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Systems Metabolic Engineering pp 335–351Cite as

Nuclear Magnetic Resonance Methods for Metabolic Fluxomics

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 985))

Abstract

Fluxomics, through its core methodology of metabolic flux analysis (MFA), enables quantification of carbon traffic through cellular biochemical pathways. Isotope labeling experiments aid MFA by providing information on intracellular fluxes, especially through parallel and cyclic pathways. Nuclear magnetic resonance (NMR) and mass spectrometry (MS) are two complementary methods to measure abundances of isotopomers generated in these experiments. 2-D [13C, 1H] heteronuclear correlation NMR spectra can detect 13C isotopes coupled to protons and thus noninvasively separate molecules and atoms with a specific isotopic content from a mixture of molecular species. Furthermore, the fine structures of the peaks in these spectra can reveal scalar couplings between chemically bonded carbon atoms in the sample, from which isotopomer abundances can be quantified. This chapter introduces methods for NMR sample preparation and spectral acquisition of 2-D [13C, 1H] correlation maps, followed by a detailed presentation of methods to process the spectra and quantify isotopomer abundances. We explain the use of the software NMRViewJ for spectral visualization and processing, as well as MATLAB scripts developed by us for peak extraction, deconvolution of overlapping peaklets, and isotopomer abundance quantification. Finally, we discuss the applications of NMR-derived isotopomer data toward quantitatively understanding metabolic pathways.

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Notes

  1. 1.

    Shilpa Nargund and Max E. Joffe contributed equally to this work.

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Acknowledgments

This work was partially funded by the National Science Foundation (award number IOS 0922650) as well as Department of Chemical and Biomolecular Engineering, University of Maryland, and A. James Clark School of Engineering, University of Maryland (faculty startup grant to GS).

Author information

Authors and Affiliations

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

    Shilpa Nargund, Max E. Joffe, Dennis Tran & Ganesh Sriram

  2. Interdisciplinary Graduate Program in the Biomedical and Biological Sciences, Vanderbilt University, Nashville, TN, USA

    Max E. Joffe

  3. Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA

    Vitali Tugarinov

Authors
  1. Shilpa Nargund
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  2. Max E. Joffe
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  3. Dennis Tran
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  4. Vitali Tugarinov
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  5. Ganesh Sriram
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Corresponding author

Correspondence to Ganesh Sriram .

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Editors and Affiliations

  1. Cockrell School of Engineering, Dept. of Chemical Engineering, The University of Texas at Austin, E. Dean Keeton Street 200, Austin, 78712, Texas, USA

    Hal S. Alper

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Nargund, S., Joffe, M.E., Tran, D., Tugarinov, V., Sriram, G. (2013). Nuclear Magnetic Resonance Methods for Metabolic Fluxomics. In: Alper, H. (eds) Systems Metabolic Engineering. Methods in Molecular Biology, vol 985. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-299-5_16

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  • DOI: https://doi.org/10.1007/978-1-62703-299-5_16

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-298-8

  • Online ISBN: 978-1-62703-299-5

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