Biophysical And Structural Aspects of Bioenergetics

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ISBN: 9780854043460 | 0854043462
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Copyright: 1/30/2006

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Bioenergetics is a term used to describe the events of primary energy transduction in biology. The field has seen tremendous advances in recent years thanks to developments in the biophysical and computational techniques used to solve the three-dimensional structures of the membrane-bound proteins, which often act as catalysts in these reactions. This has enabled researchers to bring, otherwise static, structures to life and decipher the dynamic function of these intriguing systems. Biophysical and Structural Aspects of Bioenergetics brings together contributions from internationally respected experts, all of whom helped shape and develop the field of bioenergetics. It provides a representative snapshot of the very latest key developments in this multidisciplinary subject, with an emphasis on molecular structure, and how this changes during the bioenergetic function. Offering a comprehensive overview of the current state of the art, and complete with extensive citations in each chapter, this book is the ideal reference for both biochemists and biophysicists studying this fascinating topic.

Principles of Molecular Bioenergetics and the Proton Pump of Cytochrome Oxidase

(25)

Robert B. Gennis

Introduction: General Principles of Bioenergetic Systems

(6)

Oxidoreduction Loops

(3)

Proton Pumps

(2)

Cytochrome Oxidase Uses Both Mechanisms of Energy Coupling

(1)

The Structure of Cytochrome Oxidase

(6)

The Active Site of Cytochrome Oxidase

(2)

Wiring for Electron Transfer

(1)

Proton-conducting Channels

(1)

The K-channel

(1)

The D-channel

(1)

The H-channel

(1)

The Exit Channel

(1)

Hysteretic Properties of Cytochrome Oxidase

(1)

The Mechanism of Oxygen Reduction to Water

(5)

Some Considerations Concerning the Mechanism of the Proton Pump

(3)

Four Pumping Steps per Cycle but One Common Mechanism

(1)

What Do the Decoupled Mutants of Cytochrome Oxidase Tell Us?

(1)

The Operation of the Proton Pump Depends on Kinetic Considerations

(1)

The Energetics of Proton Pumping

(1)

Where Do We Go From Here?

(5)

References

(4)

Proton Entry, Exit and Pathways in Cytochrome Oxidase: Insight from `Conserved' Water

(29)

Martyn A. Sharpe

Ling Qin

Shelagh Ferguson-Miller

Overview

(1)

Heme-copper Oxidases, their Evolution and General Function

(1)

Water and Protein Function

(14)

Water Interactions Within Protein Structures

(1)

Water Interactions in Cytochrome Oxidase: Overall Features

(1)

The Position of Metals and Water in Cytochrome Oxidases

(3)

Subunit II and Water

(1)

Subunit I and Water

(1)

The D-channel

(2)

The Gate: E286 and Variants

(4)

The K-channel

(1)

The Sodium/Calcium and Magnesium Binding Sites

(1)

The Subunit I/II Interface

(1)

The Water Exit Pathway?

(1)

The Proton Exit Pathway?

(1)

Water and the Proton Pumping Function

(7)

Role of Heme a

(2)

The Role of the Heme a3/CuB Center and Associated Water

(2)

What Evolution Tells Us About the Minimal Structural Requirements for Oxidase to Pump Protons

(1)

The Importance of Metal Center Charge in Oxidase Function

(2)

Gating of the Pump

(1)

The H284-Y288 Gate

(1)

The Wla3-H334 Gate

(1)

Summary

(5)

Acknowledgements

(1)

References

(4)

Structural Chemical Studies on the Reaction Mechanism of Cytochrome c Oxidase

(17)

Shinya Yoshikawa

Introduction

(1)

The Mechanism of O2 Reduction

(2)

Chemistry of O2 Reduction

(1)

The Intermediate Species Detectable during the Course of the O2 Reduction

(1)

X-ray Structure of the O2 Reduction Site

(1)

The Mechanism of Proton Pumping

(14)

Structural Requirements for Proton Pumping by Cytochrome c Oxidase

(1)

Redox-coupled Conformational Changes in the X-ray Structure of Bovine Heart Cytochrome c Oxidase

(4)

FTIR Analyses for Redox-coupled Conformational Changes in Bovine Heart Cytochrome c Oxidase

(2)

Mutation Analysis for Asp51

(1)

The Function of Heme a

(1)

Comparison of the Proton-Pumping Mechanisms Proposed

(3)

Acknowledgements

(1)

References

(3)

