Supplementary Materials

Total Page：16

File Type：pdf, Size：1020Kb

supplementary materials Nonnative energetic frustrations in protein folding at residual level: a simulation study of homologous immunoglobulin-like β-sandwich proteins Running title: Energetic frustrations in β-sandwich proteins Key words: nonnative energetic frustration; non-native contact; frustrated Gō-like model; β- sandwich protein; hydrophilic-hydrophobic mutation Authors: Yunxiang Suna,b Feng Dingb and Dengming Minga* a College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, Jiangsu 211816, PR China, b Department of Physics and Astronomy, Clemson University, Clemson, South Carolina 29634, USA *Contact information: Dengming Ming Biotech Building Room B1-404 College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, 30 South Puzhu Road Jiangsu 211816, PR China Tel: 8625-58139942 Email: [email protected] Figure S1. Compare the conventional constant temperature folding (CTF) simulation with that of Variable Temperature Folding (VTF) simulation. A) CTF simulation of all-β sandwich domains HC19, B) VTF simulation of HC19, C) the free energy distribution of the two simulations as log inverse of distribution probability. Compared with CTF, VTF experiences double transition between the two states within the same number of simulation steps, and the resulted free energy landscape has a wider sampling distribution. A B C Figure S2. Comparison of residual ϕ-values (black) calculated using the conventional Gō-like minimal model and those (red) using the frustrated Gō-like model for the 9 -sandwich domains that have the same sequence except a single mutation; the difference in residual ϕ- value changes reveal, to some extent, how the different local environment of mutation-site affects the folding dynamics of the -sandwich structure. Figure S3. Comparison experimental residual ϕ-values with simulated ϕ-values for HC19 domain. The experimental residue index is derived through sequence-alignment. Figure S4. The contact maps of transition states for the 9 -sandwich domains. In each map, the upper left triangle is derived from the frustrated Gō-like model which is compared with the lower right triangle derived from the conventional Gō-like minimal model. .

Copy Link

Recommended publications

Xiaoqiang Chen DEVELOPING LIGHT- RESPONSIVE DRUG CARRIERS and DIAGNOSTIC SENSORS
Developing Light- Responsive Drug Carriers and Diagnostic Sensors Dr Xiaoqiang Chen DEVELOPING LIGHT- RESPONSIVE DRUG CARRIERS AND DIAGNOSTIC SENSORS Delivering drugs to their target site and conducting medical diagnostics non-invasively are two major goals of biomedical researchers across the globe. Dr Xiaoqiang Chen and his team of scientists at Nanjing Tech University in China are developing advanced materials and procedures that can keep drugs protected before they reach their target site in the body. The group is also developing materials that can be used to detect certain substances in the body, towards providing non-invasive diagnostic tools for clinicians. Drug Delivery and Diagnostics in a more controlled manner at its intended site. At the same time, the Developing new ways of administering team is also developing biological drugs to where they are required in sensors that can monitor cell activity in the body is a challenging pursuit. For a non-invasive manner. instance, drug molecules not only need to reach their target site, but must also Central to Dr Chen’s research is the be protected in order to survive the study of how light interacts with body’s natural defences along the way. molecules. In his drug delivery research, The search for new materials that can he employs UV as an energy source to transport drugs safely to their target is break molecular bonds, allowing drug Dr Chen’s team investigated how current thus an active field of research. molecules to be released on cue. In light-based sensors, some of which his team’s diagnostic research, they have limited detection ranges, could Similarly, countless researchers are also utilise excited light to cause biological be improved.
