Molecular dynamics simulations of lipid bilayers

Computer simulation methods are becoming increasingly widespread as tools for studying the structure and dynamics of lipid bilayer membranes. The length scale and time scale accessible to atomic-level molecular dynamics simulations are rapidly increasing, providing insight into the relatively slow motions of molecular reorientation and translation and demonstrating that effects due to the finite size of the simulation cell can influence simulation results. Additionally, significant advances have been made in the complexity of membrane systems studied, including bilayers with cholesterol, small solute molecules, and lipid-protein and lipid-DNA complexes. Especially promising is the progress that continues to be made in the comparison of simulation results with experiment, both to validate the simulation algorithms and to aid in the interpretation of existing experimental data.

[1]  Daniel Huster,et al.  Interpretation of NOESY Cross-Relaxation Rates from Molecular Dynamics Simulation of a Lipid Bilayer , 1999 .

[2]  A. Kusumi,et al.  Cholesterol effects on the phosphatidylcholine bilayer polar region: a molecular simulation study. , 2000, Biophysical journal.

[3]  T. Xiang,et al.  Molecular dissolution processes in lipid bilayers: A molecular dynamics simulation , 1999 .

[4]  A. Smondyrev,et al.  Molecular dynamics simulation of dipalmitoylphosphatidylcholine membrane with cholesterol sulfate. , 2000, Biophysical journal.

[5]  T. Woolf,et al.  Indoles at interfaces: Calculations of electrostatic effects with density functional and molecular dynamics methods , 1999 .

[6]  G. R. Smith,et al.  Homology modeling and molecular dynamics simulation studies of an inward rectifier potassium channel. , 2000, Biophysical journal.

[7]  A. Pohorille,et al.  Computer simulation of ion channel gating: the M(2) channel of influenza A virus in a lipid bilayer. , 2000, Biophysical Journal.

[8]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[9]  E. Dufourc,et al.  Conformational Order of DMPC sn-1 versus sn-2 Chains and Membrane Thickness: An Approach to Molecular Protrusion by Solid State 2H-NMR and Neutron Diffraction , 1996 .

[10]  D. Marsh.  Renormalization of the tension and area expansion modulus in fluid membranes. , 1997, Biophysical journal.

[11]  Michael M. Clark,et al.  Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer , 1999, J. Comput. Chem..

[12]  A. Smondyrev,et al.  Structure of dipalmitoylphosphatidylcholine/cholesterol bilayer at low and high cholesterol concentrations: molecular dynamics simulation. , 1999, Biophysical journal.

[13]  E. Jakobsson,et al.  Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. II. Rates and mechanisms of water transport. , 1999, Biophysical journal.

[14]  E Jakobsson,et al.  Combined Monte Carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. , 1999, Biophysical journal.

[15]  Bernard R. Brooks,et al.  Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water , 1995 .

[16]  J. Nagle,et al.  Lipid bilayer structure. , 2000, Current opinion in structural biology.

[17]  M S Sansom,et al.  An alamethicin channel in a lipid bilayer: molecular dynamics simulations. , 1999, Biophysical journal.

[18]  D. Tieleman,et al.  Defining the transmembrane helix of M2 protein from influenza A by molecular dynamics simulations in a lipid bilayer. , 1999, Biophysical journal.

[19]  M. Klein,et al.  Constant pressure and temperature molecular dynamics simulation of a fully hydrated liquid crystal phase dipalmitoylphosphatidylcholine bilayer. , 1995, Biophysical journal.

[20]  B. Brooks,et al.  Molecular dynamics simulations of gel (LβI) phase lipid bilayers in constant pressure and constant surface area ensembles , 2000 .

[21]  M. Klein,et al.  Distribution of halothane in a dipalmitoylphosphatidylcholine bilayer from molecular dynamics calculations. , 2000, Biophysical journal.

[22]  A. Pohorille,et al.  Chapter 13 – Interactions of Small Molecules and Peptides with Membranes , 1999 .

[23]  D. Tieleman,et al.  Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer. , 2000, Biophysical journal.

[24]  Richard W. Pastor,et al.  Constant surface tension simulations of lipid bilayers: The sensitivity of surface areas and compressibilities , 1999 .

[25]  A. Smondyrev,et al.  Molecular dynamics simulation of DPPC bilayer in DMSO. , 1999, Biophysical journal.

[26]  Andrew Pohorille,et al.  Chapter 3 Insights from Computer Simulations into the Interaction of Small Molecules with Lipid Bilayers , 1999 .

