Cysteine Proteinases of Microorganisms and Viruses
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Subtiligase-Catalyzed Peptide Ligation Amy M
Review Cite This: Chem. Rev. 2020, 120, 3127−3160 pubs.acs.org/CR Subtiligase-Catalyzed Peptide Ligation Amy M. Weeks*,† and James A. Wells*,†,‡ † Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94143, United States ‡ Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, California 94143, United States ABSTRACT: Subtiligase-catalyzed peptide ligation is a powerful approach for site- specific protein bioconjugation, synthesis and semisynthesis of proteins and peptides, and chemoproteomic analysis of cellular N termini. Here, we provide a comprehensive review of the subtiligase technology, including its development, applications, and impacts on protein science. We highlight key advantages and limitations of the tool and compare it to other peptide ligase enzymes. Finally, we provide a perspective on future applications and challenges and how they may be addressed. CONTENTS 6.1. Subtiligase-Catalyzed Thioester and Thioa- cid Synthesis for Peptide and Protein 1. Introduction 3128 Bioconjugation 3138 2. Using Proteases in Reverse for Peptide Bond 6.2. Peptide Segment Condensation 3139 Formation 3129 6.3. Peptide Cyclization 3140 2.1. Protease-Catalyzed Peptide Bond Synthesis 6.4. Total Protein Synthesis 3140 under Thermodynamic Control 3129 7. Application of Subtiligase for Site-Specific 2.2. Protease-Catalyzed Peptide Bond Synthesis Protein Bioconjugation 3141 under Kinetic Control 3129 7.1. Sequence and Structural Requirements for 3. Protein Engineering of Subtilisin for Improved N-Terminal Modification by Subtiligase 3142 Peptide Bond Synthesis 3129 7.1.1. Characterization of Sequence and 3.1. Mutation of the Catalytic Serine to Cysteine 3129 Structural Requirements 3142 3.2. -
Neutrophil Chemoattractant Receptors in Health and Disease: Double-Edged Swords
Cellular & Molecular Immunology www.nature.com/cmi REVIEW ARTICLE Neutrophil chemoattractant receptors in health and disease: double-edged swords Mieke Metzemaekers1, Mieke Gouwy1 and Paul Proost 1 Neutrophils are frontline cells of the innate immune system. These effector leukocytes are equipped with intriguing antimicrobial machinery and consequently display high cytotoxic potential. Accurate neutrophil recruitment is essential to combat microbes and to restore homeostasis, for inflammation modulation and resolution, wound healing and tissue repair. After fulfilling the appropriate effector functions, however, dampening neutrophil activation and infiltration is crucial to prevent damage to the host. In humans, chemoattractant molecules can be categorized into four biochemical families, i.e., chemotactic lipids, formyl peptides, complement anaphylatoxins and chemokines. They are critically involved in the tight regulation of neutrophil bone marrow storage and egress and in spatial and temporal neutrophil trafficking between organs. Chemoattractants function by activating dedicated heptahelical G protein-coupled receptors (GPCRs). In addition, emerging evidence suggests an important role for atypical chemoattractant receptors (ACKRs) that do not couple to G proteins in fine-tuning neutrophil migratory and functional responses. The expression levels of chemoattractant receptors are dependent on the level of neutrophil maturation and state of activation, with a pivotal modulatory role for the (inflammatory) environment. Here, we provide an overview -
Role of Extracellular Proteases in Biofilm Disruption of Gram Positive
e Engine ym er z in n g E Mukherji, et al., Enz Eng 2015, 4:1 Enzyme Engineering DOI: 10.4172/2329-6674.1000126 ISSN: 2329-6674 Review Article Open Access Role of Extracellular Proteases in Biofilm Disruption of Gram Positive Bacteria with Special Emphasis on Staphylococcus aureus Biofilms Mukherji R, Patil A and Prabhune A* Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India *Corresponding author: Asmita Prabhune, Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune 411008, India, Tel: 91-020-25902239; Fax: 91-020-25902648; E-mail: [email protected] Rec date: December 28, 2014, Acc date: January 12, 2015, Pub date: January 15, 2015 Copyright: © 2015 Mukherji R, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Abstract Bacterial biofilms are multicellular structures akin to citadels which have individual bacterial cells embedded within a matrix of a self-synthesized polymeric or proteinaceous material. Since biofilms can establish themselves on both biotic and abiotic surfaces and that bacteria residing in these complex molecular structures are much more resistant to antimicrobial agents than their planktonic equivalents, makes these entities a medical and economic nuisance. Of late, several strategies have been investigated that intend to provide a sustainable solution to treat this problem. More recently role of extracellular proteases in disruption of already established bacterial biofilms and in prevention of biofilm formation itself has been demonstrated. The present review aims to collectively highlight the role of bacterial extracellular proteases in biofilm disruption of Gram positive bacteria. -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
