High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination

Journal of Biomolecular NMR

Volumn 48, Issue 3, 2010, Pages 137-145

  Jaipuria, Garima ^a   Thakur, Anushikha ^a   D'Silva, Patrick ^a   Atreya, Hanudatta S ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

GFT NMR; Methyl edited NOESY; NOESY; Protein structure; TOCSY

Indexed keywords

CHAPERONE; J PROTEIN COCHAPERONE; METHYL GROUP; UNCLASSIFIED DRUG;

ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; FOURIER TRANSFORMATION; G MATRIX FOURIER TRANSFORMATION NUCLEAR MAGNETIC RESONANCE; HETERONUCLEAR SINGLE QUANTUM COHERENCE; MOLECULAR IMAGING; NUCLEAR MAGNETIC RESONANCE; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SENSITIVITY AND SPECIFICITY; SPECTROSCOPY; THREE DIMENSIONAL IMAGING; TOTAL CORRELATION SPECTROSCOPY;

AMINO ACID SEQUENCE; CARBON ISOTOPES; DEUTERIUM; ESCHERICHIA COLI; FOURIER ANALYSIS; HUMANS; ISOLEUCINE; LEUCINE; METHYLATION; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN STRUCTURE, QUATERNARY; PROTEINS; VALINE;

EID: 78149416435     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-010-9444-6     Document Type: Article

References (44)

