Suppression of sampling artefacts in high-resolution four-dimensional NMR spectra using signal separation algorithm

Journal of Magnetic Resonance

Volumn 214, Issue , 2012, Pages 91-102

  Stanek, Jan ^a   Augustyniak, Rafal ^b,c,d   Koźmiński, Wiktor ^a  

^a UNIVERSITY OF WARSAW   (Poland)

^b ECOLE NORMALE SUPÉRIEURE   (France)

^c SORBONNE UNIVERSITÉ   (France)

^d CNRS   (France)

Author keywords

C,N edited NOESY; CLEAN; Engrailed 2; Four dimensional spectroscopy; HCCH TOCSY; Signal separation algorithm; Sparse sampling

Indexed keywords

C,N-EDITED NOESY; CLEAN; ENGRAILED 2; HCCH-TOCSY; SIGNAL SEPARATION ALGORITHMS; SPARSE SAMPLING;

AMIDES; EXPERIMENTS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SEPARATION;

ALGORITHMS;

ENGRAILED 2 PROTEIN; HOMEODOMAIN PROTEIN; NERVE PROTEIN;

ALGORITHM; ANIMAL; ARTICLE; ARTIFACT; CHEMISTRY; CHICKEN; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING; ULTRASTRUCTURE;

ALGORITHMS; ANIMALS; ARTIFACTS; CHICKENS; HOMEODOMAIN PROTEINS; MAGNETIC RESONANCE SPECTROSCOPY; NERVE TISSUE PROTEINS; SAMPLE SIZE; SENSITIVITY AND SPECIFICITY; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 84855649071     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2011.10.009     Document Type: Article

References (39)

