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Molecular Simulations and Biomembranes : From Biophysics to Function - Mark S.P. Sansom

Molecular Simulations and Biomembranes

From Biophysics to Function

By: Mark S.P. Sansom (Editor), Philip C. Biggin (Editor), Stephen Neidle (Editor), David M. J. Lilley (Editor), Marius Clore (Editor)

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Published: 19th July 2010
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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 Simulationsp. 1
Introductionp. 1
Force Fields/Descriptions of Interactionsp. 4
Current Atomistic Force Fieldsp. 5
Development of Force Field Parametersp. 6
Issues with Combining Force Fieldsp. 7
Starting Structuresp. 7
Bilayersp. 8
Membrane Proteinsp. 9
Embedding Proteins in Bilayersp. 9
Samplingp. 11
Improving Samplingp. 14
Coarse Grainingp. 14
Pressure Couplingp. 16
Electrostaticsp. 18
Periodicityp. 19
Future Developmentsp. 20
Acknowledgementsp. 21
Referencesp. 21
Lateral Pressure Profiles in Lipid Membranes: Dependence on Molecular Compositionp. 26
Introductionp. 26
Theoretical Conceptsp. 31
Lateral Pressure Profilep. 31
Calculation of Lateral Pressure Profile from Simulationp. 32
Elastic Propertiesp. 33
Interplay of Pressure Profile and Membrane Protein Activationp. 34
Gauging Pressure Profilep. 35
Dependence of Pressure Profiles on Molecular Compositionp. 38
Dependence on Unsaturation Levelp. 38
Effects of Different Sterols in Two-component Membranesp. 39
Pressure Profiles in Three-component Bilayersp. 41
Implications of Anesthetics on Pressure Profilep. 43
Elastic Properties Calculated from Lateral Pressure Profilep. 45
Free Energy of Protein Activation and Lateral Pressure Profilep. 48
Concluding Remarksp. 50
Abbreviationsp. 51
Acknowledgementsp. 51
Referencesp. 51
Coarse-grained Molecular Dynamics Simulations of Membrane Proteinsp. 56
Introductionp. 56
Coarse-grained Simulations: Methodologyp. 57
CG-MD and Lipid Bilayersp. 57
CG-MD and Membrane Peptides and Proteinsp. 59
Evaluation of CG-MD: Model Membrane Peptidesp. 61
Simulation Studies of Membrane Peptide Oligomerizationp. 64
Glycophorin Ap. 64
Influenza M2 Channelsp. 66
Coarse-grained MD: Larger Systemsp. 67
Vesicle Simulationsp. 67
More Complex Membrane Proteinsp. 69
Concluding Remarks and Future Directionsp. 73
Acknowledgementsp. 73
Referencesp. 73
Passive Permeation Across Lipid Bilayers: a Literature Reviewp. 76
Introductionp. 76
Experimental Methodsp. 78
Water and Small Organic Moleculesp. 78
Drugsp. 78
The Solubility-Diffusion Modelp. 80
The z-Constraint Methodp. 81
Small Moleculesp. 82
Drugsp. 83
Fullerenep. 85
Discussionp. 87
Conclusionsp. 87
Referencesp. 88
Implicit Membrane Models For Peptide Folding and Insertion Studiesp. 91
Introductionp. 91
Implicit Membrane Modelsp. 94
Overviewp. 94
Implicit Membrane Models for Studying Membrane Protein Foldingp. 95
The Generalized Born Modelp. 96
Non-polar Interactionsp. 99
Accuracy and Partitioning Propertiesp. 100
Transmembrane and Surface-bound Helices, Insertion Energy Landscapep. 102
Thermodynamic Analysisp. 102
Simulating Peptide Folding and Partitioningp. 104
Summaryp. 104
Transbilayer Peptide Foldingp. 104
Peptide Adsorption, Insertion and Foldingp. 111
Comparison with Explicit Methodsp. 124
Sampling Performancep. 128
Conclusionsp. 134
Acknowledgementsp. 135
Referencesp. 135
Multi-scale Simulations of Membrane Sculpting by N-BAR Domainsp. 146
