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Quantifying epistatic interactions among the components constituting the protein translation system

In principle, the accumulation of knowledge regarding the molecular basis of biological systems should allow the development of large-scale kinetic models of their functions. However, the development of such models requires vast numbers of parameters, which are difficult to obtain in practice. Here,...

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Autores principales: Matsuura, Tomoaki, Kazuta, Yasuaki, Aita, Takuyo, Adachi, Jiro, Yomo, Tetsuya
Formato: Texto
Lenguaje:English
Publicado: Nature Publishing Group 2009
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736649/
https://www.ncbi.nlm.nih.gov/pubmed/19690566
http://dx.doi.org/10.1038/msb.2009.50
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author Matsuura, Tomoaki
Kazuta, Yasuaki
Aita, Takuyo
Adachi, Jiro
Yomo, Tetsuya
author_facet Matsuura, Tomoaki
Kazuta, Yasuaki
Aita, Takuyo
Adachi, Jiro
Yomo, Tetsuya
author_sort Matsuura, Tomoaki
collection PubMed
description In principle, the accumulation of knowledge regarding the molecular basis of biological systems should allow the development of large-scale kinetic models of their functions. However, the development of such models requires vast numbers of parameters, which are difficult to obtain in practice. Here, we used an in vitro translation system, consisting of 69 defined components, to quantify the epistatic interactions among changes in component concentrations through Bahadur expansion, thereby obtaining a coarse-grained model of protein synthesis activity. Analyses of the data measured using various combinations of component concentrations indicated that the contributions of larger than 2-body inter-component epistatic interactions are negligible, despite the presence of larger than 2-body physical interactions. These findings allowed the prediction of protein synthesis activity at various combinations of component concentrations from a small number of samples, the principle of which is applicable to analysis and optimization of other biological systems. Moreover, the average ratio of 2- to 1-body terms was estimated to be as small as 0.1, implying high adaptability and evolvability of the protein translation system.
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spelling pubmed-27366492009-09-02 Quantifying epistatic interactions among the components constituting the protein translation system Matsuura, Tomoaki Kazuta, Yasuaki Aita, Takuyo Adachi, Jiro Yomo, Tetsuya Mol Syst Biol Article In principle, the accumulation of knowledge regarding the molecular basis of biological systems should allow the development of large-scale kinetic models of their functions. However, the development of such models requires vast numbers of parameters, which are difficult to obtain in practice. Here, we used an in vitro translation system, consisting of 69 defined components, to quantify the epistatic interactions among changes in component concentrations through Bahadur expansion, thereby obtaining a coarse-grained model of protein synthesis activity. Analyses of the data measured using various combinations of component concentrations indicated that the contributions of larger than 2-body inter-component epistatic interactions are negligible, despite the presence of larger than 2-body physical interactions. These findings allowed the prediction of protein synthesis activity at various combinations of component concentrations from a small number of samples, the principle of which is applicable to analysis and optimization of other biological systems. Moreover, the average ratio of 2- to 1-body terms was estimated to be as small as 0.1, implying high adaptability and evolvability of the protein translation system. Nature Publishing Group 2009-08-18 /pmc/articles/PMC2736649/ /pubmed/19690566 http://dx.doi.org/10.1038/msb.2009.50 Text en Copyright © 2009, EMBO and Nature Publishing Group http://creativecommons.org/licenses/by-nc-sa/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits distribution and reproduction in any medium, provided the original author and source are credited. Creation of derivative works is permitted but the resulting work may be distributed only under the same or similar licence to this one. This licence does not permit commercial exploitation without specific permission.
spellingShingle Article
Matsuura, Tomoaki
Kazuta, Yasuaki
Aita, Takuyo
Adachi, Jiro
Yomo, Tetsuya
Quantifying epistatic interactions among the components constituting the protein translation system
title Quantifying epistatic interactions among the components constituting the protein translation system
title_full Quantifying epistatic interactions among the components constituting the protein translation system
title_fullStr Quantifying epistatic interactions among the components constituting the protein translation system
title_full_unstemmed Quantifying epistatic interactions among the components constituting the protein translation system
title_short Quantifying epistatic interactions among the components constituting the protein translation system
title_sort quantifying epistatic interactions among the components constituting the protein translation system
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736649/
https://www.ncbi.nlm.nih.gov/pubmed/19690566
http://dx.doi.org/10.1038/msb.2009.50
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