Molecular Simulations and Biomembranes: From Biophysics to Function (Rsc Biomolecular Sciences, 20, Band 20) - Hardcover

Hardcover

ISBN 10: 0854041893 ISBN 13: 9780854041893

Verlag: Royal Society of Chemistry, 2010

Inhaltsangabe

Molecular Simulations and Biomembranes: From Biophysics to Function highlights recent advances in the way computer simulation can be applied to the field of membranes and membrane proteins. The authors demonstrate how simulation methods provide an important contribution to the understanding of these systems. The scope of the book covers simulation of membranes and membrane proteins, in addition to the more recent methodological developments such as coarse-grained molecular dynamics. There is currently no up-to-date book that covers the application of simulation methods to membrane systems directly, and this authoritative reference source will prove indispensible to a large scientific readership.

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Über die Autorin bzw. den Autor

Philip Biggin is a Senior Research Associate in the Department of Biochemistry at the University of Oxford. His research interests lie in receptor-ligand interactions, comparative dynamics of proteins and bioinformatics of ligand-gated ion channels. He is the author of over 30 peer-reviewed papers and he sits on the Oxford Supercomputing Centre management committee. He is currently a consultant to BioMedCentral on the development and implementation of cysloopDB, a database that stores all of the physiological and pharmacological data for the cys-loop family of ligand-gated ion channels. He is a member of the Royal Society of Chemistry, the British Biophysical Society, the Biochemical Society, the US Biophysical Society, and the Molecular Graphics and Modelling Society. Mark Sansom is a Professor in the Department of Biochemistry at the University of Oxford, and Director of the Structural Bioinformatics and Computational Biochemistry Unit (http://sbcb.bioch.ox.ac.uk). He has worked on modelling and simulations of membrane proteins for over 15 years. He heads a research group of about 25 people working on topics ranging from the dynamics of water in nanopores to large scale MD simulations of bacterial membranes. This is currently funded by BBSRC, the Wellcome Trust, the EPSRC (as part of the bionanotechnology IRC), and MRC. He is the author of about 275 papers and reviews. He has an interest in HPC and in GRID computing for biomolecular simulation applications, and heads the BioSimGrid (www.biosimgrid.org) and IntBioSim (www.intbiosim.org) projects, in addition to a project (funded by BBSRC and IBM/HPCx) to develop a virtual outer membrane. He is a member of the High End Computing Strategy Committee, and the HPC Trends and Opportunities Panel (representing BBSRC interests on both), and chairs the Hector Science Board.

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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.

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Molecular Simulations and Biomembranes

From Biophysics to Function

By Mark S.P. Sansom, Philip C. Biggin

The Royal Society of Chemistry

Copyright © 2010 Royal Society of Chemistry
All rights reserved.

ISBN: 978-0-85404-189-3

Contents

Chapter 1 Methods and Parameters for Membrane Simulations D. Peter Tieleman, 1, 
Chapter 2 Lateral Pressure Profiles in Lipid Membranes: Dependence on Molecular Composition O. H. Samuli Ollila and Ilpo Vattulainen, 26, 
Chapter 3 Coarse-grained Molecular Dynamics Simulations of Membrane Proteins Sarah Rouse, Timothy Carpenter and Mark S. P. Sansom, 56, 
Chapter 4 Passive Permeation Across Lipid Bilayers: a Literature Review Mario Orsi and Jonathan W. Essex, 76, 
Chapter 5 Implicit Membrane Models For Peptide Folding and Insertion Studies Martin B. Ulmschneider and Jakob P. Ulmschneider, 91, 
Chapter 6 Multi-scale Simulations of Membrane Sculpting by N-BAR Domains Ying Yin, Anton Arkhipov and Klaus Schulten, 146, 
Chapter 7 Continuum Electrostatics and Modeling of K+ Channels Janice L. Robertson, Vishwanath Jogini and Benoît Roux, 177, 
Chapter 8 Computational Approaches to Ionotropic Glutamate Receptors Ranjit Vijayan, Bogdan Iorga and Philip C. Biggin, 203, 
Chapter 9 Molecular Dynamics Studies of Outer Membrane Proteins: a Story of Barrels Syma Khalid and Marc Baaden, 225, 
Chapter 10 Molecular Mechanisms of Active Transport Across the Cellular Membrane Po-Chao Wen, Zhijian Huang, Giray Enkavi, Yi Wang, James Gumbart and Emad Tajkhorshid, 248, 
Chapter 11 Molecular Dynamics Studies of the Interactions Between Carbon Nanotubes and Biomembranes E. Jayne Wallace and Mark S. P. Sansom, 287, 
Subject Index, 306, 

CHAPTER 1

Methods and Parameters for Membrane Simulations

D. PETER TIELEMAN

Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta, T2N 1N4, Canada

1.1 Introduction

Computer simulation is a powerful approach to studying the properties of models of biological membranes. Because lipids have a certain degree of intrinsic disorder in biologically relevant states, direct structural and spectroscopic experimental methods necessarily average over a large number of different lipid conformations. Experimental methods to study membrane proteins are also complicated by their lipid environment. Although much progress has been made, experimental structural, dynamic and functional data on membrane proteins lag behind water-soluble proteins. In principle, simulation can be used to track the behaviour of individual atoms, with the potential for very high-resolution information, provided that the simulation models are sufficiently accurate for the properties of interest.

