Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

Bin Du; Daniel C Zielinski; Bernhard O Palsson

doi:10.1016/j.tibs.2018.09.009

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

Trends Biochem Sci. 2018 Dec;43(12):960-969. doi: 10.1016/j.tibs.2018.09.009. Epub 2018 Oct 24.

Authors

Bin Du¹, Daniel C Zielinski², Bernhard O Palsson³

Affiliations

¹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
² Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. Electronic address: dczielin@ucsd.edu.
³ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kongens Lyngby, Denmark.

PMID: 30472988
DOI: 10.1016/j.tibs.2018.09.009

Abstract

Reaction equilibrium constants (K_eqs) are key parameters that impose thermodynamic constraints on the function of a metabolic network. An important approach for K_eq estimation is the group contribution method, which utilizes chemical moiety-based estimates of compound formation energies. In this Opinion, we delineate a number of current challenges with the group contribution method, specifically: (i) problems related to the completeness and quality of data necessary for reliable estimation; and (ii) inadequacies of the method to represent the physical properties of compounds. We then highlight a number of promising approaches to deal with the limitations of group contribution methods. Further advancements should lead to more accurate prediction of equilibrium constants and a better representation of cellular function under biophysical constraints.

Keywords: equilibrium constants; group contribution; metabolism; thermodynamics.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Kinetics
Models, Chemical*
Thermodynamics