Covariance NMR in higher dimensions: Application to 4D NOESY spectroscopy of proteins

Journal of Biomolecular NMR

Volumn 39, Issue 3, 2007, Pages 165-175

  Snyder, David A ^a   Zhang, Fengli ^a   Brüschweiler, Rafael ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

4D NMR spectroscopy; Covariance NMR; Cros speak assignment; Distance constraints; NOESY

Indexed keywords

UBIQUITIN;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CONTROLLED STUDY; COVARIANCE; FOURIER TRANSFORMATION; HUMAN; IMAGE RECONSTRUCTION; NITROGEN NUCLEAR MAGNETIC RESONANCE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DETERMINATION; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; QUALITATIVE ANALYSIS;

HUMANS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEINS; REPRODUCIBILITY OF RESULTS; UBIQUITIN;

EID: 35448988389     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-007-9187-1     Document Type: Article

References (53)

1. Altieri AS, Byrd RA (2004) Automation of NMR structure determination of proteins. Curr Opin Struc Biol 14:547-553
2. Babu CR, Flynn PF, Wand AJ (2001) Validation of protein structure from preparations of encapsulated proteins dissolved in low viscosity fluids. J Am Chem Soc 123:2691-2692
3. Bax A, Clore GM, Gronenborn AM (1990) H-1-H-1 correlation via isotropic mixing of C-13 magnetization, a new 3-dimensional approach for assigning H-1 and C-13 spectra of C-13-enriched proteins. J Magn Reson 88:425-431
4. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucl Acids Res 28:235-242
5. Brüschweiler R (2004) Theory of covariance nuclear magnetic resonance spectroscopy. J Chem Phys 121:409-414
6. Brüschweiler R, Zhang F (2004) Covariance nuclear magnetic resonance spectroscopy. J Chem Phys 120:5253-5260
7. Brutscher B, Cordier F, Simorre JP, Caffrey M, Marion D (1995) High-resolution 3D HNCOCA experiment applied to a 28-kDa paramagnetic protein. J Biomol NMR 5:202-206
8. Celda B, Montelione GT (1993). Total correlation spectroscopy (TOCSY) of proteins using coaddition of spectra recorded with several mixing times. J Magn Reson Ser B 101: 189-193
9. Chen Y, Zhang F, Bermel W, Brüschweiler R (2006) Enhanced covariance spectroscopy from minimal datasets. J Am Chem Soc 128:15564-15565
10. Chen Y, Zhang F, Snyder DA, Gan Z, Brüschweiler-Li L, Brüschweiler R (2007) Quantitative covariance NMR by regularization. J Biomol NMR 38:73-77
11. Clore GM, Gronenborn AM (1991) Structures of larger proteins in solution: Three- and four-dimensional heteronuclear NMR spectroscopy. Science 252:1390-1399
12. Clore GM, Kay LE, Bax A, Gronenborn AM (1991) 4-Dimensional C-13/ C-13-edited nuclear Overhauser enhancement spectroscopy of a protein in solution - application to interleukin 1-beta. Biochemistry 30:12-18
13. Coggins BE, Zhou P (2007) Sampling in the NMR time domain along concentric rings. J Magn Reson 184:207-221
14. 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
15. Eghbalnia HR, Bahrami A, Tonelli M, Hallenga K, Markley JL (2005) High-resolution iterative frequency identification for NMR as a general strategy for multidimensional data collection. J Am Chem Soc 127:12528-12536
16. Farmer BT, Venters RA, Spicer LD, Wittekind MG, Muller L (1992) A refocused and optimized HNCA - increased sensitivity and resolution in large macromolecules. J Biomol NMR 2:195-202
17. Freeman R, Kupce E (2006) New ways to record multidimensional NMR spectra. Curr Anal Chem 2:101-105
18. Goddard TD, Kneller DG (1998) SPARKY v. 3. University of California, San Francisco, CA
19. Grzesiek S, Bax A (1992) Improved 3D triple-resonance NMR techniques applied to a 31-kDa protein. J Magn Reson 96:432-440
20. Havel TF, Najfeld I, Yang J-X (1994) Matrix decompositions of two-dimensional nuclear magnetic resonance spectra. Proc Natl Acad Sci USA 91:7962-7966
21. Hiller S, Fiorito F, Würthrich K, Wider G (2005) Automated projection spectroscopy (APSY). Proc Natl Acad Sci USA 102:10876-10881
22. Hoch JC, Stern AS (2001) Maximum entropy reconstruction, spectrum analysis and deconvolution in multidimensional nuclear magnetic resonance. Method Enzymol 338:159-178
