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Books | August 2005 | Protein-Lipid Interactions | Table of contents
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Contents  
 
Preface VII
List of Contributors XIX
Part 1 How Lipids Shape Proteins  
1 Lipid Bilayers, Translocons and the Shaping of Polypeptide Structure
Stephen H. White, Tara Hessa, and Gunnar von Heijne
3
1.1 Introduction 3
1.2 Membrane Proteins: Intrinsic Interactions 5
1.2.1 Physical Determinants of Membrane Protein Stability: The Bilayer Milieu 5
1.2.2 Physical Determinants of Membrane Protein Stability: Energetics of Peptides in Bilayers 9
1.2.3 Physical Determinants of Membrane Protein Stability: Helix--Helix Interactions in Bilayers 13
1.3 Membrane Proteins: Formative Interactions 14
1.3.1 Connecting Translocon-assisted Folding to Physical Hydrophobicity Scales: The Interfacial Connection 14
1.3.2 Connecting Translocon-assisted Folding to Physical Hydrophobicity Scales: Transmembrane Insertion of Helices 16
1.4 Perspectives 21
References 22
2 Folding and Stability of Monomeric -Barrel Membrane Proteins
Jörg H. Kleinschmidt
27
2.1 Introduction 27
2.2 Stability of -Barrel Membrane Proteins 29
2.2.1 Thermodynamic Stability of FepA in Detergent Micelles 29
2.2.2 Thermodynamic Stability of OmpA in Phospholipids Bilayers 30
2.2.3 Thermal Stability of FhuA in Detergent Micelles 31
2.3 Insertion and Folding of Transmembrane -Barrel Proteins 32
2.3.1 Insertion and Folding of -Barrel Membrane Proteins in Micelles 32
2.3.2 Oriented Insertion and Folding into Phospholipid Bilayers 32
2.3.3 Assemblies of Amphiphiles Induce Structure Formation in -Barrel Membrane Proteins 33
2.3.4 Electrophoresis as a Tool to Monitor Insertion and Folding of -Barrel Membrane Proteins 34
2.3.5 pH and Lipid Headgroup Dependence of the Folding of -Barrel Membrane Proteins 35
2.4 Kinetics of Membrane Protein Folding 35
2.4.1 Rate Law for -Barrel Membrane Protein Folding and Lipid Acyl Chain Length Dependence 35
2.4.2 Synchronized Kinetics of Secondary and Tertiary Structure Formation of the -Barrel OmpA 36
2.4.3 Interaction of OmpA with the Lipid Bilayer is Faster than the Formation of Folded OmpA 36
2.5 Folding Mechanism of the -Barrel of OmpA into DOPC Bilayers 37
2.5.1 Multistep Folding Kinetics and Temperature Dependence of OmpA Folding 37
2.5.2 Characterization of Folding Intermediates by Fluorescence Quenching 38
2.5.3 The -Barrel Domain of OmpA Folds and Inserts by a Concerted Mechanism 40
2.6 Protein--Lipid Interactions at the Interface of -Barrel Membrane Proteins 42
2.6.1 Stoichiometry of the Lipid--Protein Interface 42
2.6.2 Lipid Selectivity of -Barrel Membrane Proteins 42
2.7 Orientation of -Barrel Membrane Proteins in Lipid Bilayers 43
2.7.1 Lipid Dependence of the -Barrel Orientation Relative to the Membrane 43
2.7.2 Inclination of the -Strands Relative to the -Barrel Axis in Lipid Bilayers 44
2.7.3 Hydrophobic Matching of the -Barrel and the Lipid Bilayer 44
2.8 In vivo Requirements for the Folding of OMPs 45
2.8.1 Amino Acid Sequence Constraints for OmpA Folding in vivo 45
2.8.2 Periplasmic Chaperones 45
2.8.3 Insertion and Folding of the -Barrel OmpA is Assisted by Skp and LPS 46
2.8.4 Role of Omp85 in Targeting or Assembly of -Barrel Membrane Proteins 48
2.9 Outlook 51
References 52
3 A Paradigm of Membrane Protein Folding: Principles, Kinetics and Stability of Bacteriorhodopsin Folding
