RNA Polymerase pushing

Abstract

Abstract Molecular motors can exhibit Brownian ratchet or power stroke mechanisms. These mechanistic categories are related to transition state position: An early transition state suggests that chemical energy is stored and then released during the step (stroke) while a late transition state suggests that the release of chemical energy rectifies thermally activated motion that has already occurred (ratchet). Cellular RNA polymerases are thought be ratchets that can push each other forward to reduce pausing during elongation. Here, by constructing a two-dimensional energy landscape from the individual landscapes of active and backtracked enzymes, we identify a new pushing mechanism which is the result of a saddle trajectory that arises in the two-dimensional energy landscape of interacting enzymes. We show that this mechanism is more effective with an early transition state suggesting that interacting RNAPs might function via a power stroke translocation mechanism.

Graphical abstract

Highlights ► A simple model of collisions between elongating and backtracked RNA polymerases. ► Two-dimensional energy landscapes reveal the path for active enzyme pushing. ► Early translocation transition states are better for molecular motor pushing. ► Suggest that RNA polymerase has access to a power stroke mechanism.