Permeation and gating in ion channels

Our goal is to achieve the speedup provided by multiscale modeling, yet preserve the atomic details of the molecules. With a complete structure [24] and a multiscale description of the $K^+$ channel through MUSICO, the goal of simulating the gating mechanism may be attainable. We will perform the simulations with the atomistic molecular dynamics and then through substructuring the protein, from grouping a small number of atoms together to the larger scale of simulating at the secondary structure level of the protein. This will provide a spectrum of simulations as a foundation for future molecular modeling. We will also analyze the molecular dynamics trajectories to discover the slow hinge-like motions for gating events and the permeation of ions. The results will provide insights on exploring the gating mechanism of other ion channels as well as enzyme movements for future development in molecular modeling and drug design. This project is in collaboration with Prof. J. Andrew McCammon in the Department of Chemistry and Biochemistry at the University of California in San Diego.