Structure and Fluctuations of Bacteriorhodopsin in the Purple Membrane: A Molecular Dynamics Study

Molecular dynamics simulations on bacteriorhodopsin were performed starting from the model structure described by Hendersonet al.The simulations were gradually improved by first treating a monomer in vacuum and then adding further monomers, lipids, and water to finally simulate a unit cell of the hexagonal lattice of the purple membrane containing a trimer and lipids and water on both sides. During all simulations, the protein structure moved away from the model structure to reach a root-mean-square (r. m. s.) deviation of 2 to 3 Å. In the simulations with the trimer, the structures of the three monomers differed by about the same amount and averaging over them led to an average structure with a considerably smaller r.m.s. deviation. The best average structure obtained had an r. m. s. deviation from the model structure of 1.3 Å. Fluctuations of the protein, the lipids, and water were analyzed in detail. As expected, the membrane-spanning helices of the protein fluctuate less than peripheral loops. Unexpected, however, was the finding that the fluctuations of the protein are asymmetric with respect to the midplane of the membrane. The fluctuations of the loops and the ends of the helices on the inner side of the membrane are much stronger than on the outer side. This asymmetry is also reflected by the fluctuations for the lipids, the lipids of the inner leaflet fluctuating more strongly than those of the leaflet. The asymmetry was observed only in the presence of water on both sides of the membrane. On the average, nine water molecules were found inside the protein, most of them undergoing exchange with external water.f2f2Present address: O. Edholm, Royal Institute of Technology, Department of Theoretical Physics, S-10044 Stockholm, Sweden.Abbreviations used: BR, bacteriorhodopsin; PGP, phosphatidyl glycerophosphate; SB, Schiff base; ECM, electron cryo-microscopy; MD, molecular dynamics; r. m. s., root-mean-square; cuph, central processor unit hour.