United atom force field for phospholipid membranes: Constant pressure molecular dynamics simulation of dipalmitoylphosphatidicholine/water system

We refined the united atom field for the simulations of phospholipid membranes. To validate this potential we performed 1000‐ps constant pressure simulation of a dipalmitoylphosphatidicholine (DPPC) bilayer at T=50° C. The average area per head group (61.6±0.6) Å2 obtained in our simulation agrees well with the measured one of (62.9±1.3) Å2. The calculated SCD order parameters for the Sn‐2 hydrocarbon tail also display a good agreement with the experiment. The conformations of head groups in our simulations of the liquid crystal phase are different than the ones observed in the crystal structure. ©1999 John Wiley & Sons, Inc. J Comput Chem 20, 531–545, 1999

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

[2]  J. Nagle,et al.  Lecithin bilayers. Density measurement and molecular interactions. , 1978, Biophysical journal.

[3]  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.

[4]  K. Merz,et al.  Head group-water interactions in lipid bilayers: a comparison between DMPC- and DLPE-based lipid bilayers , 1993 .

[5]  E. Dufourc,et al.  Restatement of order parameters in biomembranes: calculation of C-C bond order parameters from C-D quadrupolar splittings. , 1995, Biophysical journal.

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

[7]  R. Pearson,et al.  The molecular structure of lecithin dihydrate , 1979, Nature.

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

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

[10]  Wataru Shinoda,et al.  Molecular dynamics study of a lipid bilayer: Convergence, structure, and long-time dynamics , 1997 .

[11]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[12]  U. Singh,et al.  A NEW FORCE FIELD FOR MOLECULAR MECHANICAL SIMULATION OF NUCLEIC ACIDS AND PROTEINS , 1984 .

[13]  R. Mendelsohn,et al.  CD2 rocking modes as quantitative infrared probes of one-, two-, and three-bond conformational disorder in dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylcholine/cholesterol mixtures. , 1991, Biochemistry.

[14]  V A Parsegian,et al.  Membrane dipole potentials, hydration forces, and the ordering of water at membrane surfaces. , 1992, Biophysical journal.

[15]  N. L. Owen,et al.  Spectroscopic studies of some substituted methyl formates. Part 1.—Microwave spectra and internal rotation barriers of methyl-fluoroformate, -propiolate, -cyanoformate, -acrylate and -acetate , 1971 .

[16]  H. Akutsu.  Direct determination by Raman scattering of the conformation of the choline group in phospholipid bilayers. , 1981, Biochemistry.

[17]  Richard W. Pastor,et al.  Computer Simulation of a DPPC Phospholipid Bilayer: Structural Changes as a Function of Molecular Surface Area , 1997 .

[18]  Jean-Paul Ryckaert,et al.  Molecular dynamics of liquid n-butane near its boiling point , 1975 .

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

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

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

[22]  G Büldt,et al.  Neutron diffraction studies on phosphatidylcholine model membranes. I. Head group conformation. , 1979, Journal of molecular biology.

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

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

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

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

[27]  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 .

[28]  Alexander D. MacKerell,et al.  An all-atom empirical energy function for the simulation of nucleic acids , 1995 .

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

[30]  M. Karplus,et al.  CHARMM: A program for macromolecular energy, minimization, and dynamics calculations , 1983 .

[31]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[32]  A. Kusumi,et al.  Hydrogen Bonding of Water to Phosphatidylcholine in the Membrane As Studied by a Molecular Dynamics Simulation: Location, Geometry, and Lipid-Lipid Bridging via Hydrogen-Bonded Water , 1997 .

[33]  G. Vanderkooi,et al.  Multibilayer structure of dimyristoylphosphatidylcholine dihydrate as determined by energy minimization. , 1991, Biochemistry.

[34]  W. Richards,et al.  Head group and chain behavior in biological membranes: a molecular dynamics computer simulation. , 1994, Biophysical journal.

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

[36]  J. Nagle,et al.  Structure of fully hydrated bilayer dispersions. , 1988, Biochimica et biophysica acta.

[37]  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.

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

[39]  K. G. Brown,et al.  Conformation‐dependent Raman bands of phospholipid surfaces. 3—head group Ortho‐phosphate stretching vibrations , 1982 .