Characterization of Cathepsin L Genes and Their Cdnas in the Brine Shrimp, Artemia Franciscana
University of Windsor Scholarship at UWindsor Electronic Theses and Dissertations Theses, Dissertations, and Major Papers 2006 Characterization of cathepsin L genes and their cDNAs in the brine shrimp, Artemia franciscana. Jian Ping Cao University of Windsor Follow this and additional works at: https://scholar.uwindsor.ca/etd Recommended Citation Cao, Jian Ping, "Characterization of cathepsin L genes and their cDNAs in the brine shrimp, Artemia franciscana." (2006). Electronic Theses and Dissertations. 1398. https://scholar.uwindsor.ca/etd/1398 This online database contains the full-text of PhD dissertations and Masters’ theses of University of Windsor students from 1954 forward. These documents are made available for personal study and research purposes only, in accordance with the Canadian Copyright Act and the Creative Commons license—CC BY-NC-ND (Attribution, Non-Commercial, No Derivative Works). Under this license, works must always be attributed to the copyright holder (original author), cannot be used for any commercial purposes, and may not be altered. Any other use would require the permission of the copyright holder. Students may inquire about withdrawing their dissertation and/or thesis from this database. For additional inquiries, please contact the repository administrator via email ([email protected]) or by telephone at 519-253-3000ext. 3208. CHARACTERIZATION OF CATHEPSIN L GENES AND THEIR cDNAs IN THE BRINE SHRIMP, ARTEMIA FRANCISCANA By: JianPing Cao A Thesis Submitted to the Faculty of Graduate Studies and Research through the Department of Biological Sciences in Partial Fulfillment of the Requirements for the Degree of Master of Science at the University of Windsor Windsor, Ontario, Canada 2006 Reproduced with permission of the copyright owner. -
Proteolytic Enzymes in Grass Pollen and Their Relationship to Allergenic Proteins
Proteolytic Enzymes in Grass Pollen and their Relationship to Allergenic Proteins By Rohit G. Saldanha A thesis submitted in fulfilment of the requirements for the degree of Masters by Research Faculty of Medicine The University of New South Wales March 2005 TABLE OF CONTENTS TABLE OF CONTENTS 1 LIST OF FIGURES 6 LIST OF TABLES 8 LIST OF TABLES 8 ABBREVIATIONS 8 ACKNOWLEDGEMENTS 11 PUBLISHED WORK FROM THIS THESIS 12 ABSTRACT 13 1. ASTHMA AND SENSITISATION IN ALLERGIC DISEASES 14 1.1 Defining Asthma and its Clinical Presentation 14 1.2 Inflammatory Responses in Asthma 15 1.2.1 The Early Phase Response 15 1.2.2 The Late Phase Reaction 16 1.3 Effects of Airway Inflammation 16 1.3.1 Respiratory Epithelium 16 1.3.2 Airway Remodelling 17 1.4 Classification of Asthma 18 1.4.1 Extrinsic Asthma 19 1.4.2 Intrinsic Asthma 19 1.5 Prevalence of Asthma 20 1.6 Immunological Sensitisation 22 1.7 Antigen Presentation and development of T cell Responses. 22 1.8 Factors Influencing T cell Activation Responses 25 1.8.1 Co-Stimulatory Interactions 25 1.8.2 Cognate Cellular Interactions 26 1.8.3 Soluble Pro-inflammatory Factors 26 1.9 Intracellular Signalling Mechanisms Regulating T cell Differentiation 30 2 POLLEN ALLERGENS AND THEIR RELATIONSHIP TO PROTEOLYTIC ENZYMES 33 1 2.1 The Role of Pollen Allergens in Asthma 33 2.2 Environmental Factors influencing Pollen Exposure 33 2.3 Classification of Pollen Sources 35 2.3.1 Taxonomy of Pollen Sources 35 2.3.2 Cross-Reactivity between different Pollen Allergens 40 2.4 Classification of Pollen Allergens 41 2.4.1 -
Final Program
In Memoriam: Final Program XXV Congress of the International Society on Thrombosis and Haemostasis and 61st Annual SSC Meeting June 20 – 25, 2015 Toronto, Canada www.isth2015.org 1 Final Program Table of Contents 3 Venue and Contacts 5 Invitation and Welcome Message 12 ISTH 2015 Committees 24 Congress Support 25 Sponsors and Exhibitors 27 ISTH Awards 32 ISTH Society Information 37 Program Overview 41 Program Day by Day 55 SSC and Educational Program 83 Master Classes and Career Mentorship Sessions 87 Nurses Forum 93 Scientific Program, Monday, June 22 94 Oral Communications 1 102 Plenary Lecture 103 State of the Art Lectures 105 Oral Communications 2 112 Abstract Symposia 120 Poster Session 189 Scientific Program, Tuesday, June 23 190 Oral