INVESTIGATION OF THE PROTON RELEASE CHANNEL OF BACTERIORHODOPSIN IN DIFFERENT INTERMEDIATES OF THE PHOTO CYCLE - A MOLECULAR-DYNAMICS STUDY

Molecular dynamics simulations on bacteriorhodopsin were performed sta rting from a conformation based on electron cryomicroscopy studies [He nderson, R., et al. (1990) J. Mol. Biol. 213, 899-929]. We examined th e proton release channel in different intermediates of the bacteriorho dopsin photocycle. In the simulations of the ground state, two stable sets of conformations were observed differing in the distance of the g uanidinium group of Arg82 to the Schiff base. The set of conformations in which Arg82 is located closer to the Schiff base has a lower poten tial energy and agrees better with experimental data than the other se t. With both sets, we performed a series of simulations in which the c hromophore was isomerized to different states using purposive and nonp urposive methods. The energetic consideration of the different states argues for the location of the guanidinium group of Arg82 close to the Schiff base. The results also show that no C-13-C-14, C-14-C-15 dicis conformation of the retinal occurs in the K/L-intermediate of the pho tocycle instead supporting the occurrence of C-13-C-14 cis in these in termediates. In a last series of simulations, we modeled the M-interme diate of the bacteriorhodopsin photocycle. Again, comparison to differ ent experimental data indicates that Arg82 points toward the Schiff ba se. We conclude that the guanidinium group of Arg82 is located close t o the Schiff base at a distance of approximately 4.5 Angstrom and stay s there at least up to the M-intermediate of the photocycle.