| | 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 |