Multiscale Responsive\nKinetic Modeling: Quantifying\nBiomolecular Reaction Flux under Varying Electrochemical Conditions

Attaining a complete thermodynamic and kinetic characterization\nfor processes involving multiple interconnected rare-event transitions\nremains a central challenge in molecular biophysics. This challenge\nis amplified when the process must be understood under a range of\nreaction conditions. Herein, we present a novel condition-responsive\nkinetic modeling framework that can combine the strengths of bottom-up\nrate quantification from multiscale simulations with top-down solution\nrefinement using both equilibrium and nonequilibrium experimental\ndata. Although this framework can be applied to any process, we demonstrate\nits use for electrochemically driven transport through channels and\ntransporters via the development of electrochemically responsive rates.\nUsing the Cl<sup>–</sup>/H<sup>+</sup> antiporter ClC-ec1 as\na model system, we show how optimal and predictive kinetic solutions\ncan be obtained when the solution space is grounded by thermodynamic\nconstraints, seeded through multiscale rate quantification, and further\nrefined with experimental data, such as electrophysiology assays.\nTurning to the Shaker K<sup>+</sup> channel, we demonstrate that optimal\nsolutions and biophysical insights can also be obtained with sufficient\nexperimental data. This multi-pathway method also proves capable of\nidentifying single-pathway dominant channel mechanisms but reveals\nthat competing and off-pathway flux is still essential to replicate\nexperimental findings and to describe concentration-dependent channel\nrectification.