Investigating the Rotary Mechanism of ATP Synthase Using Molecular Dynamics Simulations

Abstract

F1-ATPase is a motor protein that can use ATP hydrolysis to drive rotation of the central subunit. The γ C-terminal helix constitutes of the rotor tip that is seated in an apical bearing formed by the α3β3 head. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we develop a molecular dynamics (MD) strategy to model the off-axis forces acting on γ in F1-ATPase. MD runs showed stalling of the rotor tip and unfolding of the γ C-terminal helix. MD-predicted H-bond opening events coincided with experimental HDX patterns obtained in our laboratory. HDX-MS data suggests that in vitro operation of F1-ATPase is associated with significant rotational resistance in the apical bearing. These conditions cause the γ C-terminal helix to get “stuck” while the remainder of γ continues to rotate. This scenario contrasts the traditional “greasy bearing” model that envisions smooth rotation of the γ C-terminal helix. Our work also demonstrates that MD simulations can provide insights into protein dynamic features that are invisible in static X-ray crystal structures