Stochastic analysis of amino acid substitution in protein synthesis

D. Bosnacki; H.M.M. Eikelder, ten; M.N. Steijaert; E.P. Vink, de

doi:10.1007/978-3-540-88562-7_25

Stochastic analysis of amino acid substitution in protein synthesis

D. Bosnacki, H.M.M. Eikelder, ten, M.N. Steijaert, E.P. Vink, de

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

7 Citations (Scopus)

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. Partially supported by EU FP6-project ESIGNET.

Original language	English
Title of host publication	Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings)
Editors	M. Heimer, A.M. Uhrmacher
Place of Publication	Berlin
Publisher	Springer
Pages	367-386
ISBN (Print)	978-3-540-88561-0
DOIs	https://doi.org/10.1007/978-3-540-88562-7_25
Publication status	Published - 2008

Publication series

Name	Lecture Notes in Computer Science
Volume	5307
ISSN (Print)	0302-9743

Access to Document

10.1007/978-3-540-88562-7_25

Cite this

Bosnacki, D., Eikelder, ten, H. M. M., Steijaert, M. N., & Vink, de, E. P. (2008). Stochastic analysis of amino acid substitution in protein synthesis. In M. Heimer, & A. M. Uhrmacher (Eds.), Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings) (pp. 367-386). (Lecture Notes in Computer Science; Vol. 5307). Springer. https://doi.org/10.1007/978-3-540-88562-7_25

Bosnacki, D. ; Eikelder, ten, H.M.M. ; Steijaert, M.N. et al. / Stochastic analysis of amino acid substitution in protein synthesis. Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings). editor / M. Heimer ; A.M. Uhrmacher. Berlin : Springer, 2008. pp. 367-386 (Lecture Notes in Computer Science).

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title = "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. Partially supported by EU FP6-project ESIGNET.",

author = "D. Bosnacki and {Eikelder, ten}, H.M.M. and M.N. Steijaert and {Vink, de}, E.P.",

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booktitle = "Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings)",

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Bosnacki, D , Eikelder, ten, HMM, Steijaert, MN & Vink, de, EP 2008, Stochastic analysis of amino acid substitution in protein synthesis. in M Heimer & AM Uhrmacher (eds), Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings). Lecture Notes in Computer Science, vol. 5307, Springer, Berlin, pp. 367-386. https://doi.org/10.1007/978-3-540-88562-7_25

Stochastic analysis of amino acid substitution in protein synthesis. / Bosnacki, D.; Eikelder, ten, H.M.M.; Steijaert, M.N. et al.
Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings). ed. / M. Heimer; A.M. Uhrmacher. Berlin: Springer, 2008. p. 367-386 (Lecture Notes in Computer Science; Vol. 5307).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › Academic › peer-review

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N2 - 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. Partially supported by EU FP6-project ESIGNET.

AB - 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. Partially supported by EU FP6-project ESIGNET.

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Bosnacki D , Eikelder, ten HMM, Steijaert MN, Vink, de EP. Stochastic analysis of amino acid substitution in protein synthesis. In Heimer M, Uhrmacher AM, editors, Computational Methods in Systems Biology (6th International Conference, CMSB 2008, Rostock, Germany, October 12-15, 2008, Proceedings). Berlin: Springer. 2008. p. 367-386. (Lecture Notes in Computer Science). doi: 10.1007/978-3-540-88562-7_25

Stochastic analysis of amino acid substitution in protein synthesis

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