Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V‑Type ATPases

ATP
synthase is the most prominent bioenergetic macromolecular
motor in all life forms, utilizing the proton gradient across the
cell membrane to fuel the synthesis of ATP. Notwithstanding the wealth
of available biochemical and structural information inferred from
years of experiments, the precise molecular mechanism whereby vacuolar
(V-type) ATP synthase fulfills its biological function remains largely
fragmentary. Recently, crystallographers provided the first high-resolution
view of ATP activity in Enterococcus hirae V1-ATPase. Employing a combination of transition-path sampling
and high-performance free-energy methods, the sequence of conformational
transitions involved in a functional cycle accompanying ATP hydrolysis
has been investigated in unprecedented detail over an aggregate simulation
time of 65 μs. Our simulated pathways reveal that the chemical
energy produced by ATP hydrolysis is harnessed via the concerted motion
of the protein–protein interfaces in the V1-ring,
and is nearly entirely consumed in the rotation of the central stalk.
Surprisingly, in an ATPase devoid of a central stalk, the interfaces
of this ring are perfectly designed for inducing ATP hydrolysis. However,
in a complete V1-ATPase, the mechanical property of the
central stalk is a key determinant of the rate of ATP turnover. The
simulations further unveil a sequence of events, whereby unbinding
of the hydrolysis product (ADP + Pi) is followed by ATP
uptake, which, in turn, leads to the torque generation step and rotation
of the center stalk. Molecular trajectories also bring to light multiple
intermediates, two of which have been isolated in independent crystallography
experiments.