Vishnuvardhan Mahamkali1, Tim McCubbin1, Moritz Emanuel Beber2, Elad Noor3, Esteban Ma1, Lars Keld Marcellin1, Lars Keld Nielsen1,2. 1. Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, 4072 Brisbane, Australia. 2. The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark. 3. Department of Plant and Environmental Sciences, Weizmann Institute of Science, Herzl st. 234, Rehovot 7610001, Israel.
Abstract
SUMMARY: We achieve a significant improvement in thermodynamic-based flux analysis (TFA) by introducing multivariate treatment of thermodynamic variables and leveraging component contribution, the state-of-the-art implementation of the group contribution methodology. Overall, the method greatly reduces the uncertainty of thermodynamic variables. RESULTS: We present multiTFA, a Python implementation of our framework. We evaluated our application using the core Escherichia coli model and achieved a median reduction of 6.8 kJ/mol in reaction Gibbs free energy ranges, while three out of 12 reactions in glycolysis changed from reversible to irreversible. AVAILABILITY AND IMPLEMENTATION: Our framework along with documentation is available on https://github.com/biosustain/multitfa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
SUMMARY: We achieve a significant improvement in thermodynamic-based flux analysis (TFA) by introducing multivariate treatment of thermodynamic variables and leveraging component contribution, the state-of-the-art implementation of the group contribution methodology. Overall, the method greatly reduces the uncertainty of thermodynamic variables. RESULTS: We present multiTFA, a Python implementation of our framework. We evaluated our application using the core Escherichia coli model and achieved a median reduction of 6.8 kJ/mol in reaction Gibbs free energy ranges, while three out of 12 reactions in glycolysis changed from reversible to irreversible. AVAILABILITY AND IMPLEMENTATION: Our framework along with documentation is available on https://github.com/biosustain/multitfa. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Moritz E Beber; Mattia G Gollub; Dana Mozaffari; Kevin M Shebek; Avi I Flamholz; Ron Milo; Elad Noor Journal: Nucleic Acids Res Date: 2022-01-07 Impact factor: 16.971