Molecular dynamics simulations of the isolated β subunit of F1-ATPase

F1-ATPase is an ATP-driven rotary motor enzyme. We investigated the structural fluctuations of the β subunits in F1-ATPase using molecular dynamics (MD) simulations. MD simulations were performed for the isolated βE subunits over 100 ns. Consistent with NMR experiments, the average conformations remained open, and large hinge-bending motions were observed for two species. Principal component analysis shows that motions in low-frequency modes are well correlated with the functionally important structural transition of the β subunit from the open to closed conformation, suggesting that flexibility in the direction of the structural transition is an intrinsic structural feature for the β subunit.