RNA Translocation Coupled to Large-Scale Conformational Transitions of a Hexameric Helicase

Abstract

Rho is an exemplary hexameric helicase that participates in transcription termination utilizing the energy from ATP hydrolysis. It remains unclear how mRNA translocation through the Rho central pore is coupled to the ATP hydrolysis cycle of this ring-shaped motor. Rho has structural and sequence homology with F1-/V1-ATPase; a general rotary ATP-hydrolysis mechanism, similar to Boyer's mechanism for F1-ATPase, has been proposed for Rho based on structural and biochemical evidence. Here we investigate long-time (millisecond) conformational transitions of Rho during one rotary reaction step at the atomic-level in silico. To overcome the challenging time scale for molecular dynamics simulations, we employ transition pathway techniques combined with the milestoning method. Free energy profile and kinetics of the Rho-RNA conformational transition along the pathway are determined, suggesting a critical role of ATP hydrolysis product release in triggering RNA translocation. The resulting pathway suggests that the six subunits of Rho remain largely unaltered in their interior, but translate and rotate relative to each other through surface-surface generated forces stemming from the ATPase cycle. The six-subunits-motion induces translocation through the six K326 residues’ engagement with and disengagement from the RNA; the movement of K326 is coupled to the ATPase cycle through an allosteric pathway that controls phosphate (Pi) release.