Multiscale Kinetic Modeling of a Cl-/H+ Antiporter: Integrating Simulation and Experiment to Characterize Ion Exchange

One of the central challenges in modern biophysics is understanding the molecular nature of coupled biomolecular transport mechanisms. The coupled ion exchange mechanism in Cl-/H+ antiporters offers an intriguing case study for this challenge. In this talk I will present our new approach to multiscale kinetic modeling (MKM) and its application to characterize Cl-/H+ exchange in ClC-ec1. We combine rate coefficients, calculated with reactive and polarizable molecular dynamics simulations, in a kinetic (Markov state) model, and then optimize the rate coefficients within their calculated error to reproduce experimental data. This produces a set of solutions that predict new, testable properties (e.g., rates at different pH values and the relative contribution of protein orientations). These solutions also reveal insight into the series of transitions that define the mechanism, the balance of rate-limiting steps, the molecular origin of the 2.2:1 Cl -/H+ stoichiometry, and the influence of protein orientation. Our results suggest that the consistent exchange ratio is a consequence of kinetic coupling wherein residue E148 plays an essential role through protonation-dependent anion transport, and an anion-dependent pKa value. They further demonstrate that a large conformational change is not essential at this level of modeling for the ion exchange mechanism, suggesting a more facile possible evolutionary connection to chloride channels. Finally, the results demonstrate how an ensemble of different exchange pathways, as opposed to a single series of transitions, culminates in the macroscopic observables and thereby explains the molecular mechanism.