1. J Anglister S Grzesiek AC Wang H Ren CB Klee A Bax 1994 H-1, C-13, N-15 nuclear-magnetic-resonance backbone assignments and secondary structure of human Calcineurin-B Biochemistry 33 3540 3547 10.1021/bi00178a010
2. 3 groups in Val and Leu residues J Biomol NMR 19 267 272 10.1023/A:1011262916235 (Pubitemid 32288266)
3. HS Atreya T Szyperski 2005 Rapid NMR data collection Methods Enzymol 394 78 108 10.1016/S0076-6879(05)94004-4 (Pubitemid 40460913)
4. RP Barnwal HS Atreya KVR Chary 2008 Chemical shift based editing of CH3 groups in fractionally C-13-labelled proteins using GFT (3, 2)D CT-HCCH-COSY: stereospecific assignments of CH3 groups of Val and Leu residues J Biomol NMR 42 149 154 10.1007/s10858-008-9273-z
5. C Bartels TH Xia M Billeter P Güntert K Wüthrich 1995 The program Xeasy for computer-supported NMR spectral-analysis of biological macromolecules J Biomol NMR 6 1 10 10.1007/BF00417486
6. Cavanagh J, Fairbrother WJ, Palmer AG, Rance M, Skelton NJ (2007) Protein NMR spectroscopy. Elsevier Academic Press, San Diego
7. GM Clore LE Kay A Bax AM Gronenborn 1991 Four-dimensional C-13/C-13-edited nuclear overhauser enhancement spectroscopy of a protein in solution-application to Interleukin 1-Beta Biochemistry 30 12 18 10.1021/bi00215a002
8. BE Coggins RA Venters P Zhou 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 10.1021/ja053110k (Pubitemid 41208719)
9. F Delaglio S Grzesiek GW Vuister G Zhu J Pfeifer A Bax 1995 Nmrpipe-a multidimensional spectral processing system based on unix pipes J Biomol NMR 6 277 293 10.1007/BF00197809
10. BT Farmer L Mueller 1994 Simultaneous acquisition of C-13, N-15 -separated and N-15, N-15 -separated 4D gradient-enhanced NOESY spectra in proteins J Biomol NMR 4 673 687 10.1007/BF00404277
11. V Galius C Leontiou T Richmond G Wider 2008 Projected H-1, N-15 -HMQC- H-1, H-1-NOESY for large molecular systems: application to a 121 kDa protein-DNA complex J Biomol NMR 40 175 181 10.1007/s10858-008-9219-5
12. KH Gardner R Konrat MK Rosen LE Kay 1996 An (H)C(CO)NH-TOCSY pulse scheme for sequential assignment of protonated methyl groups in otherwise deuterated N-15, C-13-labeled proteins J Biomol NMR 8 351 356 10.1007/BF00410333
13. KH Gardner MK Rosen LE Kay 1997 Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR Biochemistry 36 1389 1401 10.1021/bi9624806 (Pubitemid 27074963)
14. JD Gross VM Gelev G Wagner 2003 A sensitive and robust method for obtaining intermolecular NOEs between side chains in large protein complexes J Biomol NMR 25 235 242 10.1023/A:1022890112109 (Pubitemid 36410587)
15. S Grzesiek P Wingfield S Stahl JD Kaufman A Bax 1995 Four-dimensional N-15-separated NOESY of slowly tumbling perdeuterated N-15-enriched proteins-application to Hiv-1 Nef J Am Chem Soc 117 9594 9595 10.1021/ja00142a040
16. M Kainosho T Torizawa Y Iwashita T Terauchi A Mei Ono P Güntert 2006 Optimal isotope labeling for NMR protein structure determination Nature 440 52 57 10.1038/nature04525 2006Natur.440...52K (Pubitemid 43336263)
17. LE Kay M Ikura G Zhu A Bax 1991 Four-dimensional heteronuclear triple resonance NMR spectroscopy of isotopically enriched proteins for sequential assignments of backbone atoms J Magn Reson 91 422 428
18. LE Kay GY Xu AU Singer DR Muhandiram JD Forman-kay 1993 A gradient-enhanced HCCH TOCSY experiment for recording side-chain H-1 and C-13 correlations in H2O samples of proteins J Magn Reson Ser B 101 333 337 10.1006/jmrb.1993.1053
19. S Kim T Szyperski 2003 GFT NMR, a new approach to rapidly obtain precise high-dimensional NMR spectral information J Am Chem Soc 125 1385 1393 10.1021/ja028197d (Pubitemid 36159850)
20. M Kock C Griesinger 1994 Fast NOESY experiments-an approach for fast structure determination Angew Chem Intl Ed 33 332 334 10.1002/anie.199403321
21. W Lee MJ Revington C Arrowsmith LE Kay 1994 A pulsed-field gradient isotope-filtered 3D C-13 HMQC-NOESY experiment for extracting intermolecular NOE contacts in molecular-complexes FEBS Lett 350 87 90 10.1016/0014-5793(94)00740- 3 (Pubitemid 24261402)
22. TM Logan ET Olejniczak RX Xu SW Fesik 1992 Side-chain and backbone assignments in isotopically labeled proteins from 2 heteronuclear triple resonance experiments FEBS Lett 314 413 418 10.1016/0014-5793(92)81517-P (Pubitemid 23005701)