[Show full text]
Enzymes Are Nature's Catalysts, Featuring High Reactivity, Selectivity
************************* Report Title************************************* Dr. Yao Chen Full Professor personal State Key Laboratory of Medicinal photograph Chemical Biology College of Pharmacy Nankai University Tianjin, China 300071 Phone: 01186-18222132527 E-mail: [email protected] Abstract Enzymes are nature’s catalysts, featuring high reactivity, selectivity, and specificity under mild conditions. Enzymatic catalysis has long been of great interest to chemical, pharmaceutical, and food industries. However, the use of enzymes for industrial applications is often handicapped by their low operational stability, difficult recovery, and lack of reusability under operational conditions. Immobilization of enzymes on solid supports can enhance enzyme stability as well as facilitate separation and recovery for reuse while maintaining activity and selectivity. As new classes of crystalline solid- state materials, porous frameworks materials (such as covalent-organic frameworks, COFs and metal-organic frameworks, MOFs) feature high surface area, tunable pore size, high stability, and easily tailored functionality, which entitle them as ideal supports for encapsulation of biomolecules to form novel composite materials for various applications. Our researches mainly focus on their biocatalysis, biomimetic and medicinal applications. This novel platform based on those biomolecule-incorporation composite materials exhibited various functionality and superior separation efficiency, biocatalytic performances and great potentials on biopharmaceutical formulations. Brief Biography Dr. Yao Chen obtained master degree from Nanjing Tech University, then obtained Ph.D degree from University of South Florida. After finished a posdoc training at UC San Diego, she moved back to China, and is now a full professor of State Key Laboratory of Medicinal Chemical Biology and College of Pharmacy at Nankai University. Her research interest mostly focuses on incorporating biomolecule into porous supports (e.g.
[Show full text]
PLENARY SESSIONS PROGRAMME 15:40 Building Relationships with China in Research and Education D
MONDAY, OCTOBER 22nd 2018 14:00 Welcome and Opening Session Taihua Mu, Prof. (CAAS, China), Lujia Han, Prof. (CAU, China) Up-Cycling N. Gontard, Prof. (INRA, France), S. Ward, Prof. (UCD, Ireland) Agricultural Session A1. Circular Economy in EU and China: Shared Cooperation Priorities, Co-funding Residue into Mechanisms, Policies and Implementation Bio-Products 14:20 Introduction of the Situation in China-EU Cooperation Project Application Keqin Dong, Ministry of Science and Technology, China 14:40 Government Policy and National Practice for Promoting the Recycling Utilisation of Waste in China Zhenhai Yang, Ministry of Agriculture and Rural Affairs, China 15:00 European Policy in Relation to the Circular Economy J. Ruiz, Dr, tbc, Research Policy Officer, DG Agriculture and Rural Development, European Commission 15:20 INRA’s Policy to Strengthen Collaboration between France and China tbc, INRA, France PLENARY SESSIONS PROGRAMME 15:40 Building relationships with China in Research and Education D. O’Riordan, Prof.,Vice-President for Global Engagement, Univ. College Dublin, Ireland 16:00 Cooperation between China & EU in Agriculture: the 13thFive-Year Period Agricultural waste and residue management for a circular Xifeng Gong, Dr., Department of International Cooperation, CAAS, China bio-economy: Shared EU and China impact-oriented 16:20 Coffee Break solutions Session A2. Challenges and Perspectives of Up-Cycling Agricultural Wastes and Residues into Sustainable Bio-Products using Eco-Friendly Technologies 22nd - 23rd October 2018 16:45 Diversified Agro-Waste in China: Multiscale Approaches for Better Understanding and Efficient Utilisation Lujia Han, Prof., College of Engineering, China Agricultural University (CAU), China Beijing, China 17:00 Converting Waste/Wastewater Organic Matter into Valuable Biodegradable Plastics: 3 Pilot-Scale Studies in the frame of H2020 Programme M.
