Structural Biology of Membrane Proteins

, by Grisshammer, Reinhard; Buchanan, Susan K.

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ISBN: 9780854043613 | 0854043616
Cover: Hardcover
Copyright: 6/30/2006

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In the last few years there have been many exciting and innovative developments in the field of membrane protein structure and this trend is set to continue. Structural Biology of Membrane Proteins is a new monograph covering a wide range of topics with contributions from leading experts in the field.The book will be split into three sections: the first will discuss topics such as expression, purification and crystallisation; the second will cover characterisation techniques and the final section will look at new protein structures. The book will hence have wide appeal to researchers working in and around the field and provide an up-to-date reference source. Introductory sections to each topic are accompanied by more detailed discussions for the more experienced biochemist. Detailed descriptions of experimental methods are included to demonstrate practical approaches to membrane protein structure projects. The book also offers an up-to-date reference source in addition to descriptions of new and emerging developments, including state-of-the-art techniques for solving membrane protein structures. Structural Biology of Membrane Proteins encompasses both basic introductions and detailed descriptions of themes and should appeal to a wide range of biochemical scientists, both experienced and beginner.

Section 1 Expression and Purification of Membrane Proteins

Chapter 1 Refolding of G-Protein-Coupled Receptors

(12)

Jean-Louis Banères

1 Introduction

(1)

2 Refolding of Membrane Proteins

(2)

3 In Vitro Protein Refolding

(1)

4 GPCR In Vitro Refolding

(6)

4.1 Resolubilization from Inclusion Bodies

(1)

4.2 Refolding

(1)

4.3 Refolding of GPCR Fragments

(1)

4.4 Refolding of Intact GPCRs

(3)

5 Conclusion

(1)

References

(2)

Chapter 2 Expression of Genes Encoding Eukaryotic Membrane Proteins in Mammalian Cells

(14)

Philip J. Reeves

1 Introduction

(1)

2 Mammalian Cell Hosts and Gene Expression Vectors

(1)

3 Delivery and Maintenance of Expression Vectors in Mammalian Cells

(4)

3.1 Transient Transfection

(1)

3.2 Stable Transfection

(1)

3.2.1 A Procedure for Stable Transfection of HEK293S Cells

(1)

3.3 Stable Episomal Replication

(1)

3.4 Viral Infection

(1)

4 HEK293S Stable Cell Lines for High-Level Expression of Eukaryotic Membrane Proteins

(4)

4.1 Constitutive Expression

(1)

4.2 Tetracycline-Regulated Gene Expression

(1)

4.3 A Plasmid for Tetracycline-Regulated Expression of Opsin

(1)

4.3.1 Construction and Characterization of HEK293S Stable Cell Lines for Inducible Gene Expression

(1)

5 Scale Up of Culture Growth and Rhodopsin Purification

(1)

5.1 Growth of HEK293S Cells in Suspension Culture Using a Bioreactor

(1)

5.2 Immunoaffinity Purification of Rhodopsin

(1)

6 Preparation of Eukaryotic Membrane Proteins Containing Simple N-Glycans

(1)

7 Outlook for the Use of HEK293S Tetracycline-Inducible Cell Lines for Large-Scale Preparation of Other Eukaryotic Membrane Proteins

(2)

References

(1)

Chapter 3 Expression of Recombinant G-Protein Coupled Receptors for Structural Biology

(22)

Filippo Mancia and Wayne A. Hendrickson

1 Introduction

(5)

1.1 Signal Transduction through G-protein Coupled Receptors

(1)

1.2 Structural and Functional Characteristics of GPCRs

(2)

1.3 Structure Determination of GPCRs

(2)

2 Expression of Recombinant GPCRs

(10)

2.1 Overview

(1)

2.2 Bacteria as Hosts for the Production of Functional GPCRs

(4)

2.3 Production of GPCRs in Stably Transfected Mammalian Cells

(3)

