Stochastic theory of protein synthesis and polysome: ribosome profile on a single mRNA transcript

DOI10.1016/J.JTBI.2011.08.023zbMATH Open1397.92234arXiv1106.0674OpenAlexW2050184092WikidataQ48113776 ScholiaQ48113776MaRDI QIDQ1786501FDOQ1786501

Authors: A. K. Sharma, Debashish Chowdhury 

Publication date: 24 September 2018

Published in: Journal of Theoretical Biology (Search for Journal in Brave)

Abstract: The process of polymerizing a protein by a ribosome, using a messenger RNA (mRNA) as the corresponding template, is called {it translation}. Ribosome may be regarded as a molecular motor for which the mRNA template serves also as the track. Often several ribosomes may translate the same (mRNA) simultaneously. The ribosomes bound simultaneously to a single mRNA transcript are the members of a polyribosome (or, simply, {it polysome}). Experimentally measured {it polysome profile} gives the distribution of polysome {it sizes}. Recently a breakthrough in determining the instantaneous {it positions} of the ribosomes on a given mRNA track has been achieved and the technique is called {it ribosome profiling} cite{ingolia10,guo10}. Motivated by the success of these techniques, we have studied the spatio-temporal organization of ribosomes by extending a theoretical model that we have reported elsewhere cite{sharma11}. This extended version of our model incorporates not only (i) mechano-chemical cycle of individual ribomes, and (ii) their steric interactions, but also (iii) the effects of (a) kinetic proofreading, (b) translational infidelity, (c) ribosome recycling, and (d) sequence inhomogeneities. The theoretical framework developed here will serve in guiding further experiments and in analyzing the data to gain deep insight into various kinetic processes involved in translation.

Full work available at URL: https://arxiv.org/abs/1106.0674

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zbMATH Keywords

master equationTASEPdistance-headwayextremum current hypothesisribosome traffic

Mathematics Subject Classification ID

Biochemistry, molecular biology (92C40) Kinetics in biochemical problems (pharmacokinetics, enzyme kinetics, etc.) (92C45)

Cites Work

• A model of protein translation including codon bias, nonsense errors, and ribosome recycling
• Local inhomogeneity in asymmetric simple exclusion processes with extended objects
• Asymmetric simple exclusion model with local inhomogeneity
• Totally asymmetric exclusion processes with particles of arbitrary size
• Title not available (Why is that?)
• Modeling translation in protein synthesis with TASEP: a tutorial and recent developments

Cited In (7)

• Generic nonequilibrium steady states in an exclusion process on an inhomogeneous ring
• A generalized Michaelis-Menten equation in protein synthesis: effects of mis-charged cognate tRNA and mis-reading of codon
• Fluctuations in interacting particle systems with memory
• On the stationary frequency of programmed ribosomal \(-1\) frameshift
• Ribosome dwell times and the protein copy number distribution
• Exclusion model of mRNA translation with collision-induced ribosome drop-off
• Dynamics of tRNA occupancy and dissociation during translation by the ribosome

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