title: Potential proton-release channels in bacteriorhodopsin.
abstract: The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton-transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen-bonded networks, which may include internal water molecules. The terminal step of the proton-transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton-release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen-bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.
authors.affiliation: Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
authors.forename: Alain
authors.initials: A
authors.lastname: Chaumont
authors.forename: Marcel
authors.initials: M
authors.lastname: Baer
authors.forename: Gerald
authors.initials: G
authors.lastname: Mathias
authors.forename: Dominik
authors.initials: D
authors.lastname: Marx
mesh_terms: D000596:Amino Acids; D001436:Bacteriorhodopsins / Q000737:chemistry*; D003198:Computer Simulation; D006860:Hydrogen Bonding; D008958:Models, Molecular; D011487:Protein Conformation; D017494:Proton Pumps / Q000737:chemistry* / Q000378:metabolism; D011522:Protons; D014867:Water
chemical_list: D000596:Amino Acids; D017494:Proton Pumps; D011522:Protons; D014867:Water; D001436:Bacteriorhodopsins