MOLECULAR-DYNAMICS SIMULATION OF A BILAYER OF 200 LIPIDS IN THE GEL AND IN THE LIQUID-CRYSTAL PHASES

We have constructed and simulated a membrane-water system which consis ts of 200 molecules of almitoyl-2-oleoyl-sn-glycero-3-phosphatidylchol ine forming a rectangular patch of a bilayer and of 5483 water molecul es covering the head groups on each side of the bilayer. The total num ber of atoms is approximately 27 000. The lateral dimensions of the bi layer are 85 angstrom x 100 angstrom, and the distance between the bil ayer surfaces as given by the average phosphorus to phosphorus distanc e is 35 angstrom. The thickness of each water layer is up to 15 angstr om. In all, we simulated 263 ps of the dynamics of the system. To prev ent system disintegration, atoms within 5 angstrom from the surface we re harmonically restrained and treated by Langevin dynamics, forming a stochastic boundary. Interior lipids and water molecules were unrestr ained. The first 120 ps of the dynamics calculation were used to equil ibrate the system and to achieve a low internal pressure. We performed two simulations for analysis: simulation I of the system that resulte d from the equilibration; simulation II of the system after an increas e of the area per head group from 46 to 70 angstrom2. The decrease of the lateral lipid density was achieved by scaling the atomic x-, y-, a nd z-coordinates independently, leaving the volume of the system const ant. For both simulations I and II, we determined the internal pressur e, the lipid self-diffusion coefficients, the order parameter profile, the distribution of molecular groups, and other properties. The param eters extracted from simulation II are in good agreement with observat ions on bilayers in the liquid-crystal phase. We provide evidence that the bilayer of simulation I corresponds to the gel phase. The membran e structures resulting from this work can be used for molecular dynami cs investigations of membrane proteins, e.g., for the study of lipid-p rotein interactions or for the equilibration of structural models.