title: Investigation of the proton release channel of bacteriorhodopsin in different intermediates of the photo cycle. A molecular dynamics study.
abstract: Molecular dynamics simulations on bacteriorhodopsin were performed starting from a conformation based on electron cryomicroscopy studies [Henderson, R., et al. (1990) J. Mol. Biol. 213, 899-929]. We examined the proton release channel in different intermediates of the bacteriorhodopsin photocycle. In the simulations of the ground state, two stable sets of conformations were observed differing in the distance of the guanidinium group of Arg82 to the Schiff base. The set of conformations in which Arg82 is located closer to the Schiff base has a lower potential energy and agrees better with experimental data than the other set. With both sets, we performed a series of simulations in which the chromophore was isomerized to different states using purposive and nonpurposive 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 C13-C14, C14-C15 dicis conformation of the retinal occurs in the K/L-intermediate of the photocycle instead supporting the occurrence of C13-C14 cis in these intermediates. In a last series of simulations, we modeled the M-intermediate of the bacteriorhodopsin photocycle. Again, comparison to different experimental data indicates that Arg82 points toward the Schiff base. We conclude that the guanidinium group of Arg82 is located close to the Schiff base at a distance of approximately 4.5 A and stays there at least up to the M-intermediate of the photocycle.
authors.affiliation: Max-Planck-Institut fur Biologie, Abteilung Membranbiochemie, Tubingen, Germany.
authors.forename: J
authors.initials: J
authors.lastname: Nagel
authors.forename: O
authors.initials: O
authors.lastname: Edholm
authors.forename: O
authors.initials: O
authors.lastname: Berger
authors.forename: F
authors.initials: F
authors.lastname: Jähnig
mesh_terms: D001120:Arginine / Q000378:metabolism; D001436:Bacteriorhodopsins / Q000737:chemistry*; D003198:Computer Simulation; D007536:Isomerism; D008854:Microscopy, Electron; D008958:Models, Molecular; D008968:Molecular Conformation; D015394:Molecular Structure; D011487:Protein Conformation; D011522:Protons; D012172:Retinaldehyde / Q000737:chemistry / Q000378:metabolism; D012984:Software
chemical_list: D011522:Protons; D001436:Bacteriorhodopsins; D001120:Arginine; D012172:Retinaldehyde