Computational Modeling of Membrane Bilayers (eBook)

Cover 1
Computational Modeling of Membrane Bilayers 4
Copyright page 5
Contents 6
Contributors 12
Preface 18
Previous Volumes in Series 24
Chapter 1. Considerations for Lipid Force Field Development 28
I. Introduction 29
II. Quantum Mechanics and Molecular Dynamics Based Parameter Optimization 31
III. Membrane Targets and Related Issues 47
IV. Summary and Perspectives 66
References 69
Chapter 2. Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading? 76
I. Introduction 77
II. Importance of Long-Range Interactions in Simulations of Biological Systems 78
III. Overview of Methods and Their Applicability 79
IV. Non-Periodic Systems and Different Boundary Conditions 96
V. Applications and Latest Methodological Developments 98
VI. Final Notes on Software, Accuracy, and Speed 107
References 108
Chapter 3. Time and Length Scales in Lipid Bilayer Simulations 118
I. Introduction 118
II. Area per Lipid and Finite Size Effects 121
III. Undulations 123
IV. Peristaltic Fluctuations 128
V. Hydrocarbon Chain Dynamics 131
VI. Lateral Diffusion of Lipids 132
References 134
Chapter 4. Molecular Dynamics Simulation of Lipid-Protein Interactions 138
I. Introduction 139
II. Force Fields 141
III. Combining Force Fields 144
IV. Sampling Concerns 150
V. Validation of Lipid-Protein Simulations 152
VI. Conclusion and Perspective 154
References 155
Chapter 5. Implicit Modeling of Membranes 158
I. Introduction 158
II. Classes of Models 160
III. Interesting Problems in Implicit Membrane Modeling 173
IV. Conclusion 177
References 177
Chapter 6. Blue Matter: Scaling of N-Body Simulations to One Atom per Node 186
I. Introduction 187
II. Background on Massively Parallel Biomolecular Simulation 189
III. Inherent Concurrency of Molecular Dynamics 191
IV. Parallel Decompositions 194
V. Results 198
VI. Summary and Conclusions 203
References 205
Chapter 7. Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior 208
I. Multiscale Aspects of Membrane Simulation: A Brief Review 209
II. New Multiscale Methods for Membrane Simulations 214
III. Selected Applications 228
IV. Summary 246
References 246
Chapter 8. Interactions between Small Molecules and Lipid Bilayers 254
Abbreviations 255
I. Introduction 255
II. Partitioning of Small Molecules in Lipid Bilayers 259
III. Conclusions 279
References 280
Chapter 9. On the Nature of Lipid Rafts: Insights from Molecularly Detailed Simulations of Model Biological Membranes Containing Mixtures of Cholesterol and Phospholipids 284
I. Introduction 284
II. Simulations 289
III. Concluding Remarks 302
References 303
Chapter 10. Atomistic and Mean Field Simulations of Lateral Organization in Membranes 308
I. Introduction 308
II. Molecular Dynamics Simulation of Hydrated Lipid Bilayers 311
III. General Issues in Force Feld Development for Biomolecular Simulations 312
IV. Simulation of Heterogeneous Lipid membranes 320
V. Application: A Mean Field Based Lipid Bilayer Model Based on MDSimulations 327
VI. Summary 335
References 336
Chapter 11. Molecular Modeling of the Structural Properties and Formation of High-Density Lipoprotein Particles 340
I. Introduction 340
II. Methods 345
III. Structure of Discoidal HDL 349
IV. Formation of Discoidal HDL 354
V. Conclusions 363
References 364
Chapter 12. Gas Conduction of Lipid Bilayers and Membrane Channels 370
I. Introduction 371
II. Computational Methodology 373
III. Lipid-Mediated Gas Conduction 375
IV. Protein-Mediated Gas Conduction 382
V. Concluding Remarks 389
References 390
Chapter 13. A Brief Introduction to Voltage-Gated K+ Channels 396
I. Introduction 396
II. Structure of Kv Channels and Gating Mechanisms 397
III. Free Energy and Membrane Voltage 406
IV. Conclusion 409
References 410
Chapter 14. Computational Models for Electrified Interfaces 412
I. Introduction 412
II. General Concepts of Surface Charge and Co/Counter Ions 413
III. Continuum Models 414
IV. Bridging from the Continuum to Molecular Calculations 416
V. All-Atom Models 420
VI. Long-Term Trends 424
VII. Summary 427
References 427
Chapter 15. Charged Protein Side Chain Movement in Lipid Bilayers Explored with Free Energy Simulation 432
I. Introduction 433
II. Theoretical Perspectives 436
III. Experimental Hydrophobicity and Membrane Partitioning Models 438
IV. Fully Atomistic Computer Simulations 442
V. Reconciling Simulation and Experiment 468
VI. Conclusion and Implications 475
References 480
Index 488