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

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.

6 pages, 7 figures

References in corpus (8)

• The totally asymmetric exclusion process with extended objects, a model for protein synthesis
• Physics of Transport and Traffic Phenomena in Biology: from molecular motors and cells to organisms
• Traffic of molecular motors through tube-like compartments
• Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination
• Interacting RNA polymerase motors on DNA track: effects of traffic congestion and intrinsic noise on RNA synthesis
• Traffic of interacting ribosomes on mRNA during protein synthesis: effects of chemo-mechanics of individual ribosomes
• Traffic of interacting ribosomes: effects of single-machine mechano-chemistry on protein synthesis
• Exclusion process for particles of arbitrary extension: Hydrodynamic limit and algebraic properties

Cited by in corpus (4)

• Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective
• Minimal model of transcriptional elongation processes with pauses
• Efficiency at maximum power of motor traffic on networks
• Stochastic kinetics of a single headed motor protein: dwell time distribution of KIF1A