Simulations of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine lipid bilayer interacting with a solid surface of hydroxylated nanoporous amorphous silica have been carried out over a range of lipid-solid substrate distances. The porous solid surface allowed the water layer to dynamically adjust is thickness, maintaining equal pressures above and below the membrane bilayer. Qualitative estimates of the force between the surfaces leads to an estimated lipid-silicon distance in very good agreement with the results of neutron scattering experiments. Detailed analysis of the simulation at the separation suggested by experiment shows that for this type of solid support the water layer between surfaces is very narrow, consisting only of bound waters hydrating the lipid headgroups and hydrophilic silica surface. The reduced hydration, however, has only minor effects on the headgroup hydration, the orientation of water molecules at the interface, and the membrane dipole potential. While these structural properties were not sensitive to the presence of the solid substrate, the calculated diffusion coefficient for translation of the lipid molecules was altered significantly by the silica surface.

A 100 ns simulation of a fluid phase dioleoylphosphatidylcholine bilayer, consisting of 288 lipid molecules at full hydration, has been studied to describe in detail the lateral translational motion of individual lipid molecules. Analysis of the simulation trajectories suggests that correlated motion between neighboring lipid molecules is an important aspect of lipid dynamics. The correlation among neighboring lipids within a monolayer is substantial and surprisingly long-ranged with a decay length of approximately 25 A. This provides a mechanism for the previously published observation that lateral diffusion coefficients computed from molecular dynamics simulations exhibited a strong dependence on the size of the unit cell and for the recent suggestion that lipid flows on that nanoscale are an important component of translational diffusion within membranes. Additionally, we show that diffusive motion is only weakly correlated between lipids in opposing monolayers.

The lipid modified human N-Ras protein, implicated in human cancer development, is of particular interest due to its membrane anchor that determines the activity and subcellular location of the protein. Previous solid-state NMR investigations indicated that this membrane anchor is highly dynamic, which may be indicative of backbone conformational flexibility. This article aims to address if a dynamic exchange between three structural models exist that had been determined previously. We applied a combination of solid-state nuclear magnetic resonance (NMR) methods and replica exchange molecular dynamics (MD) simulations using a Ras peptide that represents the terminal seven amino acids of the human N-Ras protein. Analysis of correlations between the conformations of individual amino acids revealed that Cys 181 and Met 182 undergo collective conformational exchange. Two major structures constituting about 60% of all conformations could be identified. The two conformations found in the simulation are in rapid exchange, which gives rise to low backbone order parameters and nuclear spin relaxation as measured by experimental NMR methods. These parameters were also determined from two 300 ns conventional MD simulations, providing very good agreement with the experimental data.

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The Ras family of proteins plays crucial roles in a variety of cell signaling networks where they have the function of a molecular switch. Their particular medical relevance arises from mutations in these proteins that are implicated in ~30% of human cancers. The various Ras proteins exhibit a high degree of homology in their soluble domains but extremely high variability in the membrane anchoring regions that are crucial for protein function and are the focus of this study. We have employed replica exchange molecular dynamics computer simulations to study a doubly lipidated heptapeptide, corresponding to the C-terminus of the human N-Ras protein, incorporated into a dimyristoylphosphatidylcholine lipid bilayer. This same system has previously been investigated experimentally utilizing a number of techniques, including neutron scattering. Here we present results of well converged simulations that describe the subtle changes in scattering density in terms of the location of the peptide and its lipid modifications and in terms of changes in phospholipid density arising from the incorporation of the peptide into the membrane bilayer. The detailed picture that emerges from the combination of experimental and computational data exemplifies the power of combining isotopic substitution neutron scattering with atomistic molecular dynamics simulation. This article is part of a Special Issue entitled: Membrane protein structure and function.