The distortion-push mechanism for the γ-subunit rotation in F1-ATPase

Abstract

F1-ATPase comprises the stator ring consisting of {beta} subunits and the rotor {gamma} subunit. The {gamma} subunit rotation mechanism has been extensively investigated by biochemical analyses, structural studies, single-molecule measurements, and computational studies. Recent cryo-electron microscopy (cryo-EM) structures of F1-ATPase from the thermophilic bacterium Bacillus PS3 (TF1) provide us with further possibilities for a better understanding of the {gamma}-rotation mechanisms. Using cryo-EM structures having the {gamma}-rotation angles close to the binding dwell and catalytic dwell states, we investigate the relationships between the {gamma} subunit rotation, conformational changes of the stator 3{beta}3 subunits, and the nucleotide-binding and release. We performed targeted molecular dynamics (MD) simulations with external forces on the {beta} subunits and observed 80{degrees} substep rotations of the {gamma} subunit. Then, we optimized the most probable transition pathway through the mean-force string method simulations with 64 images. Finally, using umbrella sampling, we calculated the potential of mean forces along the minimum free energy pathway during the 80{degrees} substep rotation. Our MD simulations suggest that 80{degrees} substep rotation is divided into the first rotation, resting, and the second rotation. Notably, the first rotation is driven by the distortion of the stator 3{beta}3 subunits, and the second rotation is induced mainly by direct {beta}/{gamma} subunit interactions. This model, which we call the distortion-push mechanism, is consistent with the residue-level experimental analysis on F1-ATPase and the atomic structures determined by X-ray crystallography and cryo-EM.