Structural fluctuation and concerted motions in F 1 ‐ATPase: A molecular dynamics study

F 1 ‐ATPase is an adenosine tri‐phosphate (ATP)‐driven rotary motor enzyme. We investigated the structural fluctuations and concerted motions of subunits in F 1 ‐ATPase using molecular dynamics (MD) simulations. An MD simulation for the α 3 β 3 γ complex was carried out for 30 ns. Although large fluctuations of the N‐terminal domain observed in simulations of the isolated β E subunit were suppressed in the complex simulation, the magnitude of fluctuations in the C‐terminal domain was clearly different among the three β subunits (β E , β TP , and β DP ). Despite fairly similar conformations of the β TP and β DP subunits, the β DP subunit exhibits smaller fluctuations in the C‐terminal domain than the β TP subunit due to their dissimilar interface configurations. Compared with the β TP subunit, the β DP subunit stably interacts with both the adjacent α DP and α E subunits. This sandwiched configuration in the β DP subunit leads to strongly correlated motions between the β DP and adjacent α subunits. The β DP subunit exhibits an extensive network of highly correlated motions with bound ATP and the γ subunit, as well as with the adjacent α subunits, suggesting that the structural changes occurring in the catalytically active β DP subunit can effectively induce movements of the γ subunit. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010