[Show full text]
Blossom —— 2019 International Bamboo Construction Competition (IBCC2019)
Blossom —— 2019 International Bamboo Construction Competition (IBCC2019) ORGANISATIONS: • Organiser: International Bamboo and Rattan Organization (INBAR) • Co-organisers: Zhejiang University Zhejiang University-University of Illinois at Urbana Champaign Institute (ZJUI) Tsinghua University World Architecture Federation of Hong Kong Industries Bamboo Industry Committee Italian Bamboo Association Base Bahay Foundation Labirinto dealla Masone • Participating Universities include (AlpHabetical order witH continually updated): Beijing Jiaotong University Centre for Corporate Responsibility and Sustainability, University of Zürich Chinese University of Hong Kong Federal University of Rio de Janeiro Hunan University Kunming University of Science and Technology Mediterranean University of Reggio Calabria Nanjing University Nanjing Forestry University Polytechnic University of Milano Polytechnic University of Turin San Martin University Sapienza University of Rome Southeast University Universidad Nacional de Colombia (National University of Colombia) University of Addis Ababa University of British Colombia University of Bologna Coventry University University of Naples Federico II University of Southern California University of Turin University of Pittsburgh University of Queensland Xi’an Jiaotong-Liverpool University • TecHnical Supports: INBAR Construction Task Force Arup • Sponsors: 1 Ganzhou Sentai Bamboo Wood Company of China Hongyazhuyuan science and technology Company of China Zhujing Bamboo Company of China Beijing Sinobamboo Culture and
[Show full text]
Title: Abstract: Scope and Topics: Program Committee Chairs
ICAIS 2021 Workshop Proposal Title: Precise Task Control in Teleoperation. Abstract: Teleoperation technology could help and substitute human to perform tasks conveniently in the long-distance or dangerous environment. One key point of teleoperation is how to make the operator get the force information which is generated when the slave robot interfaces with the environment, and make the slave robot follow the movement of the master hand controller in an accurate and timely manner. The teleoperation system becomes more and more popular and has been applied in nuclear power, space and telemedicine and also other areas. However, precise task control, as for a teleoperation control for the eye, heart surgery, is now still a hot and hard topic in the teleoperation area, because it is usually not easy to establish the precise unknown working environment model in the slave robot side, and the operator always could not feel the exact force he imposed to the master hand controller and the contact force generated by the slave robot during the interface with the environment. The ultimate goal of precise task control in teleoperation is help the operator know clearly and precisely the location of the end of slave robot and also master how much force the robot has imposed to the precise task object, and make the operator could succeed to fulfil the precise task smootly and safely. Scope and Topics: Potential topics include but are not limited to: Human-Robot Interface Human-Computer Interface High Precision Torque Sensors Information Fusion in Bilateral Control Haptics Tactile Perception High Precise Control Method Optimizing Bilateral Control Program Committee Chairs: Xiaozhen He, Rensselaer Polytechnic Institute, USA Email: [email protected] Homepage: http://homepages.rpi.edu/~hex6/ Bio: He received the B.S.
[Show full text]
3Rd Work Meeting at NFU and FAFU University, October 2018
Training Capacities in Agriculture and Urban Rural Interactions and Sustainable development of Megacitites Agenda of the Erasmus+ TAURUS Public Workshop & Project Meeting, Nanjing Forestry University (NFU), China 9 - 12 October 2018 1st day 10/09/2018 Tuesday Time Event 12:00-18:00 Arrive at Nanjing, Accommodations at Hotel 18:00 Social dinner at Nanling Hotel 2nd day 10/10/2018 Wednesday 8:30 Meeting at the Jinling Star Hotel lobby Meeting with the Vice president, International Cooperation Department and Dean of College of Biology and the Environment Hong Zhang, Vice-president of NFU Xinwu Xu, Director of International Affairs Office 9:00-9:30 Shenzuo Fang，Director of science and Technology Division Jiangang Zhu, Dean of College of International Education Gao handong, Secretary, College of Biology and the Environment Xia Xu,Vice