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 journalArticle

25 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 languageEnglish
Pages (from-to)128-140
Number of pages13
JournalJournal of Theoretical Biology
Volume303
Issue number-
Early online date16 Mar 2012
DOIs
Publication statusPublished - 21 Jun 2012

Fingerprint

Protein Biosynthesis
ribosomes
Ribosomes
Messenger RNA
translation (genetics)
Max-plus Algebra
Proteins
Protein
Discrete Event
Deterministic Model
Transfer RNA
Petri nets
codons
Codon
Petri Nets
Algebra
Amino Acids
Amino acids
Reading
Availability

Keywords

  • protein biosynthesis
  • elongation
  • Petri net
  • tropical algebra

Cite this

A max-plus model of ribosome dynamics during mRNA translation. / Brackley, Christopher A.; Broomhead, David S. ; Romano, M Carmen; Thiel, Marco.

In: Journal of Theoretical Biology, Vol. 303, No. -, 21.06.2012, p. 128-140.

Research output: Contribution to journalArticle

Brackley, Christopher A. ; Broomhead, David S. ; Romano, M Carmen ; Thiel, Marco. / A max-plus model of ribosome dynamics during mRNA translation. In: Journal of Theoretical Biology. 2012 ; Vol. 303, No. -. pp. 128-140.
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