title: Functional interactions in bacteriorhodopsin: a theoretical analysis of retinal hydrogen bonding with water.
abstract: The light-driven proton pump, bacteriorhodopsin (bR) contains a retinal molecule with a Schiff base moiety that can participate in hydrogen-bonding interactions in an internal, water-containing channel. Here we combine quantum chemistry and molecular mechanics techniques to determine the geometries and energetics of retinal Schiff base-water interactions. Ab initio molecular orbital calculations are used to determine potential surfaces for water-Schiff base hydrogen-bonding and to characterize the energetics of rotation of the C-C single bond distal and adjacent to the Schiff base NH group. The ab initio results are combined with semiempirical quantum chemistry calculations to produce a data set used for the parameterization of a molecular mechanics energy function for retinal. Using the molecular mechanics force field the hydrated retinal and associated bR protein environment are energy-minimized and the resulting geometries examined. Two distinct sites are found in which water molecules can have hydrogen-bonding interactions with the Schiff base: one near the NH group of the Schiff base in a polar region directed towards the extracellular side, and the other near a retinal CH group in a relatively nonpolar region, directed towards the cytoplasmic side.
authors.affiliation: Département de Biologie Cellulaire et Moléculaire, C.E.A., Centre d'Etudes Saclay, Gif-sur-Yvette, France.
authors.forename: M
authors.initials: M
authors.lastname: Nina
authors.forename: B
authors.initials: B
authors.lastname: Roux
authors.forename: J C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D001436:Bacteriorhodopsins / Q000737:chemistry*; D001665:Binding Sites; D055592:Biophysical Phenomena; D001703:Biophysics; D018360:Crystallography, X-Ray; D004563:Electrochemistry; D019617:Halobacterium salinarum / Q000737:chemistry; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation; D011522:Protons; D012172:Retinaldehyde / Q000737:chemistry; D012545:Schiff Bases / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D011522:Protons; D012545:Schiff Bases; D014867:Water; D001436:Bacteriorhodopsins; D012172:Retinaldehyde