Molecular Dynamics: Studies of Lipid Bilayers

1 ESR Electron Spin Resonance NMR Nuclear Magnetic Resonance MD Molecular Dynamics DPPC dipalmitoylphosphatidylcholine DPPS dipalmitoylphosphatidylserine DMPC dimyristoylphosphatidylcholine DLPE dilaureoylphosphatidylethanolamine POPC dalmitoyloleoylphosphatidylcholine NPT constant number of particles, pressure and temperature NVT constant number of particles, volume and temperature NT constant number of particles, surface tension and temperature

[1]  Jill Trewhella,et al.  Structure, dynamics, and function of biomolecules , 1998 .

[2]  O. Berger,et al.  Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations. , 1998, Biophysical journal.

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

[4]  K. Merz.  Molecular dynamics simulations of lipid bilayers. , 1997, Current opinion in structural biology.

[5]  M. Mehedintu.  Biological membranes. A molecular perspective from computation and experiment , 1997 .

[6]  O. Berger,et al.  Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature. , 1997, Biophysical journal.

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

[8]  Herman J. C. Berendsen,et al.  Permeation Process of Small Molecules across Lipid Membranes Studied by Molecular Dynamics Simulations , 1996 .

[9]  R. Gabdoulline,et al.  Comparison of the Structures of Dimyristoylphosphatidylcholine in the Presence and Absence of Cholesterol by Molecular Dynamics Simulations , 1996 .

[10]  H. Berendsen,et al.  Molecular dynamics simulations of a fully hydrated dipalmitoylphosphatidylcholine bilayer with different macroscopic boundary conditions and parameters , 1996 .

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

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

[13]  H. Berendsen,et al.  Proton transport across transient single-file water pores in a lipid membrane studied by molecular dynamics simulations. , 1996, Biophysical journal.

[14]  H. Berendsen,et al.  Free volume properties of a simulated lipid membrane , 1996 .

[15]  Ulrich Essmann,et al.  Role of water in the hydration force acting between lipid bilayers , 1996 .

[16]  H. Berendsen,et al.  Molecular Dynamics Simulation of Water between Two Charged Layers of Dipalmitoylphosphatidylserine , 1996 .

[17]  K. Schulten,et al.  Molecular dynamics study of phospholipase A2 on a membrane surface , 1996, Proteins.

[18]  R. Suter,et al.  X-ray structure determination of fully hydrated L alpha phase dipalmitoylphosphatidylcholine bilayers. , 1996, Biophysical journal.

[19]  P. Tavan,et al.  Ligand Binding: Molecular Mechanics Calculation of the Streptavidin-Biotin Rupture Force , 1996, Science.

[20]  H. Berendsen,et al.  Molecular dynamics simulation of a charged biological membrane , 1996 .

[21]  M. Klein,et al.  Molecular dynamics investigation of the structure of a fully hydrated gel-phase dipalmitoylphosphatidylcholine bilayer. , 1996, Biophysical journal.

[22]  Håkan Wennerström,et al.  Role of hydration and water structure in biological and colloidal interactions , 1996, Nature.

[23]  B. Roux,et al.  Structure, energetics, and dynamics of lipid–protein interactions: A molecular dynamics study of the gramicidin A channel in a DMPC bilayer , 1996, Proteins.

[24]  Alexander D. MacKerell,et al.  An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications , 1996 .

[25]  H. Berendsen,et al.  Membranes and water: An interesting relationship , 1996 .

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

[27]  R. Pastor,et al.  Computer simulation of liquid/liquid interfaces. II. Surface tension-area dependence of a bilayer and monolayer , 1995 .

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

[29]  T. Xiang,et al.  MEAN MOLECULAR POTENTIALS IN A MODEL LIPID BILAYER: A MOLECULAR DYNAMICS SIMULATION , 1995 .

[30]  U. Essmann,et al.  The origin of the hydration interaction of lipid bilayers from MD simulation of dipalmitoylphosphatidylcholine membranes in gel and liquid crystalline phases , 1995 .

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

[32]  Terry R. Stouch,et al.  Force field studies of cholesterol and cholesteryl acetate crystals and cholesterol–cholesterol intermolecular interactions , 1995, J. Comput. Chem..

[33]  O. Berger,et al.  Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study. , 1995, Journal of molecular biology.

[34]  Douglas J. Tobias,et al.  Constant Pressure and Temperature Molecular Dynamics Simulations of Crystals of the Lecithin Fragments: Glycerylphosphorylcholine and Dilauroylglycerol , 1995 .

[35]  Terry R. Stouch,et al.  Orientation and Diffusion of a Drug Analog in Biomembranes: Molecular Dynamics Simulations , 1995 .

[36]  Terry R. Stouch,et al.  Mechanism of Solute Diffusion through Lipid Bilayer Membranes by Molecular Dynamics Simulation , 1995 .

[37]  P. Huang,et al.  Interaction of an amphiphilic peptide with a phospholipid bilayer surface by molecular dynamics simulation study. , 1995, Journal of biomolecular structure & dynamics.

[38]  Wataru Shinoda,et al.  Molecular dynamics simulation of the dipalmitoylphosphatidylcholine (DPPC) lipid bilayer in the fluid phase using the Nosé-Parrinello-Rahman NPT ensemble , 1995 .

[39]  Klaus Schulten,et al.  Molecular dynamics study of a membrane - Water interface , 1995 .

