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Nonuniform Sampling in Biomolecular NMR

  • Tomas Marko Miljenović
  • Xinying Jia
  • Mehdi Mobli
Reference work entry

Abstract

Nonuniform sampling (NUS) is no longer an ethereal promise for future NMR spectroscopists. Freedom from comprehensively sampling the Nyquist grid has facilitated an increasing variety of applications in biomolecular NMR studies. We introduce the concepts of multidimensional experiments, sampling, and signal processing before looking at the basics of nonuniform sampling and its benefits. This chapter also includes some practical guidelines for applying NUS to protein NMR studies, and looks at more recent uses of NUS in a wide range of applications in biomolecular NMR.

Keywords

Nonuniform sampling Non–uniform sampling Multidimensional NMR spectroscopy NMR Proteins Peptides 

Notes

Acknowledgments

The authors would like to acknowledge financial support from the Australian Research Council (ARC Future Fellowship and ARC Discovery Project), the National Health and Medical Research Council (NHMRC Project), and The University of Queensland (Strategic Research Fellowship).

References

  1. 1.
    King GF, Mobli M. Determination of peptide and protein structures using NMR spectroscopy. In: Mander L, Liu H, editors. Comprehensive natural products II: chemistry and biology. Elsevier Science & Technology; Oxford: England; 2010. p. 280–325.CrossRefGoogle Scholar
  2. 2.
    Abraham RJ, Mobli M. Modelling 1H NMR spectra of organic compounds: theory, applications and NMR prediction software. Chichester: Wiley; 2008.CrossRefGoogle Scholar
  3. 3.
    Bieri M, Kwan AH, Mobli M, King GF, Mackay JP, Gooley PR. Macromolecular NMR spectroscopy for the nonspectroscopist: beyond macromolecular solution structure determination. FEBS J. 2011;278(5):704–15.CrossRefGoogle Scholar
  4. 4.
    Keeler J. Understanding NMR spectroscopy. Chichester: Wiley; 2011.Google Scholar
  5. 5.
    Jeener J. Oral presentation. Ampere International Summer School; Baško Polje: Yugoslavia; 1971.Google Scholar
  6. 6.
    Hoch JC, Maciejewski MW, Mobli M, Schuyler AD, Stern AS. Nonuniform sampling and maximum entropy reconstruction in multidimensional NMR. Acc Chem Res. 2014;47(2):708–17.CrossRefGoogle Scholar
  7. 7.
    Claridge TDW. High-resolution NMR techniques in organic chemistry. Amsterdam: Elsevier; 2009.Google Scholar
  8. 8.
    Kwan AH, Mobli M, Gooley PR, King GF, Mackay JP. Macromolecular NMR spectroscopy for the nonspectroscopist. FEBS J. 2011;278(5):687–703.CrossRefGoogle Scholar
  9. 9.
    Mobli M, Hoch JC, King GF. Fast acquisition methods in multidimensional NMR. In: Dingley AJ, Pascal SM, editors. Advances in biomedical spectroscopy, vol. 3. Amsterdam: IOS Press; 2011. p. 305–37.Google Scholar
  10. 10.
    Ernst RR. Sensitivity enhancement in NMR spectroscopy. Adv Magn Reson. 1966;2:1–135.CrossRefGoogle Scholar
  11. 11.
    Jansson PA, Hunt RH, Plyler EK. Resolution enhancement of spectra. J Opt Soc Am. 1970;60(5):596–9.CrossRefGoogle Scholar
  12. 12.
    Barkhuijsen H, de Beer R, Bovée WMMJ, van Ormondt D. Retrieval of frequencies, amplitudes, damping factors, and phases from time-domain signals using a linear least-squares procedure. J Magn Reson (1969). 1985;61(3):465–81.CrossRefGoogle Scholar
  13. 13.
    Mobli M, Hoch JC. Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR. Prog Nucl Magn Reson Spectrosc. 2014;83:21–41.CrossRefGoogle Scholar
  14. 14.
    Stern AS, Donoho DL, Hoch JC. NMR data processing using iterative thresholding and minimum l1-norm reconstruction. J Magn Reson. 2007;188(2):295–300.CrossRefGoogle Scholar
  15. 15.
    Mobli M, Stern AS, Hoch JC. Spectral reconstruction methods in fast NMR: reduced dimensionality, random sampling and maximum entropy. J Magn Reson. 2006;182(1):96–105.CrossRefGoogle Scholar
  16. 16.
    Mobli M. Reducing seed dependent variability of non-uniformly sampled multidimensional NMR data. J Magn Reson. 2015;256:60–9.CrossRefGoogle Scholar
  17. 17.
    Kupce E, Freeman R. Fast multi-dimensional NMR by minimal sampling. J Magn Reson. 2008;191(1):164–8.CrossRefGoogle Scholar
  18. 18.
    Mobli M, Maciejewski MW, Schuyler AD, Stern AS, Hoch JC. Sparse sampling methods in multidimensional NMR. Phys Chem Chem Phys. 2012;14(31):10835–43.CrossRefGoogle Scholar
  19. 19.
    Palmer M, Wenrich B, Stahlfeld P, Rovnyak D. Performance tuning non-uniform sampling for sensitivity enhancement of signal-limited biological NMR. J Biomol NMR. 2014;58(4):303–14.CrossRefGoogle Scholar
