Sundararajan Computational Modeling of Membrane Bilayers

1. Auflage 2011
ISBN: 978-0-08-092050-4
Verlag: Elsevier Science & Techn.
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, Band Volume 60, 448 Seiten, Web PDF

Reihe: Current Topics in Membranes

Current Topics in Membranes provides a systematic, comprehensive, and rigorous approach to specific topics relevant to the study of cellular membranes. Each volume is a guest edited compendium of membrane biology.
*Discusses the current stat of electrostatics in biomolecular simulations and future directions
*Includes information on time and length scales in lipid bilayer simulations
*Includes a chapter on the nature of lipid rafts

Autoren/Hrsg.

Sundararajan, V.

Inhaltsverzeichnis

1;Cover;1
2;Computational Modeling of Membrane Bilayers;4
3;Copyright page;5
4;Contents;6
5;Contributors;12
6;Preface;18
7;Previous Volumes in Series;24
8;Chapter 1. Considerations for Lipid Force Field Development;28
8.1;I. Introduction;29
8.2;II. Quantum Mechanics and Molecular Dynamics Based Parameter Optimization;31
8.3;III. Membrane Targets and Related Issues;47
8.4;IV. Summary and Perspectives;66
8.5;References;69
9;Chapter 2. Electrostatics in Biomolecular Simulations: Where Are We Now and Where Are We Heading?;76
9.1;I. Introduction;77
9.2;II. Importance of Long-Range Interactions in Simulations of Biological Systems;78
9.3;III. Overview of Methods and Their Applicability;79
9.4;IV. Non-Periodic Systems and Different Boundary Conditions;96
9.5;V. Applications and Latest Methodological Developments;98
9.6;VI. Final Notes on Software, Accuracy, and Speed;107
9.7;References;108
10;Chapter 3. Time and Length Scales in Lipid Bilayer Simulations;118
10.1;I. Introduction;118
10.2;II. Area per Lipid and Finite Size Effects;121
10.3;III. Undulations;123
10.4;IV. Peristaltic Fluctuations;128
10.5;V. Hydrocarbon Chain Dynamics;131
10.6;VI. Lateral Diffusion of Lipids;132
10.7;References;134
11;Chapter 4. Molecular Dynamics Simulation of Lipid-Protein Interactions;138
11.1;I. Introduction;139
11.2;II. Force Fields;141
11.3;III. Combining Force Fields;144
11.4;IV. Sampling Concerns;150
11.5;V. Validation of Lipid-Protein Simulations;152
11.6;VI. Conclusion and Perspective;154
11.7;References;155
12;Chapter 5. Implicit Modeling of Membranes;158
12.1;I. Introduction;158
12.2;II. Classes of Models;160
12.3;III. Interesting Problems in Implicit Membrane Modeling;173
12.4;IV. Conclusion;177
12.5;References;177
13;Chapter 6. Blue Matter: Scaling of N-Body Simulations to One Atom per Node;186
13.1;I. Introduction;187
13.2;II. Background on Massively Parallel Biomolecular Simulation;189
13.3;III. Inherent Concurrency of Molecular Dynamics;191
13.4;IV. Parallel Decompositions;194
13.5;V. Results;198
13.6;VI. Summary and Conclusions;203
13.7;References;205
14;Chapter 7. Multiscale Simulation of Membranes and Membrane Proteins: Connecting Molecular Interactions to Mesoscopic Behavior;208
14.1;I. Multiscale Aspects of Membrane Simulation: A Brief Review;209
14.2;II. New Multiscale Methods for Membrane Simulations;214
14.3;III. Selected Applications;228
14.4;IV. Summary;246
14.5;References;246
15;Chapter 8. Interactions between Small Molecules and Lipid Bilayers;254
15.1;Abbreviations;255
15.2;I. Introduction;255
15.3;II. Partitioning of Small Molecules in Lipid Bilayers;259
15.4;III. Conclusions;279
15.5;References;280
16;Chapter 9. On the Nature of Lipid Rafts: Insights from Molecularly Detailed Simulations of Model Biological Membranes Containing Mixtures of Cholesterol and Phospholipids;284
16.1;I. Introduction;284
16.2;II. Simulations;289
16.3;III. Concluding Remarks;302
16.4;References;303
17;Chapter 10. Atomistic and Mean Field Simulations of Lateral Organization in Membranes;308
17.1;I. Introduction;308
17.2;II. Molecular Dynamics Simulation of Hydrated Lipid Bilayers;311
17.3;III. General Issues in Force Feld Development for Biomolecular Simulations;312
17.4;IV. Simulation of Heterogeneous Lipid membranes;320
17.5;V. Application: A Mean Field Based Lipid Bilayer Model Based on MDSimulations;327
17.6;VI. Summary;335
17.7;References;336
18;Chapter 11. Molecular Modeling of the Structural Properties and Formation of High-Density Lipoprotein Particles;340
18.1;I. Introduction;340
18.2;II. Methods;345
18.3;III. Structure of Discoidal HDL;349
18.4;IV. Formation of Discoidal HDL;354
18.5;V. Conclusions;363
18.6;References;364
19;Chapter 12. Gas Conduction of Lipid Bilayers and Membrane Channels;370
19.1;I. Introduction;371
19.2;II. Computational Methodology;373
19.3;III. Lipid-Mediated Gas Conduction;375
19.4;IV. Protein-Mediated Gas Conduction;382
19.5;V. Concluding Remarks;389
19.6;References;390
20;Chapter 13. A Brief Introduction to Voltage-Gated K+ Channels;396
20.1;I. Introduction;396
20.2;II. Structure of Kv Channels and Gating Mechanisms;397
20.3;III. Free Energy and Membrane Voltage;406
20.4;IV. Conclusion;409
20.5;References;410
21;Chapter 14. Computational Models for Electrified Interfaces;412
21.1;I. Introduction;412
21.2;II. General Concepts of Surface Charge and Co/Counter Ions;413
21.3;III. Continuum Models;414
21.4;IV. Bridging from the Continuum to Molecular Calculations;416
21.5;V. All-Atom Models;420
21.6;VI. Long-Term Trends;424
21.7;VII. Summary;427
21.8;References;427
22;Chapter 15. Charged Protein Side Chain Movement in Lipid Bilayers Explored with Free Energy Simulation;432
22.1;I. Introduction;433
22.2;II. Theoretical Perspectives;436
22.3;III. Experimental Hydrophobicity and Membrane Partitioning Models;438
22.4;IV. Fully Atomistic Computer Simulations;442
22.5;V. Reconciling Simulation and Experiment;468
22.6;VI. Conclusion and Implications;475
22.7;References;480
23;Index;488