We report molecular dynamics simulations of water hydrating a lipid (dimyristoylphosphatidylcholine) monolayer under conditions chosen to eliminate simulation artifacts. These simulations provide a description of the behavior of the membrane–water interface that agrees with recent experimental studies. In particular, we find that the hydrating water orients to contribute the positive end of its dipole to the substantially positive electrostatic potential of the membrane interior, consistent with interpretations of recent experiments. In addition, recent experiments show that this water reorients rapidly on the NMR time scale. Our results concur, however the relatively rapid water motion does not preclude the preferential ordering that we observe. The limiting behavior of the system shows three hydration shells about the lipid PC headgroups and significant hydrogen bonding of water to the phosphate groups. The choline group experiences different environments, and the structure of the first hydration shell clearly corresponds to a clathrate. The motion of the hydrating water was found to be slower than that of bulk water, and the computed residence times for water about the lipids (20 ps about choline, 10 ps about phosphate) were in excellent agreement with results of NMR experiments. This further shows that water resides in a clathrate shell longer than in a shell about ions. In addition, we show that the structure and dynamics of water hydrating the lipids are very sensitive to the treatment of the long-range interactions. In particular, the radial structure sharpens considerably, a third hydration shell about the phosphate was observed only with large cutoffs, and hydrogen bonding of water to the lipids increased by 25%. The water moved more slowly than bulk when large cutoffs were employed but moved faster than bulk water when small cutoffs were used and the residence times for water about the lipids were twofold–fivefold larger using large cutoffs. In general it was found that the lipids significantly influence water out to several hydration shells, and that water hydrating the lipids behaves differently than bulk water.

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To elucidate the mechanism of solute diffusion through lipid bilayer membranes, nearly 4 ns of molecular dynamics simulations of solutes in phospholipid bilayers was conducted. The study, the first atomic level study of solute diffusion in a lipid bilayer, involved four simulations of an all-atom representation of a fully solvated dimyristoylphosphatidylcholine (DMPC) bilayer in the L alpha phase with benzene molecules as solutes, totaling over 7100 atoms. These simulations agree with experimental evidence that the presence of small solutes does not affect bilayer thickness but does result in slight perturbations in the ordering of the hydrocarbon chains. At room temperature, the benzene molecules have essentially isotropic motion and rotate freely. The rate of translational diffusion varies with position within the bilayer and is faster in the center than near the zwitterionic headgroups and is in excellent agreement with experimental values for the diffusion of small solutes in a bilayer. These simulations have elucidated the mechanism of diffusion in a bilayer to be similar to the "hopping" mechanism found for the diffusion of gases through soft polymers. Jumps of up to 8 A can occur in as little as 5 ps whereas average motions for that time period are only approximately 1.5 A. In many cases, the jumps are moderated by torsional changes in the hydrocarbon chains which serve as "gates" between voids through which the benzene molecules move. Comparison of these simulations with another 1000-ps simulation of benzene in a pure alkane provides evidence that lipid bilayers should not be treated as a homogeneous bulk hydrocarbon phase.

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Summary We describe the proceedings and conclusions from a “Workshop on Applications of Protein Models in Biomedical Research” that was held at University of California at San Francisco on 11 and 12 July, 2008. At the workshop, international scientists involved with structure modeling explored (i) how models are currently used in biomedical research, (ii) what the requirements and challenges for different applications are, and (iii) how the interaction between the computational and experimental research communities could be strengthened to advance the field.