move the same way in z direction as they behave granules remained for analysis after selection. Moreover, in lateral direction, suggesting the missing z direction infor- although the density of our selected AO-labeled granules mation in 2-D tracking probably will not impose significant (0.12 6 0.02/mm2) is lower than that of NPY-labeled granules distortion in assessing the lateral mobility of granules. observed under TIRFM (0.358/mm2, Taraska et al., 2003) in However, 3-D tracking does offer the advantage of following PC12 cells, it is comparable with the density of cytosolic granules in a larger 3-D space, not restricting to a single granules in chromaffin cells observed using electron optical plane. microscopy (0.11/mm2, Steyer et al., 1997). We have demonstrated that appropriate threshold selection The characterization of particle motion imposes demands is very critical for the precision of granule tracking. Specific on the temporal and spatial resolution required for the threshold should be selected for each given SNR to assure measurement. When there is only simple free diffusion, as the best result in 3-D tracking. We have found that higher indicated by the linear dependence of MSD on time, the time SNRs give better accuracy in SPT, thus improving SNR will resolution of the measurement does not influence the determi- help to get better precision in granule tracking. With our NA nation of the diffusion coefficient from the slop of the plot of 1.65 objective, a theoretical resolution of 0.18 mminx, y MSD(nDt). In contrast, when diffusion is constrained by plane and 0.45 mminz direction is expected. The evident a cage or tether, a characteristic time of observation is required discrepancy between lateral and axial resolution caused by together with a corresponding requirement for sufficient diffraction limit leads to nonisotropic resolution and pre- temporal resolution to resolve the dynamic motion (Qian et al., cision in 3-D particle tracking. In fact, we found that the 1991). Previous study has suggested that granules wander threshold optimized (optimizing procedure, see Fig. 2) for rapidly with a diffusion coefficient of 19 3 104 mm2/s within lateral tracking performance was different from that opti- a cage that leaves ;70 nm space around granules, whereas the mized for axial tracking (data not shown) at a given SNR. cage itself diffuses in random 10-fold more slowly over longer Increases in resolutions along x, y directions and z direction, distances (Steyer and Almers, 1999). The slow effective especially breaking the distortion occurred in z direction, will sampling rate (0.2 Hz) used in this study due to 3-D stack balance the tracking performance in different directions. The generation will miss the fine movement of granules within the recently developed stimulated emission depletion technique cage. However, it will accurately track the long range (Klar et al., 2000) and beam-scanning multifocal multipho- diffusion of granules, which presumably reflects the move- ton 4Pi-confocal microscopy (Egner et al., 2002) have finally ment of the cage. broken the diffraction barrier and achieved a nearly spherical Imaging under TIRFM is restricted to a thin layer resolution of ;100 nm. These techniques will find more underneath the plasma membrane, which adheres unphysio- application in the demand for more precise and isotropic 3-D logically to the coverglass. Whether the adhesion of plasma particle tracking. However, the drawbacks of these tech- membrane to coverglass will affect the mobility of neighbor- niques inherited with confocal microscopy, i.e., low time ing granules and their fusion remains to be examined. resolution, high photobleaching, and photodamage, will Interestingly, we found that GPs residing far away from the limit their use when long-term 3-D tracking in living cell is basal plasma membrane exhibit similar diffusion coefficient demanded. as that measured by TIRFM (Steyer and Almers, 1999, Becherer et al., 2003). GP in this study also traveled in a similar cage as that observed under TIRFM. Along with the 3-D mobility of secretory granules in PC12 cells fact that diffusion of fluorescent dyes could be observed as AO accumulates within granules as well as nonvesicular a ‘‘cloud’’ after fusion, it is likely the adhesion of basal compartments like lyso- or endosome. By choosing fluores- membrane to coverglass does not exert significant effect on cence spots with SNR $ 6 and by applying high-pass the surrounding granules. filtering, the selected fluorescence spots has single Gaussian Secretory granules have long been assumed to belong to profiles in fluorescence with lateral and axial FWHMs distinct functional pools (Bratanova-Tochkova et al., 2002; indistinguishable from those of NPY-DsRed labeled dense- Duncan et al., 2003). By simultaneously tracking near- core granules, suggesting we were mainly analyzing AO- membrane and cytosolic granules, we have found significant labeled large dense-core granules in this study. AO-loaded differences between these two groups of granules in their granules are much brighter than NPY-DsRed labeled ones, as D(3), radius of cage, and scope of movement. The mobility of 5 ms exposure of AO-loaded granules gave similar SNR to these two groups of granules is also differentially affected by

Biophysical Journal 87(3) 1991–2001

224 2000 Li et al. disruption of F-actin. These results suggest that the motion of underlying molecular mechanisms employing similar tech- the two groups of granules is mediated by different mecha- niques used in this study. nisms. However, we failed to distinguish subgroups within either GPs or GCs. The distributions of diffusion coefficient We thank J. Yao and T. Liang for assistance in the cell preparation, L. Xu for either GP or GC did not exhibit multiple distinct peaks, and L. Bai for help in the adjustment of the imaging system, and J. Ding for helpful comments on the manuscript. suggesting granules are smoothly organized into one population, rather than into distinct pools, and most of them This work was supported by National Science Foundation of China Grants No. 60071030 to A. Qu, Nos. 30025023, 3000062, and 30130230 to T. Xu, travel with lower mobility. This result is consistent with and National Basic Research Program of China (973) Grant G1999054000 a recent study in the neurites of differentiated PC12 cells and 2001CCA04100 to T. Xu. We are grateful for the support from the Li under TIRFM by Ng et al. (2003), who reported a broad and Foundation and the Sinogerman Scientific Center. The laboratory of T. Xu asymmetric distribution in diffusion coefficient without belongs to a Partner Group Scheme of the Max Planck Institute for a separation of a distinct pool of granules. With the advan- Biophysical Chemistry, Go¨ttingen, Germany. tage of our method to study the mobility of granules deep inside the cytosol, we now extend this feature to cytosolic REFERENCES granules. Angleson, J. K., A. J. Cochilla, G. Kilic, I. Nussinovitch, and W. J. Betz. 1999. Regulation of dense core release from neuroendocrine cells Correlation of granules with cortical revealed by imaging single exocytic events. Nat. 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Biophysical Journal 87(3) 1991–2001

OVEREXPRESSION OF CAVEOLIN-1 INDUCES ALTERATION OF MULTIDRUG RESISTANCE IN Hs578T BREAST ADENOCARCINOMA CELLS

Chuanxi CAI and Jianwen CHEN* National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

Caveolin-1 is a major caveolae-coat protein involved in a development and progression of MDR in cancer cells is largely variety of cell signaling processes. Some studies have sug- unknown. To identify the possible effects of caveolin-1 on multi- gested that the level of caveolin-1 expression positively cor- drug resistance and P-gp transport activity, we overexpressed relates with multi-drug resistance in cancer cells. We dem- caveolin-1 in Hs578T breast adenocarcinoma cells, and examined onstrated for the first time that Hs578T doxorubicin the changes of drug resistance and P-gp transport activity in these resistant cells (Hs578T/Doxo), which contain low levels of endogenous caveolin-1 and high levels of P-glycoprotein, are cells. In addition, we examined colocalization, co-fractionation rendered drug-sensitive by overexpression of exogenous and co-immunoprecipitation of caveolin-1 and P-gp. Our results caveolin-1. MTT assays showed that after overexpressing suggest that overexpression of caveolin-1 in Hs578T breast cancer caveolin-1, the drug resistance of Hs578T/Doxo cells to doxo- cells renders the cells drug-sensitive by inhibiting P-gp drug- .rubicin and cisplatin was reduced from 25.4 ؎ 1.5 and 65.3 ؎ transport activity .␮g/ml to 0.8 ؎ 0.15 and 23.2 ؎ 2.1 ␮g/ml, respectively (i.e 2.5 reduced by 97% and 64%, respectively). Furthermore, using rhodamine-123 efflux assays, we observed a significant de- MATERIAL AND METHODS crease in P-glycoprotein activity in caveolin-1 overexpressing Materials cells, similar to that observed with 5 ␮M cyclosporine A or 10 ␮M verapamil, 2 inhibitors of P-glycoprotein activity. Using Monoclonal antibody (mAb) and polyclonal antibody (pAb) confocal microscopy, subcellular fractionation and co-immu- against caveolin-1 were purchased from Transduction Laboratories noprecipitation assays, a possible physical interaction be- (Lexington, KY) and Santa Cruz Biotechnology (Santa Cruz, CA), tween caveolin-1 and P-glycoprotein in the caveolae mem- respectively. Anti-human P-gp mAb (C219) was obtained from brane was observed in Hs578T/Doxo cells overexpressing Signet Laboratories (Dedham, MA). FITC-labeled goat anti-mouse caveolin-1. These results suggest that overexpression of IgG and Texas Red-labeled goat anti-rabbit IgG were purchased caveolin-1 changes the state of the cells from drug-resistant to drug-sensitive by inhibiting P-glycoprotein transport activ- from Molecular Probe Inc. Cell culture supplies (RPMI 1640 ity. medium, geneticin, FBS, L-glutamine, trypsin-EDTA, Lipo- © 2004 Wiley-Liss, Inc. fectamine 2000, penicillin/streptomycin and Opti-Prep) were all from Life Technologies, Inc. (Carlsbad, CA). Percoll was pur- Key words: caveolin-1; Hs578T breast adenocarcinoma cells; MDR; chased from Amersham Pharmacia Biotech. BCIP/NBT reagents P-glycoprotein were purchased from Promega. The pCI-neo and pCI-neo-cav-1 plasmids were generous gifts from Dr. Eric J. Smart (Kentucky A major pitfall with chemotherapy in cancer patients is the Medical School, KY).16 Protein-G Sepharose, verapamil, cyclo- development of tumor cells that are resistant to a broad range of sporine A and Rhodamine-123 were purchased from Sigma (St. therapeutic drugs commonly used in clinical treatment.1 Although Louis, MO). All other reagents were obtained from regular com- the precise mechanism of multi-drug resistance (MDR) remains mercial sources with highest purity. largely unclear, there is abundant evidence that many cases of Cell lines, plasmids and transfections MDR are due to overexpression of a plasma membrane ATPase called P-glycoprotein (P-gp).2 As an energy-dependent drug efflux The parental human breast cancer cell line Hs578T/S and its transporter, P-gp decreases the effective concentration of active doxorubicin-resistant subclone Hs578T/Doxo were the generous drugs in the cytosol and thereby reduces their cytotoxic efficacy. gifts of Dr. Kjell Grankvist (Umea University, Sweden).17 The This is a very important mechanism of MDR in cancer cells. cells were all cultured at 37°C, 5% CO2 in RPMI 1640 medium Caveolae are invaginations of the plasma membrane that are enriched in cholesterol and sphingolipids, which impart unique Abbreviations: Cav-1, caveolin-1; CsA, cyclosporine A; DDP or cis, physical properties to these membrane sub domains. Caveolae cisplatin; DMSO, dimethyl sulphoxide Doxo, doxorubicin; mAb, mono- have been shown to play an important role in many signal trans- clonal antibody; MDR, multidrug resistance; pAb, polyclonal antibody; duction processes, by acting as a compartmentalization center for P-gp, P-glycoprotein; Rh-123, rhodamine-123; S, sensitive; Vm, vera- signaling molecules.3–9 Caveolin-1 is a major caveolar coat pro- pamil. tein10 that has the ability to engage in complex interactions with other protein components in the caveolae and to affect their func- 11 Grant sponsor: National Laboratory of Biomacromolecules; Grant num- tions. Some studies have shown that the expression level of ber: 881613; Grant sponsor: Natural Science Foundation of China; Grant caveolin-1 closely correlates with the development of MDR in number: 30070186, 30230120). cancer cells. High expression levels of caveolin-1 and high surface density of caveolae have been identified in a number of MDR cancer cell lines, including adriamycin-resistant MCF-7 breast *Correspondence to: National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Datun Road 15, Chaoyang adenocarcinoma cells, colchicine-resistant HT-29 colon carcinoma ϩ 12 District, Beijing 100101, China. Fax: 86-10-6487-2026. cells, vinblastine-resistant SKVLB1 ovarian carcinoma cells and E-mail: [email protected] Taxol-resistant A549-T24 lung carcinoma cells.13 Thus, it has been proposed that the acquisition of resistance to different drugs by various cell types might be associated with high expression of Received 20 August 2003; Revised 17 December 2003, 12 February caveolin-1. A more recent clinical study, however, showed that 2004; Accepted 26 February 2004 caveolin-1 expression in ovarian carcinoma showed no correlation 14 with MDR. Although several studies have suggested colocaliza- DOI 10.1002/ijc.20300 tion of caveolin and P-gp in caveolae,12,15 the functional effect of Published online 4 May 2004 in Wiley InterScience (www.interscience. caveolin-1 interaction with P-gp and its overall impact on the wiley.com).

