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How important is thermodynamics for identifying elementary flux modes?

Sabine Peres, Mario Jolicoeur, Cécile Moulin, Philippe Dague and Stefan Schuster

Article (2017)

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Cite this document: Peres, S., Jolicoeur, M., Moulin, C., Dague, P. & Schuster, S. (2017). How important is thermodynamics for identifying elementary flux modes? PLoS ONE, 12(2), p. 1-20. doi:10.1371/journal.pone.0171440
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Abstract

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.

Uncontrolled Keywords

Research Article; Physical Sciences; Physics; Thermodynamics; Biology and Life Sciences; Biochemistry; Metabolism; Metabolites; Computer and Information Sciences; Network Analysis; Metabolic Networks; Chemistry; Physical Chemistry; Chemical Equilibrium; Cell Biology; Cell Physiology; Cell Metabolism; Metabolic Pathways; Free Energy; Gibbs Free Energy; Enzymology; Enzyme Chemistry; Enzyme Metabolism; CHO Cells; Animals; Cricetulus; Carbon; Monosaccharides; Models; Biological; Computer Simulation; Cricetinae; Metabolic Networks

Open Access document in PolyPublie
Subjects: 1800 Génie chimique > 1800 Génie chimique
1800 Génie chimique > 1802 Génie biochimique
1900 Génie biomédical > 1900 Génie biomédical
Department: Département de génie chimique
Research Center: Autre
Date Deposited: 06 Dec 2018 12:54
Last Modified: 07 Dec 2018 01:20
PolyPublie URL: https://publications.polymtl.ca/3538/
Document issued by the official publisher
Journal Title: PLoS ONE (vol. 12, no. 2)
Publisher: PLOS
Official URL: https://doi.org/10.1371/journal.pone.0171440

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