It is increasingly apparent that proteins can utilize kinetic selection between competing pathways, each with a different sequence of transitions between intermediates. This offers an additional level of complexity to the ‘structure—dynamics—function’ paradigm revolutionized by molecular dynamics simulations: namely, it suggests that ‘kinetics’ can be an essential layer in mechanistic outcomes. Here we present strategies in multiscale kinetic modeling (MKM) as applied to coupled ion exchange in chloride channel antiporters. By combining bottom-up quantification of transition rates from experiments and multi-scale simulations (including reactive and polarizable molecular dynamics and Brownian dynamics) with top-down refinement based on experimental data, ion-exchange networks are constructed and the flux through those networks analyzed. The kinetic solutions reveal the molecular origin of the unusual 2.2:1 Cl–/H+ stoichiometry and influence of protein orientation. The dominance of different pathways will be shown to shift as a function of pH, highlighting the importance of the lower H+ binding site in maintaining the ion exchange ratio over a range of pH values. The flux will also be shown to shift in response to transmembrane electrical gradient distinctly from that due to a chemical gradient of the same magnitude, pointing to a more nuanced influence of electrochemical potentials than commonly assumed by the Nernst relationship. Collectively, our work demonstrates how simulations can build mechanistic insight from the conformational dynamics behind local transitions to phase space connecting metastable intermediates to kinetic networks that map out the flux of reactive processes and the response of that flux to reaction conditions. Most importantly, it calls out the fascinating role that kinetic selection can play in biology.

From molecular dynamics to kinetic network analysis: When does kinetic selection between competing mechanistic pathways matter?

ACS Spring 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.