Multiscale Responsive Kinetic Modeling: Quantifying Biomolecular Reaction Flux under Varying Electrochemical...

Area of Science:

• Molecular Biophysics
• Computational Biology
• Biophysical Chemistry

Background:

• Characterizing complex molecular processes with multiple transitions under diverse conditions is a significant challenge in molecular biophysics.
• Existing methods struggle to integrate simulation and experimental data effectively for a comprehensive understanding of kinetic and thermodynamic properties.

Purpose of the Study:

• To develop a novel condition-responsive kinetic modeling framework.
• To combine bottom-up rate quantification from multiscale simulations with top-down experimental data refinement.
• To apply and validate the framework for electrochemically driven transport in channels and transporters.

Main Methods:

• Developed a condition-responsive kinetic modeling framework.
• Integrated multiscale simulations for bottom-up rate quantification.
• Utilized equilibrium and nonequilibrium experimental data (e.g., electrophysiology) for top-down solution refinement.
• Applied the framework to the Cl^-/H⁺ antiporter ClC-ec1 and the Shaker K⁺ channel.

Main Results:

• Demonstrated optimal and predictive kinetic solutions for ClC-ec1 by grounding the solution space with thermodynamic constraints and seeding with simulation data.
• Showed that optimal solutions and biophysical insights for the Shaker K⁺ channel can be obtained with sufficient experimental data.
• Identified that while single-pathway mechanisms can be dominant, competing and off-pathway flux are crucial for accurately replicating experimental findings and describing channel rectification.

Conclusions:

• The novel framework enables a complete thermodynamic and kinetic characterization of complex molecular processes under varying conditions.
• Integrating simulation and experimental data provides a powerful approach for understanding transport mechanisms in membrane proteins.
• The study highlights the importance of considering multi-pathway dynamics, including off-pathway fluxes, for accurate modeling of channel function.