RNA polymerase motor on DNA track: effects of interactions, external force and torque

TL;DR

This paper presents a theoretical model of RNA polymerase movement on DNA, accounting for interactions, force, and torque, predicting velocity behaviors and effects on RNA synthesis, with testable experimental implications.

Contribution

The model uniquely incorporates mechanochemical cycles and steric interactions to explain velocity dependence on force and torque, advancing understanding of RNAP dynamics.

Findings

Velocity depends on external load force.

Velocity exhibits nonmonotonic behavior with external torque.

Steric interactions influence overall RNA synthesis rate.

Abstract

RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the steric interactions of the RNAPs and their mechanochemical cycles which explicitly captures the cyclical shape changes of each motor. Using this model, we explain not only the dependence of the average velocity of a RNAP on the externally applied load force, but also predict a {\it nonmotonic} variation of the average velocity on external torque. We also show the effect of steric interactions of the motors on the total rate of RNA synthesis. In principle, our predictions can be tested by carrying out {\it in-vitro} experiments which we suggest here.