Mechanisms of Redox-coupled Proton Pumping by Respiratory Oxidases

(27)

Peter Brzezinski

Pia Addelroth

Abbreviations

(1)

Introduction

(3)

Redox-driven Proton Pumping - General Principles

(1)

Structure

(5)

Oxygen Channels

(1)

Proton-transfer Pathways

(1)

D-pathway

(2)

K-pathway

(1)

H-pathway

(1)

Proton Exit Pathway

(1)

Structural Requirements for Combining Rapid O2 Delivery to the Catalytic Site with Gating of Protons

(1)

Electron and proton transfer during CcO turnover

(5)

Reduction of the Oxidised CcO in the Absence of O2

(2)

Reaction of the Reduced CcO with O2

(1)

Reaction of the Two-electron Reduced CcO with O2

(1)

Reaction of the Four-electron Reduced CcO with O2

(1)

The P3 → F3 transition

(1)

The F3 → O4(0) transition

(1)

Proton Pumping

(3)

Proton Pumping During the P3 → F3 Transition

(1)

Uncoupled Mutant Forms of Cytochrome c Oxidase

(1)

The role of E286

(1)

Molecular Mechanisms for Proton Pumping

(3)

Final Remarks

(8)

Acknowledgement

(1)

References

(8)

Quantum Chemical Models of O2 Bond Cleavage and Proton Pumping in Cytochrome Oxidase

(24)

Per E.M. Siegbahn

Margareta R.A. Blomberg

Introduction

(4)

Methods and Models

103

(2)

The A to PM Step: Mechanism for O--O Bond Cleavage

105

(5)

The Catalytic Cycle: Mechanism for Proton Pumping

110

(7)

Proton Gating or Guiding

117

(3)

Summary

120

(3)

References

121

(2)

The bc1 Complex: What is There Left to Argue About?

123

(33)

Antony R. Crofts

Introduction

123

(6)

Control of Turnover by the Bifurcated Reaction at the Qo Site

129

(1)

The ES Complex

130

(2)

Constraints from the ES-complex Model

132

(1)

Proton-coupled Electron Transfer

133

(1)

The Second Electron Transfer, From SQ to Heme bL

134

(2)

Kinetic Estimation of SQ Occupancy

136

(4)

Estimation of SQ Occupancy from Bypass Rates

137

(3)

Mobility in the Qo site

140

(1)

Other Problematic Short Circuits and Their Prevention

141

(4)

Double-gating

142

(1)

Coulombic Gating in a Sequential Mechanism

142

(2)

Double Occupancy

144

(1)

Location of the ES-Complex or Activated State at Some Alternative Position

144

(1)

Studies Using Glu-272 Mutants to Explore the Role of This Residue in Control of the Qo site Reaction and Protection Against Excess ROS Production

145

(2)

Conclusions

147

(9)

Acknowledgements

148

(1)

References

148

(5)

Appendix 1

153

(1)

Marcus Treatment of Endergonic Reactions

153

(2)

References

155

(1)

Insights into the Mechanism of Mitochondrial Complex I from its Distant Relatives, the [NiFe] Hydrogenases

156

(29)

Stefan Kerscher

Volker Zickermann

Klaus Zwicker

Ulrich Brandt

Introduction

156

(2)

The Three Modules of Complex I

158

(4)

The N-module

158

(1)

The Q-module

159

(1)

The P-module

160

(2)

[NiFe] Hydrogenases, a Model for the Q-Module of Complex I

162

(12)

Conserved Structural Elements

162

(6)

Natural and Site-directed Mutations in Complex I

168

(4)

Human Pathogenic Mutations

172

(2)

Addressing the Function of Cluster N2 by EPR Spectroscopy and Site-Directed Mutagenesis

174

(4)

Subunit Assignment of Iron--Sulfur Cluster N2

174

(1)

The Fourth Ligand of Iron--Sulfur Cluster N2

175

(1)

Redox-dependent Protonations/Deprotonations

176

(1)

Ubiquinone reduction

177

(1)

Implications for the Mechanism of Proton Pumping by Complex I

178

(7)

Acknowledgements

179

(1)

References

180

(5)

Current Knowledge About the Mechanism of Energy Transduction by Respiratory Complex I

185

(16)

Judy Hirst

Introduction

185

(1)

Complex I in Energy Transduction

185

(2)

The Location of the Cofactors and Substrate Binding Sites in Complex I

187

(5)

