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Steady-State and Instationary Modeling of Proteinogenic and Free Amino Acid Isotopomers for Flux Quantification

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Plant Metabolic Flux Analysis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1090))

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Abstract

Metabolic flux analysis (MFA) is a powerful tool for exploring and quantifying carbon traffic in metabolic networks. Accurate flux quantification requires (1) high-quality isotopomer measurements, usually of biomass components including proteinogenic/free amino acids or central carbon metabolites, and (2) a mathematical model that relates the unknown fluxes to the measured isotopomers. Modeling requires a thorough knowledge of the structure of the underlying metabolic network, often available from many databases, as well as the ability to make reasonable assumptions that will enable simplification of the model. Here we describe a general methodology underlying computer-aided mathematical modeling of a flux–isotopomer relationship and some of the accompanying data-processing steps. One of two modeling strategies will need to be employed, depending on the type of isotope labeling experiment performed. These strategies—steady-state modeling and instationary modeling—have different experimental and computational demands. We discuss the concepts underlying these two types of modeling and demonstrate steady-state modeling in a step-by-step manner. Our methodology should be applicable to most isotope-assisted MFA applications and should serve as a general framework applicable to many realistic metabolic networks with little modification.

Yuting Zheng and Ganesh Sriram conceived the chapter. Yuting Zheng wrote the first draft and prepared data displays. Ganesh Sriram critically edited the draft and prepared a final version. Both authors approved the final version of the chapter.

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Acknowledgments

This work was funded by the National Science Foundation (award numbers CBET 1134115 and IOS 0922650).

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Authors and Affiliations

  1. Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA

    Yuting Zheng

  2. A. James Clark School of Engineering, University of Maryland, College Park, MD, USA

    Ganesh Sriram

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  1. Yuting Zheng
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  2. Ganesh Sriram
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Editor information

Editors and Affiliations

  1. INRA Bordeaux Université Bordeaux Segalen, Villenave d'Ornon, France

    Martine Dieuaide-Noubhani

  2. Department of Molecular Genetics, The Ohio State University, Columbus, Ohio, USA

    Ana Paula Alonso

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Zheng, Y., Sriram, G. (2014). Steady-State and Instationary Modeling of Proteinogenic and Free Amino Acid Isotopomers for Flux Quantification. In: Dieuaide-Noubhani, M., Alonso, A. (eds) Plant Metabolic Flux Analysis. Methods in Molecular Biology, vol 1090. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-688-7_11

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  • DOI: https://doi.org/10.1007/978-1-62703-688-7_11

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-687-0

  • Online ISBN: 978-1-62703-688-7

  • eBook Packages: Springer Protocols

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