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Molecular Motors

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Molecular Motors. Editors of compilations such as this tend to stress in their prefaces that significantconceptual advances have been made recently, that novel technical developmentshave opened extraordinary opportunities for unprecedented discoveries and thatthe time seemed ripe to take stock and to point out developments which will advancethe field in the near future. Well, all of this is true for this book too. It isalso true that on such occasions we realize how much we have learned and yethow little we know. Since the publication nearly 40 years ago, of the landmark treatiseon cell movement edited by Robert D. Allen and Noburô Kamiya....

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Molecular Motors Edited by M. Schliwa Molecular Motors. Edited by Manfred Schliwa Copyright  2003 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim ISBN 3-527-30594-7 Molecular Motors Edited by Manfred Schliwa Edited by This book was carefully produced. Never- Prof. Dr. Manfred Schliwatheless, editors, authors and publisher do not Ludwig-Maximilians-Universitätwarrant the information contained therein to Adolf-Butenandt-Institutbe free of errors. Readers are advised to keep Zellbiologie in mind that statements, data, illustrations, Schillerstrasse 42 procedural details or other items may 80336 München inadvertently be inaccurate. Germany Library of Congress Card No.: applied for A catalogue record for this book is available from the British Library. Bibliographic information published by Die Deutsche Bibliothek Die Deutsche Bibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data is available in the internet at http://dnb.ddb.de. 2003 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim All rights reserved (including those of translation in other languages). No part of this book may be reproduced in any form – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trade- marks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law. Printed in the Federal Republic of Germany. Printed on acid-free paper. CompositionHagedorn Kommunikation, Viernheim PrintingDruckhaus Darmstadt GmbH, Darmstadt BookbindingBuchbinderei Schaumann GmbH, Darmstadt ISBN 3-527-30594-7 PrefaceV Preface Editors of compilations such as this tend to stress in their prefaces that significant conceptual advances have been made recently, that novel technical developments have opened extraordinary opportunities for unprecedented discoveries and that the time seemed ripe to take stock and to point out developments which will ad- vance the field in the near future. Well, all of this is true for this book too. It is also true that on such occasions we realize how much we have learned and yet howlittle we know. Since the publication nearly 40 years ago, of the landmark trea- tise on cell movement edited by Robert D. Allen and Noburô Kamiya and entitled Primitive Motile Systems in Cell Biology, the field has moved from the phenomeno- logical to the mechanistic and from the largely structural to the primarily molecu- lar. We have come to appreciate that at every level of complexity the cell operates through molecular machines. Some of these machines are single molecules that carry out one specific task, undergoing only small structural changes in the pro- cess. Others are macromolecular complexes composed of dozens, even hundreds of different components engaged in elaborate biochemical operations. Among the multitude of molecular machines of a cell, one group stands out owing to its ability to generate one of the hallmark characteristics of living systems: move- ment. The chapters of this book offer insights into the workings, interactions and functions of these remarkable molecules which are responsible for various forms of movement encountered in cells. The subdivision of the book into five sections developed naturally. First we learn about the basic designs of some of the most pro- minent cellular motors before considering their mechanochemistry; the role of mo- tors in the context of elaborate cellular activities is considered next, followed by ex- amples of defects which result when motors run ‘wild’; finally, biomotors are put into perspective with regard to nanobiotechnological applications and other types of molecular motors. The outcome is a pretty sizeable book, as can plainly be seen. Nevertheless, it is but an introduction to the subject, as other types of biolo- gical machines exist that could also, with some justification, be called motors but are not considered here for reasons of space. It is my hope, however, that salient features of cellular motors are covered even though gaps undoubtedly remain. I would like to express my sincere gratitude first and foremost to the authors who have managed to complete their chapters under pretty tight time constraints. I would also like to thank the staff at Wiley-VCH, in particular Dr. Andreas VIPreface Sendtko, who have helped me in every respect and to Ursula Euteneuer for critical reading and helpful comments and discussions. Thanks to the efforts of everyone concerned less than one