227 CAVEOLIN-1 ALTERATION OF MULTIDRUG RESISTANCE 523 supplemented with 10% FBS, 2 mM glutamine, 100 U/ml peni- Cell survival MTT assay cillin, 100 ␮g/ml streptomycin. The entire cDNA sequence of The 3-(4,5-dimethylthiazol-2-yl)-2,5-di-phenyltetrazolium bro- caveolin-1 was cloned into the EcoRI site of pCI-neo, to generate mide (MTT) colorimetric assay was used to assess the sensitivity pCI-neo-cav-1. PCI-neo-cav-1 and its empty vector were trans- of the cells to agents in vitro as described.19 Cells were trypsinized fected into Hs578T cell lines as described.16 Briefly, 5 ␮gof and harvested during exponential growth, and equal numbers of pCI-neo-cav-1 plasmid was transfected into ϳ106 cells in a cells (5,000 for Hs578T/S, Hs578T/S ϩ pCI-neo and Hs578T/S ϩ 100-mm dish, using Lipofectamine reagent according to the man- pCI-Cav-1 or 10,000 for Hs578T/Doxo, Hs578T/Doxo ϩ pCI-neo ufacturer’s instruction. Twenty-four hours after transfection, the and Hs578T/ Doxo ϩ pCI-Cav-1) were inoculated into each well culture medium was changed to a selection medium containing 1.5 with 150 ␮l of culture medium. After overnight incubation, 100 ␮l mg/ml geneticin for two days. Stable clones of cells overexpress- of culture medium containing various concentrations of drugs were ing caveolin-1 were subsequently maintained in a culture medium added, and the cells were incubated for 48 hr. Thereafter, 20 ␮lof containing 500 ␮g/ml geneticin. As controls, the cells were trans- MTT (2 mg/ml in PBS) were added to each well and incubated for fected with the mock pCI-neo vector, and subjected with same a further 4 hr. The resulting formazan product was dissolved in 100 selection treatment with geneticin. ␮l of dimethyl sulfoxide after aspiration of the culture medium. Plates were placed on a plate shaker for 5 min and read immedi- Isolation of caveolae-enriched membrane fraction ately at 550 nm using a microplate reader. The survival percent was calculated by the following equation: cell survival percent ϭ Detergent-free caveolae fractions were prepared using the mod- (mean OD of one grade)/(mean OD of the blank control) ϫ 100%. ified method of Smart et al.18 Briefly, cells were homogenized with The IC50 for doxorubicin or cisplatin was defined as the doxoru- a tight Dounce homogenizer. The post-nuclear supernatant frac- bicin or cisplatin concentration at which the survival rate was 50%. tion, obtained after centrifugation at 1,000g for 10 min, was layered on top of a 30% Percoll solution and centrifuged at Efflux of Rhodamine-123 84,000g for 30 min in a Beckman Ti60 rotor. The plasma mem- To examine the transport activity of P-glycoprotein, efflux of brane (PM) faction was collected from the top of the gradient, and 20,21 then sonicated with a Vibra Cell sonicator (Sonics & Materials, Rhodamine-123 (Rh-123) was measured as described. Briefly, the cells were harvested and adjusted to 106 /ml cells, then incu- Danbury, CT). The sonicate was mixed with 50% Opti Prep to bated with 2 ␮M of Rh-123 for 30 min at 37°C. After 3 times of make a 23% Opti Prep solution. This was placed on the bottom of washing to remove the extracellular free dye, the cells were incu- a Beckman SW41 centrifuge tube, and a linear 20–10% Opti-Prep bated in dye-free media or media containing 10 ␮M verapamil or gradient was layered on the top. The sample was then centrifuged 5 ␮M cyclosporine A (dissolved in DMSO) at 37°C. The efflux of at 52,000g for 90 min in a SW41 Beckman swinging bucket rotor. Rh-123 was analyzed at successive time points by flow cytometry A sample of the bottom fraction (fractions 12 and 13) was col- using a Becton-Dickinson FACS-420 instrument. lected and designated non-caveolae membrane (NCM). The top 5 ml of the gradient (fractions 1–6) was collected and mixed with Transmission electron microscopy 50% Opti-Prep. This was overlaid with 2 ml of 5% Opti-Prep and centrifuged at 52,000g for 90 min. An opaque band located just Samples were fixed with glutaraldehyde, postfixed with osmium tetroxide, and stained with uranyl acetate and lead citrate, as above the 5% interface was collected and designated caveolae described.12 Samples were examined under a Philips TECAI 20 fraction (CM). TEM.

Western blot and immunoprecipitation Confocal microscopy imaging Proteins were separated by SDS-PAGE with a standard reducing Cells were cultured in 35-mm glass-bottom dishes or on a cover condition protocol. Samples were resuspended in sample buffer glass and the following protocol was used:4 fixation was in PBS and loaded on 7.5% acrylamide-bisacrylamide gels for P-gp or containing 4% paraformaldehyde at room temperature for 20 min. 12.5% acrylamide-bisacrylamide gels for caveolin-1. After elec- Fixed cells were rinsed with PBS and treated with 25 mM NH4Cl trophoresis, proteins were electroblotted on to a nitrocellulose in PBS for 10 min to quench free aldehyde groups. The cells were membrane. Blots were blocked by 5% nonfat dry milk, 0.05% permeabilized by incubation for 15 min in freshly prepared 0.1% Tween 20 in Tris-buffered saline (10 mM Tris, pH 8.0, 135 mM Triton X-100/ PBS. The cells were preincubated for 1 hr in PBS NaCl). Immunoblotting was carried out with designated antibodies containing 5% normal goat serum, and then incubated for 2 hr in and detection was carried out with the BCIP/NBT reagents accord- diluted P-gp (1:25) or caveolin-1 (1:100) antibody in PBS con- ing to the manufacturer’s instructions. taining 2.5% goat serum. Immunostaining was carried out by A standard protocol was used for co-immunoprecipitation stud- incubation for 1 hr in 1:200 diluted FITC-labeled goat anti-mouse ies of P-gp and caveolin-1. In brief, confluent Hs578T/Doxo ϩ IgG or Taxes Red-labeled goat anti-rabbit IgG. After extensive pCI-Cav-1 cells were harvested by trypsin/EDTA solution and PBS washes, immunostained cells were examined with a Bio-Rad washed two times with ice cold PBS containing 0.1 mM PMSF. Radiant-2100 confocal microscope. More than 100 cells were The cells were pelleted and resuspended in 0.5 ml modified RIPA inspected per experiment, and the results displayed are typical. buffer (150 mM NaCl, 50 mM Tris-Cl, pH 8.0, 1 mM EGTA, 1% Triton X-100, 0.1% SDS, 1% sodium deoxy cholate) containing Data analysis protease inhibitors (0.1 mM PMSF, 1 ␮M pepstatin A, 1 mM All data points represented the mean value of at least 3 inde- Benzamidine, 10 ␮M Leupeptin, 1 ␮g/ml Aprotinin). The whole pendent experiments, with 5 duplicates for each. Values are rep- cell lysate (100 ␮g) was pre-washed with protein G-Sepharose resented as the mean Ϯ SE. Statistical significance was determined beads and then incubated overnight with 1 ␮g of monoclonal by Student’s t-test with p Ͻ 0.05. anti-P-gp antibodies (C219) or 1 ␮g of anti-caveolin-1 pAb (N- 20). As a negative control, another 0.5 ml of RIPA buffer without cell lysate was processed in the same way as the whole cell lysate. RESULTS The immune complexes were collected on protein G-Sepharose Resistance to cisplatin and doxorubicin in Hs578T cells beads by incubating for 2 hr and then washed extensively (4 times) Through subclonal selections, we have obtained the following with RIPA buffer. The beads were re-suspended in 40 ␮l of 2-fold stable clones of cancer cells: parental human breast cancer cell line concentrated Laemmli electrophoresis buffer, separated by SDS- Hs578T (Hs578T/S) and its doxorubicin-resistant derivative cell PAGE and electroblotted onto PVDF membranes for the detection line Hs578T/Doxo. The drug sensitivity or resistance of these cells of caveolin-1 or P-gp.15 was assayed using the MTT method. As shown in Table I, the

228 524 CAI AND CHEN

Hs578T/Doxo cells were around 2-fold and 24-fold more resistant The different expression patterns of P-gp and caveolin-1 in to cisplatin and doxorubicin than the parental Hs578T/S cells, these cells raise an intriguing possibility that the mutual inter- respectively, suggesting that doxorubicin is a more specific sub- action between caveolin-1 and P-gp may impact the develop- strate of P-gp than cisplatin. ment of MDR in these cells. To test this possibility, we introduced exogenous caveolin-1 into these cells and therefore Overexpression of caveolin-1 and increase of caveolae altered the ratio of caveoline-1 to P-gp, The subsequent re- organelles in Hs578T/S and Hs578T/Doxo cells sponse to different drugs was then studied. The densitometry Hs578T cells were transfected with the pCI-neo-cav-1 plasmid, results confirmed that the expression level of caveolin-1 in or with the pCI-neo vector as a control. After culture in geneticin Hs578T/S ϩ pCI-Cav-1 or Hs578T/Doxo ϩ pCI-Cav-1 cells selection medium for two weeks, the expression of caveolin-1 and was 2.5–4-fold higher than in Hs578T/S ϩ pCI-neo or Hs578T/ P-gp were detected by Western-blot assay. As shown in Figure 1a Doxo ϩ pCI-neo cells. Under the same conditions, the expres- (lane 1,3), the expression levels of endogenous caveolin-1 were sion level of P-gp in Hs578T/Doxo ϩ pCI-neo and Hs578T/ similar in Hs578T/S and Hs578/Doxo cell lines transfected with Doxo ϩ pCI-Cav-1 cells was about 20-fold higher than in pCI-neo vectors, but the expression level of P-gp was significantly Hs578T/S ϩ pCI-neo and Hs578T/S ϩ pCI-Cav-1 cells, as higher in the drug-resistant cells (Hs578/Doxo ϩ vector) than in detected by densitometry, irrespective of whether these cells the drug-sensitive cells (Hs578T/S ϩ vector). were transfected with pCI-Cav-1 or empty vector (Fig. 1a, lane 1 vs. lane 2, lane 3 vs. lane 4). To further test the impact of overexpressing caveolin-1 on the TABLE I – RESISTANCE TO CISPLATIN AND DOXORUBICIN IN Hs578T CELLS formation of caveolae in Hs578T cells, we studied the changes of ␮ 1 caveolae organelles using electron microscopy. As shown in Fig- IC50( g/ml) Reagent ure 1b, the number of caveolae increased greatly in Hs578T cells Hs578T/S Hs578T/Doxo overexpressing caveolin-1. These caveolae appeared as attached Cisplatin 32.7 Ϯ 1.52 63.2 Ϯ 1.7 (1.9ϫ)3 omega-shaped flasks and bunches like clusters of grapes. Interest- Doxorubicin 1.03 Ϯ 0.07 24.8 Ϯ 1.4 (24ϫ) ingly, a significant amount of caveolae-like intracellular vesicles could be detected in the cells overexpressing caveolin-1. Studies 1Cell survival was determined by MTT assay.– 2Data are displayed as the mean Ϯ SD of 3 determinations, each obtained from 5 duplicate from Lavie et al. have shown that the caveolae-like vesicular cultures.–3The values in parentheses represent the relative resistance, compartments contain both caveolin-1 and P-gp.12,15 The changes determined by dividing the IC50 value of the resistant cells by that of in membrane ultrastructure could in principle alter the MDR the sensitive cells. property of the Hs578T cells.

FIGURE 1 – Stable overexpression of caveolin-1 in Hs578T cells and the changes in caveolae organelles. (a) Drug sensitive (Hs578T/S) and drug resistant (Hs578T/Doxo) cells were stably transfected with caveolin-1,orvector as control. The expression levels of caveolin-1 in Hs578T/S and Hs578T/Doxo were about 2.5- or 4-fold higher than their control cell lines, respectively. The expression level of P-gp in Hs578T/Doxo is about 20-fold higher than in Hs578T/S cells, regardless of the caveolin-1 expression level. Each lane contained 30 ␮g of total protein from whole cell lysates. The results shown are representative of three separate experiments. (b) Cells were ﬁxed with osmium tetroxide, and stained with uranyl acetate and lead citrate. Representative electron micrographs display views of the plasma membrane, showing a large increase in the number of caveolae organelles in cells overexpressing caveolin-1.

229 CAVEOLIN-1 ALTERATION OF MULTIDRUG RESISTANCE 525

FIGURE 2 – Reduced multi-drug resistance in Hs578T cells overexpressing caveolin-1. The cell survival percentages of (a) Hs578T/S and (b) Hs578T/Doxo cells stably transfected with caveolin-1 (solid circle) or vector only (open square) were analyzed by MTT uptake assay with various doses of either cisplatin (left panels)or doxorubicin (right panels). (c) The relative drug resistances (%) were determined by dividing the IC50 value of the drug for each individual cell line by that of their control cell line. The decrease in IC50 of both cisplatin and doxorubicin in caveolin-1-transfected Hs578T/Doxo cells was signiﬁcant (*p Ͻ 0.01). The data shown are the mean (ϮSE) of 3 independent experiments, each with 5 duplicates.

Reduced multi-drug resistance in Hs578T cells overexpressing Cav-1 cells were reduced to 23.2 Ϯ 2.1 and 0.8 Ϯ 0.15 ␮g/ml, caveolin-1 respectively (p Ͻ 0.01) (Fig. 2b). This equates to a decrease in We examined the effect of overexpressed caveolin-1 on the drug drug resistance in terms of the IC50 values of 64% for cisplatin and resistance in Hs578T cells. We selected a specific substrate of 97% for doxorubicin (Fig. 2c). These data demonstrate that over- P-gp, doxorubicin, and a non-specific substrate, cisplatin, to study expression of caveolin-1 markedly reduces the drug resistance in the changes of multidrug resistance in these cells. As shown in Hs578T/Doxo cells, particularly for doxorubicin, a specific sub- ϩ strate of P-gp. This suggests that overexpressed caveolin-1 may Figure 2a, the IC50 values for cisplatin in Hs578T/S pCI-neo and Hs578T/S ϩ pCI-Cav-1 cells were about 40.3 Ϯ 2.0 and inhibit P-gp transport activity in Hs578T/Doxo cells. This would Ϯ ␮ Ͻ also be consistent with the high expression of P-gp in these cells 30.5 1.5 g/ml, respectively (p 0.05) (left panel), and the IC50 values for doxorubicin in Hs578T/S ϩ pCI-neo and Hs578T/S ϩ compared to the parent strain, after selection in the presence of pCI-Cav-1 cells were about 1.15 Ϯ 0.10 and 0.86 Ϯ 0.09 ␮g/ml, doxorubicin. respectively (p Ͻ 0.05) (right panel). This indicated that although the Hs578T/S cells overexpressing caveolin-1 seem to be more Reduced P-gp transport activity in Hs578T cells overexpressing sensitive to these drugs than the Hs578T/S cells transfected with caveolin-1 the pCl-neo vector, the difference is not very large. In contrast, the Because the overexpression of caveolin-1 did not change the difference in drug sensitivity could be observed more clearly in protein levels of P-gp (Fig. 1a, lane 1 vs. lane 2, lane 3 vs. lane 4), Hs578T/Doxo cells. The IC50 values for cisplatin and doxorubicin the reduced drug resistance in cells overexpressing caveolin-1 is in Hs578T/Doxo ϩ pCI-neo were 65.3 Ϯ 2.5 ␮g/ml and 25.4 Ϯ likely to be due to the inhibition of P-gp transport activity. To 1.5 ␮g/ml, respectively, whereas those in Hs578T/Doxo ϩ pCI- verify this hypothesis, we examined the activity of P-gp by mea-

230 526 CAI AND CHEN

FIGURE 3.