Biomolecular simulation, initially focused on proteins, has matured into a widely used method over the past 30 years, while more recently simulations of lipids have made significant progress. Figure 1.1 gives a graphical view of a typical simulation setup for simulating a bilayer, in this case a mixture of several lipids with a peptide. Review articles in 1994 and 1997 could still be comprehensive, but after that the field became too large and even reviews of sub-topics such as membrane protein simulations are now rarely comprehensive. A recent book volume gives a good overview of the state of the field, with a broad range of chapters. Other recent reviews include reviews on membrane protein simulations, simulations including cholesterol and simulations involving significant changes in the basic bilayer structure, including lipid defects, pores, domain formation, phase transitions and curvature.

Biomolecular simulation in general is a combination of an interaction model to describe the interactions between atoms or molecules and a sampling algorithm to explore this model numerically, using the methods of statistical mechanics. Molecular dynamics (MD) simulation is the most commonly used method, but not the only one. Because most other methods are important primarily to explore interaction models that contain less detail (coarse-grained models), this chapter will focus exclusively on MD simulation. In molecular dynamics, the force field consists of the equations chosen to model the potential energy and their associated parameters, while the standard sampling algorithm is a numerical solution of classical equations of motion based on the forces given by the energy function. The general form of the potential energy is a sum of terms similar to

[MATHEMATICAL EXPRESSION OMITTED] (1.1)

The potential function V depends on r, the position vector of particles in the system, expressed in terms of distances (rij and b - b0) and angles θ, φ and ψ between atoms. Despite occasional extra terms in some force fields, the functional form of the potential function is essentially the same in all common force fields, so that they are not fundamentally different. Indeed, the potential function embodies the most serious assumptions and will provide an upper limit to the accuracy of any parameter set to describe the interactions between atoms.

In practice, the parameters in equation (1.1) are generally stored in data files with lists corresponding to each term in the sum. The force field includes a list of particle types corresponding to the different types of atoms that occur in a system of interest. For example, the carbon atom in a methyl group CH3 and in a carbonyl group C=O can be described by two different particle types with two different charges [q in equation (1.1)] and potentially different Lennard-Jones parameters (ε, σ), and also specific bonds, angles and dihedral parameters. The Lennard-Jones parameters may be different for each pair of different atom types or they may be systematically derived from parameters attached to a single type of atom. The force field also includes a list of parameters to describe bonds (force constant kb, equilibrium bond length b0), angles (force constant kθ, equilibrium angle θ0), dihedrals (force constant kθ, phase angle θ0, multiplicity n ) to describe rotation around a central bond and improper dihedrals (force constant kψ, equilibrium angle ψ0) to enforce certain specific geometries such as planar or tetrahedral groups. Combined, these parameters describe all combinations of different particle types necessary to model a particular molecule or class of molecules, e.g. proteins, nucleic acids or lipids, or in several modern force fields nearly every molecule one can think of.

The scale of the systems that have been studied continues to increase with increasing computer power and with more efficient simulation software. The range of applications has become extremely broad, but generally a reasonable limit on simulations at the moment is 106 particles, corresponding to ca. 5000 all-atom lipids or ca. 50 000 lipids in coarse-grained models. Simulation times of hundreds of nanoseconds have become routine in simple bilayer simulations, while microsecond simulations for all-atom and millisecond simulations at the coarse-grained level are pushing current limits. In terms of both time and length scales, although more prominently in time scale (which increases linearly with computer power), simulations can now probe into the microscopic regime, allowing a direct bridge to new classes of experiments such as vesicle aspiration, fluorescence imaging and atomic force microscopy (AFM)...

Details zur Ausgabe

• Verlag: Royal Society of Chemistry
• Erscheinungsdatum: 2010
• Sprache: Englisch
• ISBN 10: 0854041893
• ISBN 13: 9780854041893
• Einband: Gebundene Ausgabe
• Anzahl der Seiten: 332
• Herausgeber: Sansom Mark S P, Biggin Philip C
• Kontakt zum Hersteller: Nicht verfügbar
• Verantwortliche Person: GPSR Kontakt; gpsr@libri.de; ; Europaallee 1; Bad Hersfeld; 36244; Deutschland