Consistent Estimation of Gibbs Energy Using Component Contributions

By Elad Noor, Hulda S. Haraldsdóttir, Ron Milo, Ronan M. T. Fleming. PLoS Comput. Biol., 2013

301 citations recorded by the source corpus.

Standard Gibbs energies of reactions are increasingly being used in metabolic modeling for applying thermodynamic constraints on reaction rates, metabolite concentrations and kinetic parameters. The increasing scope and diversity of metabolic models has led scientists to look for genome-scale solutions that can estimate the standard Gibbs energy of all the reactions in metabolism. Group contribution methods greatly increase coverage, albeit at the price of decreased precision. We present here a way to combine the estimations of group contribution with the more accurate reactant contributions by decomposing each reaction into two parts and applying one of the methods on each of them. This method gives priority to the reactant contributions over group contributions while guaranteeing that all estimations will be consistent, i.e. will not violate the first law of thermodynamics. We show that there is a significant increase in the accuracy of our estimations compared to standard group contribution. Specifically, our cross-validation results show an 80% reduction in the median absolute residual for reactions that can be derived by reactant contributions only. We provide the full framework and source code for deriving estimates of standard reaction Gibbs energy, as well as confidence intervals, and believe this will facilitate the wide use of thermodynamic data for a better understanding of metabolism.

Subfields: Control and Systems Engineering, Molecular Biology, Physical and Theoretical Chemistry

View Paper: https://www.semanticscholar.org/paper/41077554170f019b084901222e566e3106ec814b

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Control and Systems Engineering

Kiran Raosaheb Patil

In Molecular Biology

In Physical and Theoretical Chemistry

Citations in the corpus

Recon3D: A Resource Enabling A Three-Dimensional View of Gene Variation in Human Metabolism (2018, unknown): “…mass-charge balancing of reactions, (iv) a leak test, checking for stoichiometric and flux consistency and checking for thermodynamic feasibility 52 , (v) debugging and curation for removal of dead-end metabolites, and (vi) checking for network accomplishment of defined functions/tests…”
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities (2018, methodology): “Lower and upper bounds for the Gibbs free energy change for each reaction ( (cid:2) G r ) were estimated using the formula: was calculated using the component contribution method (31), R is the universal gas constant, and the temperature T was set to 298.15 K (25 C).”
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease (2018, background): “When this process is completed, the user can download the flux values to integrate in his experiments (18).”