F-1-ATPase is an ATP-driven rotary motor enzyme. We investigated the structural fluctuations of the beta subunits in F-1-ATPase using molecular dynamics (MD) simulations. MD simulations were performed for the isolated beta(E) 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 beta subunit from the open to closed conformation, suggesting that flexibility in the direction of the structural transition is an intrinsic structural feature for the beta subunit. (C) 2010 Elsevier B.V. All rights reserved.