Automated sequence- and stereo-specific assignment of methyl-labeled proteins by paramagnetic relaxation and methyl-methyl nuclear overhauser enhancement spectroscopy

Journal of Biomolecular NMR

Volumn 51, Issue 3, 2011, Pages 319-328

  Venditti, Vincenzo ^a   Fawzi, Nicolas L ^a   Clore, G Marius ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

Author keywords

1H 13C HMQC; Methyl group labeling; Methyl TROSY; Paramagnetic relaxation enhancement; Paramagnetic spin labeling

Indexed keywords

CYSTEINE DERIVATIVE; LEUCINE; METHYL GROUP; NITROXIDE; VALINE;

AMINO ACID SEQUENCE; ANALYTICAL PARAMETERS; ARTICLE; CARBON NUCLEAR MAGNETIC RESONANCE; CARBOXY TERMINAL SEQUENCE; HETERONUCLEAR MULTIPLE QUANTUM COHERENCE; MOLECULAR INTERACTION; NUCLEAR OVERHAUSER EFFECT; PARAMAGNETIC RELAXATION ENHANCEMENT; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SPIN LABELING; STEREOSPECIFICITY;

LEUCINE; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEINS; STEREOISOMERISM; VALINE;

EID: 80755190088     PISSN: 09252738     EISSN: 15735001     Source Type: Journal    
DOI: 10.1007/s10858-011-9559-4     Document Type: Article

References (36)

