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How important is thermodynamics for identifying elementary flux modes?
We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reac...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2017
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319754/ https://www.ncbi.nlm.nih.gov/pubmed/28222104 http://dx.doi.org/10.1371/journal.pone.0171440 |
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author | Peres, Sabine Jolicœur, Mario Moulin, Cécile Dague, Philippe Schuster, Stefan |
author_facet | Peres, Sabine Jolicœur, Mario Moulin, Cécile Dague, Philippe Schuster, Stefan |
author_sort | Peres, Sabine |
collection | PubMed |
description | We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of elementary flux modes (EFMs) by a factor of two. Declaring in advance some reactions as irreversible, based on reliable biochemical expertise, can in general reduce the number of EFMs by a greater factor. But, even in this case, computing tEFMs can rule out some EFMs which are biochemically irrelevant. We applied our method to two published models described with binary distinction: the monosaccharide metabolism and the central carbon metabolism of Chinese hamster ovary cells. The results show that the binary distinction is in good agreement with biochemical observations. Moreover, the suppression of the EFMs that are not consistent with the equilibrium constants appears to be biologically relevant. |
format | Online Article Text |
id | pubmed-5319754 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-53197542017-03-03 How important is thermodynamics for identifying elementary flux modes? Peres, Sabine Jolicœur, Mario Moulin, Cécile Dague, Philippe Schuster, Stefan PLoS One Research Article We present a method for computing thermodynamically feasible elementary flux modes (tEFMs) using equilibrium constants without need of internal metabolite concentrations. The method is compared with the method based on a binary distinction between reversible and irreversible reactions. When all reactions are reversible, adding the constraints based on equilibrium constants reduces the number of elementary flux modes (EFMs) by a factor of two. Declaring in advance some reactions as irreversible, based on reliable biochemical expertise, can in general reduce the number of EFMs by a greater factor. But, even in this case, computing tEFMs can rule out some EFMs which are biochemically irrelevant. We applied our method to two published models described with binary distinction: the monosaccharide metabolism and the central carbon metabolism of Chinese hamster ovary cells. The results show that the binary distinction is in good agreement with biochemical observations. Moreover, the suppression of the EFMs that are not consistent with the equilibrium constants appears to be biologically relevant. Public Library of Science 2017-02-21 /pmc/articles/PMC5319754/ /pubmed/28222104 http://dx.doi.org/10.1371/journal.pone.0171440 Text en © 2017 Peres et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Article Peres, Sabine Jolicœur, Mario Moulin, Cécile Dague, Philippe Schuster, Stefan How important is thermodynamics for identifying elementary flux modes? |
title | How important is thermodynamics for identifying elementary flux modes? |
title_full | How important is thermodynamics for identifying elementary flux modes? |
title_fullStr | How important is thermodynamics for identifying elementary flux modes? |
title_full_unstemmed | How important is thermodynamics for identifying elementary flux modes? |
title_short | How important is thermodynamics for identifying elementary flux modes? |
title_sort | how important is thermodynamics for identifying elementary flux modes? |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319754/ https://www.ncbi.nlm.nih.gov/pubmed/28222104 http://dx.doi.org/10.1371/journal.pone.0171440 |
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