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Proteins Structure, Function, and Motion Second Edition INTRODUCTION TO CopyrightedPROTEINS STRUCTURE, FUNCTION, AND MOTION SECOND EDITION Materials - Taylor and Francis CHAPMAN & HALL/CRC Mathematical and Computational Biology Series Aims and scope: This series aims to capture new developments and summarize what is known over the entire spectrum of mathematical and computational biology and medicine. It seeks to encourage the integration of mathematical, statistical, and computational methods into biology by publishing a broad range of textbooks, reference works, and handbooks. The titles included in the series are meant to appeal to students, researchers, and professionals in the mathematical, statistical and computational sciences, fundamental biology and bioengineering, as well as interdisciplinary researchers involved in the field.Copyrighted The inclusion of concrete examples and applications, and programming techniques and examples, is highly encouraged. Series Editors N. F. Britton Department of Mathematical Sciences University of Bath Materials Xihong Lin Department of Biostatistics Harvard University Nicola Mulder University of Cape Town - South Africa Taylor Maria Victoria Schneider European Bioinformatics Institute and Mona Singh Department of Computer Science Princeton University Francis Proposals for the series should be submitted to one of the series editors above or directly to: CRC Press, Taylor & Francis Group 3 Park Square, Milton Park Abingdon, Oxfordshire OX14 4RN UK Published Titles An Introduction to Systems Biology: Bayesian Phylogenetics: Methods, Design Principles of Biological Circuits Algorithms, and Applications Uri Alon Ming-Hui Chen, Lynn Kuo, and Paul O. Lewis Glycome Informatics: Methods and Statistical Methods for QTL Mapping Applications Zehua Chen Kiyoko F. Aoki-Kinoshita An Introduction to Physical Oncology: Computational Systems Biology of How Mechanistic Mathematical Cancer Modeling Can Improve Cancer Therapy Emmanuel Barillot, Laurence Calzone, Outcomes PhilippeCopyrighted Hupé, Jean-Philippe Vert, and Vittorio Cristini, Eugene J. Koay, Andrei Zinovyev and Zhihui Wang Python for Bioinformatics, Second Edition Normal Mode Analysis: Theory and Sebastian Bassi Applications to Biological and Chemical Quantitative Biology: From Molecular to Systems Cellular Systems Qiang Cui and Ivet Bahar Sebastian Bassi Materials Kinetic Modelling in Systems Biology Methods in Medical Informatics: Oleg Demin and Igor Goryanin Fundamentals of Healthcare Data Analysis Tools for DNA Microarrays Programming in Perl, Python, and Ruby Sorin Draghici Jules J. Berman Statistics and Data Analysis for Chromatin: Structure, Dynamics, Microarrays Using R and Bioconductor, Regulation - Second Edition Ralf Blossey SorinTaylor Draghici˘ Computational Biology: A Statistical Computational Neuroscience: Mechanics Perspective A Comprehensive Approach Ralf Blossey Jianfeng Fengand Game-Theoretical Models in Biology Mathematical Models of Plant-Herbivore Mark Broom and Jan Rychtáˇr Interactions Francis Computational and Visualization Zhilan Feng and Donald L. DeAngelis Techniques for Structural Bioinformatics Biological Sequence Analysis Using Using Chimera the SeqAn C++ Library Forbes J. Burkowski Andreas Gogol-Döring and Knut Reinert Structural Bioinformatics: An Algorithmic Gene Expression Studies Using Approach Affymetrix Microarrays Forbes J. Burkowski Hinrich Göhlmann and Willem Talloen Spatial Ecology Handbook of Hidden Markov Models Stephen Cantrell, Chris Cosner, in Bioinformatics and Shigui Ruan Martin Gollery Cell Mechanics: From Single Scale- Meta-analysis and Combining Based Models to Multiscale Modeling Information in Genetics and Genomics Arnaud Chauvière, Luigi Preziosi, Rudy Guerra and and Claude Verdier Darlene R. Goldstein Published Titles (continued) Differential Equations and Mathematical Computational Hydrodynamics of Biology, Second Edition Capsules and Biological Cells D.S. Jones, M.J. Plank, and B.D. Sleeman C. Pozrikidis Knowledge Discovery in Proteomics Modeling and Simulation of Capsules Igor Jurisica and Dennis Wigle and Biological Cells Introduction to Proteins: Structure, C. Pozrikidis Function, and Motion, Second Edition Cancer Modelling and Simulation Amit Kessel and Nir Ben-Tal Luigi Preziosi RNA-seq Data Analysis: A Practical Computational Exome and Genome ApproachCopyrighted Analysis Eija Korpelainen, Jarno Tuimala, Peter N. Robinson, Rosario M. Piro, Panu Somervuo, Mikael Huss, and Garry Wong and Marten Jäger Introduction to Mathematical Oncology Introduction to Bio-Ontologies Yang Kuang, John D. Nagy, and Peter N. Robinson and Sebastian Bauer Steffen E. Eikenberry Dynamics of Biological Systems Biological