  20. 20.
    Schuyler AD, Maciejewski MW, Arthanari H, Hoch JC. Knowledge-based nonuniform sampling in multidimensional NMR. J Biomol NMR. 2011;50(3):247–62.CrossRefGoogle Scholar
  21. 21.
    Maciejewski MW, Qui HZ, Rujan I, Mobli M, Hoch JC. Nonuniform sampling and spectral aliasing. J Magn Reson. 2009;199(1):88–93.CrossRefGoogle Scholar
  22. 22.
    Szyperski T, Yeh DC, Sukumaran DK, Moseley HNB, Montelione GT. Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment. Proc Natl Acad Sci USA. 2002;99(12):8009–14.CrossRefGoogle Scholar
  23. 23.
    Rovnyak D, Sarcone M, Jiang Z. Sensitivity enhancement for maximally resolved two-dimensional NMR by nonuniform sampling. Magn Reson Chem. 2011;49(8):483–91.CrossRefGoogle Scholar
  24. 24.
    Grage H, Akke M. A statistical analysis of NMR spectrometer noise. J Magn Reson. 2003;162(1):176–88.CrossRefGoogle Scholar
  25. 25.
    Miljenović T, Jia X, Lavrencic P, Kobe B, Mobli M. A non-uniform sampling approach enables studies of dilute and unstable proteins. J Biomol NMR. 2017.  https://doi.org/10.1007/s10858-017-0091-z.
  26. 26.
    Rovnyak D, Frueh DP, Sastry M, Sun Z-YJ, Stern AS, Hoch JC, Wagner G. Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction. J Magn Reson. 2004;170(1):15–21.CrossRefGoogle Scholar
  27. 27.
    Inomata K, Ohno A, Tochio H, Isogai S, Tenno T, Nakase I, Takeuchi T, Futaki S, Ito Y, Hiroaki H, Shirakawa M. High-resolution multi-dimensional NMR spectroscopy of proteins in human cells. Nature. 2009;458(7234):106–9.CrossRefGoogle Scholar
  28. 28.
    Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Walchli M, Smith BO, Shirakawa M, Guntert P, Ito Y. Protein structure determination in living cells by in-cell NMR spectroscopy. Nature. 2009;458(7234):102–5.CrossRefGoogle Scholar
  29. 29.
    Fiorito F, Hiller S, Wider G, Wüthrich K. Automated resonance assignment of proteins: 6 DAPSY-NMR. J Biomol NMR. 2006;35(1):27–37.CrossRefGoogle Scholar
  30. 30.
    Le Guennec A, Dumez J-N, Giraudeau P, Caldarelli S. Resolution-enhanced 2D NMR of complex mixtures by non-uniform sampling. Magn Reson Chem. 2015;53(11):913–20.CrossRefGoogle Scholar
  31. 31.
    Saxena S, Stanek J, Cevec M, Plavec J, Koźmiński W. C4′/H4′ selective, non-uniformly sampled 4D HC(P)CH experiment for sequential assignments of 13C-labeled RNAs. J Biomol NMR. 2014;60(2–3):91–8.CrossRefGoogle Scholar
  32. 32.
    Sergeyev IV, Itin B, Rogawski R, Day LA, McDermott AE. Efficient assignment and NMR analysis of an intact virus using sequential side-chain correlations and DNP sensitization. Proc Natl Acad Sci U S A. 2017;114(20):201701484.CrossRefGoogle Scholar
  33. 33.
    Mobli M, Stern AS, Bermel W, King GF, Hoch JC. A non-uniformly sampled 4D HCC (CO) NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment. J Magn Reson. 2010;204(1):160–4.CrossRefGoogle Scholar
  34. 34.
    Lafon O, Hu B, Amoureux J-P, Lesot P. Fast and high-resolution stereochemical analysis by nonuniform sampling and covariance processing of anisotropic natural abundance 2D 2H NMR datasets. Chem Eur J. 2011;17(24):6716–24.CrossRefGoogle Scholar
  35. 35.
    Maltsev AS, Ying J, Bax A. Deuterium isotope shifts for backbone 1H, 15N and 13C nuclei in intrinsically disordered protein α-synuclein. J Biomol NMR. 2012;54(2):181–91.CrossRefGoogle Scholar
  36. 36.
    Stanek J, Podbevšek P, Koźmiński W, Plavec J, Cevec M. 4D Non-uniformly sampled C,C-NOESY experiment for sequential assignment of 13C,15N-labeled RNAs. J Biomol NMR. 2013;57(1):1–9.CrossRefGoogle Scholar
  37. 37.
    Pudakalakatti SM, Chandra K, Thirupathi R, Atreya HS. Rapid characterization of molecular diffusion by NMR spectroscopy. Chem Eur J. 2014;20(48):15719–22.CrossRefGoogle Scholar
  38. 38.
    Klint JK, Chin YKY, Mobli M. Rational engineering defines a molecular switch that is essential for activity of spider-venom peptides against the analgesics target NaV1.7. Mol Pharmacol. 2015;88(6):1002–10.CrossRefGoogle Scholar
  39. 39.
    Das BB, Opella SJ. Simultaneous cross polarization to 13C and 15N with 1H detection at 60kHz MAS solid-state NMR. J Magn Reson. 2016;262:20–6.CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Tomas Marko Miljenović
    • 1
  • Xinying Jia
    • 1
  • Mehdi Mobli
    • 1
  1. 1.Centre for Advanced ImagingThe University of QueenslandBrisbaneAustralia

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