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CMSB
2008
Springer

Stochastic Analysis of Amino Acid Substitution in Protein Synthesis

10 years 6 months ago
Stochastic Analysis of Amino Acid Substitution in Protein Synthesis
Abstract. We present a formal analysis of amino acid replacement during mRNA translation. Building on an abstract stochastic model of arrival of tRNAs and their processing at the ribosome, we compute probabilities of the insertion of amino acids into the nascent polypeptide chain. To this end, we integrate the probabilistic model checker Prism in the Matlab environment. We construct the substitution matrix containing the probabilities of an amino acid replacing another. The resulting matrix depends on various parameters, including availability and concentration of tRNA species, as well as their assignment to individual codons. We draw a parallel with the standard mutation matrices like Dayhoff and PET91, and analyze the mutual replacement of biologically similar amino acids.
Dragan Bosnacki, Huub M. M. ten Eikelder, M. N. St
Added 18 Oct 2010
Updated 18 Oct 2010
Type Conference
Year 2008
Where CMSB
Authors Dragan Bosnacki, Huub M. M. ten Eikelder, M. N. Steijaert, Erik P. de Vink
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