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Plant Metabolism

Volume 1083 of the series Methods in Molecular Biology pp 109-131

Date:

Mathematical Modeling of Isotope Labeling Experiments for Metabolic Flux Analysis

  • Shilpa NargundAffiliated withUniversity of Maryland
  • , Ganesh SriramAffiliated withDepartment of Chemical and Biomolecular Engineering, University of Maryland

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Abstract

Isotope labeling experiments (ILEs) offer a powerful methodology to perform metabolic flux analysis. However, the task of interpreting data from these experiments to evaluate flux values requires significant mathematical modeling skills. Toward this, this chapter provides background information and examples to enable the reader to (1) model metabolic networks, (2) simulate ILEs, and (3) understand the optimization and statistical methods commonly used for flux evaluation. A compartmentalized model of plant glycolysis and pentose phosphate pathway illustrates the reconstruction of a typical metabolic network, whereas a simpler example network illustrates the underlying metabolite and isotopomer balancing techniques. We also discuss the salient features of commonly used flux estimation software 13CFLUX2, Metran, NMR2Flux+, FiatFlux, and OpenFLUX. Furthermore, we briefly discuss methods to improve flux estimates. A graphical checklist at the end of the chapter provides a reader a quick reference to the mathematical modeling concepts and resources.

Key words

Metabolic flux analysis Isotope labeling experiment Mathematical model Isotopomer balance Cumomer Elementary metabolite unit Bondomer 13CFLUX2 Metran NMR2Flux+ FiatFlux OpenFLUX