231 CAVEOLIN-1 ALTERATION OF MULTIDRUG RESISTANCE 527 suring the efflux of rhodamine-123,21–23 a P-gp specific substrate, Hs578T/S cells. This not only suggests that the drug resistance of in Hs578T cells. Cells were loaded with Rhodamine-123, and then Hs578T/Doxo cells can be attributed to augmented P-gp levels, but washed with dye-free medium to remove the extracellular dye. The also confirms that overexpressing caveolin-1 in Hs578T/Doxo fluorescence of remaining Rh-123 in the cells was monitored by cells has a similar effect on the activity of P-gp as known inhibitors flow cytometry. The fluorescence intensity change of Rh-123 of P-gp transport activity (Fig. 3d,e). reflects the change of P-gp transport activity in the membrane. The higher the fluorescence intensity of remaining Rh-123 in the cells, Localization of P-gp in caveolae membrane and the lower the P-gp transport activity. As shown in Figure 3a, the co-immunoprecipitation of P-gp and caveolin-1 Rh-123 fluorescence intensities at time 0 min were different in the Our data show that overexpression of caveolin-1 can function- Ͼ ӷ 4 cell lines: FHs578T/S ϩ pCI-cav-1 FHs578T/S ϩ pCI-neo FHs578T/ ally inhibit the transport activity of P-gp in Hs578T cells. This ϩ Ͼ Doxo pCI-cav-1 FHs578T/Doxo ϩ pCI-neo. This indicates that P-gp inhibition effect could be due to direct interaction, which would transport activity is lower in Hs578T/S cells than in Hs578T/Doxo require physical contact between caveolin-1 and P-gp, presumably cells, consistent with the relative expression levels of P-gp. It also in the caveolae membrane region. To test this possibility, we used indicates, however, that P-gp transport activity is lower when the true co-localization confocal microscopy experiments of intact expression level of caveolin-1 is increased. The Rh-123 fluores- cells to detect P-gp and caveolin-1 in the caveolae domain of the cence intensity at time ϭ 0 is related to the equilibrium of dye plasma membrane. As shown in Figure 4a, we found that P-gp uptake and efflux, and the passive dye uptake rate is expected to be colocalizes with caveolin-1. identical in the 4 cell lines. Therefore, the reduced intensity of We also found that P-gp and caveolin-1 co-fractionate in the Rh-123 fluorescence in drug-resistant cells and in those overex- caveolae fraction of the plasma membrane. As shown in Figure pressing caveolin-1 implies a reduction in efflux rate, which may 4b, we employed a detergent-free method to isolate the caveolae be mediated by the function of P-gp. This was investigated further fraction from Hs578T/Doxo ϩ pCI-Cav-1 cells. The data show by measuring the rate of decrease of Rh-123 fluorescence intensity that caveolin-1 and P-gp could be detected in the whole plasma in the 4 cell lines (Fig. 3b,c). As shown in Figure 3b (right vs. left), membrane fraction (PM). The strong bands of caveolin-1 and Hs578T/S ϩ pCI-Cav-1 cells and Hs578T/S ϩ pCI-neo cells had P-gp immunoreactive proteins in the caveolae membrane frac- similar rates of decrease of Rh-123 fluorescence. This suggests that tion (CM) indicates, however, that the majority of caveolin-1 overexpression of caveolin-1 has little effect on the efflux of and P-gp is localized in the caveolar membrane sub domain. Rhodamine-123 when P-gp expression is low. Compared to drug Caveolin-1 and P-gp proteins were undetectable in the non- resistant cells transfected with only the pCI-neo vector, however, caveolae membrane fraction (NCM). We also carried out co- Hs578T/Doxo ϩ pCI-Cav-1 cells had a much lower rate of de- immunoprecipitation in Hs578T/Doxo ϩ pCI-Cav-1 whole cell crease of Rh-123 fluorescence (Fig. 3c, right vs. left). The rate of lysates using protein G-Sepharose beads and antibodies against fluorescence decrease in Hs578T/Doxo ϩ pCI-neo cells was sig- caveolin-1 and P-gp. As shown in Figure 4c, caveolin-1 protein nificantly faster than in Hs578T/S ϩ pCI-neo cells, indicating that could be pulled down by anti-P-gp antibody and P-gp could also the rate of efflux correlates with the level of P-gp expression. To be co-immunoprecipitated with caveolin-1 by anti-caveolin-1 quantify these changes, we took the mean fluorescence intensity of antibody. Taken together, these results suggest that caveolin-1 each sample at time ϭ 0 as 100% and plotted the relative fluores- and P-gp may be able to interact directly within the caveolae cence intensity at various time points as a percentage of this (Fig. membrane compartment. 3d). The data demonstrate that Hs578T/Doxo ϩ Cav-1 cells have a similar fluorescence decline rate to Hs578T/S cells. This suggests that over-expression of caveolin-1 reduces the efflux rate of Rho- DISCUSSION damine-123 in Hs578T/Doxo cells to the level observed in drug Controlling the overexpression of particular proteins in the sensitive cells. cell is increasingly employed as a tool to investigate their To compare the inhibitory effect of caveolin-1 on the Rh-123 function and physiological significance.24,25 We used this efflux from Hs578T cells with that of P-gp inhibitors, we used the method in Hs578T carcinoma cells and their MDR derivatives drugs, verapamil and cyclosporine A, 2 known inhibitors of P-gp to investigate the role of caveolin-1 in the reduction of the transport activity.21 The results are shown in Figure 3e. We found transport activity of P-gp, and hence the ability of caveolin-1 that 5 ␮M cyclosporine A or 10 ␮M verapamil were able to reduce overexpression to cause multidrug resistant Hs578T/Doxo cells the efflux rate of Rh-123 from Hs578T/Doxo cells to the level of to become drug sensitive. We also observed that P-gp and caveolin-1 co-localize and co-fractionate in the caveolar membrane fraction, meaning that a direct physical interaction between these proteins is possible. It is generally believed that FIGURE 3 – Inhibition of P-gp transport activity in Hs578T cells overexpressing caveolin-1. P-gp transport activity was measured by the development of MDR in cells is due to the increased expression changes in Rhodamine-123 fluorescence intensity as described in “Exper- of P-gp. Our data, however, suggest that changes in the expres- imental Procedures.” (a) The Rhodamine-123 fluorescence intensity dis- sion of caveolin-1 also play an important role in regulating the tribution was different in the 4 cell lines after 30 min of dye loading (red, resistant nature of cells in response to multi-drug treatment. Hs578/Doxo ϩ pCI-neo; blue, Hs578T/Doxo ϩ pCI-Cav-1; orange, Conflicting results have been reported in the literature on the ϩ ϩ Hs578T/S pCI-neo; green, Hs578T/S pCI-Cav-1). The left shift of role of caveolins in the development of MDR. On the one hand, the fluorescent intensity in (b) Hs578T/S or (c) Hs578T/Doxo cells at differ- caveolin-1 expression level is upregulated in MDR phenotypes of ent time points (0, 5, 10, 20, 30, 50 min as indicated) was due to the efflux of dye by P-gp-mediated transport. The efflux rate in Hs578T/Doxo cells a number of human cell lines, including colon, ovarian, breast and overexpressing caveolin-1 (c, right panel) has been markedly reduced lung carcinoma.12–14 On the other hand, expression of caveolin-1 compared to control cells containing only vector (left panel). (d) The and caveolin-2 was not detected in several MDR cell lines that dynamic changes in Rhodamin-123 fluorescence intensity were re-plotted express high levels of P-glycoprotein, such as J7.V1-1 and J7.T3- as relative intensity compared to time ϭ 0 (mean Ϯ SE, n ϭ 3). Compared 1.6 derived from murine macrophage, and Caco-V100 derived to drug sensitive Hs578T cells (circles), Hs578T/Doxo ϩ pCI-neo cells from human colon carcinoma cells.13 Unlike epothilone B-resistant (open triangles) showed a sharper decline, which is consistent with higher A549 cells, epothilone B-resistant MCF-7 cells do not express any P-gp transport activity in drug-resistant cells. The decreased decline rate in ϩ caveolins. It has also been shown that caveolin-1 expression has no Hs578T/Doxo pCl-Cav-1 cells (solid triangles) indicates that overex- association with that of P-gp protein or MDR1 mRNA in human pression of caveolin-1 rendered the drug-resistant cells drug-sensitive. (e) 14 P-gp transport activity in Hs578T/Doxo cells (open triangles) was inhib- ovarian carcinoma. In our study, we observed comparable ited by verapamil (solid circles) and cyclosporine A (solid triangles) to a amounts of caveolin-1 in Hs578T cells, irrespective of whether level similar to Hs578/S cells (open circles). The traces represent the they were drug-sensitive or drug-resistant (Fig. 1a, lane 1,3). Thus, combine results of three independent experiments. it is possible that the expression level of caveolin-1 in MDR cells

232 528 CAI AND CHEN

FIGURE 4 – Co-localization and co-immunoprecipitation of caveolin-1 and P-gp. (a) Co-localization of P-gp with caveolin-1 in Hs578T/ Doxo cells. Cells were double stained and examined by confocal microscopy. For each experiment, at least 100 cells were examined, and the figures shown represent the typical staining pattern for the majority of cells. The yellow fluorescent points (right hand panel) indicate co- localization of P-gp and caveolin-1 in the same domain of the plasma membrane. (b) Hs578T/ Doxo cells stably transfected with pCI-neo-Cav-1 were processed to isolate plasma membrane (PM), non-caveolae membrane (NCM) and caveolae membrane (CM) using a detergent-free method. Most of caveolin-1 and P-gp were localized in the caveolae membrane fraction, and there was no detectable caveolin-1 or P-gp in the non- caveolae membrane fraction. (c) P-gp and caveolin-1 could be co-immunoprecipitated (co-IP) from cell lysates using either anti-P-gp or anti- caveolin-1 antibody (lane 2). Lane 1 was the negative control lacking cell lysate. The experiments were carried out at least 3 times with the same results. varies in a tissue-dependent, cell-dependent or drug-dependent factor receptor, can directly interact with a specific scaffolding manner. Most importantly, our data show that overexpression of domain of caveolin-1, which consequently results in a strong caveolin-1 reduces P-gp transport activity and renders multi-drug inhibition of their biological activities.11,26 The proteins inter- resistant cancer cells sensitive to anticancer drugs. The inhibitory acting with caveolin-1 have a consensus caveolin-binding mo- effect of overexpressing caveolin-1 on P-gp transport activity was tif, termed ‘scaffold’ site, which contains the sequences found to be similar to the effect of verapamil or cyclosporine A, ⌽XXXX⌽XX⌽ or ⌽XX⌽XXXX⌽, where ⌽ is an aromatic which are known inhibitors of P-gp activity (Fig. 3e). These residue, and X is any amino acid.27 By BLAST searching, we functional studies not only provide some clues as to the role of found that this caveolin-binding motif is also present in human caveolin-1 in multi-drug resistance of cancer cells, but also indi- P-gp between amino acid residues 36 and 44 (FSMFRYSNW). cate that caveolin-1 may function as an important regulator of P-gp This is similar to the equivalent residues in hamster MDR1 transport activity. (FTMFRYAGW), which has already been identified as a puta- Co-fractionation and co-immunoprecipitation assays in tive caveolin-binding motif.15 Taken together, this implies that Hs578T/Doxo-Cav-1 cells (Fig. 4) indicate that P-gp and caveo- the mechanism of this functional inhibition of the enzymatic lin-1 are predominantly found in the caveolae membrane frac- activity may be caused by direct interaction between caveolin-1 tion. Confocal microscopy confirms that caveolin-1 and P-gp and P-gp. colocalize in intact cells, meaning that direct association of these proteins in the caveolae membrane may occur. This is Nevertheless, other possible mechanisms of the inhibitory ef- consistent with previous findings that caveolin-1 and P-gp co- fects of caveolin-1 on P-gp transport activity and drug-resistance localize in the low density detergent-insoluble membrane frac- in cancer cells must be considered. One possible mechanism is that tion and that there is a physical interaction between these caveolin-1 regulation of cellular cholesterol may be important in proteins in resistant CHRC5 cells and brain capillaries.15 This the regulation of P-gp drug transport activity. Caveolin-1 has been indicates that co-localization of caveolin-1 and P-gp as well as reported to functionally bind to cholesterol.28 In addition, recom- their physical association is not depend on the cells selected for binant expression of caveolin-1 has been shown to facilitate the their resistance. In our study, the functional inhibitory effect of transport of newly synthesized cholesterol from the ER to the caveolin-1 on P-gp transport activity was further investigated. plasma membrane, where cholesterol rapidly diffuses out of caveo- Caveolin-1, as an important structural protein of caveolae, plays lae.29 Thus, it is possible that the overexpression of caveolin-1 a key role in signal transduction and lipid homeostasis. There is might indirectly affect P-gp transport activity through modulation a growing body of evidence that a number of proteins, such as of the availability of cholesterol at the level of the plasma mem- Ras, Src, protein kinase C␣, eNOS, and the epidermal growth brane.

233 CAVEOLIN-1 ALTERATION OF MULTIDRUG RESISTANCE 529

Although the precise mechanism by which overexpression of ACKNOWLEDGEMENTS caveolin-1 alters multidrug resistance is worthy of further inves- We thank Dr. E.J. Smart (Kentucky Medical School, Kentucky) tigation, our present data suggest that enhancing the expression or for providing the pCI-neo and pCI-neo-Cav-1 expression vectors function of caveolin-1 could downregulate the multidrug resis- and Dr. K. Grankvist (Umea University, Sweden) for providing tance of cancer cells and thus might serve as an alternative mech- Hs578T cell line. We are grateful to Dr. Zui Pan (Piscataway, NJ) anism for improving the efﬁcacy of chemotherapy in cancer pa- and Dr. Sarah Perrett (Institute of Biophysics, Beijing, P.R. China) tients. for editing the manuscript.