2.4 Production of GPCRs via Transient Transfection or Viral Infection of Mammalian Cells

(1)

2.5 Production of GPCRs in Yeast

(1)

2.6 Production of GPCRs in Insect Cells

(1)

2.7 "In Vivo" Expression in the Eye

(1)

2.8 Extra-Membranous Expression Systems

(1)

3 Conclusions

(1)

Acknowledgments

(1)

References

(6)

Chapter 4 The Purification of G-Protein Coupled Receptors for Crystallization

(21)

Tony Warne and Gebhard F.X. Schertler

1 Introduction

(1)

1.1 Structural Studies of G-Protein Coupled Receptors

(1)

1.2 The Turkey Erythrocyte Beta-Adrenergic Receptor

(1)

2 Heterogeneity of Overexpressed Receptors

(3)

2.1 Heterogeneity of GPCRs due to Post-Translational Modifications

(1)

2.1.1 N-Glycosylation

(1)

2.1.2 Palmitoylation

(1)

2.1.3 Phosphorylation

(1)

2.2 Other Sources of Heterogeneity

(1)

3 Membrane Fractionation, Solubilization, and Detergent Selection

(5)

3.1 Detergents for Solubilization

(1)

3.2 Detergents for Final Purification Steps and Crystallization

(3)

4 Purification

(6)

4.1 Use of Purification Tags and Fusions

(3)

4.2 Removal of Tags and Fusions

(1)

4.3 Ligand Affinity Chromatography

(1)

4.4 Final Purification Steps before Crystallization and Assembly of Complexes

(2)

4.5 Lipid Content during Purification

(1)

5 Final Quality Control, Monitoring Protein Stability, Aggregational State, Lipid, and Bound Detergent

(2)

6 Conclusions

(1)

Acknowledgments

(1)

References

(4)

Chapter 5 An Introduction to Detergents and Their Use in Membrane Protein Studies

(27)

Fabien Walas, Hiroyoshi Matsumura and Ben Luisi

1 Introduction

(1)

2 Physical Properties of Detergents Used in Membrane Protein Studies

(6)

2.1 Properties and Classification of Detergents

(1)

2.1.1 Properties of Detergents

(1)

2.1.2 Ionic Detergents

(1)

2.1.3 Non-Ionic Detergents

(1)

2.1.4 Zwitterionic Detergents

(1)

2.1.5 Amphipols

(1)

2.2 Lipopeptide Detergents

(1)

2.3 Supplements and Additives for Detergents

(1)

3 Extraction and Purification Procedure Using Common Detergents

(3)

3.1 Choice of Detergent

(1)

3.2 Purification of Membrane Proteins in the Presence of Detergents

(1)

3.2.1 Strategy and Method

(1)

3.2.2 Detergent Exchange or Removal

(1)

4 Use of Detergents in Membrane Protein Crystallization

(7)

4.1 Introduction

(1)

4.2 Membrane Protein Crystallization in Lipid Cubic Phase

(1)

4.3 Crystal Lattice Organization

(1)

4.4 Example of Detergent Interactions with β-Sheet Membrane Proteins

(1)

4.4.1 Crystal Structure of VceC, an Outer Membrane Protein from Vibrio Cholerae

(1)

4.4.2 Detergent Organization in Crystals of Monomeric Outer Membrane Phospholipase A

(1)

4.5 Example of Detergent and α-Helical Type Membrane Protein Contact

(1)

4.5.1 Crystal Structure of Rotor Rings

(1)

4.5.2 Structure of Bovine Rhodopsin in a Trigonal Crystal Form

(1)

4.6 A Synopsis of Detergent–Protein Interactions in Crystals

(2)

5 Conclusion

(1)

Acknowledgements

(1)

References

(9)

Section 2 Methods for Structural Characterization of Membrane Proteins

Chapter 6 Solution NMR Approaches to the Structure and Dynamics of Integral Membrane Proteins

(19)

John H. Bushweller, Tomasz Cierpicki and Yunpeng Zhou

1 Introduction

(1)

2 Protein Production and Optimization for NMR Studies

100

(2)

2.1 Protein Production

100

(1)

2.2 Sample Optimization

101

(1)

3 NMR Methodology for the Study of Integral Membrane Proteins

102

(5)

3.1 High Level Deuteration and Assignment Strategies Using TROSY-Based Experiments

102

(2)

3.2 Carbon Detected Experiments: Breaking the Limit of Sensitivity

104

(1)

3.3 Use of Methyl Protonation to Increase the Number of Nuclear Overhauser Effect-Derived Distance Constraints

105

(1)

3.4 Application of Electron-Nuclear Relaxation for Long Range Distances

106

(1)

3.5 Residual Dipolar Couplings

106

(1)

4 Solution NMR Structures of Helical Integral Membrane Proteins

107

(2)

4.1 F1Fo ATP Synthase Subunit c from E. coli

107

(1)

4.2 MerF

108

(1)

4.3 Mistic

109

(1)

5 Solution NMR Structures of β-Barrel Membrane Proteins

109

(2)

5.1 OmpA

110

(1)

5.2 OmpX

110

(1)

5.3 PagP

111

(1)

6 Solution NMR Characterization of Membrane Protein Dynamics

111

(2)

6.1 OmpA

112

(1)

6.2 PagP

112

(1)

7 Future Directions

113

(1)

References

114

(4)

Chapter 7 Membrane Proteins Studied by Solid-State NMR

118

(13)

Adam Lange and Marc Baldus

1 Introduction

118

(1)

2 Sample Preparation and Methodology

118

(3)

2.1 Isotope Labelling and Solid-State NMR Sample Preparation

118

(2)

2.2 Resonance Assignments and Structure Determination

120

(1)

3 Applications

121

(4)

3.1 Membrane Protein Structure

121

(1)

3.2 Ligand Binding to Membrane Proteins

121

(3)

3.3 Membrane Protein Dynamics

124

(1)

4 Conclusions

125

(1)

Acknowledgements

126

(1)

References

126

(5)

Chapter 8 Assessing Structure and Dynamics of Native Membrane Proteins

131

(21)

W. Kukulski, T. Kaufmann, T. Braun, H. Remigy, D. Fotiadis and A. Engel

Abstract

131

(1)

1 Introduction

131

(1)

2 Assembly of 2D Crystals

132

(3)

3 Electron Microscopy

135

(7)

3.1 Image Formations

135

(3)

3.2 Electron Diffraction

138

(1)

3.3 Specimen Preparation

138

(1)

3.4 Data Processing

139

(3)

4. Atomic Force Microscopy

142

(5)

4.1 Image Formation

142

(1)

4.2 Sample Preparation

143

(1)

4.3 Optimized Imaging Conditions

143

(1)

4.4 Imaging Native Membranes

144

(1)

4.5 Nanodissection

144

(1)

4.6 Image Processing

145

(2)

5 Conclusion and Perspectives

147

(1)

References

147

(5)

Chapter 9 State-of-the-Art Methods in Electron Microscopy, including Single-Particle Analysis

152

(21)

Vinzenz M. Unger

1 Introduction

152

(1)

2 Sample Preparation

153

(1)

3 Low-Dose Microscopy

154

(5)

3.1 Sample Holders

154

(3)

3.2 Radiation Damage and Low-Dose Imaging

157

(2)

4 Applications of CryoEM

159

(11)

4.1 Single-Particle Approaches

159

(1)

4.1.1 Generating a Data Set

160

(1)

4.1.2 Particle Classification

160

(1)

4.1.3 Euler Angle Determination

163

(1)

4.1.4 Structure Calculation

163

(1)

4.2 Electron Crystallography

164

(1)

4.2.1 2D Crystallization and Advantages of Crystalline Samples over Single Particles

165

(1)

4.2.2 Image Filtering and Lattice Straightening

166

(1)