1. T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, and G.T. Montelione Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment Proc. Natl. Acad. Sci. U. S. A. 99 2002 8009 8014 (Pubitemid 34650996)
2. K. Kazimierczuk, J. Stanek, A. Zawadzka-Kazimierczuk, and W. Koźminski Random sampling in multidimensional NMR spectroscopy Prog. Nucl. Magn. Reson. Spectrosc. 57 2010 420 434
3. B.E. Coggins, R.A. Venters, and P. Zhou Radial sampling for fast NMR: concepts and practices over three decades Prog. Nucl. Magn. Reson. Spectrosc. 57 2010 381 419
4. K. Pervushin, R. Riek, G. Wider, and K. Wüthrich Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution Proc. Natl. Acad. Sci. U. S. A. 94 1997 12366 12371
5. L. Frydman, T. Scherf, and A. Lupulescu The acquisition of multidimensional NMR spectra within a single scan Proc. Natl. Acad. Sci. U. S. A. 99 2002 15858 15862 (Pubitemid 35462712)
6. S. Hiller, F. Fiorito, K. Wüthrich, and G. Wider Automated projection spectroscopy (APSY) Proc. Natl. Acad. Sci. U. S. A. 102 2005 10876 10881 (Pubitemid 41105960)
7. V.A. Jaravine, and V.Y. Orekhov Targeted acquisition for real-time NMR spectroscopy J. Am. Chem. Soc. 128 2006 13421 13426 (Pubitemid 44583026)
8. J.C.J. Barna, E.D. Laue, M.R. Mayger, J. Skilling, and S.J.P. Worrall Exponential sampling, an alternative method for sampling in two-dimensional NMR experiments J. Magn. Reson. 73 1987 69 77
9. K. Kazimierczuk, A. Zawadzka, W. Koźmiński, and I. Zhukov Random sampling of evolution time space and Fourier transform processing J. Biomol. NMR 36 2006 157 168 (Pubitemid 44740879)
10. . Kupče, and R. Freeman Projection-reconstruction of three-dimensional NMR spectra J. Am. Chem. Soc. 125 2003 13958 13959 (Pubitemid 37420891)
11. M. Mobli, A.S. Stern, and J.C. Hoch Spectral reconstruction methods in fast NMR: reduced dimensionality, random sampling and maximum entropy J. Magn. Reson. 182 2006 96 105 (Pubitemid 44293436)
12. K. Kazimierczuk, A. Zawadzka, W. Koźmiński, and I. Zhukov Lineshapes and artifacts in Multidimensional Fourier Transform of arbitrary sampled NMR data sets J. Magn. Reson. 188 2007 344 356 (Pubitemid 47562815)
13. V.Y. Orekhov, I. Ibraghimov, and M. Billeter Optimizing resolution in multidimensional NMR by three-way decomposition J. Biomol. NMR 27 2003 165 173 (Pubitemid 37045648)
14. J.C. Hoch, and A.S. Stern NMR Data Processing 1996 Wiley-Interscience New York
15. K. Kazimierczuk, A. Zawadzka, and W. Koźmiński Narrow peaks and high dimensionalities: exploiting the advantages of random sampling J. Magn. Reson. 197 2009 219 228
16. B.E. Coggins, and P. Zhou High resolution 4-D spectroscopy with sparse concentric shell sampling and FFT-CLEAN J. Biomol. NMR 42 2008 225 239
17. J. Stanek, and W. Koźmiński Iterative algorithm of discrete Fourier transform for processing randomly sampled NMR data sets J. Biomol. NMR 47 2010 65 77
18. S.G. Hyberts, D.P. Frueh, H. Arthanari, and G. Wagner FM reconstruction of non-uniformly sampled protein NMR data at higher dimensions and optimization by distillation J. Biomol. NMR 45 2009 283 294
19. K. Kazimierczuk, and V.Y. Orekhov Accelerated NMR spectroscopy by using compressed sensing Angew. Chem., Int. Ed. 50 2011 5556 5559
20. Y. Matsuki, M.T. Eddy, R.G. Griffin, and J. Herzfeld Rapid three-dimensional MAS NMR spectroscopy at critical sensitivity Angew. Chem., Int. Ed. 49 2010 9215 9218
21. M.W. Maciejewski, A.S. Stern, G.F. King, and J.C. Hoch Nonuniform sampling in biomolecular NMR G.A. Webb, Modern Magnetic Resonance 2006 Springer Dordrecht, The Netherland 1287 1293
22. M. Mobli, and J.C. Hoch Maximum entropy spectral reconstruction of nonuniformly sampled data Concepts Magn. Reson. A 32A 2008 436 448
23. J.A. Högbom Aperture synthesis with a non-regular distribution of interferometer baselines Astron. Astrophys., Suppl. Ser. 15 1974 417 426
24. M. Mobli, A.S. Stern, W. Bermel, G.F. King, and J.C. Hoch A non-uniformly sampled 4D HCC(CO)NH-TOCSY experiment processed using maximum entropy for rapid protein sidechain assignment J. Magn. Reson. 204 2010 160 164
25. S. Hiller, R. Joss, and G. Wider Automated NMR assignment of protein side chain resonances using automated projection spectroscopy (APSY) J. Am. Chem. Soc. 130 2008 12073 12079
26. R. Augustyniak, S. Balayssac, F. Ferrage, G. Bodenhausen, and O. Lequin 1H, 13C and 15N resonance assignment of a 114-residue fragment of Engrailed 2 homeoprotein, a partially disordered protein Biomol. NMR Assignments 5 2011 229 231
27. J. Wen, J.H. Wu, and P. Zhou Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins J. Magn. Reson. 209 2011 94 100
28. V. Motáčková, J. Nováček, A. Zawadzka-Kazimierczuk, K. Kazimierczuk, L. Žídek, H. Šanderová, L. Krásný, W. Koźmiński, and V. Sklenář Strategy for complete NMR assignment of disordered proteins with highly repetitive sequences based on resolution-enhanced 5D experiments J. Biomol. NMR 48 2010 169 177
29. H.J. Dyson, and P.E. Wright Intrinsically unstructured proteins and their functions Nat. Rev. Mol. Cell Biol. 6 2005 197 208 (Pubitemid 40314921)
30. R.A. Chylla, B.F. Volkman, and J.L. Markley Practical model fitting approaches to the direct extraction of NMR parameters simultaneously from all dimensions of multidimensional NMR spectra J Biomol. NMR 12 1998 277 297 (Pubitemid 128511291)
31. K. Kazimierczuk, M. Misiak, J. Stanek, A. Zawadzka-Kazimierczuk, and W. Koźmiński Generalized Fourier transform for non-uniform sampled data Top. Curr. Chem. 2011 10.1007/128-2011-186
32. W.H. Press, S.A. Teukolsky, W.T. Vetterling, and B.P. Flannery Numerical Recipes: The Art of Scientific Computing 3rd ed. 2007 Cambridge University Press Cambridge, UK, New York
33. V.A. Jaravine, A.V. Zhuravleva, P. Permi, I. Ibraghimov, and V.Y. Orekhov Hyperdimensional NMR spectroscopy with nonlinear sampling J. Am. Chem. Soc. 130 2008 3927 3936 (Pubitemid 351429859)
34. D. Rovnyak, M. Sarcone, and Z. Jiang Sensitivity enhancement for maximally resolved two-dimensional NMR by nonuniform sampling Magn. Res. Chem. 49 2011 483 491
35. M. Sattler, J. Schleucher, and C. Griesinger Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulsed field gradients Prog. Nucl. Magn. Reson. Spectrosc. 34 1999 93 158 (Pubitemid 129595216)
36. T. Luan, V. Jaravine, A. Yee, C.H. Arrowsmith, and V.Y. Orekhov Optimization of resolution and sensitivity of 4D NOESY using multi-dimensional decomposition J. Biomol. NMR 33 2005 1 14 (Pubitemid 41573965)
37. J.W. Werner-Allen, B.E. Coggins, and P. Zhou Fast acquisition of high resolution 4-D amide-amide NOESY with diagonal suppression, sparse sampling and FFT-CLEAN J. Magn. Reson. 204 2010 173 178
38. S. Hiller, I. Ibraghimov, G. Wagner, and V.Y. Orekhov Coupled decomposition of four-dimensional NOESY spectra J. Am. Chem. Soc. 131 2009 12970 12978
39. Y. Xu, Z. Lin, C. Ho, and D. Yang A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins J. Am. Chem. Soc. 127 2005 11920 11921 (Pubitemid 41233701)