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BMC Syst Biol. 2012 Nov 12;6:140. doi: 10.1186/1752-0509-6-140.

A proof for loop-law constraints in stoichiometric metabolic networks.

Author information

1
Department of Plant Sciences, 234 Herzl St., Weizmann Institute of Science, Rehovot 76100, Israel. elad.noor@weizmann.ac.il

Abstract

BACKGROUND:

Constraint-based modeling is increasingly employed for metabolic network analysis. Its underlying assumption is that natural metabolic phenotypes can be predicted by adding physicochemical constraints to remove unrealistic metabolic flux solutions. The loopless-COBRA approach provides an additional constraint that eliminates thermodynamically infeasible internal cycles (or loops) from the space of solutions. This allows the prediction of flux solutions that are more consistent with experimental data. However, it is not clear if this approach over-constrains the models by removing non-loop solutions as well.

RESULTS:

Here we apply Gordan's theorem from linear algebra to prove for the first time that the constraints added in loopless-COBRA do not over-constrain the problem beyond the elimination of the loops themselves.

CONCLUSIONS:

The loopless-COBRA constraints can be reliably applied. Furthermore, this proof may be adapted to evaluate the theoretical soundness for other methods in constraint-based modeling.

PMID:
23146116
PMCID:
PMC3560238
DOI:
10.1186/1752-0509-6-140
[Indexed for MEDLINE]
Free PMC Article
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