A new strategy for structure determination of large proteins in solution without deuteration

Nature Methods

Volumn 3, Issue 11, 2006, Pages 931-937

  Xu, Yingqi ^a   Zheng, Yu ^a   Fan, Jing Song ^a   Yang, Daiwen ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

HEMOGLOBIN; HYDROGEN; MALTOSE BINDING PROTEIN;

ARTICLE; CHEMICAL LABELING; CONTROLLED STUDY; CORRELATION ANALYSIS; EXPERIMENTAL DESIGN; HYDROGEN BOND; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CARRIER PROTEINS; CRYSTALLOGRAPHY, X-RAY; DEUTERIUM; HEMOGLOBINS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SENSITIVITY AND SPECIFICITY; SOLUTIONS;

EID: 33750309630     PISSN: 15487091     EISSN: 15491676     Source Type: Journal    
DOI: 10.1038/nmeth938     Document Type: Article

References (29)

1. Wuthrich, K. NMR of Proteins and Nucleic Acids, (Wiley, New York, 1986).
2. Kainosho, M. et al. Optimal isotope labelling for NMR protein Structure determinations. Nature 440, 52-57 (2006).
3. LeMaster, D.M. & Richards, F.M. NMR sequential assignment of Escherichia coli thioredoxin utilizing random fractional deuteriation. Biochemistry 27, 142-150 (1988).
4. Grzesiek, S., Anglister, J., Ren, H. & Bax, A. Carbon-13 line narrowing by deuterium decoupling in deuterium/carbon-13/nitrogen-15 enriched proteins. Application to triple resonance 4D J connectivity of sequential amides. J. Am. Chem. Soc. 115, 4369-4370 (1993).
5. Venters, R.A., Farmer, B.T., II, Fierke, C.A. & Spicer, L.D. Characterizing the use of perdeuteration in NMR studies of large proteins: 13C, 15N and 1H assignments of human carbonic anhydrase II. J. Mol. Biol. 264, 1101-1116 (1996).
6. Pervushin, K., Riek, R., Wider, G. & Wuthrich, K. 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 (1997).
7. Yang, D.W. & Kay, L.E. TROSY triple-resonance four-dimensional NMR spectroscopy of a 46 ns tumbling protein. J. Am. Chem. Soc. 121, 2571-2575 (1999).
8. Salzmann, M., Pervushin, K., Wider, G., Senn, H. & Wuthrich, K. NMR assignment and secondary structure determination of an octameric 110 kDa protein using TROSY in triple resonance experiments. J. Am. Chem. Soc. 122, 7543-7548 (2000).
9. Tugarinov, V., Muhandiram, R., Ayed, A. & Kay, L,E. Four-dimensional NMR spectroscopy of a 723-residue protein: Chemical shift assignments and secondary structure of malate synthase G. J. Am. Chem. Soc. 124, 10025-10035 (2002).
10. Grzesiek, S., Wingfield, P., Stahl, S., Kaufman, J.D. & Bax, A. Four-dimensional 15N-separated NOESY of slowly tumbling perdeuterated 15N-enriched proteins. Application to HIV-1 Nef. J. Am. Chem. Soc. 117, 9594-9595 (1995).
11. Tjandra, N. & Bax, A. Direct measurement of distances and angles in biomolecuLes by NMR in a dilute liquid crystalline medium. Science 278, 1111-1114 (1997).
12. Delaglio, F., Kontaxis, G. & Bax, A. Protein structure determination using molecular fragment replacement and NMR dipolar couplings. J. Am. Chem. Soc. 122, 2142-2143 (2000).
13. Giesen, A.W., Homans, S.W. & Brown, J.M. Determination of protein global folds using backbone residual dipolar coupling and long-range NOE restraints. J. Biomol. NMR 25, 63-71 (2003).
14. Rosen, M.K. et al. Selective methyl group protonation of perdeuterated proteins. J. Mol. Biol. 263, 627-636 (1996).
15. Tugarinov, V., Choy, W.Y., Orekhov, V.Y. & Kay, L.E. Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc. Natl. Acad. Sci. USA 102, 622-627 (2005).
16. Yang, D., Zheng, Y., Liu, D. & Wyss, D.F. Sequence-specific assignments of methyl groups in high-molecular weight proteins. J. Am. Chem. Soc. 126, 3710-3711 (2004).
17. Zheng, Y., Giovannelli, J.L., Ho, N.T., Ho, C. & Yang, D.W. Side-chain assignments of methyl-containing residues in a uniformly 13C-labeled hemoglobin in the carbonmonoxy form. J. Biomol. NMR 30, 423-429 (2004).
18. Xu, Y., Lin, Z., Ho, C. & Yang, D.W. A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins. J. Am. Chem. Soc. 127, 11920-11921 (2005).
19. Ikura, M., Kay, L.E. & Bax, A. A novel approach for sequential assignment of proton, carbon-13, and nitrogen-15 spectra of larger proteins: Heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry 29, 4659-4667 (1990).
20. Lin, Z., Huang, H., Siu, C-H. & Yang, D.W. 1H, 13C, and 15N resonance assignments of Ca2+-free DdCAD-1: A Ca2+-dependent cell-cell adhesion molecule. J. Biomol. NMR 30, 375-376 (2004).
21. Gardner, K.H., Zhang, X., Gehring, K. & Kay, L.E. Solution NMR studies of a 42 KDa Escherichia coli maltose binding protein/β-cyclodextrin complex: Chemical shift assignments and analysis. J. Am. Chem. Soc. 120, 11738 (1998).
22. Lukin, J.A. et al. Backbone resonance assignments ofhuman adult hemoglobin in the carbonmonoxy form. J. Biomol. NMR 28, 203-204 (2004).
23. Lin, Z., Xu, Y.Q., Yang, S. & Yang, D.W. Sequence-specific assignment of aromatic resonances of uniformly 13C,15N-labeled proteins by using 13C- and 15N-edited NOESY spectra. Angew. Chem. Int. Edn. Engl. 45, 1960-1963 (2006).
24. Skrynnikov, N.R. et al. Orienting domains in proteins using dipolar couplings measured by liquid-state NMR: Differences in solution and crystal forms of maltodextrin binding protein loaded with beta-cyclodextrin. J. Mol. Biol. 295, 1265-1273 (2000).
25. Lukin, J.A. et al. Quatemary structure of hemoglobin in solution. Proc. Natl. Acad. Sci. USA 100, 517-520 (2003).
26. Wagner, G. & Wüthrich, K. Sequential resonance assignments in protein 1H NMR spectra: Basic pancreatic trypsin inhibitor. J. Mol. Biol. 155, 347-366 (1982).
27. Tugarinov, V., Kay, L.E., Ibraghimov, I. & Orekhov, V.Y. High-resotution four-dimensional 1H-13C NOE spectroscopy using methyl-TROSY, sparse data acquisition, and multidimensional decomposition. J. Am. Chem. Soc. 127, 2767-2775 (2005).
28. Coggins, B.E., Venters, R.A. & Zhou, P. Filtered back projection 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 (2005).
29. Delaglio, F. et al. NMRPipe: A multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 (1995).