23. DR Muhandiram NA Farrow GY Xu SH Smallcombe LE Kay 1993 A gradient C-13 NOESY-HSQC experiment for recording NOESY spectra of C-13-labeled proteins dissolved in H2O J Magn Reson Ser B 102 317 321 10.1006/jmrb.1993.1102
24. DR Muhandiram GY Xu LE Kay 1993 An enhanced-sensitivity pure absorption gradient 4D N-15, C-13-edited NOESY experiment J Biomol NMR 3 463 470 10.1007/BF00176011
25. XB Qiu YM Shao S Miao L Wang 2006 The diversity of the DnaJ/Hsp40 family, the crucial partners for Hsp70 chaperones Cell Mol Life Sci 63 2560 2570 10.1007/s00018-006-6192-6 (Pubitemid 44800711)
26. MK Rosen KH Gardner RC Willis WE Parris T Pawson LE Kay 1996 Selective methyl group protonation of perdeuterated proteins J Mol Biol 263 627 636 10.1006/jmbi.1996.0603 (Pubitemid 26395055)
27. Y Shen HS Atreya G Liu T Szyperski 2005 G-matrix fourier transform NOESY-based protocol for high-quality protein structure determination J Am Chem Soc 127 9085 9099 10.1021/ja0501870 (Pubitemid 40897602)
28. DA Snyder YQ Xu DW Yang R Bruschweiler 2007 Resolution-enhanced 4D N-15/C-13 NOESY protein NMR spectroscopy by application of the covariance transform J Am Chem Soc 129 14126 14127 10.1021/ja075533n (Pubitemid 350171409)
29. DA Snyder F Zhang R Brueschweiler 2007 Covariance NMR in higher dimensions: application to 4D NOESY spectroscopy of proteins J Biomol NMR 39 165 175 10.1007/s10858-007-9187-1 (Pubitemid 47617501)
30. S Swain HS Atreya 2008 A method to selectively detect a desired linear combination of chemical shifts in GFT projection NMR spectroscopy Open Magn Reson J 1 95 103 10.2174/1874769800801010095
31. T Szyperski HS Atreya 2006 Principles and applications of GFT projection NMR spectroscopy Magn Reson Chem 44 S51 S60 10.1002/mrc.1817 (Pubitemid 44090390)
32. V Tugarinov LE Kay 2004 An isotope labeling strategy for methyl TROSY spectroscopy J Biomol NMR 28 165 172 10.1023/B:JNMR.0000013824.93994.1f (Pubitemid 38232795)
33. V Tugarinov LE Kay 2004 Stereospecific NMR assignments of prochiral methyls, rotameric states and dynamics of valine residues in malate synthase G J Am Chem Soc 126 9827 9836 10.1021/ja048738u (Pubitemid 39031064)
34. V Tugarinov LE Kay 2005 Methyl groups as probes of structure and dynamics in NMR studies of high-molecular weight proteins ChemBioChem 6 1567 1577 10.1002/cbic.200500110 (Pubitemid 41296962)
35. V Tugarinov PM Hwang JE Ollerenshaw LE Kay 2003 Cross-correlated relaxation enhanced H-1-C-13 NMR spectroscopy of methyl groups in very high molecular weight proteins and protein complexes J Am Chem Soc 125 10420 10428 10.1021/ja030153x (Pubitemid 37022252)
36. V Tugarinov PM Hwang LE Kay 2004 Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins Ann Rev Biochem 73 107 146 10.1146/annurev.biochem.73.011303.074004 (Pubitemid 39050365)
37. V Tugarinov WY Choy VY Orekhov LE Kay 2005 Solution NMR-derived global fold of a monomeric 82-kDa enzyme Proc Natl Acad Sci USA 102 622 627 10.1073/pnas.0407792102 2005PNAS..102..622T (Pubitemid 40282715)
38. V Tugarinov LE Kay I Ibraghimov VY Orekhov 2005 High-resolution four-dimensional H-1-C-13 NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition J Am Chem Soc 127 2767 2775 10.1021/ja044032o (Pubitemid 40327839)
39. GW Vuister GM Clore AM Gronenborn R Powers DS Garrett, et al. 1993 Increased resolution and improved spectral quality in four-dimensional C-13/C-13-separated HMQC-NOESY-HMQC spectra using pulsed-field gradients J Magn Reson Ser B 101 210 213 10.1006/jmrb.1993.1035
40. Wüthrich K (1986) NMR of proteins and nucleic acids. Wiley, New York, pp 1-292
41. YL Xia A Yee CH Arrowsmith XL Gao 2003 H-1(C) and H-1(N) total NOE correlations in a single 3D NMR experiment. N-15 and C-13 time-sharing in t(1) and t(2) dimensions for simultaneous data acquisition J Biomol NMR 27 193 203 10.1023/A:1025407905478 (Pubitemid 37185121)
42. YL Xia S Veeraraghavan Q Zhu XL Gao 2008 Fast (4, 3)D GFT-TS NMR for NOESY of small to medium-sized proteins J Magn Reson 190 142 148 10.1016/j.jmr.2007.09.015 2008JMagR.190..142X (Pubitemid 350235243)
43. DY Zheng YPJ Huang HNB Moseley R Xiao J Aramini, et al. 2003 Automated protein fold determination using a minimal NMR constraint strategy Protein Sci 12 1232 1246 10.1110/ps.0300203 (Pubitemid 36597510)
44. C Zwahlen KH Gardner SP Sarma DA Horita RA Byrd LE Kay 1998 An NMR experiment for measuring methyl-methyl NOEs in C-13-labeled proteins with high resolution J Am Chem Soc 120 7617 7625 10.1021/ja981205z (Pubitemid 28383424)