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PLoS Comput Biol. 2012;8(8):e1002662. doi: 10.1371/journal.pcbi.1002662. Epub 2012 Aug 30.

Shrinking the metabolic solution space using experimental datasets.

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1
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA. reed@engr.wisc.edu

Abstract

Constraint-based models of metabolism have been used in a variety of studies on drug discovery, metabolic engineering, evolution, and multi-species interactions. These genome-scale models can be generated for any sequenced organism since their main parameters (i.e., reaction stoichiometry) are highly conserved. Their relatively low parameter requirement makes these models easy to develop; however, these models often result in a solution space with multiple possible flux distributions, making it difficult to determine the precise flux state in the cell. Recent research efforts in this modeling field have investigated how additional experimental data, including gene expression, protein expression, metabolite concentrations, and kinetic parameters, can be used to reduce the solution space. This mini-review provides a summary of the data-driven computational approaches that are available for reducing the solution space and thereby improve predictions of intracellular fluxes by constraint-based models.

PMID:
22956899
PMCID:
PMC3431291
DOI:
10.1371/journal.pcbi.1002662
[Indexed for MEDLINE]
Free PMC Article
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