REFERENCES 1. Gottesman MM. How cancer cells evade chemotherapy: sixteenth localized in caveolae in resistant cells and in brain capillaries. FEBS Richard and Hinda Rosenthal Foundation Award Lecture. Cancer Res Lett 2000;466:219–24. 1993;53:747–54. 16. Uittenbogaard A, Smart EJ. Palmitoylation of caveolin-1 is required 2. Bosch I, Croop J. P-glycoprotein multidrug resistance and cancer. for cholesterol binding, chaperone complex formation, and rapid Biochim. Biophys. Acta 1996;1288:F37–54. transport of cholesterol to caveolae. J Biol Chem 2000;275:25595–9. 3. Lisanti MP, Tang Z, Scherer PE, Kubler E, Koleske AJ, Sargiacomo 17. Jonsson O, Motlagh PB, Persson M, Henriksson R, Grankvist K. M. Caveolae, transmembrane signaling and cellular transformation. Increase in doxorubicin cytotoxicity by carvedilol inhibition of P- Mol Membr Biol 1995;12:121–4. glycoprotein activity. Biochem Pharmacol 1999;58:1801–6. 4. Li S, Couet J, Lisanti MP. Src tyrosine kinases, G␣ subunits, and 18. Smart EJ, Ying YS, Mineo C, Anderson RGW. A detergent-free H-Ras share a common membrane-anchored scaffolding protein, method for purifying caveolae membrane from tissue culture cells. caveolin. J Biol Chem 1996;271:29182–90. Proc Natl Acad Sci USA 1995;92:10104–8. 5. Li S, Okamoto T, Chun M, Sargiacomo M, Casanova JE, Hansen SH, 19. Hyafil F, Vergely C, Vignaud PD, Grand-Perret T. In vitro and in vivo Nishimoto I, Lisanti MP. Evidence for a regulated interaction between reversal of multidrug resistance by GF120918, an acridonecarboxam- heterotrimeric G proteins and caveolin. J Biol Chem 1995;270:15693– ide derivative. Cancer Res 1993;53:4595–602. 701. 20. Krishan A, Sauereig A, Gordon K, Swinkin C. Flow cytometric 6. Scherer PE, Okamoto T, Chun M, Nisimoto I, Lodish HF, Lisanti MP. monitoring of cellular anthracycline accumulation in murine leukemic Identification, sequence, and expression of caveolin-2 defines a caveo- cells. Cancer Res 1986;46:1786–73. lin gene family. Proc Natl Acad Sci USA 1996;93:131–5. 21. Patel VA, Dunn MJ, Sorokin A. Regulation of MDR-1 (P-glycopro- 7. Song SK, Li S, Okamoto T, Quilliam LA, Sargiacomo M, Lisanti MP. tein) by cyclooxygenase-2. J Biol Chem 2002;277:38915–20. Co-purification and direct interaction of Ras with caveolin, an integral 22. Jodoin J, Demeule M, Beliveau R. Inhibition of the multidrug resis- membrane protein of caveolae microdomains. J Biol Chem 1996;271: tance P-glycoprotein activity by green tea polyphenols. Biochim Bio- 9690–7. 8. Mineo C, James GL, Smart EJ, Anderson RG. Localization of epi- phys Acta 2002;1542:149–59. dermal growth factor-stimulated Ras/Raf-1 interaction to caveolae 23. Stouch TR, Gudmundsson O. Progress in understanding the structure- membrane. J Biol Chem 1996;271:11930–5. activity relationships of P-glycoprotein. Adv Drug Deliv Rev 2002; 9. Li S, Seitz R, Lisanti MP. Phosphorylation of caveolin by Src tyrosine 54:315–28. kinases. J Biol Chem 1996;271:3863–8. 24. Raziani B, Rubin CS, Lisanti MP. Regulation of cAMP mediated 10. Rothberg KG, Heuser JE, Donzell WC, Ying YS, Glenney JR, Ander- signal transduction via interaction of caveolins with the catalytic son RG. Caveolin, a protein component of caveolae membrane coats. subunit of protein kinase A. J Biol Chem 1999;274:26353–60. Cell 1992;68:673–82. 25. Pidgeon GP, Tang KQ, Rice RL, Zacharek A, Li L, Taylor JD, Honn 11. Okamoto T, Schlegel A, Scherer PE, Lisanti MP. Caveolins, a family KV. Overexpression of leukocyte-type 12-lipoxygenase promotes of scaffolding proteins for organizing “preassembled signaling com- w256 tumor cell survival by enhancing ␣v␤5 expression. Int J Cancer plexes” at the plasma membrane. J Biol Chem 1998;273:5419–22. 2003;105:459–71. 12. Lavie Y, Fiucci G, Liscovitch M. Up-regulation of caveolae and 26. Anderson RG. The caveolae membrane system. Annu Rev Biochem caveolar constituents in multidrug-resistant cancer cells. J Biol Chem 1998;67:199–225. 1998;273:32380–3. 27. Couet J, Li S, Okamoto T, Ikezu T, Lisanti MP. Identification of 13. Yang CPH, Galbiati AE, Volonte D, Horwitz SB, Lisanti MP. Up- peptide and protein ligands for the caveolin-scaffolding domain. regulation of caveolin-1 and caveolae organelles in Taxol-resistant J Biol Chem 1997;272:6525–33. A549 cells. FEBS Lett 1998;439:368–72. 28. Murata M, Peranen J, Schreiner R, Weiland F, Kurzchalia T, Simons 14. Davidson B, Goldberg I, Givant-Horwitz V, Nesland JM, Berner A, K. VIP21/Caveolin is a cholesterol-binding protein. Proc Natl Acad Bryne M, Risberg B, Kopolovic J, Kristensen GB, Trope CG, Van D, Sci USA 1995;92:10339–43. Reich R. Caveolin-1 expression in ovarian carcinoma is MDR1 inde- 29. Smart EJ, Ying YS, Donzell WC, Anderson RGW. A Role for pendent. Am J Clin Pathol 2002;117:225–34. caveolin in transport of cholesterol from endoplasmic reticulum to 15. Demeule M, Jodoin J, Gingras D, Beliveau R. P-glycoprotein is plasma membrane. J Biol Chem 1996;271:29427–35.

234 Biochem. J. (2004) 379, 697–702 (Printed in Great Britain) 697

Kinetic analysis of ligand-induced autocatalytic reactions Jiang-Hong LIU and Zhi-Xin WANG1 National Laboratory of Biomacromolecules, Center for Molecular Biology, Institute of Biophysics, Academia Sinica, Beijing 100101, People’s Republic of China

Protein phosphorylation and limited proteolysis are two most this method, the effects of calcium ions on the autoacatalytic common regulatory mechanisms involving the energy-dependent activation of trypsinogen by trypsin is re-examined. The results covalent modification of regulatory enzymes. In addition to indicate that the binding affinity for Ca2+-bound trypsinogen to modifying other proteins, many protein kinases and proteases trypsin is at least two orders of magnitude higher than that for catalyse automodification reactions (i.e. reactions in which the Ca2+-free trypsinogen, and therefore that the effect of Ca2+ ions ∗ kinase or zymogen serves as its own substrate), and their activities on Km values for trypsinogen is very much greater than that are frequently regulated by other regulatory ligands. In the present for the model peptides. Based on the experimental results, one study, a kinetic analysis of autocatalytic reaction modulated by possible molecular mechanism has been proposed. regulatory ligands is presented. On the basis of the kinetic equation, a novel procedure is developed to evaluate the kinetic Key words: autophosphorylation, limited proteolysis, protein parameters of the reaction. As an example of an application of kinase, trypsin, trypsinogen, zymogen activation.

INTRODUCTION ation process, usually a limited proteolysis, to attain their catalytic activity. The active forms of zymogens usually have power- Enzyme-catalysed covalent modification is an important mechan- ful physiological effects, and their synthesis in inactive form ism for the regulation of enzyme activity. In such a regulatory permits them to be safely stored until they are required. Zymogen process, one enzyme acts to modify the activity of another activation is a phenomenon of great importance to our under- by chemically modifying the target enzyme. Protein phosphoryl- standing of fundamental biochemical and physiological pro- ation and limited proteolysis are two most common regulatory cesses. They are involved in many physiological processes, such mechanisms involving the energy-dependent covalent modifica- as digestion, metabolism, differentiation, immunity, blood co- tion of regulatory enzymes. The control of enzyme activity through agulation, fibrinolysis, apoptosis and respose to injury [1,3–10]. a reversible covalent modification such as phosphorylation can When the activating enzyme and the activated enzyme coincide, have a variety of functions: (i) it can change the kinetic and the process is an autocatalytic zymogen activation. Physiological allosteric properties of the enzyme; (ii) by necessity it introduces examples of these processes are the activation of trypsinogen, two interconverting enzymes into the system, which may them- prekallikrein, pepsinogen and human blood coagulation factor XII selves be subject to control mechanisms; and (iii) further increases by trypsin, kallikrein, pepsin and factor XIIa (a form of activated in the regulatory potential of an enzyme can be obtained by XII), respectively [1,11–13]. introducing multiple phosphorylation or by linking two or more Recently, kinetic studies of the autoactivation of protein kinase phosphorylation/dephosphorylation cycles in sequence [1]. and zymogen have been reported [14,15]. In the present paper, Protein phosphorylation is the most prevalent form of post- kinetic analysis of an autocatalytic reaction modulated by a translational covalent modification mechanism that cells employ regulatory ligand is presented. As an example of an application to regulate enzyme activity. It is a means of superimposing the of this method, the effect of calcium ions on the autoactiv- effect of a stimulus from outside the cell on the prevailing meta- ation of trypsinogen by trypsin was re-analysed. Some years ago, bolic state within that cell. The enzymes responsible for catalysing Abita et al. [16] examined in detail the effect of Ca2+ in the this reaction are protein kinases. In addition to phosphorylat- trypsin-catalysed hydrolysis of the Lys–Ile bond in trypsinogen ing other proteins, many protein kinases catalyse autophos- and several model peptides with sequences related to the N- phorylation reactions (i.e. reactions in which the kinase serves terminal sequence of bovine trypsinogen. With trypsinogen, when 2+ as its own substrate), and their activities are frequently regulated the concentration of Ca increases from 4 to 50 mM, Km de- by phosphorylation and other regulatory ligands [2]. The auto- creased by a factor 3 and kcat was not changed. The trypsin- phosphorylation reactions can be intramolecular or inter- catalysed hydrolysis of the nonapeptide Val-Asp4-Lys-Ile-Val- 2+ molecular. The intermolecular autophosphorylation involves a Gly was also Ca -dependent, and Km decreased by a factor of bimolecular autocatalytic event. In addition to modulation by 4.3; the effect was very similar to that observed for trypsinogen. other regulatory ligands, the rate of intermolecular autophos- According to these observations, the authors suggested that phorylation is dependent on the concentration of the protein the N-terminal hexapeptide is probably randomly arranged at kinase, and thereby provides an alternative means for regulating the surface of trypsinogen and floats freely in the surrounding particular biological processes. solvent. However, our results indicate that the Km value for the Proteolytic enzymes are normally synthesized and secreted trypsinogen activation was greatly overestimated in the previous as inactive precusors, which are activated at a physiologically study, and that the binding affinity for Ca2+-bound trypsinogen appropriate time and place. These precusors are known as to trypsin is at least two orders of magnitude higher than that proenzymes, or zymogens. The zymogens must undergo an activ- for Ca2+-free trypsinogen. Therefore, the effect of Ca2+ ions

Abbreviation used: TAME, N-α-p-tosyl-L-arginine methyl ester. 1 To whom correspondence should be addressed (e-mail [email protected]).

235 c 2004 Biochemical Society 698 J.-H. Liu and Z.-X. Wang

where + ∗ = (Kd [L])KS Km (5) Kd + [L] is the apparent Michealis–Menten constant for the intermolecular autocatalytic reaction. The solution of eqn (4) for [E∗EL] is given by the quadratic formula as ∗ = [L] + ∗ [E EL] [T]0 Km 2(Kd + [L]) ∗ 2 ∗ ∗ − ([T]0 + Km ) − 4([T]0 − [ET ])[ET ] (6) Scheme 1 Mechanism of the autocatalytic reaction The rate of the modified enzyme formation is given by L represents regulatory ligand, E and E* represent unmodified and modified enzyme, respectively, and P is the product. d[E ∗] k K T = k [E∗E] + k [E∗EL] = 2 d + k [E∗EL] dt 2 2 [L] 2 ∗ ∗ kcat ∗ on Km values for trypsinogen is very much greater than that = [T]0 + Km for the model peptide, Val-Asp4-Lys-Ile-Val-Gly. Based on the 2 experimental results, one possible molecular mechanism has been ∗ 2 ∗ ∗ − ([T]0 + Km ) − 4([T]0 − [ET ])[ET ] (7) proposed. where + ∗ = k2Kd k2 [L] THEORETICAL ANALYSIS kcat (8) Kd + [L] In the cases of the autocatalytic reactions, the unmodified enzyme serves as a substrate in reactions. The general mechanism of the is the apparent turnover number (catalytic centre activity) for the intermolecular autocatalytic reaction of an enzyme can be written intermolecular autocatalytic reaction. Eqn (7) can be rewritten as as shown in Scheme 1. In Scheme 1, L represents regulatory ∗ ∗ 2d[ET ] ∗ ligand, and E and E represent unmodified and modified enzyme, √ = kcat dt + ∗ − + ∗ 2 − − ∗ ∗ respectively. It is assumed that the other substrates and products [T]0 Km ([T]0 Km ) 4([T]0 [ET ])[ET ] for modification, such as ATP, water, etc., are present at con- (9) stant levels, and can therefore be included in the kinetic constants ∗ √ without loss of generality. Since the concentrations of protein To integrate this equation, put x = 2[ET ] − [T]0 + ([T]0 + ∗ 2 ∗ ∗ substrate and enzyme are of the same order of magnitude, the Km ) − 4([T]0 − [ET ])[ET ], so that steady-state assumption is not satisfactory in this case [17]. When ∗ ∗ + 2 − ∗ + 2 there is equilibrium as far as EL, E EandE EL are concerned, i.e. ∗ (x [T]0) (Km [T]0) [ET ] = (10) when k2 and k2 are sufficiently small as not to disturb equilibrium, 4x we then have and ∗ ∗ [E ][E] [E ][EL] = = ∗ ∗ 2 ∗ ∗ KS ∗ ,KS ∗ + K − + K − − E E [E EL] [T]0 m ([T]0 m ) 4([T]0 [ET ])[ET ] ∗ ∗ ∗ (1) = + − [E][L] [E E][L] 2[ET ] Km x K = ,K = d d ∗ + 2 − ∗ + 2 [EL] [E EL] (x [T]0) (Km [T]0) ∗ = + K − x 2x m The total concentration of enzyme is (x − K ∗)(x − K ∗ − 2[T] ) = m m 0 (11) ∗ ∗ ∗ ∗ x [T]0 = [E]0 + [E ]0 = [E] + [E ] + [EL] + 2[E E] + 2[E EL] 2 (2) Differentiation of eqn (10) with respect to x gives

2 ∗ ∗2 ∗ x + 2Km [T]0 + Km where [T]0 is the total concentration of trypsin plus trypsinogen, d[E ] = dx (12) ∗ T 2 and [E]0 and [E ]0 are the initial concentrations of the unmodiﬁed 4x and modiﬁed enzyme respectively. Let Substitution of eqns (11) and (12) into eqn (9) yields

∗ ∗ ∗ ∗ = + + 2 ∗ ∗2 [ET ] [E ] [E E] [E EL] (3) x + 2K [T] + K m 0 m dx =−k ∗ dt (13) x(x − K ∗)(x − K ∗ − 2[T] ) cat From eqns (1)–(3), we have m m 0 = ∗ = ∗ With the boundary condition t 0, [ET ] [E ]0, this integrates + Kd [L] ∗ 2 ∗ ∗ to [E EL] − ([T]0 + Km )[E EL] [L] x K ∗ + [T] (x − K ∗ − 2[T] )(x − K ∗) −k ∗t = ln + m 0 ln m 0 0 m ([T] − E ∗)[E ∗][L] cat x [T] (x − K ∗ − 2[T] )(x − K ∗) + 0 T T = 0(4)0 0 0 m 0 m + Kd [L] (14)

c 2004 Biochemical Society 236 Ligand-induced autocatalytic kinetics 699 where Table 1 Effect of Ca2+ concentration on the steady-state kinetic parameters for trypsin-catalysed TAME hydrolysis ◦ ∗ ∗ 2 ∗ The kinetic experiments were carried out in 40 mM Tris/HCl buffer (pH 8.1) at 30 C. x0 = 2[E ]0 − [T]0 + (Km + [T]0) − 4[E ]0[E]0 (15) [E]0 = 50 nM and [TAME] = 50–1500 µM. k cat and K m were determined from the steady- state kinetic analysis. MATERIALS AND METHODS 2+ −1 µ Bovine pancreatic trypsinogen, trypsin and TAME (N-α-p-tosyl- [Ca ] (mM) k cat (min ) K m ( M) L-arginine methyl ester) were purchased from Sigma Chemical + + 03.33− 0.065 221 − 17 Co. The active-site normality of trypsin was 90%. Traces of + + 10 3.86 − 0.42 185 − 79 chymotryptic activity would not be expected to interfere with + + 30 4.06 − 0.23 255 − 50 the activation of trypsinogen, since the specificity does not fit the 50 3.32 + 0.16 161 + 32 activation sites. All other chemicals were local products of analyt- − − ical grade. The concentration of trypsinogen was determined by measuring the absorbance at 280 nm and using the absorption coefficient 33600 M−1 · cm−1 [18]. Trypsin activity was routinely assayed by monitoring the trypsinogen into trypsin involves the removal of the N-terminal increase in absorbance at 245 nm due to hydrolysis of TAME hexapeptide H2N-Val-Asp-Asp-Asp-Asp-Lys [20]. This process using a PerkinElmer spectrophotometer [19]. Initial rates of is strongly stimulated by calcium ions. It has been shown that the reactions were determined from the linear slope of the trypsinogen has two different binding sites for calcium ions while trypsin has only one. The high-affinity calcium-binding site progress curves obtained with a molar absorption coefficient − − − ◦ ≈ × 4 ε of 595 M 1 · cm 1. All the assays were carried out at 30 C (Kd 6.31 10 M) is common to both trypsinogen and trypsin. 245 2+ and pH 8.1 in 40 mM Tris/HCl buffer. In kinetic studies of the The binding of Ca on this site induces a stabilization of the autocatalytic conversion of trypsinogen into trypsin, aliquots conformation of these proteins which prevents the formation of of the incubation mixture of trypsinogen and trypsin were inert proteins in the course of trypsinogen activation and protects periodically removed and the activity of trypsin was determined trypsin against autolysis. The second site, with a much lower ◦ ≈ × −2 at 30 C. The assay system contained 40 mM Tris/HCl (pH 8.1), affinity for calcium ions (Kd 1.58 10 M), is found only in the zymogen and has been assigned to the two aspartyl residues 1 mM TAME and 10 mM CaCl2. Since there are many sets of constants that give essentially 13 and 14 neighbouring the important Lys-15–Ile-16 bond that is the same curve, the individual fit for each set of experimental split during activation. Binding of calcium to this site accelerates data to eqn (14) cannot give a reliable estimate for the kinetic very clearly the rate of hydrolysis by trypsin of the Lys–Ile bond parameters of the autocatalytic reaction. In practice, commercial [16,21,22]. trypsinogen always contains a trace amount of contaminating To characterize the effect of calcium ions on the trypsin- active enzyme. Therefore, the initial concentrations of enzyme catalysed reaction, the kinetic parameters of trypsin-catalysed ∗ TAME hydrolysis were determined first. The initial velocities for species can be written as [E ]0 = α[T]0 and [E]0 = (1 − α)[T]0, where α is a constant. In this case, χ in eqn (14) can be written the hydrolysis of TAME by trypsin were measured under different 0 2+ ◦ as Ca concentrations at pH 8.1, 30 C. By fitting the experimental data to the Michaelis–Menten equation, the values of kcat and Km were determined. The steady-state kinetic parameters for the = − + ∗ + 2 − − 2 x0 (2α 1)[T]0 (Km [T]0) 4α(1 α)[T]0 (16) trypsin-catalysed TAME hydrolysis are listed in Table 1. It can

be seen from Table 1 that both kcat and Km are independent of the + + and eqn (14) can then be treated as a function with two concentration of Ca2 , indicating that binding of Ca2 to trypsin is ∗ independent variables, [ET ]and[T]0, and three parameters, α, not required for activity of the enzyme. This result is in agreement ∗ ∗ Km and kcat . The problem of non-uniqueness of the estimated with the experimental observation that calcium does not affect parameters can be solved by a global-analysis approach when a activation of a trypsinogen derivative in which the carboxylate series of experiments is carried out at different initial concen- groups are blocked [23]. trations of enzyme [15]. Unlike conventional fitting methods in In order to study the stimulation mechanism of calcium ions which data corresponding to each fixed [T] are fit individually, the for the autoactivation of trypsin, the activation kinetics of trypsin 0 + kinetic parameters obtained by global analysis are constrained by was monitored at several fixed concentrations of Ca2 .The ∗ the entire matrix of [ET ]and[T]0 simultaneously. By combining trypsinogen was incubated with trypsin in 100 µl of reaction multiple experiments together in a single analysis, much more mixture containing 40 mM Tris/HCl (pH 8.0) and different con- + ◦ dramatic improvement in the fitting results can be obtained. In centrations of Ca2 at 30 C. At defined time intervals, an aliquot this study, we use a commercially available computer program (5 µl) was taken from the reaction mixture and assayed for for the non-linear regression data analysis, SigmaPlot 2000. enzyme activity. Enzyme activity assays were carried out under SigmaPlot’s non-linear curve fitter uses a least-squares procedure kinetically valid conditions with TAME as a substrate. Figure 1 (Marquardt–Levenberg algorithm) to determine the parameters shows time courses for trypsin autoactivation in the presence that minimize the sum of the squares of differences between the of 10 and 50 mM calcium ions. The time required for activation dependent variable in the equations and the observations. increases at lower enzyme concentration, and the maximal trypsin activity was proportional to the total concentration of trypsin plus RESULTS trypsinogen, indicating that the reaction went to completion in each case. As an example, fitting of eqn (14) to the experimental As an example, the new method was used to analyse the calcium- data in the presence of 10 mM Ca2+ is shown in Table 2. In Table 2 ∗ induced autoactivation of trypsinogen by trypsin. Trypsinogen, the reaction time t is the dependent variable, and [ET ]and[T]0 the zymogen form of trypsin, is secreted into the duodenum by are the two independent variables. The best-fitting results were ∗ ∗ −1 pancreatic cells. Trypsin catalyses the activation of trypsinogen obtained with α = 0.047, Km = 42.44 µMandkcat = 0.041 min in an intermolecular autocatalytic process. The conversion of by using the non-linear regression analysis program SigmaPlot

237 c 2004 Biochemical Society 700 J.-H. Liu and Z.-X. Wang

Table 2 Determination of kinetic parameters of trypsinogen autoactivation

Reaction time t is the dependent variable, and [ET*] and [T]0 are the two independent variables.

∗ t (min) [ET ](µM) [T]0 (µM)

2.1 0.90 20.29 76.8 2.27 20.29 172.6 7.09 20.29 214.4 9.88 20.29 299.3 14.68 20.29 354.8 17.68 20.29 422.2 18.84 20.29 510.5 19.88 20.29 2.1 1.50 30.43 88.3 6.12 30.43 119.0 9.43 30.43 212.6 20.98 30.43 270.4 26.20 30.43 324.8 28.22 30.43 385.4 29.74 30.43

Figure 1 Autocatalytic activation of trypsinogen by trypsin

(A) Effect of trypsinogen concentration on the time course for autoactivation in the presence of 10 mM Ca2+ at 30 ◦C. The symbols represent the experimental data. The total concentrations of trypsinogen plus trypsin are (᭹) 20.29 µMand(᭺) 30.43 µM, respectively. The lines are the theoretical curves generated by using eqn (14) with α = 0.047, K m* = 42.44 µMand −1 kcat* = 0.041 min .(B) Effect of trypsinogen concentration on the time course for autoactivation in the presence of 50 mM Ca2+ at 30 ◦C. The symbols represent the experimental data. The total concentrations of trypsinogen plus trypsin are (᭹) 11.26 µMand(᭺) 19.35 µM, respectively. The lines are the theoretical curves generated by using eqn (14) with α = 0.038, −1 K m* = 14.47 µMandkcat* = 0.043 min .

2000. Similarly, when the time courses for trypsin activation at two different enzyme concentrations were analysed by a global-fitting procedure simultaneously according to eqn (14), the values of ∗ ∗ Km , kcat and α could then be determined for each fixed concentration of Ca2+. At the same concentrations of Ca2+, the kinetic parameters so determined are quite close to those obtained by Garc´ıa-Moreno et al. [24], but are very different from those reported by Abita et al. [16]. In the presence of 50 mM Ca2+, ∗ the value of K was determined to be 14.5 µM, which is about 2+ m Figure 2 Effect of Ca concentration on K m* and kcat* 30 times lower than that obtained by Abita et al. [16] at 1 ◦C 2+ (400 µM). (A) Effect of Ca concentration on K m* for autoactivation of trypsinogen by trypsin. Inset: 2+ 2+ Figure 2 shows the effect of increasing Ca2+ concentration on plot of K m* versus 1/[Ca ]. (B) Effect of Ca concentration on kcat* for autoactivation of trypsinogen by trypsin. the kinetic parameters of trypsin autoactivation. The dominant 2+ ∗ effect of the Ca concentration appears to be on Km , but it has ∗ no significant effect on kcat . On increasing the concentration experimentally since trypsinogen is very unstable under this 2+ ∗ 2+ of Ca , Km decreases and approaches a limiting value. The condition. In the present study, the lowest concentration of Ca kinetic parameters in the absence of Ca2+ cannot be measured used was 2.5 mM when the tight Ca2+-binding site is almost

c 2004 Biochemical Society 238 Ligand-induced autocatalytic kinetics 701

does not change. Extrapolation of the experimental data to zero 2+ ∗ and high Ca concentration suggests that the Km value in the absence of Ca2+ is very much greater than that at saturating Ca2+ concentration. Therefore, the occupancy of the second site + Scheme 2 Reaction mechanism of Ca2 -induced trypsinogen auto- enhances greatly the binding afﬁnity of trypsinogen to trypsin activation without changing the rate of decomposition of the trypsinogen–

trypsin complex. Tryptic hydrolysis of the nonapeptide Val-Asp4- saturated. By fitting eqn (5) to the experimental data, the Lys-Ile-Val-Gly and of the heptapeptide Val-Asp2-Lys-Ile-Val- = + = + parameters were determined to be KS 6.19 − 0.83 µM, Kd GlyhavebeenshowntobeCa2 -dependent [16,22]. However, + =− + + 58.79 − 9.61 mM and Kd 0.0026 − 0.0074 mM. Because Ca2 ion binding to Asp-13 and Asp-14 together seems to be + Kd derived from the curve-fitting of the data to eqn (5) had a insufficient to explain the zymogen Ca2 ion effect since the small negative value with a very large standard deviation, such ∗ 2+ change in Km causedbyCa binding to the N-terminal of that its confidence interval would include the value of zero, trypsinogen is much greater than that to the model peptides. we suspected that Kd might be in fact zero. In this case, the ∗ ∗ One possible explanation for this result would be that the expressions of Km and kcat can be simplified to N-terminal aspartyl residues make an important contribution to k ∗ = k (17) the stabilization of the zymogen by forming hydrogen bonds or cat 2 salt linkages with other side chains of the protein. The binding of + 2+ ∗ (Kd [L])KS Ca to the N-terminal of zymogen disrupts this interaction and K = (18) m [L] results in exposure of the side chains, which provide an additional ‘docking site’ for trypsin binding, and therefore increase the ∗ The apparent turnover number kcat is independent of [L] and the binding affinity to trypsin. ∗ plot of Km against [L] is a descending curve. At very low [L] Most protein kinases share a common molecular organization ∗ values the plot approaches the Km axis, and at very high [L] values composed of a regulatory or inhibitory domain and a catalytic it approaches a limiting value, KS . A straight line will be obtained kinase domain having many of the conserved features. The ∗ if Km is plotted against 1/[L] as shown in the inset of Figure 2. holoenzymes are usually in an inactive or basally activated state, When the experimental data of Figure 2 were fitted to eqn (18), and cellular activation of protein kinases occurs as a result of a remarkable correspondence was observed. The continuous line conformational changes induced by binding of regulatory ligands, in Figure 2 represents the best fit of the experimental data to eqn such as cyclic nucleotides, Ras, Rho, Ca2+/calmodulin or cyclin, or = + = + (18), yielding KS 5.96 − 0.5 µMandKd 61.67 − 8.96 mM. phosphorylation by upstream protein kinases [27,28]. Although Since KS, KS , Kd and Kd are the true dissociation constants, our the events which trigger activation of protein kinases are quite data suggest that the binding affinity for Ca2+-bound trypsinogen variable, a common molecular mechanism has been proposed to trypsin is at least two orders of magnitude higher than that for [29]. A key feature in control of kinase enzymic activity is 2+ Ca -free trypsinogen. It is to be noted that Kd KS = KdKS when a regulated interaction between the inhibitory domain and the ∗ Kd is very small and KS very large, and the enzyme E can only catalytic kinase domain. The regulatory ligands bind to the in- bind to EL to form the ternary complex E∗EL, i.e. E∗ cannot form hibitory domain and disrupt this interaction, thereby relieving the complex E∗E, and the mechanism can be written as shown in initial inhibition of the kinase. The conformational changes at Scheme 2. the active site will result in increased accessibility to MgATP, a protein substrate. With some protein kinases, binding of ligand DISCUSSION to the regulatory domain can stimulate autophosphorylation of the catalytic domain, and the autophosphorylation is required As mentioned above, calcium ions have two diametrically to fully activate the enzyme. For example, PAK1 (p21-activated opposite effects on trypsinogen. They markedly increase hydro- protein kinase 1) exists in a closed conformation in the absence lysis of the Lys–Ile bond near the N-terminus of the chain and of Cdc42 due to an interaction between the inhibitory domain and almost totally suppress hydrolysis of certain other linkages, which the kinase domain [30]. The binding of Cdc42 to the inhibitory in the absence of calcium are responsible for conversion of the domain leads to a conformational change. The conformational precursor into inert proteins. The Lys–Ile bond in the inert proteins change withdraws the inhibitory domain from the cleft of the is not split by trypsin even in the presence of calcium. This double kinase domain and releases the activation loop. The activation effect is due to the binding of the calcium at two different sites. loop contains one critical phosphorylation site, Thr-423. In the The high-affinity Ca2+-binding site in trypsin was first identified absence of phosphorylation, this loop is either disordered or in a and described in detail by Bode and Schwager [25] based on conformation that is not optimal for catalysis. Cdc42-stimulated analysis of crystal structure and the Ca2+ content of their crystal. autophosphorylation of Thr-423 in the activation loop will activate Trypsinogen and trypsin have an apparently identical specific site the enzyme. Therefore, the kinetic analysis described here is also for Ca2+ [21]. The binding of Ca2+ on this site induces a structural applicable to study the ligand-induced autophosphorylation of change and stabilizes protein towards thermal denaturation or protein kinases. autolysis, but it is not essential for enzyme activity of trypsin. A second Ca2+-binding site exists only on the zymogen. This binding This work was supported in part by grants from NIH (R03TW01501), Natural Science site is on the two N-terminal aspartyl residues of trypsinogen, Asp- Foundation of China (30270327) and the Ministry of Science and Technology of China 13 and Asp-14. Binding of calcium at this site does not seem to (G1999075606). involve any structural reorganization and has no effect on the rate of formation of inert proteins, but it is required for complete and REFERENCES efficient activation of trypsinogen [16]. There is no corroborative 1 Cohen, P. (1976) Control of Enzyme Activity, John Wiley and Sons, New York 2+ crystallographic evidence as yet, since Ca was excluded from 2 Smith, J. A., Francis, S. H. and Corbin, J. D. (1993) Autophosphorylation: a salient the crystallizing solution [26]. feature of protein kinases. Mol. Cell. Biochem. 127/128, 51–70 + With trypsinogen, when the concentration of Ca2 increases 3 Hadorn, B. (1974) Pancreatic proteinases; their activation and the disturbances of this ∗ ∗ from 2.5 to 50 mM, Km decreases by a factor of 11 and kcat mechanism in man. Med. Clin. North Am. 58, 1319–1331

239 c 2004 Biochemical Society 702 J.-H. Liu and Z.-X. Wang

4 Malcinski, G. M. and Bryant, S. W. (1984) Pattern Formation: a Primer in Developmental 19 Wang, S. S. and Carpenter H. (1968) Kinetic studies at high pH of the trypsin-catalyzed Biology, Macmillan, New York hydrolysis of N-α-benzoyl derivatives of L-arginamide, L-lysinamide, and 5 MacDonald, H. R. and Nabholz, M. (1986) T-cell activation. Annu. Rev. Cell Biol. 2, S-2-aminoethyl-L-cysteinamide and related compounds. J. Biol. Chem. 243, 231–253 3702–3710 6Muller-Eberhard,¨ H. J. (1988) Molecular organization and function of the complement 20 Colomb, E. and Figarella, C. (1979) Comparative studies on the mechanism of activation system. Annu. Rev. Biochem. 57, 321–347 of the two human trypsinogens. Biochim. Biophys. Acta 571, 343–351 7 Neurath, H. and Walsh, K. A. (1976) The role of proteases in biological regulation. In 21 Delaage, M. and Lazdunski, M. (1967) The binding of Ca2+ to trypsinogen and Proteolysis and Physiological Regulation (Ribbons, E. W. and Brew, K., eds.), pp. 29–40, its relation to the mechanism of activation. Biochem. Biophys. Res. Commun. 28, Academic Press, New York 390–394 8Loffler,¨ G. and Petrides, P. E. (1988) Physiologische Chemie, pp. 832–843, Springer, 22 Delaage, M., Desnuelle, P. and Lazdunski, M. (1967) On the activation of trypsinogen. Berlin A study of peptide models related to the N-terminal sequence of the zymogen. 9 Thornberry, N. A. and Lazebnik, Y. (1998) Caspases: enemies within. Science 281, Biochem. Biophys. Res. Commun. 29, 235–240 1312–1316 23 Radhakrishnan, T. M., Walsh, K. A. and Neurath, H. (1967) Relief by modification of 10 Smith, W. L. and Borgeat, P. (1985) The eicosanoids: prostaglandins, thromboxanes, carboxylate groups of the calcium requirement for the activation of trypsinogen. leukotrienes, and hydroxy-eicosaenoic acids. In Biochemistry of Lipids and Membranes J. Am. Chem. Soc. 89, 3059–3061 (Vance, D. E. and Vance, J. E., eds.), pp. 325–360, Benjamin-Cunnings, Menlo Park, CA 24 Garc´ıa-Moreno, M., Havsteen, B. H., Varon,´ R. and Rix-Matzen, H. (1991) Evaluation 11 Tans, G., Rosing, J., Berrettini, M., Lammle, B. and Griffin, J. H. (1987) Autoactivation of of the kinetic parameters of the activation of trypsinogen by trypsin. Biochim. human plasma prekallikrein. J. Biol. Chem. 262, 11308–11314 Biophys. Acta 1080, 143–147 12 Karlson, P. (1988) Biochemie, 13th edn, pp. 160–161, Georg Thieme Verlag, Stuttgart 25 Bode, W. and Schwager, P. (1975) The single calcium-binding site of crystallin bovin 13 Tans, G., Rosing, J. and Griffin, J. H. (1983) Sulfatide-dependent autoactivation of human beta-trypsin. FEBS Lett. 56, 139–143 blood coagulation Factor XII (Hageman Factor). J. Biol. Chem. 258, 8215–8222 26 Kossiakoff, A. A., Chambers, J. L., Kay, L. M. and Stroud, R. M. (1977) Structure of 14 Wu, J. W., Wu, Y. and Wang, Z. X. (2001) Kinetic analysis of a simplified scheme of bovine trypsinogen at 1.9 A˚ resolution. Biochemistry 16, 654–664 autocatalytic zymogen activation. Eur. J. Biochem. 268, 1547–1553 27 Taylor, S. S., Knighton, D. R., Zheng, J., Ten Eyck, L. F. and Sowadski, J. M. (1992) 15 Wang, Z. X. and Wu, J. W. (2002) Autophosphorylation kinetics of protein kinases. Structural framework for the protein kinase family. Annu. Rev. Cell Biol. 8, 429–462 Biochem. J. 368, 947–952 28 Norbury, C. and Nurse, P. (1992) Animal cell cycles and their control. Annu. 16 Abita, J. P., Delaage, M. and Lazdunski, M. (1969) The mechanism of activation of Rev. Biochem. 61, 441–470 trypsinogen. The role of the four N-terminal aspartyl residues. Eur. J. Biochem. 8, 29 Kemp, B. E., Parker, M. W., Hu, S., Tiganis, T. and House, C. (1994) Substrate and 314–324 pseudosubstrate interactions with protein kinases: determinants of specificity. 17 Laidler, K. J. and Bunting P. S. (1973) The Chemical Kinetics of Enzyme Action, 2nd edn, Trends Biochem. Sci. 19, 440–444 pp. 73–74, Oxford University Press, Oxford 30 Lei, M., Lu, W., Meng, W., Parini, M. C., Eck, M. J., Mayer, B. J. and Harrison, S. C. 18 Walsh, K. A. (1970) Trypsinogens and trypsins of various species. Methods Enzymol. 19, (2000) Structure of PAK1 in an autoinhibited conformation reveals a multistage activation 41–63 switch. Cell 102, 387–397

Received 8 September 2003/26 November 2003; accepted 23 December 2003 Published as BJ Immediate Publication 5 January 2004, DOI 10.1042/BJ20031365

c 2004 Biochemical Society 240 Biochem. J. (2004) 382, 433–440 (Printed in Great Britain) 433

Thermal and conformational stability of Ssh10b protein from archaeon Sulfolobus shibattae Su XU, Sanbo QIN and Xian-Ming PAN1 National Laboratory of Biomacromolecules, Institute of Biophysics, Academia Sinica, Beijing 100101, China

The secondary structure of the DNA binding protein Ssh10b is mol residue−1), was obtained from the measured thermodynamic largely unaffected by change in temperature between 25 ◦Cand parameters. This is signiﬁcantly smaller than that of the average 85 ◦C, indicating that the protein is highly thermostable. Here, value for mesophilic proteins (50 J · K−1 · mol residue−1)or we report the temperature-dependent equilibrium denaturation of the value calculated from the Ssh10b structural data (64 J T−1 · −1 Ssh10b in the presence of guanidine hydrochloride (GdnHCl). It mol residue ). A consequence of the small Cp is that the G of was found that the transition midpoint values of the temperature Ssh10b is larger than that of mesophilic proteins, while the values ∗ (T m), and changes of enthalpy (Hm) and entropy (Sm)of of H and T S are smaller. The small Cp of Ssh10b appears to Ssh10b unfolding were linearly decreasing with increasing result mainly from the presence of compactness in the denatured GdnHCl concentration. The true values of the thermodynamic state. = = + · −1 = parameters, T m 402 K, Hm 590 − 40 kJ mol and Sm 1.4 −+ 0.15 kJ · T−1 · mol−1, were obtained by linear extrapolation Key words: compact denatured state, enthalpy change, entropy to 0 M GdnHCl. The value of the heat capacity change of Ssh10b change, equilibrium denaturation, hyperthermophilic protein, = + · −1 · −1 −1 · unfolding, Cp 3.8 − 0.2 kJ T mol (approx. 19 J T thermodynamic parameters.

INTRODUCTION ded and unfolded states to flatten the stability curve; or (3) by shifting the stability curve toward higher temperature [9,10]. Com- Hyperthermophiles constitute a group of micro-organisms with parison of the change in free energy upon unfolding (G)versus an optimum growth temperature of between 80 ◦C and 100 ◦C. temperature (T) curves for mesophilic, thermophilic and hyper- They are generally found close to the root of the phylogenetic tree, thermophilic proteins demonstrates that thermophilic and which suggests that they preceded their mesophilic counterparts hyperthermophilic proteins use various combinations of these in the course of evolution [1–3]. Proteins isolated to date from the three mechanisms to reach their superior thermodynamic stabil- hyperthermophiles are composed of the 20 common amino acids. ities [3]. For example, the greater protein stability and resistance Furthermore, homologous hyperthermophilic and mesophilic to higher temperature of Sac7d [11] and Sso7d [12] were found to proteins typically show 40–85 % sequence similarity, and their stem from an increase in stability at all temperatures, with a three-dimensional structures are superimposable [3]. Hyper- broader maximum, as compared with their mesophilic homo- thermophilic proteins show considerable thermal stability and logues (mechanisms 1 and 2, above). The thermophilic homologue thereby provide important models for the investigation of funda- of phosphoglycerate kinase [9,10] is stabilized by a small Cp mental problems in structure biology, such as the stability (mechanism 2). The maximum stability of cytochrome c-552 and folding of proteins [4–7]. However, although a number of [9,10] and cold-shock protein (CspTm) [13] is increased and hyperthermophilic and thermophilic proteins have been purified shifted to higher temperature compared with their mesophilic and compared with their mesophilic counterparts, progress in homologues (mechanisms 1 and 3). In the case of glutamate de- understanding the physicochemical basis for the stability of hydrogenase from the hyperthermophile Thermotoga maritima extremely thermophilic proteins has been hampered by the very [15], interdomain interactions play a significant role in its en- limited structural and thermodynamic data available [8]. Attempts hanced stability (mechanism 1). Deutschman and Dahlquist [22] to obtain thermodynamic information about thermostable pro- found that changes in both H and Cp are important contri- teins have been plagued by irreversibility of unfolding and/or in- butors to the thermal stability of TmY as compared with BsY accessibility of the unfolding transition to physical measurement. (mechanisms 1 and 2). Hence, studies of the thermodynamic stability of thermophilic and The free energy of stabilization, G = H − T ∗S,ofa hyperthermophilic proteins have been reported for only a few protein is the difference between the free energy of the folded select examples [9–25]. and the unfolded states of that protein, where H = H0 + 0 0 0 0 0 It has been shown that a higher transition temperature (T)ina Cp(T − T ); S = S + Cp ln(T/T ); H and S are hyperthermophilic protein could be obtained by three theoretical the standard enthalpy and entropy of unfolding at T 0 = 298 K mechanisms: (1) by shifting the stability curve to increase the respectively; and Cp is the heat capacity change between the overall unfolding free energy at any temperature; (2) by decreas- native and unfolded states of the system. The Cp is relatively ◦ ing the heat capacity change of unfolding (Cp) between the fol- independent of temperature within the range 20–80 C [26].

Abbreviations used: ASA ap, the change in solvent-accessible surface area on unfolding of apolar groups; ASA pol, the change in solvent-accessible surface area on unfolding of polar groups; cal, calculated; Cp, change in heat capacity upon unfolding; DLS, dynamic light scattering; ex, experimentally determined; G, change in free energy upon unfolding; GdnHCl, guanidine hydrochloride; H, change in enthalpy upon unfolding; H0, standard enthalpy of unfolding at T 0 = 298 K; IPTG, isopropyl β-D-thiogalactoside; S, change in entropy upon unfolding (the addition of a subscript ‘m’ to any 0 0 parameter, e.g. Sm, indicates the transition midpoint value); S , standard entropy of unfolding at T = 298 K. 1 To whom correspondence should be addressed (email [email protected]).

