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

Research output: Contribution to journal › Article

26 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

Keywords

protein biosynthesis
elongation
Petri net
tropical algebra

Access to Document

10.1016/j.jtbi.2012.03.007

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

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Brackley, C. A., Broomhead, D. S., Romano, M. C., & Thiel, M. (2012). A max-plus model of ribosome dynamics during mRNA translation. Journal of Theoretical Biology, 303(-), 128-140. https://doi.org/10.1016/j.jtbi.2012.03.007

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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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