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Biophys J. 2018 Jun 5;114(11):2691-2702. doi: 10.1016/j.bpj.2018.04.030.

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

Author information

1
Department of Bioengineering, University of California San Diego, La Jolla, California.
2
Department of Bioengineering, University of California San Diego, La Jolla, California. Electronic address: dczielin@ucsd.edu.

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 (ΔfS) using a model based on molecular properties. The median absolute error in estimating ΔfS 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.

PMID:
29874618
PMCID:
PMC6129446
[Available on 2019-06-05]
DOI:
10.1016/j.bpj.2018.04.030

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