The need for information in the understanding of membrane systems has been caused by three things - an increase in computer power; methodological developments and the recent expansion in the number of researchers working on it worldwide. However, there has been no up-to-date book that covers the application of simulation methods to membrane systems directly and this book fills an important void in the market. It provides a much needed update on the current methods and applications as well as highlighting recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The objectives are to show how simulation methods can provide an important contribution to the understanding of these systems. The scope of the book is such that it covers simulation of membranes and membrane proteins, but also covers the more recent methodological developments such as coarse-grained molecular dynamics and multiscale approaches in systems biology. Applications embrace a range of biological processes including ion channel and transport proteins. The book is wide ranging with broad coverage and a strong coupling to experimental results wherever possible, including colour illustrations to highlight particular aspects of molecular structure. With an internationally respected list of authors, its publication is timely and it will prove indispensable to a large scientific readership.

Methods and Parameters for Membrane Simulations	p. 1
Introduction	p. 1
Force Fields/Descriptions of Interactions	p. 4
Current Atomistic Force Fields	p. 5
Development of Force Field Parameters	p. 6
Issues with Combining Force Fields	p. 7
Starting Structures	p. 7
Bilayers	p. 8
Membrane Proteins	p. 9
Embedding Proteins in Bilayers	p. 9
Sampling	p. 11
Improving Sampling	p. 14
Coarse Graining	p. 14
Pressure Coupling	p. 16
Electrostatics	p. 18
Periodicity	p. 19
Future Developments	p. 20
Acknowledgements	p. 21
References	p. 21
Lateral Pressure Profiles in Lipid Membranes: Dependence on Molecular Composition	p. 26
Introduction	p. 26
Theoretical Concepts	p. 31
Lateral Pressure Profile	p. 31
Calculation of Lateral Pressure Profile from Simulation	p. 32
Elastic Properties	p. 33
Interplay of Pressure Profile and Membrane Protein Activation	p. 34
Gauging Pressure Profile	p. 35
Dependence of Pressure Profiles on Molecular Composition	p. 38
Dependence on Unsaturation Level	p. 38
Effects of Different Sterols in Two-component Membranes	p. 39
Pressure Profiles in Three-component Bilayers	p. 41
Implications of Anesthetics on Pressure Profile	p. 43
Elastic Properties Calculated from Lateral Pressure Profile	p. 45
Free Energy of Protein Activation and Lateral Pressure Profile	p. 48
Concluding Remarks	p. 50
Abbreviations	p. 51
Acknowledgements	p. 51
References	p. 51
Coarse-grained Molecular Dynamics Simulations of Membrane Proteins	p. 56
Introduction	p. 56
Coarse-grained Simulations: Methodology	p. 57
CG-MD and Lipid Bilayers	p. 57
CG-MD and Membrane Peptides and Proteins	p. 59
Evaluation of CG-MD: Model Membrane Peptides	p. 61
Simulation Studies of Membrane Peptide Oligomerization	p. 64
Glycophorin A	p. 64
Influenza M2 Channels	p. 66
Coarse-grained MD: Larger Systems	p. 67
Vesicle Simulations	p. 67
More Complex Membrane Proteins	p. 69
Concluding Remarks and Future Directions	p. 73
Acknowledgements	p. 73
References	p. 73
Passive Permeation Across Lipid Bilayers: a Literature Review	p. 76
Introduction	p. 76
Experimental Methods	p. 78
Water and Small Organic Molecules	p. 78
Drugs	p. 78
The Solubility-Diffusion Model	p. 80
The z-Constraint Method	p. 81
Small Molecules	p. 82
Drugs	p. 83
Fullerene	p. 85
Discussion	p. 87
Conclusions	p. 87
References	p. 88
Implicit Membrane Models For Peptide Folding and Insertion Studies	p. 91
Introduction	p. 91
Implicit Membrane Models	p. 94
Overview	p. 94
Implicit Membrane Models for Studying Membrane Protein Folding	p. 95
