STRUCTURE AND FLUCTUATIONS OF BACTERIORHODOPSIN IN THE PURPLE MEMBRANE - A MOLECULAR-DYNAMICS STUDY

Molecular dynamics simulations on bacteriorhodopsin were performed sta rting from the model structure described by Henderson et al. The simul ations were gradually improved by first treating a monomer in vacuum a nd then adding further monomers, lipids, and water to finally simulate a unit cell of the hexagonal lattice of the purple membrane containin g 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 Angstrom. In the simulat ions with the trimer, the structures of the three monomers differed by about the same amount and averaging over them led to an average struc ture with a considerably smaller r.m.s. deviation. The best average st ructure obtained had an r.m.s. deviation from the model structure of 1 .3 Angstrom. Fluctuations of the protein, the lipids, and water were a nalyzed in detail. As expected, the membrane-spanning helces of the pr otein fluctuate less than the peripheral loops. Unexpected, however, w as the finding that the fluctuations of the protein are asymmetric wit h respect to the midplane of the membrane. The fluctuations of the loo ps and the ends of the helices on the inner side of the membrane are m uch stronger than on the outer side. This asymmetry is also reflected by the fluctuations for the lipids, the lipids of the inner leaflet fl uctuating more strongly than those of the outer leaflet. The asymmetry was observed only in the presence of water on both sides of the membr ane. On the average, nine water molecules were found inside the protei n, most of them undergoing exchange with external water.