Determination of flux directions by thermodynamic network analysis: Computing informative metabolite pools

Frieder Hadlich, Katharina Nöh and Wolfgang Wiechert

Mathematics and Computers in Simulation (MATCOM), 2011, vol. 82, issue 3, 460-470

Abstract: Network thermodynamics focuses on the energetic analysis of complex metabolic networks. The method connects free Gibbs energies, metabolite concentrations and flux directions by fundamental thermodynamic laws. Here, a new application of network thermodynamics is presented that identifies those metabolite pools that have to be measured in order to determine as many flux directions as possible. For a medium-scaled reaction network such informative metabolite pools are computed with an approach based on Monte Carlo sampling. It turns out that some reactions can be directed with only a few measurements whereas other reactions cannot be directed even with a complete data set. High connectivity in metabolic reaction networks in alliance with concentration ranges make it impossible to intuitively foresee such results. In particular, the impact of measurements of a special type of metabolites being involved in many reactions, so called energetic currency metabolites is investigated.

Keywords: Metabolic networks; Network thermodynamics; Flux directions; Monte Carlo method; Gibbs sampler (search for similar items in EconPapers)
Date: 2011
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Persistent link: https://EconPapers.repec.org/RePEc:eee:matcom:v:82:y:2011:i:3:p:460-470

DOI: 10.1016/j.matcom.2010.10.025

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