Proton Binding at Protein and Membrane Interfaces

Abstract

Membrane-embedded proton transporters often expose to the bulk clusters of closely spaced carboxylate groups that might function as a proton antenna, binding a proton that could then be released to the bulk or transferred to an internal protein group. To characterize mechanisms of proton binding and proton transfer at protein and membrane interfaces we study membranes and proteins in membranes. Extensive computations of a proton-antenna model using classical mechanical and quantum mechanical descriptions indicate that the surface proton-binding site is part of an extensive hydrogen-bond cluster that includes caged waters. The water-mediated bridges between carboxylate groups are, however, highly dynamic, with lifetimes comparable to that of water hydrogen bonding. The energetic barrier for proton transfer within the proton antenna cluster is somewhat high, suggesting that a proton bound at this site could indeed be stored. At the interface of a membrane with negatively charged lipids, we find a rich network of dynamic lipid-water hydrogen bonds and transient clusters of water-bridged phosphate groups.We developed algorithms inspired from graph theory and social sciences and applied these algorithms to study protein conformational dynamics. Using such algorithms, we found that hydrogen-bonded waters might assist long-distance conformational coupling of the SecA protein motor. Financial support was provided in part by the DFG Collaborative Research Center SFB 1078 Project C4 (to A.-N.B.) and by the Freie Universität Berlin within the Excellence Initiative of the German Research Foundation. Computing time was provided by the HLRN, the North-German Supercomputing Alliance.