241 c 2004 Biochemical Society 434 S. Xu, S. Qin and X.-M. Pan

0 0 Thus, H , S and Cp are the intrinsic parameters for for 10 min. The lysate was centrifuged at 6000 g for 15 min at describing the thermodynamic properties of protein folding. 4 ◦C. The supernatant was maintained at 80 ◦C for 20 min in Furthermore, these three macroscopic thermodynamic parameters a temperature controller (Huber CC130) and then centrifuged of protein folding have direct microscopic interpretations. H0 at 12 000 g for 15 min at 4 ◦C. Ammonium sulphate was added is the measurement of changes (at standard temperature 298 K) gradually to the supernatant to a final concentration of 70 % (w/v). in packing forces of side chains, while S0 reflects the numbers After centrifugation at 6000 g for 30 min at 4 ◦C, the precipitate of accessible conformational states between the native and the was dissolved in 5 ml of buffer A (20 mM Na2HPO4/NaH2PO4, unfolded states, including the contribution of solvent. Cp is pH 7.5, 1 mM EDTA) and dialysed against the same buffer. After the measurement of change in accessible surface area bet- centrifugation at 13 500 g, the sample was applied to an UNO ween the native and the unfolded states of the protein. A micro- S6 column (Biorad), which had been equilibrated in buffer A. scopic understanding of hyperthermophilic protein stability in Proteins were eluted with buffer B (20 mM Na2HPO4/NaH2PO4, terms of protein structure should compare the parameters H0, pH 7.5, 1 M NaCl, 1 mM EDTA) [27]. The concentrated sample 0 S and Cp of the hyperthermophilic protein with those of the was then dialysed against buffer A. The purity of protein was mesophilic protein. verified by SDS/PAGE. The DNA binding protein Ssh10b from the archaeon Sulfo- lobus shibattae, a member of the sac10b family, is conserved in most thermophilic and hyperthermophilic archaeal genomes Unfolding studies that have been sequenced to date. The protein constitutes approx. Unfolding of Ssh10b by GdnHCl was monitored by CD using 4–5 % of the cellular protein, binds double-stranded DNA without a Jasco-J720 spectropolarimeter. The CD signal in the region apparent sequence specificity and is capable of constraining 190–250 nm (far-UV CD) was monitored using a rectangular negative DNA supercoils in a temperature-dependent fashion. quartz cuvette with a pathlength of 1 mm. The temperature was ◦ This binding ability is weak at 25 C, but is enhanced substantially increased from 298 K to 358 K, monitored using a thermometer ◦ at 45 C or higher temperature. Ssh10b is a dimeric protein com- attached to the thermosatted cell holder. The samples containing posed of two identical subunits. The monomer of Ssh10b consists various concentrations of GdnHCl were equilibrated for 3–6 h of 97 amino acid residues with no disulphide bonds, and the pro- before experiments were performed. Samples were heated at 1 ◦C tein is highly thermostable [27]. The crystal structure of Ssh10b per minute from 25 ◦Cto85◦C in a cell sealed with parafilm reveals a mixed α/β structure comprising four β-strands and to prevent evaporation, while keeping the pressure relatively two α-helixes [28]. In the present study, we report the tem- constant. At the end of each experiment the samples were cooled perature-dependent equilibrium denaturation of Ssh10b in the to room temperature to check the reversibility. presence of guanidine hydrochloride (GdnHCl), monitored by CD spectra. We found that in the presence of GdnHCl, protein unfolding is fully reversible and the temperature of the unfolding Analysis of the denaturation data transition becomes accessible to physical measurement. The The thermodynamic properties of Ssh10b were calculated thermodynamic parameters, Hm, T m and Sm, for Ssh10b un- assuming a two-state denaturation process N ←→ 2U. Concen- folding were found to decrease with increasing GdnHCl concen- 2 k trations of the folded protein [N2] (in dimer units) and the tration. The true values for these thermodynamic parameters unfolded protein [U] (in monomer units) at different temperatures were obtained by linear extrapolation to 0 M GdnHCl. The or denaturant concentrations were calculated [29]: + · −1 · −1 value of Cp of Ssh10b unfolding is 3.8 − 0.2 kJ T mol , which is significantly smaller than that of the average value for y − yU + mUT [D] mesophilic proteins. Our results suggest that the small Cp of N = P / × [ 2] t 2 + − + (1) Ssh10b results from the presence of compactness in the denatured yN mNT [D] yU mUT [D] state. yN + mNT [D] − y [U] = Pt (2) yN + mNT − yU + mUT [D] MATERIALS AND METHODS where Pt is the total protein concentration in monomer units; y is Materials the experimentally measured signal value at a given temperature T or given denaturant concentration [D]; y and y ,arethein- GdnHCl was from Gibco BRL, IPTG (isopropyl β-D-thio- N U galactoside) from Merck, and foline phenol was from Sigma. The tercepts; and mN,andmU are the slopes of the native and unfolded ssh10b gene was provided by Professor Jinfeng Wang (Institute baselines, respectively. The apparent equilibrium constant (K)and of Biophysics, Academia Sinica, Beijing, China) and Professor the corresponding free energy change (G) at temperature T or Li Huang (State Key Laboratory of Microbial resources, Institute denaturant concentration [D] were calculated according to: of Microbiology, Chinese Academy of Sciences, Beijing, China) 2×P [y +m T [D]−y]2 [27]. K = t × N N (3) yN +mNT [D]−yU +mUT [D] y −yU +mUT [D] Protein purification G =−RT ln K (4) An overnight culture of Escherichia coli (BL21) cells containing the target plasmid was added to 1 litre of Luria–Bertani media plus where R is the gas constant and T is the absolute temperature. ampicillin (60 µg/ml) and incubated at 37 ◦C with shaking at According to the linear free energy model [30–33], the changes in

220 r.p.m. At D600 = 0.8, expression was induced with 1 mM free energy, enthalpy, and entropy changes that occur on unfolding IPTG. After an additional 3 h at 37 ◦C, the cells were harvested are expected to vary linearly with the denaturant concentration, by centrifugation (6000 g at 4 ◦C for 20 min). The cell pellet was [D]: then resuspended in 5 vol. of buffer (20 mM Na2HPO4/NaH2PO4, pH 6.8, 1 mM EDTA) and the cells were sonicated on ice at 40 W G = G(H2O) − mG[D] (5)

c 2004 Biochemical Society 242 Thermal and conformational stability of Ssh10b 435

H = H (H2O) − mH[D] (6)

S = S(H2O) − mS[D] (7)

where G(H2O), H(H2O) and S(H2O) represent the free energy, enthalpy and entropy changes of unfolding in the absence of denaturant; and mG, mH and mS are the slopes of the transition for the free energy, enthalpy and entropy changes respectively.

The midpoint of the transition (Cm), where 50 % of the protein was unfolded, is a function of protein concentration Pt:

RT ln(P ) = 0 + t Cm Cm (8) mG where C0 = G(H2O) is the transition midpoint at protein concen- m mG tration Pt = 1 M. For thermal unfolding, assuming that the heat capacity change (Cp) between the native and unfolded states of the system is relatively independent of temperature within the range of the transition, then [34,35]: Figure 1 CD spectra of 50 µM Ssh10b protein in phosphate buffer at pH 6.8 Line 1, native protein measured at 25 ◦C; line 2, native protein measured at 85 ◦C; line 3, G(T ) =−RT ln(K) denatured protein in 6 M GdnHCl measured at 25 ◦C; line 4, denatured protein in 6 M GdnHCl measured at 85 ◦C; line 5, Ssh10b protein denatured in 7 M GdnHCl and then refolded by µ = H − TS + C (T − T ) 10-fold dilution to give final concentrations of 0.7 M for denaturant and 50 M for protein; m m P m line 6, Ssh10b protein denatured in 3.5 M GdnHCl at 85 ◦C and then refolded by re-equilibrating to 25 ◦C and diluting 7-fold to give final concentrations of 0.5 M for denaturant and 50 µMfor T − T protein. + T ln 1 − m (9) T Here k is the Boltzmann’s constant, T is the absolute tem- where Hm,andSm are the enthalpy and entropy changes, perature and η is the solvent viscosity. The hydrodynamic radius respectively, at the transition midpoint, where T = T . Within m RH of the protein was calculated using the native protein (in 0.5 M − T − Tm ≈ − the transition range, where T ln(1 T ) Tm T from Eq- GdnHCl) as a reference molecule: uation 9 can be simplified to the van’t Hoff plot: Rcal(N) = ex H Sm Hm RH RH ex (13) ln(K) = − (10) RH (N) R RT ex where RH (N) is the experimentally determined hydrodynamic The temperature of the transition midpoint (T m) is a function of cal radius of the native protein and RH (N) is the calculated hydro- the protein and denaturant concentration, as follows: dynamic radius of the native protein dimer. The theoretical hydrodynamic radius of the native and fully − Hm Hm(H2O) mH[D] denatured protein were calculated according to the method of Tm = = (11) Sm − R ln(Pt) Sm(H2O) − mS[D] − R ln(Pt) Wilkins et al. [36]:

+ Rcal = (4.75 −+ 1.11)N0.29−0.02 (14) Hydrodynamic radius measurements H Dynamic light scattering (DLS) measurements were performed for native protein (dimer) and: at a protein concentration of 10 mg/ml at pH 6.8 at various con- cal = + 0.57−+0.02 centrations of GdnHCl. Before the DLS measurements, the solu- RH (2.21 − 1.07)N (15) tions were centrifuged at 14 000 g for 10 min. All experiments ◦ were performed at a 90 scattering angle on a DynaPro-LSR for fully denatured protein (monomer), where N is the number of (Protein Solution, Charlottesville, VA, U.S.A.) at a wavelength residues in the protein. of 781.8 nm. During the measurements, the temperature was The compaction factor C is defined as [36]: maintained at 20 ◦C using a built-in temperature controller. The = − − diffusion coefficient (D) was calculated from the autocorrelation C [RH(D) RH]/[RH(D) RH(N)] (16) function, using the accessory software DYNAMICS provided with the instrument. Since the structure of the protein does where RH(D)andRH(N) represent the predicted hydrodynamic not change at GdnHCl concentrations lower than 4 M, and the radii of the fully denatured and native protein, respectively. viscosity of GdnHCl solutions differs significantly from that of D pure water, the diffusion coefficient was corrected not to pure RESULTS water, but to 0.5 M GdnHCl. The experimentally measured hydro- ex dynamic radius, RH , of the protein was determined from the Denaturant-induced unfolding Stokes–Einstein relationship [36]: Figure 1 shows typical CD spectra of the native protein, consistent with the native CD spectrum of Ssh10b reported previously [27], kT ◦ ◦ Rex = (12) measured at 25 C and pH 6.8 (Figure 1, line 1) and 85 C(Fig- H 6πηD ure 1, line 2). The spectra are nearly identical, indicating that the

243 c 2004 Biochemical Society 4

436 S. Xu, S. Qin and X.-M. Pan

Table 1 Thermodynamic parameters derived from GdnHCl denaturation for the conformational stability of Ssh10b

Protein concentration, P t = 50 µM.

−1 −1 −1 T (K) G(H2O) (kJ · mol ) mG (kJ · mol · M ) Cm*(M)

288 128 20 4.9 293 131 21 4.85 298 126 23 4.3 318 137 24 4.19 338 102 21 3.5 348 83 19 2.93 353 55 12 2.12 358 49 11 1.68 * Calculated according to equation 8.

Figure 2 GdnHCl induced unfolding curves ◦ ◦ ◦ The concentration (P t) of Ssh10b was 50 µMatpH6.8at15 C(ᮀ), 20 C(᭺), 25 C(᭛), 45 ◦C(᭝), 65 ◦C(᭞), 75 ◦C(᭹), 80 ◦C(᭿) and 85 ◦C(). The inset shows the protein concentration dependence of unfolding at 7 µM(᭿), 50 µM(᭹) and 70 µM(). protein is thermally stable up to 85 ◦C. Upon incubation in 8 M urea for 24 h, Ssh10b underwent no reduction in backbone CD signal (results not shown), indicating that Ssh10b is resistant to urea-induced denaturation. At 25 ◦C and pH 6.8 in 6 M GdnHCl, Ssh10b loses approx. 80% of its CD signal (Figure 1, line 3). The CD spectrum of the denatured protein measured at 25 ◦Cwas found to undergo no further change when the concentration of GdnHCl was increased to 8 M, or when the pH was varied between 2 and 10 (results not shown). The fact that the CD spectra do not change with further changes in the denaturing conditions, suggests that the residual structure may not be native-like structure, but rather an ensemble of compact states. The CD signal of the 6 M Figure 3 The unfolding free energy of Ssh10b (G) versus temperature (T) GdnHCl denatured protein increases with increasing temperature Inset shows the unfolding m value of Ssh10b versus temperature. The concentration (Pt)of (Figure 1 line 4), implying that there is more residual structure Ssh10b was 50 µM. at higher temperature. A similar phenomenon was observed in denaturation of Sac7d [11], but the reason remains unclear. the presence of different concentrations of GdnHCl. At pH 6.8, GdnHCl-induced unfolding of Ssh10b was studied at pH 6.8, ◦ ◦ at several constant temperatures between 15 ◦C and 85 ◦C, by increasing the temperature from 25 Cto85 C in the presence of measuring far-UV CD at 222 nm (Figure 2). The transitions were GdnHCl results in unfolding of the protein by an apparent two- characterized by a single sharp change in the ellipticity that looks state mechanism (Figure 4). In certain cases, although the unlike a typical two-state transition. The observed denaturation mid- folding curve of a protein shows a single observable step, the point decreases with increasing temperature (Table 1), indicating transition may involve intermediates. Computer simulation of a decrease in the free energy of unfolding with increasing temp- the Ssh10b experimental data could be fitted to both 2-state and erature. As shown in the inset to Figure 2, protein concentration 3-state equations within experimental error. However, the 3-state dependence of the transition curves was observed at GdnHCl con- values of G(H2O) and Hm are only approx. 10% larger than centrations between 3 and 4.5 M, but a much smaller protein those obtained by 2-state fitting. Thus, the choice of model does concentration dependence was seen at GdnHCl concentrations not significantly affect the thermodynamic parameters obtained. The values obtained by fitting to a two-state model were used higher than 4.5 M. The free energy of unfolding, G(H2O), and the m value for the GdnHCl-induced unfolding curve were in the subsequent analysis. obtained from the fit to Equation 9. As shown in Figure 3, The van’t Hoff plots (Figure 4, inset) demonstrate a good linear relationship between ln(K) and 1/T for each of the GdnHCl G(H2O) and the m value increased slightly with increasing temperature between 15 ◦C and 45 ◦C, then reached a maximum, concentrations measured. The slope of the van’t Hoff plot is before starting to decrease with further increase in temperature. Hm/R and the intercept is Sm/R (Equation 10). The values of Hm and Sm thus obtained are observed to decrease linearly with increasing GdnHCl concentration (Figure 5), as expected (Equations 6 and 7). Linear extrapolation to zero GdnHCl con- Heat-induced unfolding in the presence of different = + · −1 = centration gives the values Hm 590 − 40 kJ mol and Sm concentrations of GdnHCl − − 1.4 −+ 0.15 kJ · K 1 · mol 1. ◦ As Ssh10b is thermally stable up to 85 C (Figure 1, lines 1 and The observed unfolding transition temperature, T m, also appears 2), the thermal unfolding of the protein was carried out in to decrease linearly with increasing GdnHCl concentration

c 2004 Biochemical Society 244 Thermal and conformational stability of Ssh10b 437

Figure 6 The reconstructed stability curves for Ssh10b and Arc dimmer

Solid lines are for Ssh10b (a–c) and broken lines are for Arc repressor (1–3). (a,1) G versus T.(b,2) H versus T.(c,3) S*T versus T.

Figure 4 Temperature dependence of ellipticity at 222 nm at pH 6.8 of Ssh10b in the presence of different concentrations of GdnHCl

(a) 2.5 M GdnHCl, (b) 3.0 M GdnHCl, (c) 3.3 M GdnHCl, (d) 3.5 M GdnHCl, (e) 4.0 M GdnHCl, (f) 4.3 M GdnHCl, (g) 5.0 M GdnHCl, (h) 6.0 M GdnHCl, (i) 7.0 M GdnHCl. The inset shows the plots of ln(K) versus 1/T.

Figure 7 The GdnHCl concentration dependence of the hydrodynamic radius of Ssh10b

The protein concentration was 10 mg/ml at pH 6.8. The DLS measurement was performed at 20 ◦C. The data shown are corrected for the solution viscosity.

