Stochastic kinetics of ribosomes: single motor properties and collective behavior

TL;DR

This paper develops a detailed stochastic model of ribosome movement along mRNA, deriving exact analytical expressions for dwell times, velocity, and force-velocity relations, and extends it to include collective ribosome traffic with steric exclusion.

Contribution

It introduces a comprehensive mechanochemical model of individual ribosomes and extends it to describe collective traffic, providing exact analytical results and phase diagrams.

Findings

Exact dwell time distribution derived for single ribosomes

Force-velocity relation formulated for ribosomes

Phase diagram for ribosome traffic on mRNA constructed

Abstract

Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an {\it exact} analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a ``Michaelis-Menten-like'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechano-chemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes simultaneously move on the same mRNA track, while each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in 3-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions.