Modelling the effect of ribosome mobility on the rate of protein synthesis
arXiv:2009.14533 · doi:10.1140/epje/s10189-021-00019-8
Abstract
Translation is one of the main steps in the synthesis of proteins. It consists of ribosomes that translate sequences of nucleotides encoded on mRNA into polypeptide sequences of amino acids. Ribosomes bound to mRNA move unidirectionally, while unbound ribosomes diffuse in the cytoplasm. It has been hypothesized that finite diffusion of ribosomes plays an important role in ribosome recycling and that mRNA circularization enhances the efficiency of translation. In order to estimate the effect of cytoplasmic diffusion on the rate of translation, we consider a Totally Asymmetric Simple Exclusion Process (TASEP) coupled to a finite diffusive reservoir, which we call the Ribosome Transport model with Diffusion (RTD). In this model, we derive an analytical expression for the rate of protein synthesis as a function of the diffusion constant of ribosomes, which is corroborated with results from continuous-time Monte Carlo simulations. Using a wide range of biological relevant parameters, we conclude that diffusion in biological cells is fast enough so that it does not play a role in controlling the rate of translation initiation.
article, 16 pages, 5 figures
References in corpus (9)
- Anomalous transport in the crowded world of biological cells
- Nonequilibrium Steady States of Matrix Product Form: A Solver's Guide
- Traffic of molecular motors through tube-like compartments
- An introduction to Monte Carlo methods
- Modelling cytoskeletal traffic: an interplay between passive diffusion and active transport
- Feedback and Fluctuations in a Totally Asymmetric Simple Exclusion Process with Finite Resources
- Motor proteins traffic regulation by supply-demand balance of resources
- Generic transport mechanisms for molecular traffic in cellular protrusions
- Cooperative dynamics in bidirectional transport on flexible lattice