Estimation of flux distribution in metabolic networks accounting for thermodynamic constraints: The effect of equilibrium vs. blocked reactions

Thermodynamically constrained stoichiometric-based models have been widely used for the estimation of feasible flux distributions of a metabolic network. The prediction of a zero net flux through a reaction indicates that this reaction is either blocked (the enzyme is absent) or at equilibrium (the enzyme is present but the Gibbs free energy change of the reaction is zero). The estimation of the thermodynamic equilibrium of a reaction requires the exact knowledge of environmental conditions and metabolites' concentrations. This information, however, is not always available. Here, the effect of considering that a reaction is at equilibrium instead of being blocked on the metabolic flux distribution is analysed. The central carbon metabolism of Actinobacillus succinogenes for the production of succinic acid from glycerol has been used as case study, based on results from experiments in 1.8 L batch bioreactors. The impact of changes in ionic strength (I), temperature (T), intracellular pHc and medium pHe was also investigated, revealing that only I and T affect the prediction of flux distributions compared with those obtained at standard biological conditions when zero flux reactions are considered either as blocked or at equilibrium. In general, the range of fluxes estimated for the equilibrium case is narrower than that for the blocked case.