[40]  W. Richards,et al.  Behavior of cholesterol and its effect on head group and chain conformations in lipid bilayers: a molecular dynamics study. , 1995, Biophysical journal.

[41]  M. Klein,et al.  Constant pressure molecular dynamics algorithms , 1994 .

[42]  T. McIntosh,et al.  Hydration and steric pressures between phospholipid bilayers. , 1994, Annual review of biophysics and biomolecular structure.

[43]  A. Hagler,et al.  AB INITIO STUDIES OF LIPID MODEL SPECIES. II: CONFORMATIONAL ANALYSIS OF INOSITOLS , 1994 .

[44]  Herman J. C. Berendsen,et al.  Simulation of Water Transport through a Lipid Membrane , 1994 .

[45]  P. Huang,et al.  Molecular dynamics simulations of phospholipid bilayers. , 1994, Journal of biomolecular structure & dynamics.

[46]  K V Damodaran,et al.  A comparison of DMPC- and DLPE-based lipid bilayers. , 1994, Biophysical journal.

[47]  Ming-Jing Hwang,et al.  Derivation of Class II Force Fields. 2. Derivation and Characterization of a Class II Force Field, CFF93, for the Alkyl Functional Group and Alkane Molecules , 1994 .

[48]  Ming-Jing Hwang,et al.  Derivation of class II force fields. I. Methodology and quantum force field for the alkyl functional group and alkane molecules , 1994, J. Comput. Chem..

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

[50]  S. Marrink.  Permeation of small molecules across lipid membranes. A molecular dynamics study. , 1994 .

[51]  T R Stouch,et al.  Solute diffusion in lipid bilayer membranes: an atomic level study by molecular dynamics simulation. , 1993, Biochemistry.

[52]  Herman J. C. Berendsen,et al.  Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force , 1993 .

[53]  R M Venable,et al.  Molecular dynamics simulations of a lipid bilayer and of hexadecane: an investigation of membrane fluidity. , 1993, Science.

[54]  Herman J. C. Berendsen,et al.  A Molecular Dynamics Study of the Decane/Water Interface , 1993 .

[55]  Terry R. Stouch,et al.  Characterization of force fields for lipid molecules: Applications to crystal structures , 1993, J. Comput. Chem..

[56]  Terry R. Stouch,et al.  Lipid Membrane Structure and Dynamics Studied by All-Atom Molecular Dynamics Simulations of Hydrated Phospholipid Bilayers , 1993 .

[57]  K. Schulten,et al.  Molecular dynamics simulation of a bilayer of 200 lipids in the gel and in the liquid crystal phase , 1993 .

[58]  J. Nagle,et al.  Area/lipid of bilayers from NMR. , 1993, Biophysical journal.

[59]  Terry R. Stouch,et al.  Ab initio studies of lipid model species. 1. Dimethyl phosphate and methyl propyl phosphate anions , 1993 .

[60]  K V Damodaran,et al.  Structure and dynamics of the dilauroylphosphatidylethanolamine lipid bilayer. , 1992, Biochemistry.

[61]  S H White,et al.  Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. III. Complete structure. , 1992, Biophysical journal.

[62]  M. Rami Reddy,et al.  A molecular dynamics study of the structure and dynamics of water between dilauroylphosphatidylethanolamine bilayers , 1992 .

[63]  E. Jakobsson,et al.  Computational Approaches to Understanding the Ion Channel-Lipid System , 1992 .

[64]  B. Pullman,et al.  Membrane Proteins: Structures, Interactions and Models , 1992 .

[65]  Keith B. Ward,et al.  Simulations of lipid crystals: Characterization of potential energy functions and parameters for lecithin molecules , 1991 .

[66]  M. Bloom,et al.  Physical properties of the fluid lipid-bilayer component of cell membranes: a perspective , 1991, Quarterly Reviews of Biophysics.

[67]  V. Parsegian,et al.  Hydration forces between phospholipid bilayers , 1989 .

[68]  Wilfred F. van Gunsteren,et al.  Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications , 1989 .

[69]  H. Berendsen,et al.  Molecular dynamics simulation of a smectic liquid crystal with atomic detail , 1988 .

[70]  W. L. Jorgensen,et al.  The OPLS [optimized potentials for liquid simulations] potential functions for proteins, energy minimizations for crystals of cyclic peptides and crambin. , 1988, Journal of the American Chemical Society.

[71]  H. Berendsen,et al.  Molecular Dynamics of a Bilayer Membrane with Atomic Detail , 1987 .

[72]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[73]  D. Engelman,et al.  Lipid bilayer thickness varies linearly with acyl chain length in fluid phosphatidylcholine vesicles. , 1983, Journal of molecular biology.

[74]  H. Berendsen,et al.  Multipulse Fluorine NMR Experiments on Lyotropic Liquid Crystals. I. Determination of Order Parameter Tensor , 1982 .

[75]  Herman J. C. Berendsen,et al.  MOLECULAR-DYNAMICS SIMULATION OF A BILAYER-MEMBRANE , 1982 .

[76]  F. W. Wiegel,et al.  Simulation of a lipid monolayer using molecular dynamics , 1980, Nature.

[77]  J. Seelig,et al.  Lipid conformation in model membranes and biological membranes , 1980, Quarterly Reviews of Biophysics.

[78]  J. Seelig.  Deuterium magnetic resonance: theory and application to lipid membranes , 1977, Quarterly Reviews of Biophysics.

[79]  板橋 清巳.  Resonance , 1962 .