Introductionp. 146
Methodsp. 148
All-atom Simulationsp. 150
Residue-based Coarse-grained Simulationsp. 151
Shape-based Coarse-grained Simulationsp. 152
Continuum Elastic Membrane Modelp. 157
Results and Discussionp. 159
Simulations of a Single N-BAR Domainp. 159
Comparison of RBCG and SBCG Simulations for Systems with Six N-BAR Domainsp. 161
Effect of Different N-BAR Domain Lattices on Membrane Curvaturesp. 164
Comparing All-atom and SBCG Simulations of an N-BAR Domain Latticep. 167
Complete Membrane Tubulation by Lattices of BAR Domainsp. 169
Elastic Membrane Computationsp. 169
Conclusionp. 172
Acknowledgementsp. 173
Referencesp. 173
Continuum Electrostatics and Modeling of K+ Channelsp. 177
Introductionp. 177
Theory and Methodsp. 180
The Poisson-Boltzmann (PB) Equationp. 180
Calculation of Electrostatic Free Energies and Decompositionp. 181
The Modified PB Equation for Treatment of Transmembrane Voltagep. 182
Applicationsp. 184
Electrostatics in the Intracellular Vestibule of K+ Channelsp. 184
Long-pore Electrostatics in K+ Channelsp. 191
K+ Channels and the Transmembrane Potentialp. 195
Conclusionp. 200
Referencesp. 201
Computational Approaches to Ionotropic Glutamate Receptorsp. 203
Introductionp. 203
The Amino-terminal Domainp. 205
The Ligand-binding Domain (LBD)p. 207
Selectivity and Modulationp. 207
Dynamicsp. 209
The Transmembrane Domainp. 216
Conclusionp. 218
Acknowledgementsp. 218
Referencesp. 218
Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrelsp. 225
Introductionp. 225
Outer Membrane Proteinsp. 226
Simple Barrelsp. 227
OmpA and Its Homologuesp. 227
Simple OMPs in Diverse Environmentsp. 230
Leaking Barrelsp. 232
Transporting Barrelsp. 232
TonB-dependent Transportersp. 233
Autotransportersp. 235
TolCp. 237
Reacting Barrelsp. 239
Technological Barrelsp. 241
Conclusionp. 243
Acknowledgementsp. 244
Referencesp. 244
Molecular Mechanisms of Active Transport Across the Cellular Membranep. 248
Introductionp. 248
Computational Methodologyp. 250
Electrostatic Potential Calculationp. 251
Net Charge Density Distribution Calculationp. 251
ATP-driven Transport in ABC Transportersp. 252
Ion-driven Neurotransmitter Uptake by the Glutamate Transporterp. 258
Substrate Binding and Selectivity in Glycerol-3-Phosphate Transporterp. 263
Membrane Potential-driven Nucleotide Exchange in ADP/ATP Carrierp. 268
Mechanically Driven Transport Across the Outer Membranep. 272
Conclusionp. 277
Acknowledgementsp. 278
Referencesp. 278
Molecular Dynamics Studies of the Interactions Between Carbon Nanotubes and Biomembranesp. 287
Introductionp. 287
Carbon Nanotube Structurep. 288
Experimental Techniques for Studying CNTs in a Biological Environmentp. 289
Molecular Dynamics Simulationsp. 289
Methodologyp. 290
Parameterization of CNT Modelsp. 290
CNT Interactions with Lipids and Related Moleculesp. 292
Interaction of CNTs with Lipid Bilayersp. 296
CNTs as Nanoporesp. 298
Transport of Water and Ions Through CNT Nanoporesp. 299
Nanopores as Nanosyringesp. 301
Conclusionp. 302
Referencesp. 302
Subject Indexp. 306
Table of Contents provided by Ingram. All Rights Reserved.

ISBN: 9780854041893
ISBN-10: 0854041893
Series: RSC Biomolecular Sciences : Book 20
Audience: Professional
Format: Hardcover
Language: English
Number Of Pages: 353
Published: 19th July 2010
Publisher: Royal Society Of Chemistry
Country of Publication: GB
Dimensions (cm): 23.4 x 15.6  x 1.91
Weight (kg): 0.64