Computation Materials Michael Small Ehud Lamm and Ron Unger Genome Annotation Optimal Control Applied to Biological Jung Soh, Paul M.K. Gordon, and Models Christoph W. Sensen Suzanne Lenhart and John T. Workman Niche Modeling: Predictions from Clustering in Bioinformatics and Drug Statistical Distributions Discovery - David Stockwell John D. MacCuish and Norah E. MacCuish AlgorithmsTaylor for Next-Generation Spatiotemporal Patterns in Ecology Sequencing and Epidemiology: Theory, Models, Wing-Kin Sung and Simulation Algorithms in andBioinformatics: A Practical Horst Malchow, Sergei V. Petrovskii, and Introduction Ezio Venturino Wing-Kin Sung Stochastic Dynamics for Systems Biology Introduction to BioinformaticsFrancis Christian Mazza and Michel Benaïm Anna Tramontano Statistical Modeling and Machine The Ten Most Wanted Solutions in Learning for Molecular Biology Protein Bioinformatics Alan M. Moses Anna Tramontano Engineering Genetic Circuits Combinatorial Pattern Matching Chris J. Myers Algorithms in Computational Biology Pattern Discovery in Bioinformatics: Using Perl and R Theory & Algorithms Gabriel Valiente Laxmi Parida Managing Your Biological Data with Exactly Solvable Models of Biological Python Invasion Allegra Via, Kristian Rother, and Sergei V. Petrovskii and Bai-Lian Li Anna Tramontano Published Titles (continued) Cancer Systems Biology Bioinformatics: A Practical Approach Edwin Wang Shui Qing Ye Stochastic Modelling for Systems Introduction to Computational Biology, Second Edition Proteomics Darren J. Wilkinson Golan Yona Big Data in Omics and Imaging: Big Data in Omics and Imaging: Association Analysis Integrated Analysis and Causal Momiao Xiong Inference BigCopyrighted Data Analysis for Bioinformatics and Momiao Xiong Biomedical Discoveries Shui Qing Ye Materials - Taylor and Francis Copyrighted Materials - Taylor and Francis INTRODUCTION TO CopyrightedPROTEINS STRUCTURE, FUNCTION, AND MOTION SECONDMaterials EDITION - Taylor and AMIT KESSEL • NIR BEN-TALFrancis Copyrighted Materials CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487-2742 - Taylor © 2018 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed on acid-free paper and Version Date: 20180208 International Standard Book Number-13: 978-1-4987-4717-2 (Hardback) This book contains information obtained from authentic and highly regarded sources. Reasonable efforts Francishave been made to publish reliable data and information, but the author and publisher cannot assume responsibility for the validity of all materials or the consequences of their use. The authors and publishers have attempted to trace the copyright holders of all material reproduced in this publication and apologize to copyright holders if permission to publish in this form has not been obtained. If any copyright material has not been acknowledged please write and let us know so we may rectify in any future reprint. Except as permitted under U.S. Copyright Law, no part of this book may be reprinted, reproduced, transmitted, or utilized in any form by any electronic, mechanical, or other means, now known or hereafter invented, including photocopying, microfilming, and recording, or in any information storage or retrieval system, without written permission from the publishers. For permission to photocopy or use material electronically from this work, please access www.copyright.com (http://www.copyright.com/) or contact the Copyright Clearance Center, Inc. (CCC), 222 Rosewood Drive, Danvers, MA 01923, 978-750-8400. CCC is a not-for-profit organization that provides licenses and registration for a variety of users. For organizations that have been granted a photocopy license by the CCC, a separate system of payment has been arranged. Trademark Notice: Product or corporate names may be trademarks or registered trademarks, and are used only for identification and explanation without intent to infringe. Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com Contents List of Figures xxi List of Tables xxxi List of BoxesCopyrighted xxxiii Preface xxxv Changes in Second Edition xli Acknowledgments xliii Authors xlv Physical Quantities and Constants xlvii List of Acronyms Materials xlix Chapter 1 ■ Introduction 1 1.1 IMPORTANCE OF PROTEINS IN LIVING ORGANISMS 1 1.1.1 Life, proteins and mysterious forces - 1 1.1.2 Molecular organization of living organismsTaylor 2 1.1.3 Proteins have numerous biological roles 6 1.1.3.1 Catalysis of metabolic processes 6 1.1.3.2 Energy transfer and 8 1.1.3.3 Gene expression 11 1.1.3.4 Transport of solutes across biological membranes Francis13 1.1.3.5 Cellular communication 13 1.1.3.6 Molecular recognition 16 1.1.3.7 Defense 17 1.1.3.8 Forming intracellular and extracellular
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