Professor Jana Shen
Pharmaceutical Sciences
University of Maryland
Baltimore, MD

Monday, April 9, 2018
3:00 pm (CT)
3269 Beckman Institute

Abstract

Biological ion and substrate transport across the membrane is often regulated by proton translocation; however, detailed mechanisms are challenging to decipher using wet-lab experiments. In this talk I will discuss a molecular dynamics technique that can describe conformational dynamics coupled to protonation/deprotonation events. This technique, known as the continuous constant pH molecular dynamics (CpHMD), can be applied to predict pKa values, and more importantly, provide novel details of proton-coupled conformational processes that are otherwise difficult to delineate. I will discuss two examples from our recent work: 1) the conformational activation of the influenza virus M2 proton channel as a function of pH; 2) the activation and ion-proton exchange steps of the E. coli. sodium-proton antiporter NhaA. With our current effort to accelerate and disseminate the CpHMD method as well as adapt it to GPU hardware, we hope to equip the community with a powerful tool for gaining previously unattainable insights into proton-mediated processes in biology that remain poorly understood.