Paula J. Booth
57
3.1 Introduction 57
3.2 Principles of Transmembrane -Helical Membrane Protein Folding: A Thermodynamic Model for Bacteriorhodopsin 59
3.3 Bacteriorhodopsin Stability 60
3.3.1 Side-chain Contributions to Helix Interactions and the Role of Pro 61
3.3.2 Helix-connecting Loops 62
3.4 Pulling the Protein Out of the Membrane 63
3.5 Bacteriorhodopsin Folding Kinetics 64
3.5.1 Cotranslational Insertion 65
3.5.2 Retinal Binding Studies to Apomembrane 65
3.5.3 Unfolding, Refolding and Kinetic Studies in vitro 67
3.6 Controlling Membrane Protein Folding 69
3.7 Conclusions 71
3.7.1 Summary of Bacteriorhodopsin Folding 71
3.7.2 Implications for Transmembrane -Helical Membrane Protein Folding 73
References 75
4 Post-integration Misassembly of Membrane Proteins and Disease
Charles R. Sanders
81
4.1 Introduction 81
4.2 A Given IMP May be Subject to Numerous Disease-linked Mutations 82
4.3 Ligand Rescue of Misassembly-prone Membrane Proteins: Implications 84
4.4 What IMP Properties Affect Folding Efficiency in the Cell? 87
4.5 Common Mutations in Transmembrane Domains That Lead to Misassembly and Disease 89
4.6 Correlating Biophysical, Cell-biological and Biomedical Measurements 90
References 91
Part 2 How Proteins Shape Lipids  
5 A Census of Ordered Lipids and Detergents in X-ray Crystal Structures of Integral Membrane Proteins
Michael C. Wiener
97
5.1 Introduction 97
5.2 Results 98
5.3 Illustrative Examples of Selected Bound Lipids, Detergents and Related Molecules 103
5.3.1 Integral Membrane Protein Structures Contain Ordered Native Lipids 103
5.3.2 Structures of Lipids in Membrane Protein Co-crystals Differ from Those in Pure Lipid Crystals 107
5.3.3 Native Lipids can Stabilize and Preserve Protein--Protein Interfaces 108
5.3.4 Multiple Acyl Chain Conformations Exist for Efficient Packing with Protein Interfaces 108
5.3.5 Lipid Acyl Chains Interact Primarily with Aliphatic and Aromatic Amino Acid Side-chains 109
5.3.6 Unusual Lipid/Detergent Conformations Occur at the Protein--Lipid Interface 109
5.3.7 A Bilayer Structure is Present in Crystals Grown from the LCP 112
5.4 Conclusion 114
References 115
6 Lipid and Detergent Interactions with Membrane Proteins Derived from Solution Nuclear Magnetic Resonance
Ashish Arora
119
6.1 Introduction 119
6.2 Heteronuclear Solution NMR of Protein/Detergent Complexes 120
6.3 Choice of Detergents 122
6.4 Size and Shape of Pure Detergent Micelles and Detergent/Protein Complexes 124
6.5 Sample Preparation for Solution NMR Measurements 125
6.6 Protein/Detergent Interactions Monitored by NMR Spectroscopy 128
6.7 Dynamics and Conformational Transitions of Membrane Proteins in Detergent Micelles 130
6.8 MD Simulations of Protein/Detergent Complexes 131
6.9 Implications on the Structure and Function of Membrane Proteins in Biological Membranes 133
References 134
Part 3 Membrane Penetration by Toxins  
7 Lipid Interactions of -Helical Protein Toxins
Gregor Anderluh and Jeremy H. Lakey
141
7.1 Introduction 141
7.1.1 The Two Secondary Structures Compared 141
7.1.2 Lessons from a Potassium Channel 145
7.2 Pore-forming Colicins 145
7.2.1 Outer Membrane Interactions 146
7.2.2 Colicin A Requires Acidic Lipids 147
7.2.3 The Open Channel 148
7.2.4 The Colicin--Phospholipid Complex 149
7.2.5 Other Similar Proteins 150
7.3 Actinoporins 151
7.3.1 Initial Lipid Binding 152
7.3.2 Helix Insertion 154
7.3.3 The Oligomeric Pore 155