(402 K). Thus, the results are not influenced by the model chosen. = + · The value of the heat capacity change, Cp 3.8 − 0.2 kJ −1 −1 K · mol , was obtained by fitting the G(H2O) values to −1 Equation 9 using T m = 398 K, Hm = 590 kJ · mol and Sm = 1.4 kJ · T−1 · mol−1. There are no structural or thermodynamic data currently available for a mesophilic homologue of Ssh10b. Therefore, the Arc repressor was chosen as a suitable example of a typical mesophilic protein that has been well-characterized [37]. The Arc repressor is a dimeric DNA binding protein with 53 residues per monomer, and is thus the closest to Ssh10b in size, structure and function among the mesophilic proteins for which thermodynamic Figure 5 The GdnHCl concentration dependence of the (A) enthalpy parameters have been determined. Figure 6 shows a comparison change, Hm, (B) entropy change, Sm, and (C) melting temperature, T m, of the calculated stability curves for Ssh10b (solid lines) and of Ssh10b Arc repressor (broken lines). (The plots of G versus T, H ∗ The broken line in (C) was calculated using Equation 11 with the values Hm = versus T and T S versus T for Arc repressor were constructed −1 −1 −1 −1 −1 590 kJ · mol , mH = 104 kJ · mol · M , S m = 1.4 kJ · K · mol and mS = 0.26 kJ · from the published thermodynamic parameters [37] as follows: K−1 · mol−1 · M−1. −1 −1 −1 T m = 327 K, Hm = 284 kJ · mol , Cp = 6.4 kJ · K · mol and S = 0.78 kJ · K−1 · mol−1). ◦ m (Figure 5C), giving an extrapolated value of T m = 402 K (129 C) in the absence of denaturant. According to Equation 11, the depen- Hydrodynamic radius measurements in the presence GdnHCl dence of the T m value on denaturant concentration is expected to show curvature (broken line in Figure 5C). The T m was also The hydrodynamic radius of Ssh10b as a function of GdnHCl calculated according to Equation 9 using the following values: concentration is shown in Figure 7. A single transition is observed −1 −1 −1 Hm = 590 kJ · mol , mH = 104 kJ · mol · M , Sm = 1.4 kJ · in the range 4–5 M GdnHCl, which is in good agreement with −1 −1 −1 −1 −1 K · mol , mS = 0.26 kJ · K · mol · M and Pt = 50 µM. The the CD results (Figure 2). The average hydrodynamic radius T m value obtained by this calculation is 398 K, which is in of the denatured protein is approx. 2.57 nm, which is significantly good agreement with the value obtained by linear extrapolation smaller than the predicted value of 3.05 nm (Equation 15). The

245 c 2004 Biochemical Society 6

438 S. Xu, S. Qin and X.-M. Pan compaction factor (Equation 16) is approx. 57%, indicating that It has also been suggested that protein stability is determined the denatured state is non-random and compact, possibly an en- by the stability and tight packing of the hydrophobic core. The semble of compact structures. helices of thermophilic proteins are observed to contain a lower content of β-branched residues (valine, isoleucine and threonine), Reversibility which leads to greater stability of the helices of thermophilic proteins compared with those of mesopholic proteins [40]. The Reversibility of GdnHCl-induced unfolding was confirmed by structure of the Ssh10b monomer reveals a mixed α/β structure diluting protein denatured in GdnHCl concentrations of 2.5 M to comprising four β-strands and two α-helices (Protein Database 8 M and comparing the CD spectrum with that for the native pro- code 1h0x). The two α-helices in Ssh10b consist of approx. 15% tein. Figure 1 (line 5) shows a typical CD spectrum for the 10-fold valine, 7.7% threonine and 7.7% isoleucine, similarly to the dilution of 7 M GdnHCl denatured protein. Reversibility of heat- β-branched residue content of mesophilic proteins, suggesting induced unfolding in the presence of GdnHCl was confirmed by that this is not a stabilization mechanism in the case of Ssh10b comparing the CD signal at 222 nm after cooling the samples to ◦ also. On the other hand, the Ssh10b structure is stabilized by four 25 C. Figure 1 (line 4) shows a typical CD spectrum after heat- ◦ salt bridges and an ion-pair network involving four residues, and induced unfolding at 85 C in the presence of 3.5 M GdmHCl, ◦ thus the number of ion pairs in Ssh10b is clearly higher than followed by re-equilibration at 25 C and 7-fold dilution. The the average value, which is approx. 5 per 150 residues of protein refolded protein after thermal cycling was found to be identical [41]. This is a common feature of proteins from hyperthermostable to native protein by SDS/PAGE, implying that no deamidation organisms, and appears to be an important contributing factor to occurred during the thermal cycling. the remarkable stability of Ssh10b. The free energy of stabilization, G (where G = H − ∗ DISCUSSION T S), of a protein is the difference between the free energy of the folded and the unfolded states of that protein. As a protein The function of the Ssh10b protein is to compact and regulate the folds it loses considerable entropy, which must be balanced by availability of the genetic material in thermophilic archaea at their a gain of enthalpy for the free energy to favour folding. It is growth temperature, which is as high as 85 ◦C. The protein is very interesting to note that the G per residue of Ssh10b is higher than stable at ambient temperature (G = 126 kJ · mol−1 at 25 ◦C) and that of the mesophilic Arc repressor protein at any temperature, shows more typical stability at high temperature (G = 49 kJ · but the values of H and S per residue of Ssh10b are lower mol−1 at 85 ◦C). The protein has a weak ability to constrain DNA than these for the mesophilic protein at temperatures higher than ◦ −1 −1 in negative supercoils at 25 C, whereas this ability is greatly in- 298 K. This is because the Cp (19 J · K · mol · residue )of creased at 85 ◦C, supporting the speculative concept that there is Ssh10b is significantly smaller than that for the Arc repressor a trade-off between stability and activity [26,38,39]. Our results or for mesophilic proteins in general (the average value is demonstrate that the Ssh10b protein uses a combination of two around 50 J · K−1 · mol · residue−1 [42]). As a consequence of the mechanisms to increase its thermodynamic stability: (1) the free small Cp, the rate of increase in H and S of Ssh10b with energy of the Ssh10b protein is higher than that of a typical increasing temperature is more gradual than for mesophilic pro- mesophilic protein with similar functional properties (such as teins, especially in the case of the S values. This means that the Arc repressor) at any temperature, and 2) the stability curve of high thermal stability of the Ssh10b protein is due mainly to a the Ssh10b protein is more flat than that of a typical mesophilic low Cp value, as has been observed for other hyperthermophilic protein. proteins [8]. Ssh10b is a dimer in solution; some dimeric proteins show In general, the native state of a protein has many of its hydro- a 3-state denaturation curve, with population of monomeric or phobic side chains shielded from water because they are packed dimeric intermediates, while others follow a 2-state model [29]. within the hydrophobic core. Conversely, the hydrophobic side The experimental data suggest that the unfolding of Ssh10b chains of the denatured protein are exposed to solvent and the follows a 2-state transition, implying that the monomeric subunits water molecules stack around these in ‘icebergs’. This results in of Ssh10b are not significantly populated under the conditions of a decrease in the entropy of the denatured state and compensates the denaturation experiments. The X-ray structure shows that the partly for the conformational entropy decrease associated with monomer of Ssh10b is stabilized by several salt bridges and an ion- protein folding. The Cp of unfolding principally reflects the pair network, all of which are on the ‘back’ of the Ssh10b dimer. In melting of these icebergs. It has been shown that the Cp of the process of GdnHCl denaturation, the dissociation of the dimer unfolding is described by [43,44]: would expose these ion-pair residues to solution and destroy the = × − × · −1 · −1 interactions. This may explain why the monomeric subunits are Cp 0.45 ASAap 0.26 ASApol (cal degree mol ) not significantly populated during equilibrium denaturation in (17) GdnHCl.

Protein amino acid composition has long been thought to be where ASAap and ASApol are the change in solvent-accessible linked to thermostability. Statistical analysis comparing amino surface area on unfolding, for given apolar and polar groups acid composition in mesophilic and thermophilic proteins indicate respectively. The Dictionary of protein secondary structure: trends toward substitutions such as glycine → alanine and pattern (DSSP) file of Ssh10b (ih0x.dssp) [45] gives a ASAap 2 2 lysine → arginine [3]. The amino acid composition of Ssh10b value of 8952 Å (1 Å = 0.1 nm) and a ASApol value of 3409 Å , −1 −1 shows such trends to only a minor extent: the protein consists giving a Cp of 64.7 J · K · mol · residue .TheASA values of approx. 6.7% alanine and 8.2% arginine, compared with the shown refer to the dimer-to-coil transition, which assumes a average values for mesophilic proteins of 8.0% and 4.3% re- 2-state transition. However, as the area of the dimer interface spectively [3]. The known Ssh10b homologues share 35% to (1150 Å2 [28]) is only approx. 10% of the total surface area, 60% identity and 55% to 82% similarity at the amino acid se- population of the folded monomer during denaturation would not quence level [27]. Amino acid composition and sequence appears affect the conclusions drawn. not to be the most important stabilizating factor in the case of The calculated Cp is significantly larger than the measured Ssh10b. value. In general, a low Cp value reflects that the hydrophobic

c 2004 Biochemical Society 246 Thermal and conformational stability of Ssh10b 439 side chains in the native and the denatured states of the protein 6 Kelly, R. M., Peeples, T. L., Halio, S. B., Rinker, K. D. and Duffaud, G. D. (1994) Extremely are similarly accessible to the solvent water molecules. A mea- thermophilic microorganisms. Metabolic strategies, genetic characteriztics, and biotechnological potential. Ann. N.Y. Acad. Sci. 745, 409–425 sured Cp value lower than predicted implies either that some hydrophobic side chains remain relatively solvent-exposed in 7 Rees, G. C. and Adams, M. W. (1995) Hyperthermophiles: taking the heat and loving it. the native state or remain relatively buried in the denatured state. Structure 3, 251–254 8 Kumar, S., Tsai, C. J. and Nussinov, R. (2001) Thermodynamic differences among When hydrophobic side chains in the native protein structure are homologous thermophilic and mesophilic proteins. Biochemistry 40, 14152–14165 accessible to solvent water molecules, this implies the presence 9 Nojima, H., Ikai, A., Oshima, T. and Noda, H. (1977) Reversible thermal unfolding of of a cavity filled by water molecules within the core of the folded thermostable phosphoglycerate kinase. Thermostability associated with mean zero protein. This is unlikely to be the basis of the low value of Cp for enthalpy change. J. Mol. Biol. 116, 429–442 Ssh10b for the following reasons. (1) The cavity would need to be 10 Nojima, H., Ikai, A., Noda, H., Hon-nami, K. and Oshima, T. (1978) Thermodynamic unrealistically large (approx. 2/3 total surface area according to studies on reversible denaturation of thermostable proteins from an extreme thermophile. Equation 1). (2) Increasing the temperature should allow the water In Biochemistry of Thermophily (Friedman, S. M. Ed.), Academic Press, New York, molecules to escape from the cavity, which would perturb the pp. 305–323 protein structure. In contrast, the CD spectrum of Ssh10b indicates 11 McCrary, B. S., Edmondson, S. P. and Shriver, J. W. (1996) Hyperthermophile protein folding thermodynamics: differential scanning calorimetry and chemical denaturation of that no structural change takes place when the temperature is ◦ ◦ Sac7d. J. Mol. Biol. 264, 784–805 increased from 25 Cto85 C. (3) If the native state of Ssh10b 12 Knapp, S., Karshikoff, A., Berndt, K. D., Christova, P., Atanasov, B. and Ladenstein, R. contained ordered water molecules, then some of the entropic (1996) Thermal unfolding of the DNA-binding protein Sso7d from the hyperthermophile compensation of iceberg formation in the denatured state would Sulpholobus solfataricus.J.Mol.Biol.264, 1132–1144 be lost and a high S of unfolding would be predicted. As the S 13 Wassenberg, D., Welker, C. and Jaenicke, R. (1999) Thermodynamics of the unfolding of for Ssh10b is in fact lower than for the mesophilic Arc repressor, the cold-shock protein from Thermotoga maritima.J.Mol.Biol.289, 187–193 14 Backmann, J., Schafer,¨ G., Wyns, L. and Bonisch,¨ H. (1998) Thermodynamics and this therefore cannot explain the lower Cp of the thermophilic protein. kinetics of unfolding of the thermostable trimeric adenylate kinase from the archaeon As the presence of a water-filled cavity within the Ssh10b Sulpholobus acidocaldarius.J.Mol.Biol.284, 817–833 15 Consalvi, V., Chiaraluce, R., Giangiacomo, L., Scandurra, R., Christova, P., Karshikoff, A., structure seems unlikely, the low Cp is best explained by the Knapp, S. and Ladenstein, R. (2000) Thermal unfolding and conformational stability of presence of residual structure in the denatured state of Ssh10b. A the recombinant domain II of glutamate dehydrogenase from the hyperthermophile compact denatured state would explain why the Cp value is low Thermotoga maritima. Protein Eng. 13, 501–507 both in comparison to the average value for all mesophilic proteins 16 Jaenicke, R., Schurig, H., Beaucamp, N. and Ostendorp, R. (1996) Structure and stability and in comparison to the value calculated from the Ssh10b stru- of hyperstable proteins: glycolytic enzymes from hyperthermophilic bacterium ctural data. Experimental evidence in support of a compact de- Thermotoga maritime. Adv. Protein Chem. 48, 181–269 natured state ensemble for Ssh10b are as follows. (1) The CD 17 Pfeil, W., Gesierich, U., Kleemann, G. R. and Sterner, R. (1997) Ferredoxin from the spectra of denatured Ssh10b indicates compactness of the de- hyperthermophile Thermotoga maritima is stable beyond the boiling point of water. natured protein. (2) The compaction factor calculated from the J. Mol. Biol. 272, 591–596 18 Wassenberg, D., Schurig, H., Liebl, W. and Jaenicke, R. (1997) Xylanase XynA from the hydrodynamic radius measurements is approx. 57%, indicating hyperthermophilic bacterium Thermotoga maritima: structure and stability of the that the denatured state is non-random and compact, possibly recombinant enzyme and its isolated cellulose-binding domain. Protein Sci. 6, an ensemble of compact structures. (3) A compact denatured 1718–1726 state predicts that the folding entropy change, S, should be 19 Zaiss, K. and Jaenicke, R. (1999) Thermodynamic study of phosphoglycerate kinase smaller than that for a typical mesophilic protein, agreeing with from Thermotoga maritima and its isolated domains: reversible thermal unfolding the experimental observations. (4) As discussed above the number monitored by differential scanning calorimetry and circular dichroism spectroscopy. of ion pairs in Ssh10b is clearly higher than the average value. This Biochemistry 38, 4633–4639 is expected to lead to a high enthalpy of folding, H0 (298 K). 20 Motono, C., Yamagishi, A. and Oshima, T. (1999) Urea-induced unfolding and However, the H0 (298 K) for Ssh10b is smaller than that of a conformational stability of 3-isopropylmalate dehydrogenase from the thermophile typical mesophilic protein. This may reflect the presence of Thermus thermophilus and its mesophilic counterpart from Escherichia coli. Biochemistry 38, 1332–1337 stabilizing interactions in the ensemble of compact structures that 21 Fitter, J., Herrmann, R., Dencher, N. A., Blume, A. and Hauss, T. (2001) Activity and represent the denatured state. stability of a thermostable α-amylase compared to its mesophilic homologue: mechanisms of thermal adaptation. Biochemistry 40, 10723–10731 We express our sincere thanks to Professor C. L. Tsou of the Institute of Biophysics, 22 Deutschman, W. A. and Dahlquist, F. W. 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Received 4 February 2004/22 April 2004; accepted 23 April 2004 Published as BJ Immediate Publication 23 April 2004, DOI 10.1042/BJ20040191

c 2004 Biochemical Society 248