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Applications of Non-Uniform Sampling and Processing

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Novel Sampling Approaches in Higher Dimensional NMR

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 316))

Abstract

Modern high-field NMR instruments provide unprecedented resolution. To make use of the resolving power in multidimensional NMR experiment standard linear sampling through the indirect dimensions to the maximum optimal evolution times (~1.2T 2) is not practical because it would require extremely long measurement times. Thus, alternative sampling methods have been proposed during the past 20 years. Originally, random nonlinear sampling with an exponentially decreasing sampling density was suggested, and data were transformed with a maximum entropy algorithm (Barna et al., J Magn Reson 73:69–77, 1987). Numerous other procedures have been proposed in the meantime. It has become obvious that the quality of spectra depends crucially on the sampling schedules and the algorithms of data reconstruction. Here we use the forward maximum entropy (FM) reconstruction method to evaluate several alternate sampling schedules. At the current stage, multidimensional NMR spectra that do not have a serious dynamic range problem, such as triple resonance experiments used for sequential assignments, are readily recorded and faithfully reconstructed using non-uniform sampling. Thus, these experiments can all be recorded non-uniformly to utilize the power of modern instruments. On the other hand, for spectra with a large dynamic range, such as 3D and 4D NOESYs, choosing optimal sampling schedules and the best reconstruction method is crucial if one wants to recover very weak peaks. Thus, this chapter is focused on selecting the best sampling schedules and processing methods for high-dynamic range spectra.

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References

  1. Ernst RR, Anderson WA (1966) Application of Fourier transform spectroscopy to magnetic resonance. Rev Sci Instr 37:93–106

    Article  CAS  Google Scholar 

  2. Cooley JW, Tukey JW (1965) An algorithm for the machine calculation of complex Fourier series. Math Comput 19:297–301

    Article  Google Scholar 

  3. Barna JCJ, Laue ED, Mayger MR, Skilling J, Worrall SJP (1987) Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments. J Magn Reson 73:69–77

    CAS  Google Scholar 

  4. Sibisi S, Skilling J, Brereton RG, Laue ED, Staunton J (1984) Maximum entropy signal processing in practical NMR spectroscopy. Nature 311:446–447

    Article  CAS  Google Scholar 

  5. Hoch JC (1989) Modern spectrum analysis in nuclear magnetic resonance: alternatives to the Fourier transform. Meth Enzymol 176:216–241

    Article  CAS  Google Scholar 

  6. Frueh DP, Sun ZY, Vosburg DA, Walsh CT, Hoch JC, Wagner G (2006) Non-uniformly sampled double-TROSY hNcaNH experiments for NMR sequential assignments of large proteins. J Am Chem Soc 128:5757–5763

    Article  CAS  Google Scholar 

  7. Rovnyak D, Frueh DP, Sastry M, Sun ZY, Stern AS, Hoch JC, Wagner G (2004) Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction. J Magn Reson 170:15–21

    Article  CAS  Google Scholar 

  8. Rovnyak D, Hoch JC, Stern AS, Wagner G (2004) Resolution and sensitivity of high field nuclear magnetic resonance spectroscopy. J Biomol NMR 30:1–10

    Article  CAS  Google Scholar 

  9. Schmieder P, Stern AS, Wagner G, Hoch JC (1993) Application of nonlinear sampling schemes to COSY-type spectra. J Biomol NMR 3:569–576

    Article  CAS  Google Scholar 

  10. Schmieder P, Stern AS, Wagner G, Hoch JC (1994) Improved resolution in triple-resonance spectra by nonlinear sampling in the constant-time domain. J Biomol NMR 4:483–490

    Article  CAS  Google Scholar 

  11. Schmieder P, Stern AS, Wagner G, Hoch JC (1997) Quantification of maximum-entropy spectrum reconstructions. J Magn Reson 125:332–339

    Article  CAS  Google Scholar 

  12. Shimba N, Stern AS, Craik CS, Hoch JC, Dotsch V (2003) Elimination of 13Calpha splitting in protein NMR spectra by deconvolution with maximum entropy reconstruction. J Am Chem Soc 125:2382–2383

    Article  CAS  Google Scholar 

  13. Sun ZJ, Hyberts SG, Rovnyak D, Park S, Stern AS, Hoch JC, Wagner G (2005) High-resolution aliphatic side-chain assignments in 3D HCcoNH experiments with joint H-C evolution and non-uniform sampling. J Biomol NMR 32:55–60

    Article  CAS  Google Scholar 

  14. Sun ZY, Frueh DP, Selenko P, Hoch JC, Wagner G (2005) Fast assignment of 15N-HSQC peaks using high-resolution 3D HNcocaNH experiments with non-uniform sampling. J Biomol NMR 33:43–50

    Article  CAS  Google Scholar 

  15. Tugarinov V, Kay LE, Ibraghimov I, Orekhov VY (2005) High-resolution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J Am Chem Soc 127:2767–2775

    Article  CAS  Google Scholar 

  16. Chylla RA, Markley JL (1995) Theory and application of the maximum likelihood principle to NMR parameter estimation of multidimensional NMR data. J Biomol NMR 5:245–258

