title: Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway.
abstract: Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained a mystery. From an analysis of the X-ray structure of the D96G/F171C/F219L triple mutant of bR and 60 independent molecular dynamics simulations of bR photointermediates, we report that the deprotonation of D96, a key residue in proton transfer reactions, serves two roles that occur sequentially. First, D96 donates a proton to the Schiff base. Subsequently, the deprotonation of D96 serves to "unlatch" the cytoplasmic side. The latching function of D96 appears to be remarkably robust, functioning to open hydration channels in all photointermediate structures. These results suggest that the protonation state of D96 may be the critical biophysical cue controlling the opening and closing of the cytoplasmic half-channel in bR. We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality.
authors: Genome Center and Department of Biomedical Engineering, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
authors: Ting
authors: T
authors: Wang
authors: Ayla O
authors: AO
authors: Sessions
authors: Christopher S
authors: CS
authors: Lunde
authors: Shahab
authors: S
authors: Rouhani
authors: Robert M
authors: RM
authors: Glaeser
authors: Yong
authors: Y
authors: Duan
authors: Marc T
authors: MT
authors: Facciotti
mesh_terms: D019943:Amino Acid Substitution; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics; D001224:Aspartic Acid / Q000737:chemistry*; D001436:Bacteriorhodopsins / Q000737:chemistry* / Q000235:genetics; D018360:Crystallography, X-Ray; D019617:Halobacterium salinarum; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D010084:Oxidation-Reduction; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D019843:Archaeal Proteins; D001224:Aspartic Acid; D001436:Bacteriorhodopsins
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