7.4 Conclusion 156
References 157
8 Membrane Recognition and Pore Formation by Bacterial Pore-forming Toxins
Alejandro P. Heuck and Arthur E. Johnson
163
8.1 Introduction 163
8.2 Classification of Bacterial PFTs 163
8.2.1 -PFTs 164
8.2.2 -PFTs 166
8.3 A General Mechanism of Pore Formation? 166
8.4 Membrane Recognition 169
8.4.1 Recognition of Specific Membrane Lipids 170
8.4.2 Recognition of Membrane-anchored Proteins or Carbohydrates 172
8.4.3 The Role of Membrane Lipid Domains 173
8.5 Oligomerization on the Membrane Surface 175
8.5.1 Oligomerization Triggered by Lipid-induced Conformational Changes 176
8.5.2 Oligomerization Following Proteolytic Activation of Toxins 178
8.6 Membrane Penetration and Pore Formation 179
8.7 Unresolved Issues 181
References 183
9 Mechanism of Membrane Permeation and Pore Formation by Antimicrobial Peptides
Yechiel Shai
187
9.1 Introduction 187
9.2 The Cell Membrane is the Major Binding Site for Most Cationic Antimicrobial Peptides 188
9.2.1 Non-receptor-mediated Interaction of Antimicrobial Peptides with their Target Cells 189
9.2.2 A Receptor-mediated Interaction of Antimicrobial Peptides with their Target Cells 191
9.3 Parameters Involved in the Selection of Target Cells by Antimicrobial Peptides 192
9.3.1 The Role of the Composition of the Cell Wall and the Cytoplasmic Membrane 193
9.3.2 The Role of the Peptide Chain and Its Organization 194
9.3.2.1 The Extent of Hydrophobicity and Distribution of Positively-charged Amino Acids Along the Peptide Chain 194
9.3.2.2 The Stability of the Amphipathic Structure 194
9.3.2.3 The Ability of a Peptide to Self-associate in Solution and/or in Membranes 195
9.3.2.4 Fatty Acid Modification can Compensate for the Hydrophobicity and Amphipathicity of the Peptide Chain 200
9.4 The Lethal Event Caused by Antimicrobial Peptides 201
9.5 How do Antimicrobial Peptides Damage the Integrity of the Target Cell Membrane? 202
9.5.1 Membrane-imposed Amphipathic Structure 202
9.5.2 Molecular Mechanisms of Membrane Permeation 204
9.5.2.1 Pore Formation via the Barrel--Stave Model 204
9.5.2.2 The Carpet Model 205
9.5.3 The Molecular Architecture of the Permeation Pathway 208
9.5.3.1 Toroidal Pores 208
9.5.3.2 Channel Aggregates/Hydrophobic Pores 208
9.6 Summary and Conclusions 209
References 210
Part 4 Mechanisms of Membrane Fusion  
10 Cell Fusion in Development and Disease
Benjamin Podbilewicz and Leonid V. Chernomordik
221
10.1 Introduction 221
10.2 Developmental Cell Fusion for Health 221
10.2.1 Muscles 222
10.2.1.1 Vertebrates 222
10.2.1.2 Drosophila 223
10.2.2 C. elegans 226
10.2.2.1 Epithelial Cell Fusion Assay in C. elegans 227
10.2.2.2 Control of Cell Fusion 227
10.2.2.3 Developmental Genetics of Cell Fusion in C. elegans 227
10.2.2.4 eff-1 Mutant Epidermal Cells do not Initiate Cell Membrane Fusion 228
10.2.2.5 eff-1-mediated Cell Fusion is Essential for Healthy Organogenesis 228
10.2.2.6 eff-1 Encodes Novel Type I Membrane and Secreted Proteins 230
10.2.2.7 eff-1 is Highly Expressed in Epidermal Cells Ready to Fuse 230
10.2.2.8 eff-1 is Sufficient for Cell Membrane Fusion in vivo 230
10.2.2.9 Tissue-specific Fusogenic Activity of eff-1 in Pharyngeal Muscles 231
10.2.3 Comparison between Cell Fusion in a Worm, a Fly and Vertebrates 231
10.3 Cell Fusion in Diseases 233
10.3.1 Cell Fusion Mediated by Enveloped Viruses 233
10.3.1.1 Dissection of Viral Membrane Fusion 234
