BIOPHYSICS SEMINAR<br>Elucidating Roles of Protein Dynamics in Enzyme Function by Molecular Simulation

Protein dynamics connect protein structure to function. The long term goal of the Nam research lab is to understand how large-scale protein dynamics and local fluctuations determine protein function at the molecular level. In this talk, I will discuss our recent work on F1-ATPase. F1-ATPase is the catalytic moiety of the F0F1-ATP synthase, which is responsible for the synthesis of ATP in cell by harnessing the proton-motive force across a membrane. F1-ATPase by itself is an ATP-driven motor protein that converts the free energy of ATP binding and its hydrolysis into the mechanical force that rotates the ?-stalk with high energy efficiency. The main question is to understand how the enzyme couples small structural changes in the enzyme’s active sites to global rotation of the ?-stalk. By applying molecular simulation techniques, we have trapped an intermediate state structure of F1-ATPase, which has eluded its experimental determination despite biophysical evidence for its existence, and showed how the release of ATP hydrolysis product is coupled to large-scale conformational changes of the enzyme. In addition, I will discuss our recent progress on elucidating the catalytic mechanism of protein tyrosine kinase by multiscale quantum mechanical and molecular mechanical simulations. The two examples highlight the central role of protein dynamics on the control of protein activity.