Reaction lumping in metabolic networks for application with thermodynamic metabolic flux analysis.

ABSTRACT: Thermodynamic metabolic flux analysis (TMFA) can narrow down the space of steady-state flux distributions, but requires knowledge of the standard Gibbs free energy for the modelled reactions. The latter are often not available due to unknown Gibbs free energy change of formation [Formula: see text], of metabolites. To optimize the usage of data on thermodynamics in constraining a model, reaction lumping has been proposed to eliminate metabolites with unknown [Formula: see text]. However, the lumping procedure has not been formalized nor implemented for systematic identification of lumped reactions. Here, we propose, implement, and test a combined procedure for reaction lumping, applicable to genome-scale metabolic models. It is based on identification of groups of metabolites with unknown

SUBMITTER: Seep L 

PROVIDER: S-EPMC8058346 | biostudies-literature | 2021 Apr

REPOSITORIES: biostudies-literature