Wen Ma and Klaus Schulten.
Mechanism of substrate translocation by a ring-shaped ATPase motor
at millisecond resolution.
Journal of the American Chemical Society, 137:3031-3040, 2015.
(PMC: PMC4393844)
MA2015
Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as
genome replication, transcription or protein degradation, by translocating a long substrate
through their central pore powered by ATP hydrolysis. Despite intense research efforts, the
atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical
force that translocates the substrate is still unclear. Here we employ all-atom molecular
dynamics simulations combined with advanced path sampling techniques and milestoning
analysis to characterize how mRNA substrate is translocated by an exemplary homo-
hexameric motor, the transcription termination factor Rho. We find that the release of
hydrolysis product (ADP+Pi) triggers the force-generating process of Rho through a 0.1
millisecond-long conformational transition, the time scale seen also in experiment. The
calculated free energy profiles and kinetics show that Rho unidirectionally translocates the
single-stranded RNA substrate via a population shift of the conformational states of Rho;
upon hydrolysis product release, the most favorable conformation shifts from the pre-
translocation state to the post-translocation state. Via two previously unidentified
intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose
motions are induced by highly coordinated relative translation and rotation of Rho's six
subunits. The present study not only reveals in new detail the mechanism employed by
ring-shaped ATPase motors, for example the use of loosely bound and tightly bound
hydrolysis reactant and product states to coordinate motor action, but also provides an
effective approach to identify allosteric sites of multimeric enzymes in general.
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