Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

doi:10.1186/1752-0509-1-23

BMC Systems Biology

Volume 1

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Methodology article

Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks

Andreas Hoppe , Sabrina Hoffmann and Hermann-Georg Holzhütter

Charité – University Medicine Berlin, Institute for Biochemistry, Universitätsmedizin Berlin, Monbijoustr. 2, 10117 Berlin, Germany

author email corresponding author email

BMC Systems Biology 2007, 1:23doi:10.1186/1752-0509-1-23


Published:	1 June 2007

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Additional file 3:

This document shows the proof that thermodynamic realizability implies that there is no net flux in a closed loop – a consequence of the generalization of Kirchhoff's loop law.

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Additional file 1:

This archive contains three files relating to the erythrocyte network. The file "Ery-model.txt" gives the definition of the network as tab-separated text file which is organized in the sections: 'Metabolites', 'Reactions', 'Reactions excluded from the TR property', 'Equilibrium constants', 'Targetfluxes', 'Fixed concentrations', The file "Ery.sbml" gives the network description in SBML format. The file "Ery-solutions.txt" contains three solutions: the thermodynamically realizable fluxmin solution (TR-fluxmin) together with the associated metabolite concentrations and the two alternative solutions obtained in the perturbation analysis.

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Additional file 2:

This archive includes two directories relating to the E. coli iJR904 computations: "FullyReversible" and "HeuristicIrreversibilities". Both contain the file "Ecoli-model.txt", a tab-separated text file, as the definition of the network which is organized in the sections: 'Metabolites', 'Reactions', 'Reactions excluded from the TR property', 'Equilibrium constants', 'Targetfluxes', 'Concentration bounds', and 'Setpoint concentrations'. Both directories also contain the file "Ecoli.sbml", the network description in SBML format. The file "Biomax.txt" also residing in both directories contains the solution of the biomass maximization without the constraint of thermodynamic realizability as a tab-separated text file assigning a reaction identifier with a flux value if it is not zero.. Additionally the directory "FullyReversible" contains the file "TR-Biomax.txt" as the solution to the thermodynamically realizable biomass maximization together with the hypothetic metabolite concentrations compatible with the flux directions.

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