The L-shaped Structure of Complex I

187

(1)

The Location of the Cofactors in Complex I

187

(2)

The Quinone Binding Site(s)

189

(3)

The Redox Reaction: Oxidation of NADH and Reduction of Quinone

192

(2)

The Role of the FMN: Oxidation of NADH and Electron Transfer

192

(1)

Electron Transfer via the Iron--sulphur Clusters

192

(2)

Quinone Reduction

194

(1)

Mechanisms of Proton Pumping

194

(7)

The Q-cycle Mechanism

195

(1)

Coupled Reactions

196

(1)

Evidence for Directly-Coupled Proton--Electron Transfer at Cluster N2

197

(1)

Evidence for an Indirectly Coupled Proton Transfer Mechanism

198

(1)

References

198

(3)

Structure of Photosystem II from Thermosynechococcus Elongatus

201

(26)

Kristina N Ferreira

So Iwata

Introduction

201

(1)

Optimized Crystallization of Photosystem II from T. Elongatus

202

(2)

Cell Culture

202

(1)

Purification

202

(1)

Crystallization and Optimization

203

(1)

Data Collection

204

(1)

Structure of Photosystem II from T. Elongatus

204

(15)

Overall Structure

204

(1)

D1 and D2 Proteins

204

(6)

CP43 and CP47 subunits

210

(3)

Low Molecular Weight Subunits

213

(1)

PsbE and PsbF (Cyt b559)

213

(1)

PsbL, PsbM and PsbT

213

(1)

PsbI

214

(1)

PsbH and PsbX

214

(1)

PsbJ

215

(1)

PsbK

215

(1)

PsbZ

215

(1)

Putative PsbN

215

(1)

Extrinsic Subunits

215

(1)

PsbO

215

(2)

PsbU

217

(1)

PsbV (Cyt c550)

217

(1)

The Oxygen-evolving Centre (OEC)

217

(2)

Mechanism of Water Oxidation

219

(2)

Conclusion

221

(6)

Abbreviations

221

(1)

Acknowledgements

222

(1)

References

222

(5)

A Structural View of Proton Transport by Bacteriorhodopsin

227

(22)

Janos K. Lanyi

Introduction

227

(1)

Structure of Bacteriorhodopsin

228

(1)

Photochemical Reaction Cycle

228

(1)

Evaluating the Crystallography

229

(3)

Trapping the Right Structure and the Right Intermediate State

232

(1)

Retinal Motions: The Pump

233

(3)

Conformational Cascades in Response to Relaxation of the Retinal

236

(4)

Crystallographic vs. Non-crystallographic Evidence

240

(1)

Pump Energetics

241

(8)

References

243

(6)

The Dynamics of Proton Transfer Across Bacteriorhodopsin Explored by FT-IR Spectroscopy

249

(24)

Joachim Heberle

Introduction

249

(1)

FT-IR Spectroscopy

250

(4)

Selecting a Single Vibration from a Protein: Difference Spectroscopy

250

(1)

Finding a Suitable Environment: Sampling Techniques

251

(1)

Transmission Spectroscopy

251

(1)

Attenuated Total Reflection (ATR)

251

(1)

Surface-enhanced Infrared Absorption (SEIRA)

252

(1)

Resolving the Reaction Dynamics: Time-resolved Step-scan Spectroscopy

253

(1)

Bacteriorhodopsin

254

(19)

The Molecule and its Photoreaction

254

(2)

Vibrational Differences and Their Assignments

256

(1)

Retinal Modes

256

(2)

Vibrational Bands of Amino-acid Side Chains

258

(6)

Internal Water Molecules

264

(1)

The Sequence of Proton Transfer Steps

265

(1)

Proton Release

265

(1)

Proton Uptake

266

(1)

Reprotonation of the Proton-release Group

267

(1)

References

267

(6)

Intraprotein Proton Transfer--Concepts and Realities from the Bacterial Photosynthetic Reaction Center

273

(41)

Colin A. Wraight

Introduction

273

(1)

Proton Transfer vs. Electron Transfer

274

(1)

The Grotthuss Mechanism and Hydrogen-bonded Chains

275

(4)

Free Energy Relationships--Marcus and Bronsted

279

(5)

Proton Transfer in Biology

284

(3)

`Normal' Acids and Bases

287

(1)

Proton-coupled Electron Transfer in the Acceptor Quinone Function of Photosynthetic Reaction Centers

288

(12)

