FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation

Journal of Biomolecular NMR

Volumn 45, Issue 3, 2009, Pages 283-294

  Hyberts, Sven G ^a   Frueh, Dominique P ^a   Arthanari, Haribabu ^a   Wagner, Gerhard ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Data processing; Non uniform sampling; Nuclear magnetic resonance; Protein structure; Sparse sampling

Indexed keywords

ALGORITHM; ARTICLE; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DISTILLATION; ENTROPY; FORWARD MAXIMUM ENTROPY; MACROMOLECULE; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR OVERHAUSER EFFECT; PERFORMANCE MEASUREMENT SYSTEM; PRIORITY JOURNAL; PROCESS OPTIMIZATION; REPRODUCIBILITY;

NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 70350303834     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-009-9368-1     Document Type: Article

References (36)

1. 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
2. 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
3. Coggins BE, Zhou P (2006) Polar Fourier transforms of radially sampled NMR data. J Magn Reson 182:84-95
4. Coggins BE, Zhou P (2008) High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN. J Biomol NMR 42:225-239
5. 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
6. Daniell GJ, Hore PJ (1989) Maximum entropy and NMR - a new approach. J Magn Reson 84:515-536
7. Delaglio F, Grzesiek S, Vuister GW, Zhu G, Pfeifer J, Bax A (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J Biomol NMR 6:277-293
8. 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
9. Gull S, Skilling J (1991) MEMSYS5 Quantified Maximum Entropy. Royston, England
10. 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
11. Hoch JC (1989) Modern spectrum analysis in nuclear magnetic resonance: alternatives to the Fourier transform. Methods Enzymol 176:216-241
12. Hoch JC, Stern AS (1996) NMR data processing. Wiley-Liss, New York
13. Högbom JA (1974) Aperture synthesis with a non-regular distribution of interferometer baselines. Astron Astrophys Suppl 15:417-426
14. Hyberts SG, Heffron GJ, Tarragona NG, Solanky K, Edmonds KA, Luithardt H, Fejzo J, Chorev M, Aktas H, Colson K, Falchuk KH, Halperin JA, Wagner G (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
15. Kazimierczuk K, Kozminski W, Zhukov I (2006a) Two-dimensional Fourier transform of arbitrarily sampled NMR data sets. J Magn Reson 179:323-328
16. Kazimierczuk K, Zawadzka A, Kozminski W, Zhukov I (2006b) Random sampling of evolution time space and Fourier transform processing. J Biomol NMR 36:157-168
17. 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
18. 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
19. Kupce E, Freeman R (2004a) Projection-reconstruction technique for speeding up multidimensional NMR spectroscopy. J Am Chem Soc 126:6429-6440
20. Kupce E, Freeman R (2004b) Fast reconstruction of four-dimensional NMR spectra from plane projections. J Biomol NMR 28:391-395
21. Marion D (2005) Fast acquisition of NMR spectra using Fourier transform of non-equispaced data. J Biomol NMR 32:141-150
22. Orekhov VY, Ibraghimov IV, Billeter M (2001) MUNIN: A new approach to multi-dimensional NMR spectra interpretation. J Biomol NMR 20:49-60
23. Orekhov VY, Ibraghimov I, Billeter M (2003) Optimizing resolution in multidimensional NMR by three-way decomposition. J Biomol NMR 27:165-173
24. Rovnyak D, Frueh DP, Sastry M, Sun ZY, Stern AS, Hoch JC, Wagner G (2004a) Accelerated acquisition of high resolution triple-resonance spectra using non-uniform sampling and maximum entropy reconstruction. J Magn Reson 170:15-21
25. Rovnyak D, Hoch JC, Stern AS, Wagner G (2004b) Resolution and sensitivity of high field nuclear magnetic resonance spectroscopy. J Biomol NMR 30:1-10
26. Schmieder P, Stern AS, Wagner G, Hoch JC (1993) Application of nonlinear sampling schemes to COSY-type spectra. J Biomol NMR 3:569-576
27. 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
28. Schmieder P, Stern AS, Wagner G, Hoch JC (1997) Quantification of maximum-entropy spectrum reconstructions. J Magn Reson 125:332-339
29. Shannon CE (1948) A mathematical theory of communication. Bell Syst Tech J 27:379-432, 623-656
30. 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
31. Stern AS, Li KB, Hoch JC (2002) Modern spectrum analysis in multidimensional NMR spectroscopy: Comparison of linear-prediction extrapolation and maximum-entropy reconstruction. J Am Chem Soc 124:1982-1993
32. Sun ZJ, Hyberts SG, Rovnyak D, Park S, Stern AS, Hoch JC, Wagner G (2005a) 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
33. Sun ZY, Frueh DP, Selenko P, Hoch JC, Wagner G (2005b) Fast assignment of 15N-HSQC peaks using high-resolution 3D HNcocaNH experiments with non-uniform sampling. J Biomol NMR 33:43-50
34. Thakur JK, Arthanari H, Yang F, Pan SJ, Fan X, Breger J, Frueh DP, Gulshan K, Li DK, Mylonakis E, Struhl K, Moye-Rowley WS, Cormack BP, Wagner G, Naar AM (2008) A nuclear receptor-like pathway regulating multidrug resistance in fungi. Nature 452:604-609
35. 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
36. 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