A max-plus model of ribosome dynamics during mRNA translation

Christopher A. Brackley; David S.  Broomhead; M Carmen Romano; Marco Thiel

doi:10.1016/j.jtbi.2012.03.007

A max-plus model of ribosome dynamics during mRNA translation

Christopher A. Brackley, David S. Broomhead, M Carmen Romano, Marco Thiel

University of Manchester

Research output: Contribution to journal › Article › peer-review

31 Citations (Scopus)

Abstract

We examine the dynamics of the translation stage of cellular protein production, in which ribosomes move uni-directionally along an mRNA strand, building amino acid chains as they go. We describe the system using a timed event graph—a class of Petri net useful for studying discrete events, which have to satisfy constraints. We use max-plus algebra to describe a deterministic version of the model, where the constraints represent steric effects which prevent more than one ribosome reading a given codon at a given time and delays associated with the availability of the different tRNAs. We calculate the protein production rate and density of ribosomes on the mRNA and find exact agreement between these analytical results and numerical simulations of the deterministic model, even in the case of heterogeneous mRNAs.

Original language	English
Pages (from-to)	128-140
Number of pages	13
Journal	Journal of Theoretical Biology
Volume	303
Issue number	-
Early online date	16 Mar 2012
DOIs	https://doi.org/10.1016/j.jtbi.2012.03.007
Publication status	Published - 21 Jun 2012

Bibliographical note

A paid open access option is available for this journal.
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Keywords

protein biosynthesis
elongation
Petri net
tropical algebra

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10.1016/j.jtbi.2012.03.007Licence: CC BY

http://arxiv.org/abs/1105.3580v1

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title = "A max-plus model of ribosome dynamics during mRNA translation",

abstract = "We examine the dynamics of the translation stage of cellular protein production, in which ribosomes move uni-directionally along an mRNA strand, building amino acid chains as they go. We describe the system using a timed event graph—a class of Petri net useful for studying discrete events, which have to satisfy constraints. We use max-plus algebra to describe a deterministic version of the model, where the constraints represent steric effects which prevent more than one ribosome reading a given codon at a given time and delays associated with the availability of the different tRNAs. We calculate the protein production rate and density of ribosomes on the mRNA and find exact agreement between these analytical results and numerical simulations of the deterministic model, even in the case of heterogeneous mRNAs.",

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AU - Broomhead, David S.

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AU - Thiel, Marco

N1 - A paid open access option is available for this journal. Voluntary deposit by author of pre-print allowed on Institutions open scholarly website and pre-print servers Voluntary deposit by author of authors post-print allowed on institutions open scholarly website including Institutional Repository Deposit due to Funding Body, Institutional and Governmental mandate only allowed where separate agreement between repository and publisher exists Set statement to accompany deposit Published source must be acknowledged Must link to journal home page or articles' DOI Publisher's version/PDF cannot be used Articles in some journals can be made Open Access on payment of additional charge NIH Authors articles will be submitted to PubMed Central after <num>12</num> <period units="month">months</period> Authors who are required to deposit in subject-based repositories may also use Sponsorship Option

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KW - Petri net

KW - tropical algebra

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A max-plus model of ribosome dynamics during mRNA translation

Abstract

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Keywords

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