Communications 3 198 Plenary Lecture 198 State of the Art Lectures 200 Oral Communications 4 208 Plenary Lecture 209 Abstract Symposia 216 Poster Session 285 Scientific Program, Wednesday, June 24 286 Oral Communications 5 294 Plenary Lecture 294 State of the Art Lectures 296 Oral Communications 6 304 Abstract Symposia 311 Poster Session 381 Scientific Program, Thursday, June 25 382 Oral Communications 7 390 Plenary Lecture 390 Abstract Symposia 397 Highlights of ISTH 399 Exhibition Floor Plan 402 Exhibitor List 405 Congress Information 406 Venue Plan 407 Congress Information 417 Social Program 418 Toronto & Canada Information 421 Transportation in Toronto 423 Future ISTH Meetings and Congresses 2 427 Authors Index 1 Thank You to Everyone Who Supported the Venue and Contacts 2014 World Thrombosis Day -
Crystal Structure of the Parasite Inhibitor Chagasin In
Crystal structure of the parasite inhibitor chagasin in complex with papain allows identification of structural requirements for broad reactivity and specificity determinants for target proteases Izabela Redzynia1,*, Anna Ljunggren2,*, Anna Bujacz1, Magnus Abrahamson2, Mariusz Jaskolski3,4 and Grzegorz Bujacz1,4 1 Institute of Technical Biochemistry, Faculty of Biotechnology and Food Sciences, Technical University of Lodz, Poland 2 Department of Laboratory Medicine, Division of Clinical Chemistry and Pharmacology, Lund University, Sweden 3 Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, Poznan, Poland 4 Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland Keywords A complex of chagasin, a protein inhibitor from Trypanosoma cruzi, and Chagas disease; cruzipain; cysteine papain, a classic family C1 cysteine protease, has been crystallized. Kinetic proteases; papain; protein inhibitors studies revealed that inactivation of papain by chagasin is very fast ) ) (k = 1.5 · 106 m 1Æs 1), and results in the formation of a very tight, Correspondence on m G. Bujacz, Institute of Technical Biochemis- reversible complex (Ki =36p ), with similar or better rate and equilib- try, Faculty of Biotechnology and Food rium constants than those for cathepsins L and B. The high-resolution Sciences, Technical University of Lodz, ul. crystal structure shows an inhibitory wedge comprising three loops, which Stefanowskiego 4/10, 90-924 Lodz, Poland forms a number of contacts responsible for the high-affinity binding. Com- Fax: +48 42 636 66 18 parison with the structure of papain in complex with human cystatin B Tel: +48 42 631 34 31 reveals that, despite entirely different folding, the two inhibitors utilize very E-mail: [email protected] similar atomic interactions, leading to essentially identical affinities for the M. -
Developing Methods to Understand and Engineer Protease Cleavage Specificity
Developing methods to understand and engineer protease cleavage specificity A Dissertation SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Michael Douglas Lane IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Burckhard Seelig September 2016 © Michael D Lane, 2016 Acknowledgements I would like to thank the many people who supported me along the way towards completing my thesis. Above all, I thank my advisor, Dr. Burckhard Seelig, who gave me the opportunity to pursue my ideas, embraced my research with thoughtful criticism and relentless optimism, and shaped my scientific approach through challenging me to be the best I can be. I also would like to thank previous members of the Seelig lab, Dr. Misha Golynskiy, Dr. John Haugner, Dr. Dana Morrone, and Dr. Aleardo Morelli, for being good friends and the many scientific discussions we had that guided me through the rough experiments. To the new Seelig lab members, especially Dr. Matilda Newton, Dr. Yari Cabezas, and Dr. Nisha Kanwar, thank you for your critical feedback, friendship, and taking away all my lab responsibilities. To the MSTP, I would like to thank Dr. Yoji Shimizu, Susan Shurson, and Nicholas Berg for their unending help guiding through the woven MD/PhD program. In particular, I thank the MSTP leadership for allowing me to pursue the program tailored to my interests. To my thesis committee, thank you for your support through the years. From annual reviews, to informal discussions, to grant application drafts, your feedback molded my abilities and experience. To my friends and family, especially my wife, Dr. -
SVM and a Novel POOL Method Coupled with THEMATICS For