10.3.1.2 Initiation and Expansion of Membrane Fusion 234
10.3.1.3 Protein--Protein and Protein--Lipid Interactions in Membrane Fusion 235
10.3.1.4 The Role of Fusion Proteins Outside the Fusion Site 236
10.3.1.5 HA Insiders Initiate Hemifusion and HA Outsiders Expand Fusion Pores 236
10.3.1.6 Models for Final Expansion of Fusion Pores 237
10.4 Dissection of Developmental Fusion Based on Viral Fusion Analogies 239
10.4.1 Activation of a Developmental Fusogen 239
10.4.2 Dissection of Developmental Cell Fusion 239
10.4.3 Direct Cell Fusion Promotion or Indirect Relaxation of Fusion Blocks 240
10.5 Concluding Remarks 240
References 241
11 Molecular Mechanisms of Intracellular Membrane Fusion
Olga Vites and Reinhard Jahn
245
11.1 Introduction 245
11.2 Intracellular Fusion Reactions -- An Overview 246
11.3 Tethering and Docking 247
11.4 SNARE Proteins -- The Fusion Catalysts? 249
11.4.1 Assembly--Disassembly Cycle of SNARE Proteins 249
11.4.2 N-terminal Domains of SNAREs -- Recruiting Proteins or Regulating SNARE Function? 251
11.4.3 Zippering Model for SNARE-mediated Membrane Fusion 252
11.4.4 Trans-complexes -- Intermediates in the Fusion Pathway? 253
11.4.5 Acceptor Complexes, Topology and Specificity 256
11.4.5.1 SNARE Acceptor Complexes 256
11.4.5.2 Topology of SNAREs 257
11.4.5.3 Specificity of SNAREs 258
11.4.6 Challenges of the SNARE Hypothesis 259
11.4.6.1 Persistence of Fusion in Spite of SNARE Deletions 260
11.4.6.2 Late-acting Factors Uncovered in Yeast Vacuolar Fusion 260
11.4.6.3 Exocytosis of Cortical Granules in Sea Urchin Oocytes 262
11.5 SM Proteins and Other Regulators 262
11.5.1 SM Proteins 263
11.6 Fusion Pores 264
11.6.1 Measuring Fusion Pore Opening and Closure 265
11.6.2 The Role of Proteins in Controlling Fusion Pore Opening 266
11.7 Concluding Remarks 267
List of Abbreviations 267
References 268
12 Interplay of Proteins and Lipids in Virus Entry by Membrane Fusion
Alex L. Lai, Yinling Li, and Lukas K. Tamm
279
12.1 Introduction 279
12.2 Fusion of Pure Lipid Bilayers 281
12.3 Viral Protein Sequences that Mediate Lipid Bilayer Fusion 284
12.3.1 Fusion Peptides 284
12.3.2 Transmembrane Domains 285
12.3.3 Other Regions of the Fusion Protein 285
12.4 Interactions of Fusion Peptides with Lipid Bilayers 286
12.4.1 HIV Fusion Peptide--Bilayer Interactions 287
12.4.2 Influenza Fusion Peptide Structure 288
12.4.3 Influenza Fusion Peptide Mutants 290
12.4.4 Binding of Fusion Peptides to Lipid Bilayers 290
12.4.5 Sendai, Measles and Ebola Fusion Peptide--Bilayer Interactions 290
12.4.6 Perturbation of Bilayer Structure by Fusion Peptides 291
12.5 Interactions of Transmembrane Domains with Lipid Bilayers 292
12.6 Structure--Function (Fusion) Relationships of Membrane-interactive Viral Fusion Protein Domains 294
12.6.1 Fusion Peptide Mutants 294
12.6.2 Transmembrane Domain Mutants 295
12.7 Possible Mechanisms for Initiating the Formation of Viral Fusion Pores 296
References 300
Part 5 Cholesterol, Lipid Rafts, and Protein Sorting  
13 Protein--Lipid Interactions in the Formation of Raft Microdomains in Biological Membranes
Akihiro Kusumi, Kenichi Suzuki, Junko Kondo, Nobuhiro Morone, and Yasuhiro Umemura
307
13.1 Many Plasma Membrane Functions are Mediated by Molecular Complexes, Microdomains and Membrane Skeleton-based Compartments 307
13.2 Timescales, Please! 309
13.3 Four Types of Membrane Domains 310
13.4 The Cell Membrane is a Two-dimensional Non-ideal Liquid Containing Dynamic Structures on Various Time-Space Scales 314
