Protein Electron Transfer PDF
Preview Protein Electron Transfer
Protein Electron Transfer Protein E lectron Transfer Edited by s. Derek Bendall Department o f BiochemistrYJ University of CambridgeJ CambridgeJ UK /JIOS SCIENTIFIC PUBUSHERS © BIOS Scientific Publishers Limited, 1996 Copyright held by BIOS Scientific Publishers Ltd for all chapters except Chapter 10 on pp. 249-272 which is e The Nobel Foundation 1993 or LeB Prix Nobel 1992. First published 1996 Transferred to Digital Printing 2005 All rights reserved. No part of this book may be reproduced or transmitted, in any form or by any means, without permission. A CIP catalogue record for this book is available from the British Library. ISBN 1 85996 040 5 BIOS Scientific Publishers Ltd 9 Newtec Place, Magdalen Road, Oxford OX4 IRE, UK Tel. +44 (0) 1865726286. Fax +44 (0) 1865246823 World Wide Web home page: http://www.Bookshop.co.ukIBIOS/ DISTRIBUTORS Australia a nd N ew Zealand Singapore and S outh E ast A sia DA Information Services Toppan Company (S) PTE Ltd 648 Whitehorse Road, Mitcham 38 Liu Fang Road, Jurong Victoria 3132 Singapore 2262 India USA a nd C anada Viva Books Private Limited BIOS Scientific Publishers 4346/4C Ansari Road PO Box 605, Herndon Daryaganj VA 20172-0605 New Delhi 110002 Typeset by Chandos Electronic Publishing, Stanton Harcourt, UK. Front cover: Crystal structure of complex between yeast cytochrome c peroxidase and cytochrome c (2pcc) drawn using MOLSCRIPT. Kraulis PJ (1991) J. Appl. Crystallogr. 24: 946-950. Contents Contributors xi Abbreviations xiii Preface xv 1 Outline oftheory of protein electron transfer. C. C. Maser and P.L. Duttan 1 Introduction 1 Fundamental tunnelling theory 2 Simple electron tunnelling through a barrier 2 Fermi's golden rule 2 Marcus theory and nuclear geometries 3 Tunnelling in proteins 8 Characteristic free energy dependence of biological electron tunnelling 8 Characteristic distance dependence of biological electron tunnelling 9 A simple three-parameter predictor of rate 11 Variable distance dependence 11 Redox protein engineering principles 14 The dominance of distance 14 Distance and binding in interprotein electron transfer 15 Distance and stability themes in intraprotein charge separation 16 The role of adiabaticity 17 References 18 2 The protein bridge between redox centres. D.N Beratan and J N Onuchic 23 Introduction 23 What tunnels? 23 Strong versus weak electronic coupling regimes 24 Tunnelling electrons 25 Basics of vibronically coupled electron tunnelling 26 Tunnelling energetics 26 How does exponential decay arise from delocalized bridge states? 27 Through-bond and through-space decay length scales 28 Tunnelling pathways in proteins 28 What is the physical meaning of the dominant pathway? 29 When does a simple product approximate the tunnelling matrix element? 30 Key role for hydrogen bonds predicted 31 v vi CONTENTS Predictions of the tunnelling pathway model 31 Tests of pathway predictions 33 Pathways in the exponential distance regime 33 Docking and intermolecular ET 33 Concerns related to simple pathway analysis 35 Beyond the single pathway view 36 What is the physical meaning of a tunnelling pathway? 36 Multipath models and electronlhole propagators 37 Hamiltonian-based models of electronic coupling in proteins 38 Current challenges 39 References 40 3 Interprotein electron transfer. D.S. Bendall 43 Introduction 43 Kinetics of electron transfer reactions in solution 44 Diffusional kinetics of complex formation 45 The nature of diffusional encounter 45 Ionic strength effects 46 Microscopic electrostatic methods 48 Macroscopic electrostatic methods 49 Binding forces and binding energies 53 Non-covalent sources of binding energy 53 Specificity and binding energy 54 Statics and dynamics of reaction complexes 57 The static view 58 The dynamic view 59 Conclusions 63 References 64 4 Computer modelling of protein-protein interactions. S.H. N orthrup 69 Introduction 69 Model building of electron transfer complexes 69 Diffusional dynamics of protein-protein association 70 Alternative docking geometries for electron transfer 71 Influence of protein flexibility and internaI dynamics 71 Theoretical methodologies 72 Modelling of protein structure 72 Calculation of protein electrostatic fields 73 Brownian dynamics