Molecular mechanism and energetics of coupling between substrate binding and product release in the F ₁ -ATPase catalytic cycle

Abstract

F 1 -ATPase is a motor protein that couples the rotation of its rotary γ subunit with ATP synthesis or hydrolysis. Single-molecule experiments indicate that nucleotide binding and release events occur almost simultaneously during the synthesis cycle, allowing the energy gain due to spontaneous binding of ADP to one catalytic β subunit to be directly harnessed for driving the release of ATP from another rather than being dissipated as heat. Here, we examine the unknown mechanism of this coupling that is critical for an exceptionally high mechanochemical efficiency of F 1 -ATPase by means of all-atom free-energy simulations. We find that nondissipative and kinetically fast progression of the motor in the synthesis direction requires a concerted conformational change involving the closure of the ADP-binding β subunit followed by the gradual opening of the ATP-releasing β subunit over the course of the 30 to 40° rotary substep of the γ subunit. This rotary substep, preceding the ATP-dependent metastable state, allows for the recovery of a large portion of the ADP binding energy in the conformation of ATP-bound β that gradually adopts the low-affinity conformation, captured also by the recent cryo-EM structure of this elusive state. The release of ATP from this nearly open conformation leads to its further opening, which enables the progression of the motor to the next catalytic metastable state. Our simulations explain this energy conversion mechanism in terms of intersubunit and ligand–protein interactions.

Perspective on Integrative Simulations of Bioenergetic Domains

“…Metadynamics improves conformational sampling by discouraging the simulation to visit previously sampled states. , These simulations have successfully modeled protein–protein dissociation events or rearrangement of cofactors at different binding sites, , resolving some of the slowest steps in bioenergetic processes and elucidating the properties of the dissociated state. − A major advantage of metadynamics over other free energy methods is that, provided the knowledge of putative reaction coordinates, the free energy profile can be extracted from the accumulated bias potential without requiring separate simulations for each state.…”

Perspective on Integrative Simulations of Bioenergetic Domains

“…Metadynamics improves conformational sampling by discouraging the simulation to visit previously sampled states. 73,74 These simulations have successfully modeled protein-protein dissociation events or rearrangement of cofactors at different binding sites, 75,76 resolving some of the slowest steps in bioenergetic processes and elucidating the properties of the dissociated state. [77][78][79] A major advantage of metadynamics over other free energy methods is that, provided the knowledge of putative reaction coordinates, the free energy profile can be extracted from the accumulated bias potential without requiring separate simulation for each state.…”