Role of the particle's stepping cycle in an asymmetric exclusion process: A model of mRNA translation

TL;DR

This paper extends the ASEP model of mRNA translation by incorporating the ribosome's biochemical cycle, revealing that phase transition points differ from standard models and highlighting the cycle's biological significance.

Contribution

It introduces a mean-field model that includes the ribosome's stepping cycle, bridging simple ASEP models and complex detailed models for better biological insight.

Findings

Phase transition points differ from standard ASEP.

Inclusion of the biochemical cycle affects system dynamics.

Analytical characterization of different translation phases.

Abstract

Messenger RNA translation is often studied by means of statistical-mechanical models based on the Asymmetric Simple Exclusion Process (ASEP), which considers hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In this work we extend this class of models and consider the two fundamental steps of the ribosome's biochemical cycle following a coarse-grained perspective. In order to achieve a better understanding of the underlying biological processes and compare the theoretical predictions with experimental results, we provide a description lying between the minimal ASEP-like models and the more detailed models, which are analytically hard to treat. We use a mean-field approach to study the dynamics of particles associated with an internal stepping cycle. In this framework it is possible to characterize analytically different phases of the system (high density, low density or maximal current phase). Crucially, we show that the transitions between these different phases occur at different parameter values than the equivalent transitions in a standard ASEP, indicating the importance of including the two fundamental steps of the ribosome's biochemical cycle into the model.