4.2.3 Impact of CTF on Images of 2D crystals and CTF–Correction

167

(1)

4.2.4 Projection Density Maps and Calculation of 3D Structures

168

(2)

5 Examples

170

(1)

5.1 Single-Particle Reconstructions

170

(1)

5.2 Electron Crystallography

170

(1)

6 Conclusion

170

(1)

References

171

(2)

Chapter 10 Atomic Resolution Structures of Integral Membrane Proteins Using Cubic Lipid Phase Crystallization

173

(22)

Hartmut Luecke

1 Introduction

173

(4)

1.1 Nuclear Magnetic Resonance Techniques

173

(1)

1.2 Crystallography

174

(1)

1.3 Crystallization Techniques

174

(1)

1.3.1 Vapor Diffusion

174

(1)

1.3.2 Microdialysis Crystallization

175

(1)

1.4 Special Issues of Membrane Protein Crystallization

175

(1)

1.5 History of Membrane Protein Crystallization

176

(1)

1.6 Aim of this Chapter

177

(1)

2 Membrane Protein Crystals and Crystallization

177

(9)

2.1 Vapor Diffusion of Detergent-Solubilized Membrane Proteins

177

(2)

2.2 The Cubic Lipid Phase (CLP) Crystallization Method

179

(6)

2.3 Crystallization from Bicelles

185

(1)

2.4 Crystallization from Spherical Micelles

186

(1)

3 Advantages of Structures in a Native Setting at High Resolution

186

(2)

4 Conclusions

188

(1)

References

188

(7)

Section 3 New Membrane Protein Structures

Chapter 11 Aquaporins: Integral Membrane Channel Proteins

195

(17)

Robert M. Stroud, William E.C. Harries, John Lee, Shahram Khademi and David Savage

1 Introduction

195

(4)

2 The Exclusion Barrier to Ions and Protons in Aquaporins

199

(2)

2.1 Global Orientational Tuning by the NPA Motif

199

(2)

2.2 Helix Dipole

201

(1)

2.3 Electrostatic Desolvation Penalty

201

(1)

3 Selectivity in the Aquaporin Family

201

(2)

4 Permeation of Substances Other than Water and Glycerol

203

(1)

4.1 Conductance of Other Molecules

203

(1)

5 Aquaporin Monomer Associations and their Functional Implications

204

(5)

5.1 The Eye Lens: A Brief History of Aquaporin 0 Research

204

(1)

5.2 Aquaporin 0 Monomer Structure and Organization

205

(3)

5.3 Extracellular Domain Interactions

208

(1)

Acknowledgment

209

(1)

References

209

(3)

Chapter 12 Gas Channels for Ammonia

212

(23)

Shahram Khademi and Robert M. Stroud

1 Introduction

212

(1)

2 The Structure of Ammonia Channel

213

(9)

2.1 Overall Structure of AmtB: A New Family of 11-Crossing Proteins

213

(4)

2.2 A Membrane Protein with In-Plane Quasi Twofold Symmetry

217

(1)

2.3 The Ammonia Pathway

218

(4)

3 Reconstituted into Liposomes AmtB Acts as a Channel that Conducts NH3

222

(2)

4 The Mechanism of Conduction

224

(3)

4.1 pH-Dependent Effects

224

(2)

4.2 Competitive Inhibition

226

(1)

4.3 Transmembrane Potential

226

(1)

5 The Rh Proteins

227

(1)

6 Comparison with Aquaporins

228

(2)

7 Comparison with K+ Channel

230

(1)

Acknowledgment

230

(1)

References

230

(5)

Chapter 13 Channels in the Outer Membrane of Mycobacter

235

(17)

Georg E. Schulz

1 Introduction

235

(1)

2 Structure Determination

236

(4)

2.1 Protein Production

236

(2)

2.2 Crystallization

238

(1)

2.3 X-Ray Analysis

239

(1)

3 Structure Description

240

(5)

3.1 The Channel

240

(2)

