Proton Transport through E. coli CLC Chloride/Proton Antiporter in the Presence of Bound Fluoride

Abstract

A prototypical CLC antiporter from E. coli, EcCLC, regulates the influx of Cl− and efflux of H+ across membranes. Interestingly, it does not transport F-, even though F- has a smaller radius than Cl-. Here we apply multiscale quantum-mechanical/molecular-mechanical (QM/MM) simulations to study H+ migration via the Grotthuss mechanism through the transmembrane domain of EcCLC with F− present in the central binding site. Our preliminary data suggest that the F- does not prevent the protonation of the external gating residue E148, which rotates inward into the pore to receive the migrating H+. However, the protonated E148 is stabilized by F- in the pore through hydrogen-bonding interactions via 0-2 bridging water molecules. Some trajectories even show back and forth exchanges of H+ between the F- and E148. This picture differs significantly from our previous simulations of H+ transfer in the presence of a bound Cl-, where such strong interactions are not found. These strong interactions imply that it is difficult to separate the F- and protonated E148, therefore disrupting the antiporter operating cycle. Our results agree well with the “lock down” mechanism previously proposed by Miller and coworkers based on experiments (Lim, et al. Nat. Chem. Biol. 2013, 9, 721-725).