Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

TitleTemperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.
Publication TypeJournal Article
Year of Publication2018
AuthorsDu B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC
JournalBiophys J
Volume114
Issue11
Pagination2691-2702
PubMed Date06/2018
ISSN1542-0086
Abstract

Reaction-equilibrium constants determine the metabolite concentrations necessary to drive flux through metabolic pathways. Group-contribution methods offer a way to estimate reaction-equilibrium constants at wide coverage across the metabolic network. Here, we present an updated group-contribution method with 1) additional curated thermodynamic data used in fitting and 2) capabilities to calculate equilibrium constants as a function of temperature. We first collected and curated aqueous thermodynamic data, including reaction-equilibrium constants, enthalpies of reaction, Gibbs free energies of formation, enthalpies of formation, entropy changes of formation of compounds, and proton- and metal-ion-binding constants. Next, we formulated the calculation of equilibrium constants as a function of temperature and calculated the standard entropy change of formation (ΔS) using a model based on molecular properties. The median absolute error in estimating ΔS was 0.013 kJ/K/mol. We also estimated magnesium binding constants for 618 compounds using a linear regression model validated against measured data. We demonstrate the improved performance of the current method (8.17 kJ/mol in median absolute residual) over the current state-of-the-art method (11.47 kJ/mol) in estimating the 185 new reactions added in this work. The efforts here fill in gaps for thermodynamic calculations under various conditions, specifically different temperatures and metal-ion concentrations. These, to our knowledge, new capabilities empower the study of thermodynamic driving forces underlying the metabolic function of organisms living under diverse conditions.

Alternate JournalBiophys. J.
PubMed ID29874618
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