The Generalized Born Model	p. 96
Non-polar Interactions	p. 99
Accuracy and Partitioning Properties	p. 100
Transmembrane and Surface-bound Helices, Insertion Energy Landscape	p. 102
Thermodynamic Analysis	p. 102
Simulating Peptide Folding and Partitioning	p. 104
Summary	p. 104
Transbilayer Peptide Folding	p. 104
Peptide Adsorption, Insertion and Folding	p. 111
Comparison with Explicit Methods	p. 124
Sampling Performance	p. 128
Conclusions	p. 134
Acknowledgements	p. 135
References	p. 135
Multi-scale Simulations of Membrane Sculpting by N-BAR Domains	p. 146
Introduction	p. 146
Methods	p. 148
All-atom Simulations	p. 150
Residue-based Coarse-grained Simulations	p. 151
Shape-based Coarse-grained Simulations	p. 152
Continuum Elastic Membrane Model	p. 157
Results and Discussion	p. 159
Simulations of a Single N-BAR Domain	p. 159
Comparison of RBCG and SBCG Simulations for Systems with Six N-BAR Domains	p. 161
Effect of Different N-BAR Domain Lattices on Membrane Curvatures	p. 164
Comparing All-atom and SBCG Simulations of an N-BAR Domain Lattice	p. 167
Complete Membrane Tubulation by Lattices of BAR Domains	p. 169
Elastic Membrane Computations	p. 169
Conclusion	p. 172
Acknowledgements	p. 173
References	p. 173
Continuum Electrostatics and Modeling of K⁺ Channels	p. 177
Introduction	p. 177
Theory and Methods	p. 180
The Poisson-Boltzmann (PB) Equation	p. 180
Calculation of Electrostatic Free Energies and Decomposition	p. 181
The Modified PB Equation for Treatment of Transmembrane Voltage	p. 182
Applications	p. 184
Electrostatics in the Intracellular Vestibule of K⁺ Channels	p. 184
Long-pore Electrostatics in K⁺ Channels	p. 191
K⁺ Channels and the Transmembrane Potential	p. 195
Conclusion	p. 200
References	p. 201
Computational Approaches to Ionotropic Glutamate Receptors	p. 203
Introduction	p. 203
The Amino-terminal Domain	p. 205
The Ligand-binding Domain (LBD)	p. 207
Selectivity and Modulation	p. 207
Dynamics	p. 209
The Transmembrane Domain	p. 216
Conclusion	p. 218
Acknowledgements	p. 218
References	p. 218
Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrels	p. 225
Introduction	p. 225
Outer Membrane Proteins	p. 226
Simple Barrels	p. 227
OmpA and Its Homologues	p. 227
Simple OMPs in Diverse Environments	p. 230
Leaking Barrels	p. 232
Transporting Barrels	p. 232
TonB-dependent Transporters	p. 233
Autotransporters	p. 235
TolC	p. 237
Reacting Barrels	p. 239
Technological Barrels	p. 241
Conclusion	p. 243
Acknowledgements	p. 244
References	p. 244
Molecular Mechanisms of Active Transport Across the Cellular Membrane	p. 248
Introduction	p. 248
Computational Methodology	p. 250
Electrostatic Potential Calculation	p. 251
Net Charge Density Distribution Calculation	p. 251
ATP-driven Transport in ABC Transporters	p. 252
Ion-driven Neurotransmitter Uptake by the Glutamate Transporter	p. 258
Substrate Binding and Selectivity in Glycerol-3-Phosphate Transporter	p. 263
Membrane Potential-driven Nucleotide Exchange in ADP/ATP Carrier	p. 268
Mechanically Driven Transport Across the Outer Membrane	p. 272
Conclusion	p. 277
Acknowledgements	p. 278
References	p. 278
Molecular Dynamics Studies of the Interactions Between Carbon Nanotubes and Biomembranes	p. 287
Introduction	p. 287
Carbon Nanotube Structure	p. 288
Experimental Techniques for Studying CNTs in a Biological Environment	p. 289
Molecular Dynamics Simulations	p. 289
Methodology	p. 290
Parameterization of CNT Models	p. 290
CNT Interactions with Lipids and Related Molecules	p. 292
Interaction of CNTs with Lipid Bilayers	p. 296
CNTs as Nanopores	p. 298
Transport of Water and Ions Through CNT Nanopores	p. 299
Nanopores as Nanosyringes	p. 301
Conclusion	p. 302
References	p. 302
Subject Index	p. 306
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Molecular Simulations and Biomembranes

9780854041893

0854041893

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