Kinase simulations

Kinases are large family of protein found in a variety of cells that catalyze the transfer of ATP’s gamma phosphate group to target substrate. They initiate and control a large number of cellular pathways and are critical pharmaceutical targets. My research involves looking at the relationship between the sequence and dynamics of these kinases. The fundamental question that I would like to answer is what happens to the kinase’s underlying free energy landscape when its amino acid sequence is mutated, similar to mutations found in many cancers. To answer these questions, I am employing MD simulations combined with a new variation to MSMs which allows us to explicitly compare the kinetics and thermodynamics of these mutants. I have simulated over 12 milliseconds in aggregate data with three publications under preparation. These simulations are the largest set of kinase simulations ever performed.