Sparsely sampled high-resolution 4-D experiments for efficient backbone resonance assignment of disordered proteins

Journal of Magnetic Resonance

Volumn 209, Issue 1, 2011, Pages 94-100

  Wen, Jie ^a   Wu, Jihui ^a,b   Zhou, Pei ^c  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

^c DUKE UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

Fast NMR; FFT CLEAN; IDP; Sequential assignment; Sparse sampling

Indexed keywords

FAST NMR; FFT-CLEAN; IDP; SEQUENTIAL ASSIGNMENT; SPARSE SAMPLING;

CHEMICAL SHIFT; EXPERIMENTS; FAST FOURIER TRANSFORMS; OPTIMIZATION; RESONANCE;

NUCLEAR MAGNETIC RESONANCE;

PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CHEMISTRY; METHODOLOGY; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PEPTIDE MAPPING; SEQUENCE ANALYSIS;

AMINO ACID SEQUENCE; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR SEQUENCE DATA; PEPTIDE MAPPING; PROTEINS; SEQUENCE ANALYSIS, PROTEIN;

EID: 79951680178     PISSN: 10907807     EISSN: 10960856     Source Type: Journal    
DOI: 10.1016/j.jmr.2010.12.012     Document Type: Article

References (33)

1. A.L. Fink Natively unfolded proteins Curr. Opin. Struct. Biol. 15 2005 35 41 (Pubitemid 40249507)
2. V.N. Uversky, C.J. Oldfield, and A.K. Dunker Intrinsically disordered proteins in human diseases: introducing the D2 concept Annu. Rev. Biophys. 37 2008 215 246
3. N. Pannetier, K. Houben, L. Blanchard, and D. Marion Optimized 3D-NMR sampling for resonance assignment of partially unfolded proteins J. Magn. Reson. 186 2007 142 149 (Pubitemid 46635244)
4. 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)
5. S. Hiller, F. Fiorito, K. Wüthrich, and G. Wider Automated projection spectroscopy (APSY) Proc. Natl. Acad. Sci. USA 102 2005 10876 10881 (Pubitemid 41105960)
6. S. Hiller, C. Wasmer, G. Wider, and K. Wuthrich Sequence-specific resonance assignment of soluble nonglobular proteins by 7D APSY-NMR spectroscopy J. Am. Chem. Soc. 129 2007 10823 10828 (Pubitemid 350067493)
7. 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
8. R.L. Narayanan, U.H. Durr, S. Bibow, J. Biernat, E. Mandelkow, and M. Zweckstetter Automatic assignment of the intrinsically disordered protein Tau with 441-residues J. Am. Chem. Soc. 132 2010 11906 11907
9. 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
10. B.E. Coggins, R.A. Venters, and P. Zhou 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 2005 11562 11563 (Pubitemid 41208719)
11. 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
12. D. Marion Combining methods for speeding up multi-dimensional acquisition. Sparse sampling and fast pulsing methods for unfolded proteins J. Magn. Reson. 206 2010 81 87
13. A. Zawadzka-Kazimierczuk, K. Kazimierczuk, and W. Kozminski A set of 4D NMR experiments of enhanced resolution for easy resonance assignment in proteins J. Magn. Reson. 202 2010 109 116
14. 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
15. 13C NOE spectroscopy using methyl-TROSY sparse data acquisition and multidimensional decomposition J. Am. Chem. Soc. 127 2005 2767 2775 (Pubitemid 40327839)
16. X. Wang, S. Zhang, J. Zhang, X. Huang, C. Xu, W. Wang, Z. Liu, J. Wu, and Y. Shi A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR J. Biol. Chem. 285 2010 4951 4963
17. M. Wittekind, and L. Mueller HNCACB, a high-sensitivity 3D NMR experiment to correlate amide-proton and nitrogen resonances with the alpha- and beta-carbon resonances in proteins J. Magn. Reson. Ser. B 101 1993 201 205
18. R.A. Venters, B.E. Coggins, D. Kojetin, J. Cavanagh, and P. Zhou (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 2005 8785 8795 (Pubitemid 40868260)
19. F. Löhr, and H. Rüterjans A new triple-resonance experiment for the sequential assignment of backbone resonances in proteins J. Biomol. NMR 6 1995 189 197
20. W. Boucher, E.D. Laue, S. Campbell-Burk, and P.J. Domaille Four-dimensional heteronuclear triple resonance NMR methods for the assignment of backbone nuclei in proteins J. Am. Chem. Soc. 114 1992 2262 2264
21. H. Matsuo, E. Kupče, H. Li, and G. Wagner Use of selective C alpha pulses for improvement of HN(CA)CO-D and HN(COCA)NH-D experiments J. Magn. Reson. B 111 1996 194 198 (Pubitemid 126758679)
22. 2H-labeled proteins J. Biomol. NMR 14 1999 333 343 (Pubitemid 29473521)
23. J.W. Werner-Allen, L. Jiang, and P. Zhou A 'just-in-time' HN(CA)CO experiment for the backbone assignment of large proteins with high sensitivity J. Magn. Reson. 181 2006 177 180 (Pubitemid 43866548)
24. B.E. Coggins, and P. Zhou Polar Fourier transforms of radially sampled NMR data J. Magn. Reson. 182 2006 84 95 (Pubitemid 44293437)
25. K. Kazimierczuk, W. Koźmiński, and I. Zhukov Two-dimensional Fourier transform of arbitrarily sampled NMR data sets J. Magn. Reson. 179 2006 323 328
26. D. Marion Processing of ND NMR spectra sampled in polar coordinates: a simple Fourier transform instead of a reconstruction J. Biomol. NMR 36 2006 45 54 (Pubitemid 44473226)
27. K. Kazimierczuk, A. Zawadzka, and W. Kozminski Narrow peaks and high dimensionalities: exploiting the advantages of random sampling J. Magn. Reson. 197 2009 219 228
28. B.E. Coggins, and P. Zhou Sampling of the NMR time domain along concentric rings J. Magn. Reson. 184 2007 219 233
29. K. Kazimierczuk, A. Zawadzka, and W. Koźmiński Optimization of random time domain sampling in multidimensional NMR J. Magn. Reson. 192 2008 123 130 (Pubitemid 351609413)
30. 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)
31. 15N HSQC experiments optimized to retain full sensitivity J. Magn. Reson. A 102 1993 241 245
32. L. Emsley, and G. Bodenhausen Gaussian pulse cascades: new analytical functions for rectangular selective inversion and in-phase excitation in NMR Chem. Phys. Lett. 165 1990 469 476
33. L. Emsley, and G. Bodenhausen Optimization of shaped selective pulses for NMR using a quaternion description of their overall propagators J. Magn. Reson. 97 1992 135 148