Multiscale Analysis of Functional Motions in F1-ATPase: From Pi Release to Elasticity and Friction of γ-Subunit Rotation

Abstract

F1-ATPase, the catalytic domain of ATP synthase, synthesizes most of the ATP in living organisms. Running in reverse powered by ATP hydrolysis, this hexameric ring-shaped molecular motor formed by three αβ-dimers creates torque on its central γ-subunit. This reverse operation enables detailed explorations of the mechano-chemical coupling mechanisms in experiment and simulation. First, we use molecular dynamics (MD) simulations to construct an atomistic conformation of the intermediate state following the 40° substep of rotary motion, and to study the timing and molecular mechanism of inorganic phosphate (Pi) release coupled to the rotation. In response to torque-driven rotation of the γ-subunit in the hydrolysis direction, the nucleotide-free αβE interface forming the “empty” E site loosens and singly charged Pi readily escapes to the P-loop. The γ-rotation tightens the ATP-bound αβTP interface, as required for hydrolysis. On the basis of metadynamics simulations and rate calculations, we then clarify the timing and pathway of Pi release [1]. Second, from the MD simulation trajectories we introduce a simple model to estimate the elastic properties of the central γ-subunit and the friction affecting γ-subunit rotation. The estimated elastic properties are consistent with experiments. According to our analysis, the work performed in the torque-driven rotation is mostly stored as elastic energy with remarkably little dissipation even at high angular velocities. We also estimate the maximum rotational speed without load, which is not available in experiments.[1] Okazaki and Hummer PNAS 110:41 (2013) 16468-16473