1. I Ayala R Sounier N Use P Gans J Boisbouvier 2009 An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein J Biomol NMR 43 111 119 10.1007/s10858-008-9294-7
2. A Bernini V Venditti O Spiga N Niccolai 2009 Probing protein surface accessibility with solvent and paramagnetic molecules Prog Nucl Magn Reson Spectrosc 54 278 289 10.1016/j.pnmrs.2008.10.003
3. GM Clore 2011 Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation Protein Sci 20 229 246 10.1002/pro.576
4. GM Clore J Iwahara 2009 Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes Chem Rev 109 4108 4139 10.1021/cr900033p
5. 1 rotamer populations and angles of mobile surface side chains are accurately predicted by a torsion angle database potential of mean force J Am Chem Soc 124 2866 2867 10.1021/ja017712p (Pubitemid 34249951)
6. Fawzi NL, Fleissner MR, Anthis NJ, Kálai T, Hideg K, Hubbell WL, Clore GM (2011) A rigid, small, cysteine-reactive nitroxide spin label simplifies the quantitative analysis of PRE data. J Biomol NMR. doi: 10:1007/s10858-011-9545-x
7. MR Fleissner EM Brustad T Kalai C Altenbach D Cascio FB Peters K Hideg S Peuker PG Schultz WL Hubbell 2009 Site-directed spin labeling of a genetically encoded unnatural amino acid Proc Natl Acad Sci USA 106 21637 21642 2009PNAS..10621637F 10.1073/pnas.0912009106
8. 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 (15)N, (13)C-labeled proteins J Biomol NMR 8 351 356 10.1007/BF00410333 (Pubitemid 126707873)
9. DS Garrett YJ Seok DI Liao A Peterkofsky AM Gronenborn GM Clore 1997 Solution structure of the 30 kDa N-terminal domain of enzyme I of the Escherichia coli phosphoenolpyruvate: sugar phosphotransferase system by multidimensional NMR Biochemistry 36 2517 2530 10.1021/bi962924y (Pubitemid 27106644)
10. DS Garrett YJ Seok A Peterkofsky AM Gronenborn GM Clore 1999 Solution structure of the 40,000 Mr phosphoryl transfer complex between the N-terminal domain of enzyme I and HPr Nat Struct Biol 6 166 173 10.1038/5854 (Pubitemid 29069780)
11. I Gelis AM Bonvin D Keramisanou M Koukaki G Gouridis S Karamanou A Economou CG Kalodimos 2007 Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR Cell 131 756 769 10.1016/j.cell.2007.09.039 (Pubitemid 350087200)
12. R Godoy-Ruiz C Guo V Tugarinov 2010 Alanine methyl groups as NMR probes of molecular structure and dynamics in high-molecular-weight proteins J Am Chem Soc 132 18340 18350 10.1021/ja1083656
13. 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)
14. 13C-labeled methyl groups J Am Chem Soc 122 7898 7904 10.1021/ja000350l (Pubitemid 30659411)
15. 1H paramagnetic relaxation enhancement data arising from a flexible paramagnetic group attached to a macromolecule J Am Chem Soc 126 5879 5896 10.1021/ja031580d (Pubitemid 38621427)
16. M John C Schmitz AY Park NE Dixon T Huber G Otting 2007 Sequence-specific and stereospecific assignment of methyl groups using paramagnetic lanthanides J Am Chem Soc 129 13749 13757 10.1021/ja0744753 (Pubitemid 350071805)
17. D Marion M Ikura R Tschudin A Bax 1989 Rapid recording of 2D NMR spectra without phase cycling. Application to the study of hydrogen exchange in proteins J Magn Reson 85 393 399
18. N Metropolis AW Rosenbluth MN Rosenbluth AH Teller E Teller 1953 Equations of state calculations by fast computing machines J Chem Phys 21 1087 1092 1953JChPh..21.1087M 10.1063/1.1699114
19. K Pervushin R Riek G Wider K Wuthrich 1997 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 USA 94 12366 12371 1997PNAS...9412366P 10.1073/pnas.94.23.12366 (Pubitemid 27492534)
20. 15N-labeled paramagnetic proteins J Am Chem Soc 126 2963 2970 10.1021/ja039339m (Pubitemid 38314301)
21. TL Religa R Sprangers LE Kay 2010 Dynamic regulation of archaeal proteasome gate opening as studied by TROSY NMR Science 328 98 102 2010Sci...328...98R 10.1126/science.1184991
22. CD Schwieters GM Clore 2002 Reweighted atomic densities to represent ensembles of NMR structures J Biomol NMR 23 221 225 10.1023/A:1019875223132 (Pubitemid 34982254)
23. CD Schwieters JJ Kuszewski N Tjandra GM Clore 2003 The Xplor-NIH NMR molecular structure determination package J Magn Reson 160 65 73 2003JMagR.160...65S 10.1016/S1090-7807(02)00014-9
24. CD Schwieters JY Suh A Grishaev R Ghirlando Y Takayama GM Clore 2010 Solution structure of the 128 kDa enzyme I dimer from Escherichia coli and its 146 kDa complex with HPr using residual dipolar couplings and small- and wide-angle X-ray scattering J Am Chem Soc 132 13026 13045 10.1021/ja105485b
25. I Solomon N Bloembergen 1956 Nuclear magnetic interactions in the HF molecule J Chem Phys 25 261 266 1956JChPh..25..261S 10.1063/1.1742867
26. R Sprangers LE Kay 2007 Quantitative dynamics and binding studies of the 20S proteasome by NMR Nature 445 618 622 10.1038/nature05512 (Pubitemid 46232877)
27. C Tang J Iwahara GM Clore 2006 Visualization of transient encounter complexes in protein-protein association Nature 444 383 386 2006Natur.444..383T 10.1038/nature05201 (Pubitemid 44764115)
28. N Tjandra A Bax 1997 Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium Science 278 1111 1114 1997Sci...278.1111T 10.1126/science.278.5340.1111 (Pubitemid 27517889)
29. V Tugarinov LE Kay 2003 Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods J Am Chem Soc 125 13868 13878 10.1021/ja030345s (Pubitemid 37386061)
30. V Tugarinov PM Hwang JE Ollerenshaw LE Kay 2003 Cross-correlated relaxation enhanced 1H-13C 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)
31. 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 2005PNAS..102..622T 10.1073/pnas.0407792102 (Pubitemid 40282715)
32. V Tugarinov V Kanelis LE Kay 2006 Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy Nat Protoc 1 749 754 10.1038/nprot.2006.101
33. EL Ulrich H Akutsu JF Doreleijers Y Harano YE Ioannidis J Lin M Livny S Mading D Maziuk Z Miller E Nakatani CF Schulte DE Tolmie R Kent Wenger H Yao JL Markley 2008 BioMagResBank Nucleic Acids Res 36 D402 D408 10.1093/nar/gkm957 (Pubitemid 351149757)
34. A Velyvis YR Yang HK Schachman LE Kay 2007 A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylase Proc Natl Acad Sci USA 104 8815 8820 2007PNAS..104.8815V 10.1073/pnas.0703347104 (Pubitemid 47175394)
35. 13C separated HMQC-NOESY-HMQC spectra using pulsed field gradients. J Magn Reson Ser B 101:210-213
36. Y Xu M Liu PJ Simpson R Isaacson E Cota J Marchant D Yang X Zhang P Freemont S Matthews 2009 Automated assignment in selectively methyl-labeled proteins J Am Chem Soc 131 9480 9481 10.1021/ja9020233