Dean, College of Biology and the Environment Yifan Duan,Vice Dean, College of Biology and the Environment Public Workshop WP1: 1.2 Reviewing and learning EU experience in HEIs – Employers cooperation 9:30-12:00 through study visits. Workshop: Comparative analysis of University & Employers collaboration in EU and China Project meeting WP3: 3.1 Establishing the framework program to organize internships. Presentation of Internships Programmes for inclusion in the TAURUS platform 14:00-17:00 (target: TAURUS partners) WP8: 8.3 Coordination meetings - Reporting progresses on the project activities & Steering Committee 17:00-18:00 Visit the NFU Campus Training Capacities in Agriculture and Urban Rural Interactions and
[Show full text]
Conference Program Friday June 28, 2019
Organizing Committee Workshop Co-Chairs Daniel Zeng, Chinese Academy of Sciences, China Guoqing Chen, Tsinghua University, China Leon Zhao, City University of Hong Kong, China Publications Chair Daning Hu, Southern University of Science and Technology, China Junior Faculty Forum Chair Kevin Zhu, University of California, San Diego Junior Faculty Forum Co-Chair Beibei Li, Carnegie Mellon University Michael Zhang, Chinese University of Hong Kong Publicity Co-Chairs Harris Wu, Old Dominion University, USA Han Zhang, Georgia Tech, USA Career Fair Co-Chairs Yanwu Yang, Huazhong University of Science and Technology, China Xunhua Guo, Tsinghua University, China Local Arrangement Co-Chairs Wayne Huang, Xi’An Jiaotong Univesity, China Xin Li, City University of Hong Kong, China Hao Liao, Shenzhen University, China 2 Advisory Committee Ravi Bapna, University of Minnesota Anandhi Bharadwaj, Emory University Guoqing Chen, Tsinghua University Hsinchun Chen, University of Arizona Jian Chen, Tsinghua University Prabuddha De, Purdue University Anindya Ghose, New York University Paulo Goes, University of Arizona Alok Gupta, University of Minnesota Alan Hevner, University of Southern Florida Varghese Jacob, The University of Texas at Dallas Elena Karahanna, University of Georgia Robert Kauffman, Singapore Management University Ramayya Krishnan, Carnegie Mellon University T.P. Liang, National Sun Yat‐Sen University Feicheng Ma, Wuhan University Jiye Mao, Renmin University of China James Marsden, University of Connecticut Saby Mitra, Georgia Institute of Technology Vijay Mookerjee, The University of Texas at Dallas Sridhar Narasimhan, Georgia Institute of Technology Arun Rai, Georgia State University Sudha Ram, University of Arizona Vallabh Sambamurthy, Michigan State University Sumit Sarkar, The University of Texas at Dallas Michael Shaw, University of Illinois at Urbana‐Champaign Olivia R.
[Show full text]
Enhanced Detoxification and Degradation of Herbicide Atrazine
Chemosphere 165 (2016) 487e496 Contents lists available at ScienceDirect Chemosphere journal homepage: www.elsevier.com/locate/chemosphere Enhanced detoxification and degradation of herbicide atrazine by a group of O-methyltransferases in rice Yi Chen Lu a, e, 1, Fang Luo a, 1, Zhong Ji Pu c, Shuang Zhang d, Meng Tian Huang a, * Hong Yang a, b, a Jiangsu Key Laboratory of Pesticide Science, College of Sciences, Nanjing Agricultural University, Nanjing, 210095, China b State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China c School of Life Science and Biotechnology, Dalian University of Technology, Dalian, 116024, China d State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China e College of Food Science and Light Industry, Nanjing Tech University, Nanjing, 211800, China highlights graphical abstract Many ATR-responsive O-methyl- transferases were identified in rice. Yeast with MTs accumulated less ATR and more degraded products. UPLC-TOF-MS2 characterized a O- methylated-modified metabolites. O-MT and ATR-metabolites interac- tion was analyzed by molecular- docking. article info abstract Article history: Atrazine (ATR) as a toxic herbicide has become one of the seriously environmental contaminants Received 18 June 2016 worldwide due to its long-term intensive use in crop production. This study identified novel methyl- Received in revised form transferases (MTs) involved in detoxification and degradation of ATR residues in rice plants. From a 1 September 2016 subset of MTs differentially expressed in ATR-exposed rice, forty-four O-methyltransferase genes were Accepted 7 September 2016 investigated. Total activities were significantly enhanced by ATR in rice tissues.
