Multiscale Kinetic Modeling Reveals an Ensemble of Cl -/H + Exchange Pathways in ClC-ec1 Antiporter

J Am Chem Soc. 2018 Feb 7;140(5):1793-1804. doi: 10.1021/jacs.7b11463. Epub 2018 Jan 30.

Abstract

Despite several years of research, the ion exchange mechanisms in chloride/proton antiporters and many other coupled transporters are not yet understood at the molecular level. Here, we present a novel approach to kinetic modeling and apply it to ion exchange in ClC-ec1. Our multiscale kinetic model is developed by (1) calculating the state-to-state rate coefficients with reactive and polarizable molecular dynamics simulations, (2) optimizing these rates in a global kinetic network, and (3) predicting new electrophysiological results. The model shows that the robust Cl:H exchange ratio (2.2:1) can indeed arise from kinetic coupling without large protein conformational changes, indicating a possible facile evolutionary connection to chloride channels. The E148 amino acid residue is shown to couple chloride and proton transport through protonation-dependent blockage of the central anion binding site and an anion-dependent pKa value, which influences proton transport. The results demonstrate how an ensemble of different exchange pathways, as opposed to a single series of transitions, culminates in the macroscopic observables of the antiporter, such as transport rates, chloride/proton stoichiometry, and pH dependence.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Antiporters / chemistry
  • Antiporters / metabolism*
  • Chlorides / chemistry
  • Chlorides / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / metabolism*
  • Hydrogen / chemistry
  • Hydrogen / metabolism
  • Hydrogen-Ion Concentration
  • Kinetics
  • Molecular Dynamics Simulation*

Substances

  • Antiporters
  • CLC-ec1 protein, E coli
  • Chlorides
  • Escherichia coli Proteins
  • Hydrogen