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Biophysical analysis of membrane proteins : investigating structure and function / edited by Eva Pebay-Peyroula. — Weinheim : Wiley-VCH, c2008. – (58.1782/B615m) |
Contents
Contents
Preface XIII
The Editor XV
List of Contributors XVII
Part1 Introduction
1 High-Resolution Structures of Membrane Proteins: From X-Ray Crystallography to an Integrated Approach of Membranes 3
1.1 Membranes: A Soft Medium? 3
1.2 Current Knowledge on Membrane Protein Structures 4
1.3 X-Ray Crystallography 8
1.4 Recent Examples 16
1.5 Future Developments in X-Ray Crystallography of Membrane Proteins 23
1.6 Conclusions 25
Part II Structural Approaches
2 Membrane Protein Structure Determination by Electron Cryo-Microscopy 31
2.1 Introduction 32
2.2 Single-Particle Electron Microscopy 33
2.3 Structure Determination from 2-Dimensional Crystals 41
2.4 Helical Analysis of Tubes 49
2.5 Conclusions 51
3 Introduction to Solid-State NMR and its Application to Membrane Protein-Ligand Binding Studies 55
3.1 Introduction 55
3.2 Solid-State NMR 57
3.3 Examples: Receptor-Ligand Studies by Solid-State NMR 70
Part III Molecular Interaction and Large Assemblies
4 Analytical Ultracentrifugation: Membrane Protein Assemblies in the Presence of Detergent 91
4.1 Introduction 91
4.2 Instrumentation and the Principle of Typical Experiments 92
4.3 General Theoretical Background 93
4.4 Membrane Proteins: Measurement of Rs， Mb， M， and v 97
4.5 Sedimentation Equilibrium Data Analysis 103
4.6 Sedimentation Velocity Data Analysis 108
4.7 Analytical Ultracentrifugation and SANS/SAXS 116
4.8 Conclusions 116
5 Probing Membrane Protein Interactions with Real-Time Biosensor Technology 121
5.1 Rich Introduction 121
5.2 Interactions of Extracellular Domains 123
5.3 Interactions of Soluble Proteins with Lipid Layers 124
5.4 Interactions of Proteins Embedded in Lipid Layers 129
5.5 Interactions of Membrane-Solubilized Proteins 131
5.6 Summary 138
6 Atomic Force Microscopy: High-Resolution Imaging of Structure and Assembly of Membrane Proteins 141
6.1 Atomic Force Microscopy 141
6.2 Combined Imaging and Force Measurements by AFM 145
6.3 High-Resolution Imaging by AFM 147
6.4 Conclusions 153
6.5 Feasibilities， Limitations， and Outlook 153
Part IV Dynamics
7 Molecular Dynamics Studies of Membrane Proteins: Outer Membrane Proteins and Transporters 161
7.1 Introduction 161
7.2 Outer Membrane Proteins 163
7.3 Cytoplasmic Membrane Transport Proteins 172
7.4 Conclusions 179
8 Understanding Structure and Function of Membrane Proteins Using Free Energy Calculations 187
8.1 Introduction 187
8.2 Theoretical Underpinnings of Free Energy Calculations 188
8.3 Point Mutations in Membrane Proteins 196
8.4 Assisted Transport Phenomena Across Membranes 199
8.5 Recognition and Association in Membrane Proteins 204
8.6 Conclusions 206
9 Neutrons to Study the Structure and Dynamics of Membrane Proteins 213
9.1 General Introduction 213
9.2 Introduction to Neutrons 213
9.3 Introduction to Bacteriorhodopsin and the Purple Membrane 219
9.4 Methods for Labeling 221
9.5 Neutrons for Structural Studies of Membrane Proteins 222
9.6 Neutrons for Dynamical Studies of Membrane Proteins 231
9.7 Take-Home Message 237
Part V Spectroscopies
10 Circular Dichroism: Folding and Conformational Changes of Membrane Proteins 243
10.1 Introduction 243
10.2 Secondary Structure Composition 244
10.3 Tertiary Structure Fingerprint 250
10.4 Extrinsic Chromophores 252
10.5 Conformational Changes upon Ligand Binding 252
10.6 Folding/Unfolding 254
10.7 Conclusion and Perspectives 255
11 Membrane Protein Structure and Conformational Change Probed using Fourier Transform Infrared Spectroscopy 259
11.1 Introduction 259
11.2 FTIR Spectroscopy 260
11.3 Vibrational Spectra of Membrane Proteins 267
11.4 Applications of FTIR To Membrane Proteins 273
11.5 Conclusions and Future Directions 286
12 Resonance Raman Spectroscopy of a Light-Harvesting Protein 289
12.1 Introduction 289
12.2 Principles of Resonance Raman Spectroscopy 289
12.3 Primary Processes in Photosynthesis 291
12.4 Photosynthesis in Plants 292
12.5 The Light-Harvesting System of Plants 293
12.6 Protection against Oxidative Stress: Light-Harvesting Regulation in Plants 294
12.7 Raman studies of LHCII 297
12.8 Crystallographic Structure of LHCII 301
12.9 Properties of LHCII in Crystal 302
12.10 Recent Developments and Perspectives 305
Part Vl Exploring Structure-Function Relationships in Whole Cells
13 Energy Transfer Technologies to Monitor the Dynamics and Signaling Properties of G-Protein-Coupled Receptors in Living Cells 311
13.1 Introduction 311
13.2 Fluorescence Resonance Energy Transfer (FRET) 312
13.3 FRET Using GFP and its Various Mutants 314
13.4 BRET as an Alternative to FRET 315
13.5 Time-Resolved FRET (TR-FRET) and Homogeneous Time-Resolved(HTRF) 318
13.6 New Developments in Fluorescent Labeling of Membrane Proteins 320
13.7 Ligand-Receptor Interaction Monitored by FRET 322
13.8 Fast GPCR Activation Process Monitored in Living Cells 323
13.9 FRET and BRET Validated the Constitutive Oligomerization of GPCR in Living Cells 324
13.10 FRET and BRET Changed the Concept of G-Protein Activation 326
13.11 GPCRs as Part of Large Signaling Complexes 327
13.12 Conclusion and Future Prospects 328
Index 335
