Lipid Membrane Structure and Dynamics Studied by All-Atom Molecular Dynamics Simulations of Hydrated Phospholipid Bilayers

Abstract The structure and dynamics of phosphatidylcholine bilayers are examined by reviewing the results of several nanoseconds of molecular dynamics simulations on a number of bilayer and monolayer models. The lengths of these simulations, the longest single one of which was 2 nanoseconds, were sufficiently long to effectively sample many of the longer-scale motions governing the behaviour of biomembranes. These simulations reproduce many experimental observables well and provide a degree of resolution currently unavailable experimentally.

[1]  Michael L. Klein,et al.  Disorder in the pseudohexagonal rotator phase of n-alkanes: molecular-dynamics calculations for tricosane , 1989 .

[2]  S H White,et al.  Hexane dissolved in dioleoyllecithin bilayers has a partial molar volume of approximately zero. , 1985, Biochemistry.

[3]  J. Schlitter,et al.  A statistical mechanical treatment of fatty acyl chain order in phospholipid bilayers and correlation with experimental data. A. Theory. , 1981, Biochimica et biophysica acta.

[4]  H. Hauser,et al.  Polar group interaction and molecular packing of membrane lipids. The crystal structure of lysophosphatidylethanolamine. , 1981, Journal of molecular biology.

[5]  Scott H. Northrup,et al.  Molecular mechanics of kink formation in lipid monolayers , 1984 .

[6]  R B Knott,et al.  Quantitation of water in membranes by neutron diffraction and X-ray techniques. , 1986, Methods in enzymology.

[7]  Anthony Watts,et al.  The dependence of phospholipid head-group mobility on hydration as studied by deuterium-NMR spin-lattice relaxation time measurements , 1990 .

[8]  C. Y. Lee,et al.  The surface tension of lipid water interfaces: Monte Carlo simulations , 1980 .

[9]  Kenneth A. Dawson,et al.  Microscopic model of amphiphilic assembly , 1989 .

[10]  Studies on membrane hydration.: Part I. Monte Carlo simulation of the cholesterol—water interface , 1987 .

[11]  H. L. Scott,et al.  Density and bonding profiles of interbilayer water as functions of bilayer separation: a Monte Carlo study , 1987 .

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

[13]  H. Hauser,et al.  Preferred conformation and dynamics of the glycerol backbone in phospholipids. An NMR and X-ray single-crystal analysis. , 1988, Biochemistry.

[14]  Kurt Binder,et al.  Orientational ordering in lipid monolayers: A two‐dimensional model of rigid rods grafted onto a lattice , 1992 .

[15]  Donald E. Williams,et al.  Conformational dependence of electrostatic potential‐derived charges: Studies of the fitting procedure , 1993, J. Comput. Chem..

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

[17]  R. Brasseur,et al.  Orientation into the lipid bilayer of an asymmetric amphipathic helical peptide located at the N-terminus of viral fusion proteins. , 1990, Biochimica et biophysica acta.

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

[19]  J. M. Haile,et al.  Internal structure of a model micelle via computer simulation. II: Spherically confined aggregates with mobile head groups , 1986 .

[20]  D. Gruen,et al.  A statistical mechanical model of the lipid bilayer above its phase transition. , 1980, Biochimica et biophysica acta.

[21]  Donald E. Williams Nonbonded Potential Parameters Derived from Crystalline Hydrocarbons , 1967 .

[22]  T J O'Leary Lateral diffusion of lipids in complex biological membranes. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[23]  W. Hubbell,et al.  The membrane dipole potential in a total membrane potential model. Applications to hydrophobic ion interactions with membranes. , 1986, Biophysical journal.

[24]  Roger Coleman,et al.  Membranes and Their Cellular Functions , 1974 .

[25]  A. Horwitz,et al.  The fluid state of lecithin bilayers. , 1973, Journal of supramolecular structure.

[26]  Michiko Kodama,et al.  Phase transition phenomena induced by the successive appearances of new types of aggregation states of water molecules in the “l-dipalmitoylphosphatidylcholine-water” system , 1986 .

[27]  L. Verlet Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules , 1967 .

[28]  D. Pink,et al.  Theoretical studies of phospholipid bilayers and monolayers. Perturbing probes, monolayer phase transitions, and computer simulations of lipid-protein bilayers. , 1984, Canadian journal of biochemistry and cell biology = Revue canadienne de biochimie et biologie cellulaire.