3.2 0-Barrels

242

(2)

3.3 Protein Properties

244

(1)

4 The Outer Membrane

245

(4)

4.1 Membrane Structure

245

(3)

4.2 Porin Localization

248

(1)

5 Conclusion

249

(1)

Acknowledgments

249

(1)

References

249

(3)

Chapter 14 The Structure of the SecY Protein Translocation Channel

252

(18)

Bert Van Den Berg and Ian Collinson

1 Introduction

252

(3)

1.1 The Sec61/SecY Complex

253

(1)

1.2 The Three Different Translocation Modes

253

(2)

2 Structure Determination of the SecY Complex by Electron Cryo-Microscopy

255

(2)

3 Determination of the X-ray Crystal Structure of the SecY Complex

257

(2)

4 Description of the Structure of the SecY Complex

259

(4)

5 Post-Translational Translocation in Bacteria

263

(2)

5.1 A Model for Post-Translational Protein Translocation in Bacteria

265

(1)

6 Conclusions and Outlook

265

(1)

References

266

(4)

Chapter 15 Structure and Function of the Translocator Domain of Bacterial Autotransporters

270

(18)

Peter Van Ulsen, Piet Gros and Jan Tommassen

1 Introduction

270

(1)

2 The NalP Autotransporter

271

(1)

3 The Translocator Domain of Autotransporters

272

(1)

4 Purification and In Vitro Folding of the Na1P Translocator Domain

273

(4)

5 The Structure of the NalP Translocator Domain

277

(2)

6 Comparison of the NalP Translocator Domain to Other Translocator Domains and to TolC

279

(4)

7 The Autotransporter Secretion Mechanism

283

(2)

References

285

(3)

Chapter 16 X-Ray Crystallographic Structures of Sarcoplasmic Reticulum Ca²+-ATPase at the Atomic Level

288

(19)

Jesper Vuust Møller, Poul Nissen and Thomas Lykke-Møller Sørensen

1 Introduction

288

(1)

2 The Transport Scheme and Thermodynamics of Ca²+ Transport

289

(1)

3 Overall structure of Ca²+-ATPase

290

(2)

4 Transport Models

292

(1)

5 Initialization of the Cycle: Phosphorylation and Calcium Ion Occlusion

293

(4)

6 The Dephosphorylation Step and Proton Counter Transport

297

(3)

7 Getting Ca²+ in and out of the Membrane

300

(2)

8 Compact vs. Open Conformations of SERCA

302

(1)

9 Conclusions and Perspectives

303

(1)

References

303

(4)

Chapter 17 Comparison of the Multidrug Transporter EmrE Structures Determined by Electron Cryomicroscopy and X-ray Crystallography

307

(13)

C.G. Tate

1 Introduction

307

(2)

2 The Oligomeric State of EmrE

309

(3)

3 Transport Activity of EmrE

312

(1)

4 Structure of EmrE Determined by Electron Cryomicroscopy

312

(3)

5 Comparison of the EmrE Structure Determined by Electron Crystallography with a 3.8 Å Resolution Structure Determined by X-ray Crystallography

315

(2)

6 Conclusions

317

(1)

References

317

(3)

Chapter 18 Structure of Photosystems I and II

320

(29)

Raimund Fromme, Ingo Grotjohann and Petra Fromme

1 Introduction to Oxygenic Photosynthesis

320

(4)

2 Photosystem II

324

(8)

2.1 Overview

324

(1)

2.2 The Protein subunits in Photosystem II

325

(1)

2.2.1 The Core Subunits D1 and D2 (PsbA and PsbD)

325

(1)

2.2.2 The Antenna Proteins CP47 and CP43 (PsbB and PsbC)

325

(1)

2.2.3 Cytochrome b559 (PsbE and PsbF)

325

(1)

2.2.4 The Small Membrane-Intrinsic Subunits

327

(1)

2.2.5 The Lumenal Subunits PsbO, PsbV, and PsbU

327

(1)