[27]  M. Klein,et al.  Molecular dynamics simulations of supported phospholipid/alkanethiol bilayers on a gold(111) surface. , 1999, Biophysical journal.

[28]  P. Schleyer.  Encyclopedia of computational chemistry , 1998 .

[29]  R. Pastor,et al.  On simulating lipid bilayers with an applied surface tension: periodic boundary conditions and undulations. , 1996, Biophysical journal.

[30]  Eric Jakobsson,et al.  Optimization of Hydrocarbon Chain Interaction Parameters: Application to the Simulation of Fluid Phase Lipid Bilayers , 1999 .

[31]  I. Shrivastava,et al.  Structure and dynamics of K channel pore-lining helices: a comparative simulation study. , 2000, Biophysical journal.

[32]  F. Jähnig,et al.  What is the surface tension of a lipid bilayer membrane? , 1996, Biophysical journal.

[33]  E Jakobsson,et al.  Computer simulation studies of biological membranes: progress, promise and pitfalls. , 1997, Trends in biochemical sciences.

[34]  A Kusumi,et al.  Charge pairing of headgroups in phosphatidylcholine membranes: A molecular dynamics simulation study. , 1999, Biophysical journal.

[35]  Richard W. Pastor,et al.  Molecular dynamics and Monte Carlo simulations of lipid bilayers , 1994 .

[36]  E. Lindahl,et al.  Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations , 2000 .

[37]  E. Jakobsson,et al.  Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer , 1999, J. Comput. Chem..

[38]  M S Sansom,et al.  Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane. , 1999, Biophysical journal.

[39]  E. Jakobsson,et al.  Incorporation of surface tension into molecular dynamics simulation of an interface: a fluid phase lipid bilayer membrane. , 1995, Biophysical journal.

[40]  Alexander D. MacKerell,et al.  Computational Biochemistry and Biophysics , 2001 .

[41]  Simulation study of a gramicidin/lipid bilayer system in excess water and lipid. I. Structure of the molecular complex. , 1999, Biophysical journal.

[42]  J. Nagle,et al.  Analysis of simulated NMR order parameters for lipid bilayer structure determination. , 1999, Biophysical journal.

[43]  Molecular dynamics study of Sn-1 and Sn-2 chain conformations in dipalmitoylphosphatidylcholine membranes , 1999 .

[44]  M S Sansom,et al.  Membrane simulations: bigger and better? , 2000, Current opinion in structural biology.

[45]  B. Brooks,et al.  Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water , 1996 .

[46]  O. Becker,et al.  Protein-induced membrane disorder: a molecular dynamics study of melittin in a dipalmitoylphosphatidylcholine bilayer. , 2000, Biophysical journal.

[47]  I. Shrivastava,et al.  Simulations of ion permeation through a potassium channel: molecular dynamics of KcsA in a phospholipid bilayer. , 2000, Biophysical journal.

[48]  T. Xiang,et al.  Translational Diffusion in Lipid Bilayers: Dynamic Free-Volume Theory and Molecular Dynamics Simulation , 1999 .

[49]  Michael L. Klein,et al.  Molecular Dynamics Study of a Lipid−DNA Complex , 1999 .

[50]  H. Berendsen,et al.  Surface binding of alamethicin stabilizes its helical structure: molecular dynamics simulations. , 1999, Biophysical journal.

[51]  A. Baumgaertner,et al.  Stability of a melittin pore in a lipid bilayer: a molecular dynamics study. , 2000, Biophysical journal.

[52]  U. Essmann,et al.  Dynamical properties of phospholipid bilayers from computer simulation. , 1999, Biophysical journal.

[53]  B. Roux,et al.  Molecular dynamics of the KcsA K(+) channel in a bilayer membrane. , 2000, Biophysical journal.

[54]  E. Lindahl,et al.  Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations. , 2000, Biophysical journal.

[55]  D P Tieleman,et al.  A computer perspective of membranes: molecular dynamics studies of lipid bilayer systems. , 1997, Biochimica et biophysica acta.

[56]  D. Tieleman,et al.  Structure and dynamics of the pore‐lining helix of the nicotinic receptor: MD simulations in water, lipid bilayers, and transbilayer bundles , 2000, Proteins.

[57]  Douglas J. Tobias,et al.  Atomic-scale molecular dynamics simulations of lipid membranes , 1997 .

[58]  Hjc Berendsen,et al.  Molecular Dynamics: Studies of Lipid Bilayers , 1998 .

[59]  M S Sansom,et al.  Alamethicin helices in a bilayer and in solution: molecular dynamics simulations. , 1999, Biophysical journal.