23. Hu HT, De Angelis AA, Mandelshtam VA, Shaka AJ (2000) The multidimensional filter diagonalization method - II. Application to 2D projections of 2D, 3D, and 4D NMR experiments. J Magn Reson 144:357-366
24. Huang YJ, Powers R, Montelione GT (2005) Protein NMR recall, precision and F-measure scores (RPF scores): Structure quality assessment measures based on information retrieval statistics. J Am Chem Soc 127:1665-1674
25. Huang YJ, Tejero R, Powers R, Montelione GT (2006) A topology constrained distance network algorithm for protein structure determination from NOESY data. Proteins: Struct Funct Bioinfo 15:587-603
26. Jaravine V, Ibraghimov I, Orekhov VY (2006) Removal of a time barrier for high-resolution multidimensional NMR spectroscopy. Nat Methods 3:605-607
27. Johnson RA, Wichern DW (2002) Applied multivariate statistical analysis. Prentice Hall
28. Kay LE, Clore GM, Bax A, Gronenborn AM (1990). 4-Dimensional heteronuclear triple-resonance NMR-spectroscopy of interleukin-1-beta in solution. Science 249:411-414
29. Kay LE, Ikura M, Tschudin R, Bax A (1990) 3-Dimensional triple-resonance NMR-spectroscopy of isotopically enriched proteins. J Magn Reson 89:496-514
30. Kay LE, Keifer P, Saarinen T (1992) Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity. J Am Chem Soc 114:10663-10665
31. 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
32. Koehl P (1999) Linear prediction spectral analysis of NMR data. Prog Nucl Mag Res Sp 34:257-299
33. Kumar A, Ernst RR, Wüthrich K (1980) A two-dimensional nuclear Overhauser enhancement (2D NOE) experiment for the elucidation of complete proton-proton cross-relaxation networks in biological macromolecules. Biochem Bioph Res Co 95:1-6
34. Kupce E, Freeman R (2006). Hyperdimensional NMR spectroscopy. J Am Chem Soc 128:6020-6021
35. Led JJ, Gesmar H (1991) Application of the linear prediction method to NMR spectroscopy. Chem Rev 91:1413-1426
36. Macura S, Ernst RR (1980) Elucidation of cross relaxation in liquids by two-dimensional NMR-spectroscopy. Mol Phys 41:95-117
37. Malmodin D, Billeter M (2005) Multiway decomposition of NMR spectra with coupled evolution periods. J Am Chem Soc 127:13486-13487
38. Marion D (2006) Processing of nD NMR spectra sampled in polar coordinates: A simple Fourier transform instead of a reconstruction. J Biolmol NMR 36:45-54
39. Misiak M, Kozminski W (2007) Three-dimensional NMR spectroscopy of organic molecules by random sampling of evolution time space and multidimensional Fourier transform. Magn Reson Chem 45:171-174
40. Morshauser RC, Zuiderweg ERP (1999) High-resolution four-dimensional HMQC-NOESY-HSQC spectroscopy. J Magn Reson 139:232-239
41. Orekhov VY, Ibraghimov I, Billeter M (2003) Optimizing resolution in multidimensional NMR by three-way decomposition. J Biolmol NMR 27:165-173
42. Rance M (1994) Sensitivity improvement in multidimensional NMR spectroscopy. Bull Magn Reson 16:54
43. Rovnyak D, Frueh DP, Sastry M, Sun ZYJ, 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
44. Seavey BR, Farr EA, Westler WM, Markley JL (1991) A relational database for sequence-specific protein NMR data. J Biolmol NMR 1:217-236
45. Solomon I (1955) Relaxation processes in a system of 2 spins. Phys Rev 99:559-565
46. Szyperski T, Atreya HS (2006) Principles and applications of GFT projection NMR spectroscopy. Magn Reson Chem 44:S51-S60
47. Szyperski T, Wider G, Bushweller JH, Wüthrich K (1993) Reduced dimensionality in triple-resonance NMR experiments. J Am Chem Soc 115:9307-9308
48. Trbovic N, Smirnov S, Zhang F, Brüschweiler R (2004) Covariance NMR spectroscopy by singular value decomposition. J Magn Reson 171:277-283
49. 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
50. Uitenbroek DG (1997). SISA: Simple interactive statistical analysis. (http://www.home.clara.net/sisa/)
51. Vuister GW, Clore GM, Gronenborn AM, Powers R, Garrett DS, Tschudin R, Bax A (1993) Increased resolution and improved spectral quality in four-dimensional 13C/13C-separated HMQC-NOESY-HMQC spectra using pulsed field gradients. J Magn Reson B 101:210-213
52. Wüthrich K (1986) NMR of proteins and nucleic acids. John Wiley and Sons, New York
53. Yee A, Gutmanas A, Arrowsmith CH (2006) Solution NMR in structural genomics. Curr Opin Struct Biol 16:611-617