year has elapsed between conception of the book and the completion of the printed product. You might say all of us have motored along just fine. ManfredSchliwa September 2002 ContentsVII Contents PrefaceV List of ContributorsXIX Part 1 Basic Principles of Motor Design 1 The Myosin Superfamily: An Overview3 1.1 An Introduction to the Myosin Superfamily3 1.2 Functional Properties of Myosins7 1.2.1Directionality and Processivity7 1.2.2Protein Motifs Found in Myosins 8 1.2.3Myosin Regulation 10 1.3 Diverse Functions for Myosins11 1.3.1Non-muscle Contractile Structures14 1.3.2Cell Motility and Adhesion15 1.3.3Organelle/Cellular Component Transport 16 1.3.4Maintenance of Actin-rich Extensions21 1.3.5Membrane Trafficking 24 1.3.6Signal Transduction26 1.4 Myosins in Disease 28 1.4.1Griscelli Syndrome28 1.4.2Roles for Myosins in Hearing29 1.5 New Myosins and Myosin Functions on the Horizon 31 1.6 Conclusions 32 References 33 2 Dynein Motors: Structure, Mechanochemistry and Regulation45 2.1 Introduction45 2.2 Structural Organization of the Motor, Cargo-binding and Regulatory Components 46 2.2.1Heavy Chains 48 2.2.2Intermediate Chains53 VIIIContents 2.2.3Light Intermediate Chains56 2.2.4The LC8 Light Chain Class 57 2.2.5The Tctex1/Tctex2 Light Chain Class59 2.2.6The LC7/roadblock Light Chain Class 61 2.2.7Heavy Chain-associated Regulatory Light Chains62 2.2.7.1Light chain 162 2.2.7.2Calmodulin-related light chains63 2.2.7.3Thioredoxins 64 2.2.7.4p29 (cAMP-dependent phosphoprotein) 64 2.2.8Light Chains Associated with Inner Arms I2/365 2.3 Mechanochemistry and Motility 65 2.4 Dynein Deficiencies and Disease67 2.5 Conclusions 69 References 70 3 Kinesin Superfamily Proteins79 3.1 Introduction79 3.2 The Kinesin Superfamily Proteins82 3.3 N-Kinesins 87 3.3.1N-1 Kinesins 87 3.3.2N-2 Kinesins 91 3.3.3N-3 Kinesins 91 3.3.3.1The Unc104/KIF1 family 91 3.3.3.2The KIF13 family 92 3.3.3.3The KIF16 family 92 3.3.4N-4 Kinesins 92 3.3.4.1The KIF3 family 93 3.3.4.2The Osm3/KIF17 family 94 3.3.5N-5 Kinesins 94 3.3.6N-6 Kinesins 94 3.3.6.1The CHO1/KIF23 family 95 3.3.6.2The KIF20/Rab6 kinesin family 95 3.3.7N-7 Kinesins 95 3.3.8N-8 Kinesins 95 3.3.8.1The Kid/KIF22 family 95 3.3.8.2The KIF18 family 96 3.3.9N-9 Kinesins 96 3.3.10N-10 Kinesins 96 3.3.11N-11 Kinesins 96 3.4 M-Kinesins 96 3.5 C-Kinesins 97 3.5.1C-1 Kinesins97 3.5.2C-2 Kinesins97 3.6 Orphans 98 3.7 Cargoes of KIFs; Specificity and Redundancy98 Contents IX 3.8 Recognition and Binding to Cargoes 99 3.9 How to Determine the Direction of Transport 100 References 100 4 The Bacterial Flagellar Motor111 4.1 Introduction 111 4.2 Structure 114 4.2.1 Propeller and Drive-shaft117 4.2.2 Rotor 117 4.2.3 Stator 118 4.2.4 RotorStator Interactions119 4.3 Function 120   4.3.1 Motor Driven by H and Na Ion Flux 121 4.3.2 Torque versus Speed 122 4.3.3 Independent Torque Generators 126 4.3.4 Proton Motive Force, Sodium-motive Force, Ion Flux128 4.3.5 Reversibility131 4.3.6 Steps? 131 4.4 Models 132 4.4.1 Conceptual Models 133 4.4.2 Kinetic Models 135 4.5 Summary 136 References 137 5F-MotorofATPSynthase 141 1 5.1 Introduction 141 5.2 ATP Synthase 141 5.3 F1-Motor 142 5.4 Imaging of Rotation of F1-Motor 144 5.5 High-speed Imaging of F Rotation 145 1 5.6 New Crystal Structure for the F1-Motor146 5.7 Catalysis and Rotation of F1-Motor148 5.8 Perspectives 150 References 151 6 RNA and DNA Polymerases 153 6.1 Introduction 153 6.2 NTP Polymerization Mechanism 155 6.3 Basic Methods used to Study Polymerase Movement during Transcription 158 6.3.1 The Tethered Particle Motion Approach 158 6.3.2 The Surface Force Microscopy Technique 158 6.3.3 The Optical Tweezer Method 159 6.3.4 Method for Visualization of DNA Rotation during Transcription161 6.3.5 Footprinting Approach 161 X Contents 6.3.6Single Molecule Assay for DNA Polymerase 162 6.4 Mechanism of Force Generation for RNAP and DNAP 164 6.5 Molecular Model for RNAP Translocation 168 6.6 Possible Utilization of the Energy Released upon NTP Cleavage171 6.7 Single-Molecule Studies and Molecular Mechanisms of Transcription Pausing and Arrest172 6.8 Concluding Remarks 174 References 175 7 Helicases as Molecular Motors179 7.1 Introduction179 7.2 Basic Properties of Helicases182 7.3 Mechanism of Helicase Activity188 7.3.1Unidirectional Translocation188 7.3.2Step Size of the Helicase192 7.3.3NA Strand Separation 192 7.4 HCVHelicase 194 7.5 Bacteriophage T7 gp4 Helicase 196 7.6 Conclusions 197 References 198 Part 2 Mechanochemistry 8 How Protein Motors Convert Chemical Energy into Mechanical Work207 8.1 Introduction207 8.2 A Brief Description of ATP Synthase Structure208 8.3 The F1 Motor: A Power Stroke 209 8.4 The F0 Motor: A Brownian Ratchet212 8.4.1A Pure Brownian Ratchet 212 8.4.2A Pure Power Stroke 214 8.5 Coupling and Coordination of Motors 216 8.6 Measures of Efficiency218 8.7 Discussion 220 A1 Example Models to Illustrate the Difference between Ratchets and Power Strokes221 A1.1Example 1: A power stroke without Brownian fluctuations221 A1.2Example 2: A power stroke with Brownian fluctuations222 A1.3Example 3: A Brownian ratchet that biases fluctuations223 A1.4Example 4: A Brownian ratchet that rectifies fluctuations224 A2 A Closer Look at Binding Free Energy225 References 227