Abstract
| 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 | |
| Publication status | Published - 21 Jun 2012 |
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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 journal › Article
}
TY - JOUR
T1 - A max-plus model of ribosome dynamics during mRNA translation
AU - Brackley, Christopher A.
AU - Broomhead, David S.
AU - Romano, M Carmen
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
PY - 2012/6/21
Y1 - 2012/6/21
N2 - 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.
AB - 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.
KW - protein biosynthesis
KW - elongation
KW - Petri net
KW - tropical algebra
U2 - 10.1016/j.jtbi.2012.03.007
DO - 10.1016/j.jtbi.2012.03.007
M3 - Article
VL - 303
SP - 128
EP - 140
JO - Journal of Theoretical Biology
JF - Journal of Theoretical Biology
SN - 0022-5193
IS - -
ER -