    Article  CAS  Google Scholar 

  17. Marion D (2005) Fast acquisition of NMR spectra using Fourier transform of non-equispaced data. J Biomol NMR 32:141–150

    Article  CAS  Google Scholar 

  18. Gutmanas A, Jarvoll P, Orekhov VY, Billeter M (2002) Three-way decomposition of a complete 3D 15N-NOESY-HSQC. J Biomol NMR 24:191–201

    Article  CAS  Google Scholar 

  19. Hiller S, Ibraghimov I, Wagner G, Orekhov VY (2009) Coupled decomposition of four-dimensional NOESY spectra. J Am Chem Soc 131:12970–12978

    Article  CAS  Google Scholar 

  20. Korzhneva DM, Ibraghimov IV, Billeter M, Orekhov VY (2001) MUNIN: application of three-way decomposition to the analysis of heteronuclear NMR relaxation data. J Biomol NMR 21:263–268

    Article  CAS  Google Scholar 

  21. Orekhov VY, Ibraghimov I, Billeter M (2003) Optimizing resolution in multidimensional NMR by three-way decomposition. J Biomol NMR 27:165–173

    Article  CAS  Google Scholar 

  22. Orekhov VY, Ibraghimov IV, Billeter M (2001) MUNIN: a new approach to multi-dimensional NMR spectra interpretation. J Biomol NMR 20:49–60

    Article  CAS  Google Scholar 

  23. Coggins BE, Venters RA, Zhou P (2005) Filtered backprojection for the reconstruction of a high-resolution (4,2)D CH3-NH NOESY spectrum on a 29 kDa protein. J Am Chem Soc 127:11562–11563

    Article  CAS  Google Scholar 

  24. Coggins BE, Zhou P (2006) Polar Fourier transforms of radially sampled NMR data. J Magn Reson 182:84–95

    Article  CAS  Google Scholar 

  25. Coggins BE, Zhou P (2008) High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN. J Biomol NMR 42:225–239

    Article  CAS  Google Scholar 

  26. Kazimierczuk K, Kozminski W, Zhukov I (2006) Two-dimensional Fourier transform of arbitrarily sampled NMR data sets. J Magn Reson 179:323–328

    Article  CAS  Google Scholar 

  27. Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157–168

    Article  CAS  Google Scholar 

  28. Kim S, Szyperski T (2003) GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information. J Am Chem Soc 125:1385–1393

    Article  CAS  Google Scholar 

  29. Kupce E, Freeman R (2004) Fast reconstruction of four-dimensional NMR spectra from plane projections. J Biomol NMR 28:391–395

    Article  CAS  Google Scholar 

  30. Kupce E, Freeman R (2004) Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc 126:6429–6440

    Article  CAS  Google Scholar 

  31. Venters RA, Coggins BE, Kojetin D, Cavanagh J, Zhou P (2005) (4,2)D Projection–reconstruction experiments for protein backbone assignment: application to human carbonic anhydrase II and calbindin D(28K). J Am Chem Soc 127:8785–8795

    Article  CAS  Google Scholar 

  32. Hyberts SG, Frueh DP, Arthanari H, Wagner G (2009) FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation. J Biomol NMR 45:283–294

    Article  CAS  Google Scholar 

  33. Hyberts SG, Heffron GJ, Tarragona NG, Solanky K, Edmonds KA, Luithardt H, Fejzo J, Chorev M, Aktas H, Colson K et al (2007) Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction. J Am Chem Soc 129:5108–5116

    Article  CAS  Google Scholar 

  34. Hyberts SG, Takeuchi K, Wagner G (2010) Poisson-gap sampling and forward maximum entropy reconstruction for enhancing the resolution and sensitivity of protein NMR data. J Am Chem Soc 132:2145–2147

    Article  CAS  Google Scholar 

  35. Frueh DP, Arthanari H, Koglin A, Walsh CT, Wagner G (2009) A double TROSY hNCAnH experiment for efficient assignment of large and challenging proteins. J Am Chem Soc 131:12880–12881

    Article  CAS  Google Scholar 

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Acknowledgment

This research was supported by the National Institutes of Health (grants GM 47467 and EB 002026). We thank Bruker Biospin for providing access to a 700-MHz spectrometer for acquiring the experimental data.

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Authors and Affiliations

  1. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA, 02115, USA

    Sven G. Hyberts, Haribabu Arthanari & Gerhard Wagner

Authors
  1. Sven G. Hyberts
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  2. Haribabu Arthanari
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  3. Gerhard Wagner
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Correspondence to Gerhard Wagner .

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Editors and Affiliations

  1. , Department of Chemistry, University of Gothenburg, Göteborg, 405 30, Sweden

    Martin Billeter

  2. , The Swedish NMR Centre, Göteborg University, Medicinaregatan 5C, Göteborg, 413 90, Sweden

    Vladislav Orekhov

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Hyberts, S.G., Arthanari, H., Wagner, G. (2011). Applications of Non-Uniform Sampling and Processing. In: Billeter, M., Orekhov, V. (eds) Novel Sampling Approaches in Higher Dimensional NMR. Topics in Current Chemistry, vol 316. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2011_187

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