2.3 The Electron Transport Chain of Photosystem II

327

(1)

2.3.1 The Acceptor Site of the Electron Transport Chain in Photosystem II

328

(1)

2.3.2 The Donor Site of the Electron Transfer Chain of Photosystem II

329

(2)

2.4 The Antenna System of Photosystem II

331

(1)

3 Photosystem I

332

(12)

3.1 Overview

332

(1)

3.2 The Protein Subunits of Photosystem I

332

(1)

3.2.1 The Core of Photosystem I: The Large Subunits PsaA and PsaB

333

(1)

3.2.2 The Small Transmembrane Subunits in Photosystem I

336

(1)

3.2.3 The Stromal Hump of PSI: PsaC, PsaD, and PsaE

338

(1)

3.3 The Electron Transfer Chain of Photosystem I

339

(1)

3.3.1 P700: The Primary Electron Donor

340

(1)

3.3.2 A: The Initial Electron Acceptor

340

(1)

3.3.3 A0: The First Stable Electron Acceptor

341

(1)

3.3.4 A1: The Phylloquinone

341

(1)

3.3.5 Fx: The First FeS Cluster

342

(1)

3.3.6 FA and FB: The Terminal FeS Clusters

342

(1)

3.4 The Antenna System of Photosystem I

342

(1)

3.4.1 The Chlorophylls

343

(1)

3.4.2 The Carotenoids

343

(1)

3.4.3 The Lipids in Photosystem I

344

(1)

4 Conclusion and Outlook

344

(1)

References

344

(5)

Chapter 19 Glutamate Receptor Ion Channels: Structural Insights into Molecular Mechanisms

349

(24)

Avinash Gill and Dean R. Madden.

1 Introduction

349

(2)

1.1 Physiological and Pathophysiologieal Roles of the Ionotropic Glutamate Receptors

350

(1)

1.2 Medicinal Chemistry

351

(1)

1.3 Ionotropic Glutamate Receptor Subunits Are Modular

351

(1)

2 Studies of the Ligand-Binding Domain

351

(7)

2.1 Overall Structure

353

(1)

2.2 Pharmacological Specificity

353

(1)

2.3 Ligand-Binding Domain Conformational Changes

354

(1)

2.4 Correlation with Channel Activation

355

(1)

2.5 Dimerization

356

(1)

2.6 Desensitization and the Stability of the Dimer Interface

356

(2)

3 The Functional Architecture of a Glutamate Receptor Ion Channel

358

(4)

3.1 Structure of a Complete Ionotropic Glutamate Receptor

358

(2)

3.2 The Role of the N-Terminal Domain in Subunit Assembly

360

(1)

3.3 The Organization of the Transmembrane Domains

361

(1)

4 A Working Model of AMPA Receptor Function

362

(2)

4.1 LBD Mutations Affecting Binding and Gating

363

(1)

4.2 Subunit Gating Behavior

363

(1)

5 Open Questions

364

(3)

5.1 Different Models of Partial Agonism

364

(2)

5.2 Multistate Kinetic Models

366

(1)

5.3 Structural Prospects

366

(1)

5.4 Auxiliary Proteins

367

(1)

References

367

(6)

Chapter 20 The Mitochondrial ADP/ATP Carrier

373

(17)

Eva Pebay-Peyroula

1 Introduction

373

(1)

2 Mitochondrial Carriers and ADP/ATP Carrier

374

(1)

3 Crystallization

375

(3)

4 Diffraction, Phasing and Model Building

378

(2)

5 Structure Analysis

380

(4)

6 Functional Implications

384

(2)

6.1 Nucleotide Binding

384

(1)

6.2 Conformational Changes

385

(1)

6.3 Transport Regulation

386

(1)

7 Future Developments and Conclusions

386

(1)

Acknowledgments

387

(1)

References

387

(3)

Subject Index

390

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Structural Biology of Membrane Proteins

Summary

Table of Contents

Supplemental Materials