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Abstract:
Potassium (K+) ion channels are transmembrane proteins that regulate the passage of K+ ions through cell membranes. The selectivity filter is the narrowest part of the pathway of ions through the channel. It plays a determining role in the remarkably high ion selectivity and transport rates. Despite decades of work the precise mechanistic details of the transport through ion channels are still elusive. According to the so-called soft-knock mechanism water molecules alternate between K+ ions in the selectivity filter and co-transport with the ions. In contrast, the hard-knock mechanism assumes that water is absent from the selectivity filter during ion conduction. Two-dimensional infrared spectroscopy (2D IR) is an ultrafast technique that measures molecular vibrations. Carbonyl stretching vibrations of a protein backbone are sensitive probes of the local chemical environment and can be used to discriminate between water and K+ ions in the selectivity filter.
I will present our recent line shape simulations and experiments, performed by our collaborators, on a prokaryotic K+ channel KcsA. Our results are clearly consistent with all the previous 2D IR experiments and illustrate the prevalence of the soft-knock ion configurations in the closed conductive state of the KcsA channel. Additionally, I will discuss our most recent simulations and 2D IR experiments with various waiting times reporting on ion, water, and protein dynamics inside the selectivity filter of the KcsA channel.
Biography:
Alexei Kananenka is an Assistant Professor of Physics at the University of Delaware. Alexei received his undergraduate degree from Belarus State University and M. Sc. in Theoretical Chemistry from University of Western Ontario in Canada in 2013. He then joined Prof. Dominika Zgid group at University of Michigan where he developed Green's function-based embedding methods for strongly correlated electron systems receiving his Ph.D. in Theoretical Chemistry in 2017. Next two years Alexei spent as a postdoctoral scholar in Prof. Jim Skinner's group at Pritzker School of Molecular Engineering, University of Chicago where Alexei used theoretical and computational vibrational spectroscopy to study soft condensed-phase systems such as water and proteins. Alexei's current research interest include vibrational spectroscopy of biological systems, dynamics of open quantum systems, machine learning, and electrochemistry.
Seminar Series by the NYU-ECNU Center for Computational Chemistry at NYU Shanghai
This event is open to the NYU Shanghai, NYU, ECNU community and the computational chemistry community.