13.5 A Definition of Raft Domains 315
13.6 The Original Raft Hypothesis 316
13.7 Are there Raft Domains in Steady-state Cells in the Absence of Extracellular Stimulation? 316
13.7.1 Standard Immunofluorescence or Immunoelectron Microscopy Failed to Detect Raft-like Domains in the Plasma Membrane of Steady-state Cells 317
13.7.2 The Recovery of a Molecule in Detergent-resistant Membrane (DRM) Fractions Might Infer its Raft Association in the Cell Membrane, but the Relationship between DRM Fractions and Raft Domains is Complicated 317
13.7.3 The Size of Rafts in Plasma Membranes of Steady-state Cells may be 10 nm or Less 319
13.7.4 Mushroom Model for the Steady-state Raft 322
13.8 Stabilized Rafts Induced by Protein Clustering in Plasma and Golgi Membranes 324
13.8.1 Clustering of Raft Molecules by Ligand Binding or Crosslinking Induces Stabilized Rafts (Receptor-cluster Rafts) 324
13.8.2 How can Raft Molecule Clustering Induce Stabilized Rafts? 324
13.9 Can Receptor-cluster Rafts Work as Platforms to Facilitate the Assembly of Raftophilic Molecules? 326
13.9.1 Benchmarks for Experiments Examining the Colocalization of Raftophilic Molecules 326
13.9.2 Simultaneous Crosslinking of Two GPI-anchored Receptors 327
13.9.3 Sequential Crosslinking of One Species of GPI-anchored Receptors Followed by Crosslinking of a Second Species without Fixation 328
13.9.4 Examination of the Recruitment of Non-crosslinked Second Raftophilic Molecules to Crosslinked GPI-anchored Receptor Clusters 328
13.9.5 Difficulty in Colocalization Experiments using Raftophilic Molecules: Low Levels of Colocalization and Quantitative Reproducibility Due to Sensitivity to Subtle Differences in Experimental Conditions and Protocols 329
13.10 Timescales Again! Transient Colocalization of Raftophilic Molecules 329
13.11 Modified Raft Hypothesis 331
References 332
14 Protein and Lipid Partitioning in Locally Heterogeneous Model Membranes
Petra Schwille, Nicoletta Kahya, and Kirsten Bacia
337
14.1 Introduction: Why Should We Use Simple Model Membranes to Gain Insight into Complex Membrane Organization? 337
14.1.1 Relation of Domain Structure to a Biological Function 337
14.1.2 An Accessible Detection Method 338
14.1.3 The Term Raft 338
14.2 Biomimetic Membranes 340
14.2.1 GUVs: Properties and Preparation 342
14.3 Methods of Investigation of Domain Formation in Biomimetic Membranes 343
14.3.1 Electron Microscopy 343
14.3.2 Atomic Force Microscopy (AFM) 343
14.3.3 Near-field Scanning Optical Microscopy (NSOM) 344
14.3.4 Fluorescence Imaging (Confocal, Multi-photon) 344
14.3.5 Fluorescence Photobleaching Recovery (FPR) or Fluorescence Recovery after Photobleaching (FRAP) 344
14.3.6 Single Particle Tracking (SPT) 344
14.3.7 Fluorescence Correlation Spectroscopy (FCS) 345
14.4 Lipid Domain Assembly in GUVs 345
14.4.1 Phase Separation 345
14.4.1.1 Can Cellular Membrane Domains be Regarded as Phase Domains? 345
14.4.1.2 Properties of Lipid Bilayer Phases 347
14.4.1.3 Co-existence of Lipid Bilayer Phases 348
14.4.1.4 Lipid Phase Diagrams 348
14.4.2 Binary Lipid Systems 348
14.4.3 Ternary Lipid Systems 351
14.4.4 Effect of Sterols on Lipid Segregation 353
14.4.5 Lipid Dynamics in Domain-exhibiting GUVs 354
14.4.5.1 Fluidizing Effect of Cholesterol for High-Tm Lipids 355
14.4.5.2 Condensing Effect of Cholesterol for Low-Tm Lipids 356
