Many important receptor proteins are embedded in lipid bilayers, and the lipid environment significantly influences the structure, dynamics, and properties of these integral membrane proteins. While lipid bilayers have been the subject of extensive experimental study, the results have been difficult to analyze and interpret due to the systems' complexities. A large number of lipid and water molecules and counterions is required to represent a physically realistic monolayer or bilayer model. Many interesting properties of lipid assemblies occur on time scales longer than can be accommodated by typical MD simulations.
Green spheres are phosphorus atoms, and red spheres are phosphate oxygens.
Water molecules are omitted to simplify the structure. The challenging computational task of simulating lipid assemblies is being met by Terry P. Lybrand and colleagues at the University of Washington, who are studying the behavior and properties of lipid bilayer systems using detailed MD simulations as part of a major research program on membrane receptor proteins. Ultimately they seek to include full lipid bilayer models in detailed simulation studies of membrane proteins to address key issues such as conformational flexibility and protein transitions and to help analyze the results of experimental studies of membrane proteins. Studies of the latter are quite important as, for example, plasma membranes of eucaryotes are rich in cholesterol. Sj for hydrocarbon sidechains, electron-density profiles, lateral pressures, and radial distribution functions for water around the phosphate head groups.