Molecular Basis for Differential Anion Binding and Proton Coupling in the Cl–/H+ Exchanger ClC-ec1

By Tao Jiang, Wei Han, Merritt C. Maduke, and Emad Tajkhorshid.

Published in Journal of the American Chemical Society 2016 Mar 9;138(9):3066-75. PMID: 26880377. PMCID: 4898471. Link to publication page.

Projects: The Transport Cycle in Neurotransmitter Uptake Systems, Conformational Dynamics in the CLC Channel/Transporter Family . Core Facility: Computational Modeling.

Abstract

Cl^–/H⁺ transporters of the CLC superfamily form a ubiquitous class of membrane proteins that catalyze stoichiometrically coupled exchange of Cl^– and H⁺ across biological membranes. CLC transporters exchange H⁺ for halides and certain polyatomic anions, but exclude cations, F^–, and larger physiological anions, such as PO43^– and SO42^–. Despite comparable transport rates of different anions, the H⁺ coupling in CLC transporters varies significantly depending on the chemical nature of the transported anion. Although the molecular mechanism of exchange remains unknown, studies on bacterial ClC^-ec1 transporter revealed that Cl^– binding to the central anion^-binding site (S_cen) is crucial for the anion^-coupled H⁺ transport. Here, we show that Cl^–, F^–, NO3^–, and SCN^– display distinct binding coordinations at the S_cen site and are hydrated in different manners. Consistent with the observation of differential bindings, ClC^-ec1 exhibits markedly variable ability to support the formation of the transient water wires, which are necessary to support the connection of the two H⁺ transfer sites (Glu_in and Glu_ex), in the presence of different anions. While continuous water wires are frequently observed in the presence of physiologically transported Cl^–, binding of F^– or NO3^– leads to the formation of pseudo^-water^-wires that are substantially different from the wires formed with Cl^–. Binding of SCN^–, however, eliminates the water wires altogether. These findings provide structural details of anion binding in ClC^-ec1 and reveal a putative atomic^-level mechanism for the decoupling of H⁺ transport to the transport of anions other than Cl^–.