equation of motion 74 Extraction of rate constants 75 Treatment of excluded volume effects 77 Reaction criteria 77 Results 78 Cytochrome reaction rate constants with distance cut-off model 78 Protein-protein docking in the cytochrome c-CCP reaction 80 CONTENTS vii CDNP-derivatized cytochrome c reactions with CCP 83 Extension to surface side chain flexibility 84 Treatment of the cytochrome c-CCP reaction with self-consistent electrostatics 85 Self-exchange reactions using the exponential reactivity model 85 Site-directed mutants of CY: reactions with cytochrome bs 86 Energy refinement and analysis of Brownian dynamics-generated complexes 88 Summary 91 References 94 5 Structure of electron transfer proteins and their complexes. ES. Mathews and R .C.E. Durley 99 Introduction 99 Cytochromes and cupredoxins 100 Cytochromes 100 Cupredoxins 102 Two-site proteins 103 Ascorbate oxidase 103 Flavocytochromes 105 Complexes between redox proteins 112 Complex of MADH with amicyanin and cytochrome c-55l i 112 Cytochrome c peroxidase 116 Activity of crystals 119 Flavocytochrome b 119 2 The MADH system 120 Complex dynamics 120 References 121 6 Photosynthetic bacterial reaction centres. w.w. Parson 125 Introduction 125 Reaction centre structures 126 Charge separation and competing reactions 129 The free energies and enthalpies of P+QA- and P+HL- 133 Kinetics and mechanism of the initial charge separation 135 Vibrational relaxations of p* and P+HL - 137 The role of the 'accessory' BChl (BJ 139 Calculations of interaction matrix elements and radical pair energies 141 The roles of individual amino acid residues in controlling the rate, temperature dependence and directional specificity of charge separation 143 Contributions to the directional specificity from orbital overlap, internaI charge transfer states of P and dielectric asymmetry 144 Computer simulations 146 Electron transfer from bacteriophaeophytin HL - to QA 147 References 148 viii CONTENTS 7 Copper proteins. O. Farver 161 Introduction 161 Ligand structure 162 Redox potentials and spectroscopic properties 165 Role of ligand geometry on ET 168 ET pathway calculations 169 Pathways in protein-protein ET 169 Azurin 170 Plastocyanin 172 Intramolecular LRET in type-l copper proteins 175 Azurin 175 Other blue copper proteins 178 ET in type-2 copper proteins 178 Intramolecular LRET in blue oxidases 179 ET pathways in proteins: conclusion 183 References 183 8 Haemoproteins. G.R. Moore 189 Introduction 189 Structures of haems 191 Tertiary structures of haemoproteins 194 Control of redox potentials 198 Intraprotein electron transfer 202 Interprotein electron transfer 205 Coupled electron-ion transfers 210 References 212 9 Electron transfer complexes coupled to ion translocation. P.R. Rich 217 Introduction 217 Principles of coupling 217 The chemiosmotic theory 217 The vectorial redox loop 218 Protein structure and the proton weIl 219 The importance of local electroneutrality within the reaction core 220 Structure and mechanism of complexes 223 Enzymes catalysing components of larger chemiosmotic systems 224 The bc complexes 225 Ionmotive NADH dehydrogenases 229 Protonmotive oxidases 234 Applications to other systems and future prospects 241 References 242 10 Electron transfer reactions in chemistry. Theory and experiment. R.A. Marcus 249 Electron transfer experiments since the late 1940s 249 The early experience 251 CONTENTS ix Developing an electron transfer theory 252 Introduction 252 Reaction rate theory 253 Electron transfer theory. Formulation 254 Electron transfer theory. Treatment 257 Predictions 260 Comparisons of experiment and theory 262 Other applications and extensions 266 References 270 Further reading 272 Appendices A Electron transfer rate calculations. JN Onuchic and D .N Beratan 273 The ET Hamiltonian 273 Two-Ievel systems 274 E and the Condon approximation 275 tun Born-Oppenheimer approximation 276 Rate expressions 276 References 282 B Kinetic analysis. D.S. Bendall 285 Introduction 285 Observed rate constants 285 First order and pseudo-first order reactions 285 Second order reactions 287 Kinetic models 287 Reversible reactions 288 Two binding sites and rearrangement 288 Ionic strength effects 290 References 292 Index 295
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