SVM and a Novel POOL Method Coupled with THEMATICS for Protein Active Site Prediction A DISSERTATION SUBMITTED TO THE COLLEGE OF COMPUTER AND INFORMATION SCIENCE OF NORTHEASTERN UNIVERSITY IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY By Wenxu Tong April 2008 ©Wenxu Tong, 2008 ALL RIGHTS RESERVED Acknowledgements I have a lot of people to thank. I am mostly indebted to my advisor Dr. Ron Williams. He generously allowed me to work on a problem with the idea he developed decades ago and guided me through the research to turn it from just a mere idea into a useful system to solve important problems. Without his kindness, wisdom and persistence, there would be no this dissertation. Another person I am so fortunate to meet and work with is Dr. Mary Jo Ondrechen, my co-advisor. It was her who developed the THEMATICS method, which this dissertation works on. Her guidance and help during my research is critical for me. I am grateful to all the committee members for reading and commenting my dissertation. Especially, I am thankful to Dr. Jay Aslam, who provided a lot of advice for my research, and Dr. Bob Futrelle, who brought me into the field and provided much help in my writing of this dissertation. I also thank Dr. Budil for the time he spent serving as my committee member, especially during all the difficulties and inconvenience he happened to experience unfortunately during the time. I am so fortunate to work in the THEMATICS group with Dr. Leo Murga, Dr. -
Regulation and Functions of Acute Phase Proteins
ACUTE PHASE ROTEI REG ULATION AND FUNCTIONS OF ACUTE PHASE PROTEINS Edited by Fra cisco Veas INTECH ACUTE PHASE PROTEINS – REGULATION AND FUNCTIONS OF ACUTE PHASE PROTEINS Edited by Francisco Veas Acute Phase Proteins – Regulation and Functions of Acute Phase Proteins Edited by Francisco Veas Published by InTech Janeza Trdine 9, 51000 Rijeka, Croatia Copyright © 2011 InTech All chapters are Open Access articles distributed under the Creative Commons Non Commercial Share Alike Attribution 3.0 license, which permits to copy, distribute, transmit, and adapt the work in any medium, so long as the original work is properly cited. After this work has been published by InTech, authors have the right to republish it, in whole or part, in any publication of which they are the author, and to make other personal use of the work. Any republication, referencing or personal use of the work must explicitly identify the original source. Statements and opinions expressed in the chapters are these of the individual contributors and not necessarily those of the editors or publisher. No responsibility is accepted for the accuracy of information contained in the published articles. The publisher assumes no responsibility for any damage or injury to persons or property arising out of the use of any materials, instructions, methods or ideas contained in the book. Publishing Process Manager Davor Vidic Technical Editor Teodora Smiljanic Cover Designer Jan Hyrat Image Copyright Ali Mazraie Shadi, 2011. Used under license from Shutterstock.com First published September, 2011 Printed in Croatia A free online edition of this book is available at www.intechopen.com Additional hard copies can be obtained from [email protected] Acute Phase Proteins – Regulation and Functions of Acute Phase Proteins, Edited by Francisco Veas p. -
"2N Ó - H a A.N () -Si-'-RH "',O '-S'a AO Or Patent Application Publication Jul
US 2006O154325A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2006/0154325 A1 Bogyo et al. (43) Pub. Date: Jul. 13, 2006 (54) SYNTHESIS OF EPOXIDE BASED Publication Classification INHIBITORS OF CYSTEINE PROTEASES (51) Int. Cl. CI2O I/37 (2006.01) (76) Inventors: Matthew Bogyo, Redwood City, CA C07K 7/08 (2006.01) (US); Steven H.L. Verhelst, Stanford, C07D 303/08 (2006.01) CA (US) (52) U.S. Cl. ............................. 435/23: 530/402; 549/551 Correspondence Address: (57) ABSTRACT PETERS VERNY JONES & SCHMITT, L.L.P. 425 SHERMANAVENUE SUTE 230 Epoxide based cysteine protease inhibitors containing pep PALO ALTO, CA 94.306 (US) tide derivatives and methods for synthesizing them in sold phase are disclosed. Preferably, an epoxy succinyl “war head' (for binding to the enzyme) is prepared, having two (21) Appl. No.: 11/329,818 amino acid residues or residue-like structures on either side. Natural and non-natural amino acids may be used. The present process may be carried out entirely on a solid (22) Filed: Jan. 10, 2006 Support, with the proviso that a dipeptide like group is prepared prior to coupling to one side of the Supported Related U.S. Application Data complex. The method lends itself to more efficient inhibitor synthesis, and may be employed with mixtures of peptide (60) Provisional application No. 60/642,891, filed on Jan. compounds, and various modifications of epoxides to create 10, 2005. diverse libraries of inhibitors. Fmoc-NH-AA-OH 1) 20%diorari Piperdine all- AA A 1 0 2 O N-Fmoc di H 1 AA if m RNK Tentage Resin Step 1 2)) Fmoc-NH-AA-OH2 2 1) 20% Piperdine Step 2 Step 3 2) epoxide-NP ester NaOH (): N AA 1 N o al- S H AA O H O O S1NÓ H A A.