First Electron Transfer to QB and Coupled Proton Uptake (Bohr Protons)

289

(4)

Second Electron Transfer and Coupled Proton Transfer to QB (Chemical Protons)

293

(2)

Proton Transfer to the QB Pocket

295

(1)

Outline of the PT Elements in the QB Domain

295

(2)

The Proton Conduction Pathway to QB and the QB Domain

297

(1)

Investigations of Intraprotein PT Coupled to the First and Second ETs

298

(2)

Concluding Remarks

300

(14)

Acknowledgements

301

(1)

References

302

(12)

Infrared Protein Spectroscopy as a Tool to Study Protonation Reactions Within Proteins

314

(20)

Peter R. Rich

Masayo Iwaki

Abbreviations

314

(1)

Introduction

314

(1)

Types of Information from Protein (FT)IR Spectroscopy

315

(1)

Principles of (FT)IR Spectroscopy

316

(1)

ATR-FTIR Spectroscopy

317

(3)

ATR Versus Transmission FTIR Spectroscopy

317

(1)

Methods of Handling Protein Samples

317

(2)

Methods of Inducing Difference Spectra

319

(1)

Strategies to Assign IR Bands

320

(1)

IR Properties of Amino Acids

320

(7)

Strategies to Isolate Headgroup Spectra: Amino Acids versus Poly-amino Acids

320

(1)

IR Signatures of Protonation-State Changes of Amino acid Residues

321

(1)

Lysine

321

(1)

Tyrosine

322

(1)

Histidine

323

(2)

Aspartic and Glutamic Acids

325

(2)

Examples of Protein Infrared Spectroscopy Applications

327

(4)

Absolute Spectra of Proteins and Effects of Isotope Substitution

327

(2)

Redox Difference Spectra

329

(1)

Ligand Binding and Catalytic Intermediates Difference Spectra

330

(1)

Outlook

331

(3)

References

331

(3)

Inhibitors of Mitochondrial F1-ATPase

334

(25)

John E. Walker

Jonathan R. Gledhill

Introduction

334

(2)

High-resolution Structures of F1-ATPase

336

(2)

Characterised Sites of Inhibition

338

(11)

Catalytic Sites

338

(2)

Non-catalytic Sites

340

(1)

The Aurovertin B Site

340

(2)

The Efrapeptin Site

342

(2)

The Site of Binding of the Natural Inhibitor Protein, IF1

344

(2)

The Non-peptidyl Lipophilic Cation Site

346

(3)

Inhibition of F1-ATPase by Azide

349

(1)

Potential Medical Significance

349

(4)

Development of New Antibiotic Inhibitors of F1-ATPase

349

(1)

Potential Uses of the Inhibitor Protein in Medicine

350

(1)

The Ectopic ATPase as a Target for Therapy

351

(2)

Concluding Remarks

353

(6)

Abbreviations

353

(1)

Acknowledgements

353

(1)

References

353

(6)

The Passion of the Permease

359

(17)

H. Ronald Kaback

Introduction

359

(1)

Background

359

(4)

Overall Structure of LacY

363

(3)

The Substrate-binding Site

366

(2)

Residues Involved in H+ Translocation and Coupling

368

(2)

Proposed Mechanism of Lactose/H+ Symport

370

(6)

Acknowledgements

373

(1)

References

373

(3)

Hydride Transfer and Proton Translocation by Nicotinamide Nucleotide Transhydrogenase

376

(18)

J. Baz Jackson

Scott A. White

T. Harma C. Brondijk

Abbreviations

376

(1)

Residue Numbering

376

(1)

The Function of Proton-Translocating Transhydrogenase

376

(1)

The Global Architecture of Transhydrogenase

377

(1)

The dII Component

378

(1)

dI2dIII1 Complexes: Catalytic Properties and High-Resolution Structures

379

(4)

Considerations Relevant to the Mechanism of Proton Translocation by Transhydrogenase

383

(3)

Hypothesis for the Mechanism of Proton Translocation by Transhydrogenase

386

(4)

The Specificity Rules

386

(1)

The Sequence of Events During the Reduction of NADP+ by NADH in Transhydrogenase Driven by Δp (see Figure 6)

387

(1)

Conformational Changes Associated with the Hydride-Transfer Step

387

(3)

Future Directions

390

(4)

Acknowledgements

390

(1)

References

390

(4)

Subject Index

394

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Biophysical And Structural Aspects of Bioenergetics

Summary

Table of Contents

Supplemental Materials