Textbook of Structur al Bi logy Second Edition 10102_9789813142466_tp_Color.indd 1 19/9/16 11:47 AM Series in Structural Biology Series Editor: Anders Liljas (Lund University, Sweden) Published Vol. 1 Structural Aspects of Protein Synthesis (Second Edition) by Anders Liljas and Måns Ehrenberg Vol. 2 Found in Translation: Collection of Original Articles on Single-Particle Reconstruction and the Structural Basis of Protein Synthesis by Joachim Frank Vol. 3 Selected Papers of Michael G. Rossmann with Commentaries: The Development of Structural Biology by Michael G. Rossmann Vol. 4 From a Grain of Salt to the Ribosome: The History of Crystallography as seen Through the Lens of the Nobel Prize edited by Ivar Olovsson, Anders Liljas and Sven Lidin Vol. 5 The Struggles and Dreams of Robert Langer by Robert Langer Vol. 6 Structure and Action of Molecular Chaperones: Machines that Assist Protein Folding in the Cell by Lila M. Gierasch, Arthur L. Horwich, Christine Slingsby, Sue Wickner and David Agard Vol. 7 Curiosity and Passion for Science and Art by Uwe B. Sleytr Vol. 8 Textbook of Structural Biology (Second Edition) by Anders Liljas, Lars Liljas, Miriam-Rose Ash, Göran Lindblom, Poul Nissen and Morten Kjeldgaard SC - Textbook of Structural Biology.indd 1 19-09-16 10:11:21 AM Series in Structural Biology – Vol. 8 Textbook of Structur al Bi logy Second Edition Anders Liljas (Lund University, Sweden) Lars Liljas (Uppsala University, Sweden) Miriam-Rose Ash (The University of Sydney, Australia) Göran Lindblom (Umeå University, Sweden) Poul Nissen (Aarhus University, Denmark) Morten Kjeldgaard (Aarhus University, Denmark) World Scientific NEW JERSEY • LONDON • SINGAPORE • BEIJING • SHANGHAI • HONG KONG • TAIPEI • CHENNAI • TOKYO 10102_9789813142466_tp_Color.indd 2 19/9/16 11:47 AM Published by World Scientific Publishing Co. Pte. Ltd. 5 Toh Tuck Link, Singapore 596224 USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601 UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE Library of Congress Cataloging-in-Publication Data Names: Liljas, Anders, author. Title: Textbook of structural biology / Anders Liljas, Lund University, Sweden [and five others]. Description: Second edition. | [Hackensack] New Jersey : World Scientific, 2017. | Series: Series in structural biology ; vol. 8 | Includes bibliographical references and index. Identifiers: LCCN 2016033861| ISBN 9789813142466 (hardcover : alk. paper) | ISBN 9813142464 (hardcover : alk. paper) | ISBN 9789813142473 (pbk. : alk. paper) | ISBN 9813142472 (pbk. : alk. paper) Subjects: LCSH: Proteins--Structure. | Ultrastructure (Biology) | Protein folding. | Biomolecules--Structure. Classification: LCC QP551 .T45 2017 | DDC 572/.633--dc23 LC record available at https://lccn.loc.gov/2016033861 British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. Copyright © 2017 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the publisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher. Printed in Singapore SC - Textbook of Structural Biology.indd 2 19-09-16 10:11:21 AM “7.5x10.25” b2510 Textbook of Structural Biology, 2nd Edition We dedicate this textbook to the memory of our coauthor Jure Piskur. bb22551100__FFMM..iinndddd vv 1100//2244//22001166 11::2277::2211 PPMM b1754 Effective Anger Management for Children & Youth: A Training Manual TTTThhhhiiiissss ppppaaaaggggeeee iiiinnnntttteeeennnnttttiiiioooonnnnaaaallllllllyyyy lllleeeefffftttt bbbbllllaaaannnnkkkk bb11775544__FFMM..iinndddd iiii 99//33//22001144 77::3311::0044 PPMM “7.5x10.25” b2510 Textbook of Structural Biology, 2nd Edition Contents Preface to the Second Edition ix Chapter 1 I ntroduction 1 Chapter 2 B asics of Protein Structure 11 Chapter 3 T he Folding, Folds and Functions of Proteins 37 Chapter 4 B asics of Membrane Proteins 69 Chapter 5 B asics of Nucleic Acid Structure 105 Chapter 6 B asics of Lipids and Membrane Structure 161 Chapter 7 B asics of Carbohydrates 213 Chapter 8 E nzymes 227 Chapter 9 G enome Structure, DNA Replication and Recombination 269 Chapter 10 T ranscription 307 Chapter 11 P rotein Synthesis — Translation 351 Chapter 12 P rotein Folding and Degradation 385 Chapter 13 T ransmembrane Transport 425 Chapter 14 S ignal Transduction 451 Chapter 15 C ell Motility and Transport 481 Chapter 16 S tructural Aspects of Cell-Cell Interactions 507 Chapter 17 T he Immune System 521 bb22551100__FFMM..iinndddd vviiii 99//1199//22001166 1122::4400::1144 PPMM b2510 Textbook of Structural Biology, 2nd Edition “7.5x10.25” viii  Textbook of Structural Biology, 2nd Edition Chapter 18 V irus Structure and Function 535 Chapter 19 B ioinformatics Tools in Structural Biology 553 Index 577 bb22551100__FFMM..iinndddd vviiiiii 99//1199//22001166 1122::4400::1144 PPMM “7.5x10.25” b2510 Textbook of Structural Biology, 2nd Edition Preface to the Second Edition It is now over seven years ago since we published the first edition of our Textbook of Structural Biology. Our coauthor of the first edition, Jure Piskur, died prematurely in 2014 due to cancer. We very much miss his insights and skills. The field has made very rapid and extensive progress since the first edition was released. In particular, it is becoming evident that many molecular systems are highly integrated with each other and sometimes very large assemblies are formed. This com- plexity is gradually emerging and accessible for structural investigations. The field of membrane proteins is making remarkable progress and is more extensively covered in this edition with its own dedicated chapter. Furthermore, we have added a chapter on carbohydrates, which is an emerging area that is deeply integrated with protein and cellular structure and function. Given the impressive number of unique protein structures now available, it is of course impossible to cover all of these in any single volume. We have therefore tried to concentrate on the growing body of lasting knowledge of the structure and the roles of macromolecular systems. We have received help from many colleagues who have used the first edition of the textbook for courses. In addition, we have had expert help in reviewing certain chapters. We are indebted to Prof Ulf Lindahl for expert insight into carbohydrates. Furthermore, we wish to express our thanks to Lars Erik Andreas Ehnbom and Saraboji Kadhirvel for expert skills in producing parts of the illustrations. Many illustrations are produced using the program Molscript by Per Kraulis. bb22551100__FFMM..iinndddd iixx 99//1199//22001166 1122::4400::1144 PPMM