Rotation-direction-dependent regulation of ATPase inhibitory factor 1 for mitochondrial ATP synthase from atomistic simulation

ATPase inhibitory factor 1 (IF 1 ) is an endogenous regulatory protein for mitochondrial F o F 1 -ATP synthase. It blocks the catalysis and rotation of the F 1 part by deeply inserting itself into the rotor-stator interface. Recent single-molecule manipulation experiments have elucidated that forcible rotations only in the ATP-synthesis direction eject IF 1 , rescuing F 1 from the IF 1 -inhibited state. However, the molecular mechanism of the rotation-direction-dependent process at an atomic resolution is still elusive. Here, we have performed all-atom molecular dynamics (MD) simulations of the IF 1 -bound F 1 structure with a torque applied to the rotor γ subunit. In the torque-applying simulations, we first found that the core part of the γ subunit rotated more in response to an external torque in the synthesis direction than in the hydrolysis direction. Further rotations of the γ subunit up to 120° revealed that the conformational change of the IF 1 -bound αβ was only allowed in the synthesis direction. Also, the 120° rotation in the synthesis direction disrupted its contacts with IF 1 , destabilizing the short helix of IF 1 . After additional rotation up to the synthetic 240° state, the closed-to-open conformational change of the IF 1 -bound β subunit pulled IF 1 outwardly, deforming the long helix of IF 1 . These stepwise destabilizations of the IF 1 helices should be crucial for IF 1 ejection. Our simulations also provided insight into the nullification mechanism of the hydrolytic rotation, highlighting the steric clash between F22 of IF 1 and the β TP subunit. Finally, we discussed a sufficient proton motive force to rescue F o F 1 -ATP synthase from the IF 1 -inhibited state.