[Show full text]
German Teacher Required Job Description Desired Skills
German Teacher Required Nanjing Tech University is currently looking for a motivated and qualified German Teacher. If you are interested in being considered for a teaching position with Nanjing Tech University and meet the below stated requirements, please apply via email with a formal resume in Word/PDF format to Hui MA ([email protected]). We look forward to the possibility of working with you and are eager to welcome you to our team. Job Description • Courses: Speaking & Listening; Conversational German • Start date: September every year • Hours per week: 12-14 teaching hours per week • Students: College students • Class size: Small classroom environment, less than 30 students • Salary: 4,000-6,000 RMB per month • Flight allowance: Once a year round-trip economical ticket is covered • Accommodation: 1 or 2 bedroom apartment on campus provided depends on individual or family, with free electricity, water and internet fee • Documents: Z visa, Foreign Expert Certificate, and Residence Permit provided Desired Skills & Experience • Education: Bachelor's (or equivalent) or above • Age: less than 50 years old • According to Chinese law, must have two years employment experience • Native German Speaker from Germany • Previous teaching experience preferred • Knowledge of Chinese culture and language preferred • Must be willing to adapt to a foreign environment; open minded, adventurous Office of Global Engagement Nanjing Tech University April 6, 2016 INTRODUCTION OF NANJING TECH UNIVERSITY History and Facts Nanjing Tech University, a comprehensive university with engineering as its focus, has a history of more than one hundred years as a cradle of education. It is a key institution of higher learning to be constructed in Jiangsu Province, and one of the first group of institutions of higher learning approved by the Chinese Ministry of Education for the training of "Excellent Engineers".
[Show full text]
Curriculum Vitae
ZHU YUEZHAO CURRICULUM VITAE ZHU YUEZHAO College of Mechanical and Power Engineering Nanjing Tech University Nanjing, China Emai: [email protected] Research Interests Biomass AND Organic Wastes disposal and resource utilization: Biomass thermal chemical conversion, biomass gas steam boiler and power generation, organic wastes thermal chemical conversion (pyrolysis, gasification), supercritical water oxidation technology, etc. Solar thermal and high efficient heat transfer device: Compound parabolic solar collector and parabolic trough collector, solar thermal (high temperature) and chemical recycling technology (Hydrogen production), heat pipe technology for geothermal, solar thermal and heat storage applications, etc. Professional Experience Professor, School of Mechanical and Power Engineering, Nanjing University of Chemical Engineering, 2005- Deputy Party Secretary, NanjingTech University, 2013-2018 Vice President, Nanjing University of Technology, 2001-2012 Associate Professor, 1995-2005 Teaching Assistant, Nanjing Institute of Chemical Engineering, 1982-1992 Education Ph.D. Chemical Process Machinery, College of Mechanical and Power Engineering, Nanjing University of Technology, 2008 Master Degree Philosophy of Science and Technology, College of Humanities, Nanjing Agricultural University, 2005; Chemical Process Machinery, College of Mechanical and Power Engineering, Nanjing Institute of Chemical Engineering, 1992 Bachelor Degree Chemical Process Machinery, College of Mechanical and Power Engineering, Nanjing Institute of 1 ZHU YUEZHAO
[Show full text]
Introducing Some of Our Contributors, Writers and Editors
