Exploring the gap between dynamic and constraint-based models of metabolism
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Tidor_Exploring the gap.pdf
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Author(s)
Machado, Daniel
Costa, Rafael S.
Rocha, Isabel
Tidor, Bruce
Ferreira, Eugenio C.
Date Issued
January 2012
Journal
Metabolic Engineering
Publisher
Elsevier
Citation
Machado, Daniel, Rafael S. Costa, Eugenio C. Ferreira, Isabel Rocha, and Bruce Tidor. “Exploring the Gap Between Dynamic and Constraint-Based Models of Metabolism.” Metabolic Engineering 14, no. 2 (March 2012): 112–119.
Version
Author's final manuscript
Abstract
Systems biology provides new approaches for metabolic engineering through the development of models and methods for simulation and optimization of microbial metabolism. Here we explore the relationship between two modeling frameworks in common use namely, dynamic models with kinetic rate laws and constraint-based flux models. We compare and analyze dynamic and constraint-based formulations of the same model of the central carbon metabolism of Escherichia coli. Our results show that, if unconstrained, the space of steady states described by both formulations is the same. However, the imposition of parameter-range constraints can be mapped into kinetically feasible regions of the solution space for the dynamic formulation that is not readily transferable to the constraint-based formulation. Therefore, with partial kinetic parameter knowledge, dynamic models can be used to generate constraints that reduce the solution space below that identified by constraint-based models, eliminating infeasible solutions and increasing the accuracy of simulation and optimization methods.
MIT Department
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Biological Engineering
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Terms of Use
Creative Commons Attribution-NonCommercial-NoDerivs License
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DOI of Published Version
https://doi.org/10.1016/j.ymben.2012.01.003