[29]  Bo Jönsson,et al.  Molecular dynamics simulations of a sodium octanoate micelle in aqueous solution , 1986 .

[30]  P J Flory,et al.  Molecular organization in micelles and vesicles. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[31]  M. Saxton,et al.  Lateral diffusion and aggregation. A Monte Carlo study. , 1992, Biophysical journal.

[32]  G. Gompper,et al.  The conformation of fluid membranes: Monte Carlo simulations. , 1992, Science.

[33]  K. Dill,et al.  Phospholipid interactions in model membrane systems. I. Experiments on monolayers. , 1992, Biophysical journal.

[34]  E. Dufourc,et al.  Dynamics of phosphate head groups in biomembranes. Comprehensive analysis using phosphorus-31 nuclear magnetic resonance lineshape and relaxation time measurements. , 1992, Biophysical journal.

[35]  William M. Gelbart,et al.  Monte Carlo and mean‐field studies of successive phase transitions in rod monolayers , 1992 .

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

[37]  Terry R. Stouch,et al.  Conformational dependence of electrostatic potential derived charges of a lipid headgroup: Glycerylphosphorylcholine , 1992 .

[38]  O. Steinhauser,et al.  Cutoff size does strongly influence molecular dynamics results on solvated polypeptides. , 1992, Biochemistry.

[39]  J Brickmann,et al.  Molecular dynamics studies of the interface between a model membrane and an aqueous solution. , 1991, Biophysical journal.

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

[41]  K. Dill,et al.  Phospholipid interactions in model membrane systems. II. Theory. , 1992, Biophysical journal.

[42]  Michael L. Klein,et al.  Molecular dynamics study of a sodium octanoate micelle in aqueous solution , 1988 .

[43]  James H. Davis,et al.  The description of membrane lipid conformation, order and dynamics by 2H-NMR. , 1983, Biochimica et biophysica acta.

[44]  Ji-Min Yan,et al.  Point-Charge Models for Molecules Derived from Least-Squares Fitting of the Electric Potential , 1988 .

[45]  Herman J. C. Berendsen,et al.  MOLECULAR-DYNAMICS OF A BILAYER-MEMBRANE , 1983 .

[46]  H De Loof,et al.  Mean field stochastic boundary molecular dynamics simulation of a phospholipid in a membrane. , 1991, Biochemistry.

[47]  Scott H. Northrup,et al.  Molecular dynamics simulation of disorder transitions in lipid monolayers , 1985 .

[48]  J. Mccammon,et al.  Dynamics of Proteins and Nucleic Acids , 2018 .

[49]  Ken A. Dill,et al.  Molecular conformations in surfactant micelles , 1984, Nature.

[50]  H. Berendsen,et al.  Interaction Models for Water in Relation to Protein Hydration , 1981 .

[51]  Michiko Kodama,et al.  Successive phase-transition phenomena and phase diagram of the phosphatidylcholine-water system as revealed by differential scanning calorimetry , 1982 .

[52]  Martin Karplus,et al.  A simulation based model of NMR T1 relaxation in lipid bilayer vesicles , 1988 .

[53]  R. S. Mulliken Electronic Population Analysis on LCAO–MO Molecular Wave Functions. I , 1955 .

[54]  H. Hauser,et al.  Glycerol conformation and molecular packing of membrane lipids. The crystal structure of 2,3-dilauroyl-D-glycerol. , 1981, Journal of molecular biology.

[55]  Klein,et al.  Characterization of structural and dynamical behavior in monolayers of long-chain molecules using molecular-dynamics calculations. , 1988, Physical review letters.

[56]  J. Glomset,et al.  Computer-based modeling of the conformation and packing properties of docosahexaenoic acid. , 1986, Journal of lipid research.

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

[58]  Malcolm E. Davis,et al.  Electrostatics in biomolecular structure and dynamics , 1990 .

[59]  Pavel G. Khalatur,et al.  Molecular motions in a liquid-crystalline lipid bilayer. Molecular dynamics simulation , 1987 .

[60]  S H White,et al.  Structure of a fluid dioleoylphosphatidylcholine bilayer determined by joint refinement of x-ray and neutron diffraction data. I. Scaling of neutron data and the distributions of double bonds and water. , 1991, Biophysical journal.

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

[62]  J. Browning,et al.  General features of phospholipid conformation in membranes , 1978 .

[63]  Maria Luisa Foresti,et al.  A Monte Carlo simulation of water molecules near a charged wall , 1989 .

