RNA polymerase motors: dwell time distribution, velocity and dynamical phases

TL;DR

This paper models RNA polymerase as a molecular motor, deriving dwell time distributions, analyzing velocity, and exploring phase behavior in traffic scenarios, providing insights into its stochastic dynamics and collective movement.

Contribution

It introduces an exact dwell time distribution model for RNA polymerase and incorporates steric interactions to analyze traffic phases, extending previous motor models.

Findings

Derived exact dwell time distribution for RNAP.

Established a Michaelis-Menten-like relation for mean dwell time.

Mapped phase diagram for RNAP traffic with steric interactions.

Abstract

Polymerization of RNA from a template DNA is carried out by a molecular machine called RNA polymerase (RNAP). It also uses the template as a track on which it moves as a motor utilizing chemical energy input. The time it spends at each successive monomer of DNA is random; we derive the exact distribution of these "dwell times" in our model. The inverse of the mean dwell time satisfies a Michaelis-Menten-like equation and is also consistent with a general formula derived earlier by Fisher and Kolomeisky for molecular motors with unbranched mechano-chemical cycles. Often many RNAP motors move simultaneously on the same track. Incorporating the steric interactions among the RNAPs in our model, we also plot the three-dimensional phase diagram of our model for RNAP traffic using an extremum current hypothesis.