Introducing some of our contributors, writers and editors Sponsor 主办单位 SinoConnexion 贺福传媒 Contributing editor Ken Ellingwood is a former foreign and national correspondent for the Los Angeles Times and author of Hard Line: Life and Death on the U.S.- Publisher 编辑出版 Mexico Border. He teaches writing at Nanjing University. Nanjinger《南京人》杂志社特约编辑Ken Ellingwood之前是《洛杉矶时报》的国内外通讯记者，同时也是“死亡地带”的作者：描述美国与墨西哥边境的生存 Operating Organization 运营机构与死亡。他目前在南京大学教写作。 Nanjing Hefu Cultural Media Co.,Ltd 南京贺福文化传媒有限公司 Principal Deputy Editor Laura Helen Schmitt holds a masters in International Mul- Contributors 特约专稿人 timedia Journalism from Newcastle University in the UK and is fluent in English, Shahnaz Mouhamou German and Mandarin. Laura Helen Schmitt 首席副编辑Laura Helen Schmitt毕业于英国纽卡斯尔大学，硕士 Doug Hughes 专业为国际多媒体新闻学，她精通英语，德语与中文，三种语言。 Ronald Paredes Frank Hossack Jochen Schultz has more than 10 years´proven management experiences at in- Columnists 特约专稿人 ternational training and universities. He has a deep knowledge in professional Rachel Skeels trainings, personnel and organizational Development and developing relationships Maria Simonova with clients from all over the world. He is now the Managing Director in China for a Nurmira Jamangulova German Training & Consultancy Company. Jochen Shultz Jochen Schultz在国际培训和大学教育方面有着10年以上的管理经 Misha Maruma 验。同时在专业培训、个人与公司发展以及如何与世界各地的客户 Rick Staff 建立良好关系方面具备相当深厚的专业知识。现今，供职于一家德 Dan Clarke 国培训咨询公司，任中国区总经理一职。 Editor-in-chief 主编 Frank Hossack 贺福 Rick Staff is from the UK and has 20 years cumulative experience as a wine trader, taster, and writer and was editor of ‘Superplonk’, the UK’s popular wine guide, prior to moving to Nanjing in 2008. Deputy Principal Editor 首席副编辑 Rick Staff来自英国，有着二十年丰富经验的葡萄酒商人、品酒师、 Laura Helen Schmitt 王甜甜作家，并且是《Superplonk》的撰写者，英国很受欢迎的葡萄酒鉴 Contributing Editor 副主编赏家，于2008年移居南京。 Ken Ellingwood Rachel Skeels is qualified in the field of interior textile design and previously Creative Director 创意总监 worked as childrenswear designer for major UK retailers such as Marks & Spencers, Ronald Paredes 泉源 C&A and Mothercare.
[Show full text]
Download Programme
PLENARY SESSIONS PROGRAMME Agricultural waste and residue management for a circular bio-economy: Shared China and EU impact-oriented solutions 22nd - 23rd October 2018 HUBEI HOTEL Haidian District, Zhongguancun South Street, No. 36 Beijing, China TOWARDS ZERO PLASTIC: This event aims to be as plastic-free as possible MONDAY, OCTOBER 22nd 2018 14:00 Welcome and Opening Session Taihua Mu, Prof. (CAAS, China), Lujia Han, Prof. (CAU, China) Nathalie Gontard, Prof. (INRA, France), Shane Ward, Prof. (UCD, Ireland) Session A1. Circular Economy in EU and China: Shared Cooperation Priorities, Co-funding Mechanisms, Policies and Implementation Chairpersons: Nathalie Gontard, Prof. (INRA, France), Lujia Han, Prof. (CAU, China) 14:20 Introduction of the Situation in China-EU Cooperation Project Application Keqin Dong, Ministry of Science and Technology, China 14:40 Government Policy and National Practice for Promoting the Recycling Utilisation of Waste in China Zhenhai Yang, National Animal Husbandry Service (NAHS)/China Feed Industry Association (CFIA), China European Policy in Relation to the Circular Economy Nicolas Dandois, Counsellor for Agriculture, European Union Delegation to China 15:00 INRA’s Policy to Strengthen Collaboration between France and China Philippe Mauguin, President of INRA, France 15:20 Building relationships with China in Research and Education Dolores O’Riordan, Prof., Vice-President for Global Engagement, Univ. College Dublin (UCD), Ireland 15:40 Cooperation between China & EU in Agriculture: the 13th Five-Year Period Xifeng Gong, Dr., Department of International Cooperation, Chinese Academy of Agricultural Sciences (CAAS), China 16:00 Coffee Break 16:20 Session A2. Challenges and Perspectives of Up-Cycling Agricultural Wastes and Residues into Sustainable Bio- Products using Eco-Friendly Technologies Chairpersons: TaihuaDiversifiedMu, Prof Agro.
[Show full text]