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

[65]  Søren Toxvaerd,et al.  Molecular dynamics simulations of Langmuir monolayers: A study of structure and thermodynamics , 1992 .

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

[67]  Donald E. Williams,et al.  Representation of the molecular electrostatic potential by a net atomic charge model , 1981 .

[68]  H L Scott,et al.  Monte Carlo calculations of order parameter profiles in models of lipid-protein interactions in bilayers. , 1986, Biochemistry.

[69]  R. Clegg,et al.  Translational diffusion of lipids in liquid crystalline phase phosphatidylcholine multibilayers. A comparison of experiment with theory. , 1985, Biochemistry.

[70]  S. Marčelja,et al.  Chain ordering in liquid crystals. II. Structure of bilayer membranes. , 1974, Biochimica et biophysica acta.

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

[72]  K. Harlos,et al.  Interactions and space requirement of the phosphate head group of membrane lipids: The single crystal structures of a triclinic and a monoclinic form of hexadecyl-2-deoxyglycerophosphoric acid monohydrate , 1984 .

[73]  Egbert Egberts Molecular dynamics simulation of multibilayer membranes. , 1988 .

[74]  Max L. Berkowitz,et al.  Computer simulation of a water/membrane interface , 1991 .

[75]  H L Scott,et al.  Lipid chains and cholesterol in model membranes: a Monte Carlo Study. , 1989, Biochemistry.

[76]  H. Hauser,et al.  Preferred conformation and molecular packing of phosphatidylethanolamine and phosphatidylcholine. , 1981, Biochimica et biophysica acta.

[77]  S. Singer,et al.  The Fluid Mosaic Model of the Structure of Cell Membranes , 1972, Science.

[78]  A. Blaurock,et al.  Disorder in nerve myelin: Phasing the higher order reflections by means of the diffuse scatter☆ , 1978 .

[79]  J J Wendoloski,et al.  Molecular dynamics simulation of a phospholipid micelle. , 1989, Science.

[80]  C R Worthington,et al.  X-ray diffraction evidence for the presence of discrete water layers on the surface of membranes. , 1991, Biochimica et biophysica acta.

[81]  K. Harlos,et al.  Conformation and packing properties of phosphatidic acid: The crystal structure of monosodium dimyristoylphosphatidate , 1984 .

[82]  H De Loof,et al.  Conformational analysis of lipid-associating proteins in a lipid environment. , 1988, Biochimica et biophysica acta.

[83]  D. Marsh,et al.  Calorimetric studies of the gel-fluid (L beta-L alpha) and lamellar-inverted hexagonal (L alpha-HII) phase transitions in dialkyl- and diacylphosphatidylethanolamines. , 1983, Biochemistry.

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

[85]  R M Venable,et al.  Model for the structure of the lipid bilayer. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[86]  D. Small,et al.  Phase equilibria and structure of dry and hydrated egg lecithin. , 1967, Journal of lipid research.

[87]  J. Seelig,et al.  Orientation and flexibility of the choline head group in phosphatidylcholine bilayers. , 1977, Biochimica et biophysica acta.

[88]  M. Volkenstein,et al.  Statistical mechanics of chain molecules , 1969 .

[89]  Alfred D. French,et al.  Computer modeling of carbohydrate molecules , 1990 .

[90]  Hans Binder,et al.  Behaviour of water at membrane surfaces - a molecular dynamics study , 1985 .

[91]  T. Ackermann C. L. Brooks III, M. Karplus, B. M. Pettitt. Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Volume LXXI, in: Advances in Chemical Physics, John Wiley & Sons, New York 1988. 259 Seiten, Preis: US $ 65.25 , 1990 .

[92]  Jacob N. Israelachvili,et al.  Entropic forces between amphiphilic surfaces in liquids , 1992 .

[93]  Ronald G. Larson,et al.  Monte Carlo simulation of microstructural transitions in surfactant systems , 1992 .

[94]  A C Maggs,et al.  Computer simulations of self-assembled membranes. , 1991, Science.

[95]  E Goormaghtigh,et al.  Theoretical conformational analysis of phospholipids bilayers. , 1981, Biochemical and biophysical research communications.

[96]  K. Esselink,et al.  Computer simulations of a water/oil interface in the presence of micelles , 1990, Nature.

[97]  Herman J. C. Berendsen,et al.  CONFORMATIONAL ENTROPY OF A BILAYER-MEMBRANE DERIVED FROM A MOLECULAR-DYNAMICS SIMULATION , 1983 .