14.5 Spatial Organization and Dynamics of Membrane Proteins in GUVs 357
14.6 From Model to Cellular Membranes 358
14.6.1 Model Membranes Constitute Test Systems for Developing New and Improving Existing Detection Techniques 358
14.6.2 Direct Comparison Between Results Obtained on Model and Native Membranes 361
14.6.3 Model Membranes Demonstrate What Structures Can be Potentially Formed by Lipids and Proteins, and Suggest Mechanisms for Fulfilling in vivo Functions 361
References 362
Part 6 Targeting of Extrinsic Membrane Protein Modules to Membranes and Signal Transduction  
15 In vitro and Cellular Membrane-binding Mechanisms of Membrane-targeting Domains
Wonhwa Cho and Robert V. Stahelin
369
15.1 Introduction 369
15.2 Membrane Interactions of Membrane-targeting Domains 370
15.2.1 Interfacial Location of Membrane-targeting Domains 370
15.2.2 Energetics and Kinetics of Membrane--Protein Interactions 371
15.3 C1 Domains 373
15.3.1 Occurrence and Structure 373
15.3.2 Lipid Specificity 374
15.3.3 Membrane-binding Mechanisms 374
15.3.4 Subcellular Localization 375
15.4 C2 Domains 376
15.4.1 Occurrence and Structure 376
15.4.2 Lipid Specificity 376
15.4.3 Membrane Binding Mechanisms 377
15.4.4 Subcellular Localization 378
15.5 PH Domains 378
15.5.1 Occurrence, Structure and Lipid Specificity 378
15.5.2 Membrane-binding Mechanisms 380
15.5.3 Subcellular Localization 380
15.6 FYVE Domains 380
15.6.1 Occurrence, Structure and Lipid Specificity 380
15.6.2 Membrane-binding Mechanism 382
15.6.3 Subcellular Localization 383
15.7 PX Domains 384
15.7.1 Occurrence, Structure and Lipid Specificity 384
15.7.2 Membrane-binding Mechanism 385
15.7.3 Subcellular Localization 385
15.8 ENTH and ANTH Domains 387
15.8.1 Occurrence, Structure and Lipid Specificity 387
15.8.2 Membrane-binding Mechanism 387
15.9 BAR Domains 389
15.10 FERM Domains 390
15.11 Tubby Domains 391
15.12 Other Phosphoinositide-binding Domains 391
15.13 Perspectives 392
References 393
16 Structure and Interactions of C2 Domains at Membrane Surfaces
David S. Cafiso
403
16.1 Introduction 403
16.2 C2 Domains: Ca2+-dependent and Ca2+-independent Membrane Binding 404
16.3 What Drives Membrane Targeting of C2 Domains? 405
16.4 Electrostatic Binding of Simple Linear Protein Motifs 406
16.5 The Results of Electrostatic Calculations on C2 Domains 408
16.6 Determining the Interactions and Positions of C2 Domains 410
16.6.1 Site-directed Mutagenesis 410
16.6.2 Chemical Labeling 410
16.6.3 Fluorescence 411
16.6.4 Site-directed Spin Labeling (SDSL) to Determine C2 Domain Orientation 411
16.7 Proteins with Multiple C2 Domains 416
16.8 Interactions of Phosphoinositides with C2 Domains 417
References 418
17 Structural Mechanisms of Allosteric Regulation by Membrane-binding Domains
Bertram Canagarajah, William J. Smith, and James H. Hurley
423
17.1 Introduction 423
17.2 How Membranes and PH Domains Regulate Rho Family-specific Guanine Nucleotide Exchange Factors (GEFs) 424
17.2.1 DH and PH Domain Rho GEFs 425
17.2.2 Regulation of GEF Activity by PH Domains 425
17.3 Regulation of G-protein Receptor Kinase (GRK) 2 Activity by Lipids and the Gbc Subunit at the Membrane 429
17.4 Lipid Activation of Rac-GAP Activity: b2-Chimaerin 432
17.4.1 The C1 Domain of b2-Chimaerin is Buried 432
17.4.2 Mechanism of Allosteric Rac-GTPase Activation by the C1 Domain 434
References 435
Subject Index 437

 
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