Mechanisms by which water-mediated hydrogen-bond networks govern pH-dependent reactions at membrane interfaces.

Abstract

pH-dependent reactions at membrane interfaces are used by cells to maintain pH homeostasis and to ensure normal cell function. Membrane-bound proteins and peptide systems that sense pH typically bind protons using a few titratable sidechains that communicate with the bulk. The identity of these pH-sensing sidechains is central to hypotheses about protein reaction mechanisms and for the rational design of proton detectors. But, as protein groups hypothesized to sense pH in proteins and peptide systems are part of dynamic water-mediated networks, evaluating their pH-sensing functionality may prove difficult. We developed efficient graph-based algorithms and methodologies to evaluate dynamic hydrogen-bond networks of protein and peptide systems known to have a pH-sensing functionality, and to identify sites of hydrogen-bond networks where protons are likely to bind. We find that the assembly of dynamic water-mediated hydrogen-bond networks that include potential proton-sensing groups is a key event along the reaction coordinates of pH-dependent membrane proteins and membrane-bound peptides, and implement graph-based algorithms to characterize the dynamics of these water networks. We further find that polar and basic protein sidechains largely govern the dynamics of the water-mediated hydrogen-bond networks of proton-binding groups, and help maintain acidic sidechains within clusters that collectively can bind and store protons. Taken together, the ensemble of hydrogen-bond network computations we performed for pH-coupled proteins and peptide systems provide a framework to decipher the roles of dynamic water-mediated hydrogen-bond networks in proton binding at membrane interfaces. Research was supported in part by the European Union's Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie grant agreement No 860592, Innovative Training Network ‘Proton and proton-coupled transport’, and by computing time from the Physics Department of the Freie Universität Berlin and from the Forschungszentrum Jülich (JURECA-DC, allocation PHDPORES).