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Stable Isotope-Resolved Metabolomics by NMR

  • Penghui Lin
  • Andrew N. LaneEmail author
  • Teresa W.-M. Fan
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2037)

Abstract

Stable isotopes enable the tracing of atoms from precursors to products via metabolic transformations in situ and in crude extracts. NMR has some unique capabilities that are especially suited for metabolic analysis, including atom position-resolved isotope analysis and isotope editing. In this chapter we describe NMR-based analysis of positional isotopomer distribution using metabolic tracers.

Key words

Stable isotope-resolved metabolomics Isotopomers Spectral editing Quantification 

Abbreviations

DSS

2,2-Dimethyl-2-silapentane-5-sulfonate

FID

Free induction decay

rf

Radiofrequency

RoI

Region of interest

SIRM

Stable isotope-resolved metabolomics

SNR

Signal-to-noise ratio

TMS

Tetramethylsilane

Notes

Acknowledgments

This work was supported in part by NIH grants 1U24DK097215-01A1, CA163223-01A1, 5P20GM121327 (COBRE) the Carmen L. Buck endowment (to ANL), and the Edith D. Gardner Chair in Cancer Research (TWMF).

References

  1. 1.
    Lane AN, Fan TWM (2017) NMR-based stable isotope resolved metabolomics in systems biochemistry. Arch Biochem Biophys 628:123–131CrossRefGoogle Scholar
  2. 2.
    Fan TWM, Lane AN (2016) Applications of NMR to systems biochemistry. Prog NMR Spectrosc 92:18–53CrossRefGoogle Scholar
  3. 3.
    Bruntz RC, Higashi RM, Lane AN, Fan TWM (2017) Exploring cancer metabolism using stable isotope resolved metabolomics (SIRM). J Biol Chem 292:11601–11609CrossRefGoogle Scholar
  4. 4.
    Fan TWM, Lane AN (2011) NMR-based stable isotope resolved metabolomics in systems biochemistry. J Biomol NMR 49(3-4):267–280CrossRefGoogle Scholar
  5. 5.
    Fan TWM (2012) Considerations of sample preparation for metabolomics investigation. Handbook of metabolomics, Human New YorkGoogle Scholar
  6. 6.
    Fan TWM, Lane AN (2013) Assignment strategies for NMR resonances in metabolomics research. In: Lutz N, Sweedler JV, Weevers RA (eds) Methodologies for metabolomics: experimental strategies and techniques. Cambridge University Press, CambridgeGoogle Scholar
  7. 7.
    Fan TWM, WarmoesMO SQ, Song H, Turchan-Cholewo J, Martin JT et al (2016) Distinctly perturbed metabolic networks underlie differential tumor tissue damages induced by immune modulator beta-glucan in a two-case ex vivo non-small-cell lung cancer study. Cold Spring Harb Mol Case Stud 2(4):a000893CrossRefGoogle Scholar
  8. 8.
    Giraudeau P, Silvestre V, Akoka S (2015) Optimizing water suppression for quantitative NMR-based metabolomics: a tutorial review. Metabolomics 11:1041–1055CrossRefGoogle Scholar
  9. 9.
    Lane AN, Arumugam S, Lorkiewicz PK, Higashi RM, Laulhe S, Nantz MH et al (2014) Chemoselective detection of carbonyl compounds in metabolite mixtures by NMR. Magn Reson Chem 53:337–343CrossRefGoogle Scholar
  10. 10.
    Tayyari F, Nagan Gowda GA, Gu H, Raftery D (2013) 15N-cholamine--a smart isotope tag for combining NMR- and MS-based metabolite profiling. Anal Chem 85:8715–8721CrossRefGoogle Scholar
  11. 11.
