ArticlePloS one2017
How important is thermodynamics for identifying elementary flux modes?
Article in PloS one, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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5 citing papers in PubMed, 21 citations in OpenAlex.
- Unlocking Elementary Conversion Modes: ecmtool Unveils All Capabilities of Metabolic Networks.Patterns (New York, N.Y.) · 2021Article
- Dynamic metabolic resource allocation based on the maximum entropy principle.Journal of mathematical biology · 2020Article
- Thermodynamic Limits and Optimality of Microbial Growth.Entropy (Basel, Switzerland) · 2020Review
- Flux tope analysis: studying the coordination of reaction directions in metabolic networks.Bioinformatics (Oxford, England) · 2019Article
- Metabolic enzyme cost explains variable trade-offs between microbial growth rate and yield.PLoS computational biology · 2018Article
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Authors and funding
5 authors at 3 institutions in 3 countries.
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No grant is acknowledged in the PubMed record.
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.
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