    Heikkinen S, Permi P, Kilpela¨inen I (2001) Methods for the measurement of 1JNCa and 2JNCa from a simplified 2D 13Ca-coupled 15N SE–HSQC spectrum. J Magn Reson 148:53–60CrossRefGoogle Scholar
  12. 12.
    Niu C, Bertrand RD, Shindo H, Cohen JS (1079) Cross-peptide bond 13C--15N coupling constants by 13C and J cross-polarization 15N NMR. J Biochem Biophys Methods 1(3):135–143CrossRefGoogle Scholar
  13. 13.
    Wishart DS, Bigam CG, Yao J, Abildgaard F, Dyson HJ, Oldfield E et al (1995) 1H, 13C and 15N chemical shift referencing in biomolecular NMR. J Biomol NMR 6(2):135–140CrossRefGoogle Scholar
  14. 14.
    Clore GM, Gronenborn AM (1998) NMR structure determination of proteins and protein complexes larger than 20 kDa. Curr Opin Chem Biol 2(5):564–570CrossRefGoogle Scholar
  15. 15.
    Otting G, Wuthrich K (1990) Heteronuclear filters In 2-dimensional H-1, H-1 NMR-spectroscopy—combined use with isotope labeling for studies of macromolecular conformation and intermolecular interactions. Q Rev Biophys 23(1):39–96CrossRefGoogle Scholar
  16. 16.
    Gardner KH, Kay LE (1998) The use of H-2, C-13, N-15 multidimensional NMR to study the structure and dynamics of proteins. Annu Rev Biophys Biomol Struct 27:357–406CrossRefGoogle Scholar
  17. 17.
    Fan TWM, Lane AN (2013) Assignment strategies for NMR resonances in metabolomics research. In: Lutz N, Sweedler JV, Wevers RA (eds) Methodologies for metabolomics: experimental strategies and techniques. Cambridge University Press, Cambridge, p 525Google Scholar
  18. 18.
    Fan TWM (1996) Metabolite profiling by one- and two-dimensional NMR analysis of complex mixtures. Prog Nucl. Magn Reson Spectro 28:161–219CrossRefGoogle Scholar
  19. 19.
    Fan TWM, Lane AN (2008) Structure-based profiling of metabolites and isotopomers by NMR. Prog NMR Spectrosc 52:69–117CrossRefGoogle Scholar
  20. 20.
    Fan TW, Lane AN (2016) Applications of NMR spectroscopy to systems biochemistry. Prog Nucl Magn Reson Spectrosc 92–93:18–53CrossRefGoogle Scholar
  21. 21.
    Lane AN, Fan TW (2007) Quantification and identification of isotopomer distributions of metabolites in crude cell extracts using 1H TOCSY. Metabolomics 3:79–86CrossRefGoogle Scholar
  22. 22.
    Le Guennec A, Tayyari F, Edison AS (2017) Alternatives to nuclear overhauser enhancement spectroscopy presat and Carr−Purcell−Meiboom−Gill presat for NMR-based metabolomics. Anal Chem 89:8582–8588CrossRefGoogle Scholar
  23. 23.
    Hwang TL, Shaka AJ (1995) Water suppression that works. excitation sculpting using arbitrary wave-forms and pulsed-field gradients. J Magn Reson Ser A 112:275–279CrossRefGoogle Scholar
  24. 24.
    Lane AN (2012) In: Fan TW-M, Lane AN, Higashi RM (eds) NMR applications in metabolomics in Handbook of metabolomics. Humana, New YorkGoogle Scholar
  25. 25.
    Lane AN, Fan TW, Higashi RM (2008) Isotopomer-based metabolomic analysis by NMR and mass spectrometry. Methods Cell Biol 84:541–588CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Penghui Lin
    • 1
  • Andrew N. Lane
    • 1
    • 2
    Email author
  • Teresa W.-M. Fan
    • 1
    • 2
  1. 1.Center for Environmental and Systems BiochemistryUniversity of KentuckyLexingtonUSA
  2. 2.Department of Toxicology and Cancer BiologyUniversity of KentuckyLexingtonUSA

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