Protein chemical shift analysis: A practical guide

Biochemistry and Cell Biology

Volumn 76, Issue 2-3, 1998, Pages 153-163

  Wishart, David S ^a   Nip, Alex M ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Chemical shift; NMR; Prediction; Protein; Structure

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; CARBON NUCLEAR MAGNETIC RESONANCE; PREDICTION; PROTEIN ANALYSIS; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; REVIEW; SPECTROMETER;

EID: 0032454094     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o98-038     Document Type: Review

References (57)

1. Bax, A., and Subramanian, J. 1986. Sensitivity-enhanced two-dimensional shift correlation NMR spectroscopy. J. Magn. Reson. 67: 565-570.
2. Beger, R.D., and Bolton, P.H. 1997. Protein phi and psi dihedral restrainst determined from multidimensional hypersurface correlations of backbone chemical shifts and their use in the determination of protein tertiary structures. J. Biomol. NMR, 10: 129-142.
3. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.V., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M.J. 1977. The protein data bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112: 535-542.
4. 15N "random coil" chemical shifts. J. Am. Chem. Soc. 116: 8466-8469.
5. 1H-NMR parameters of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers, 18: 285-297.
6. Case, D.A., Dyson, H.J., and Wright, P.E. 1994. Use of chemical shifts and coupling constants in nuclear magnetic resonance structural studies on peptides and proteins. Methods Enzymol. 239: 392-416.
7. 13C alpha heteronuclear NOE data in monitoring a protein NMR structure refinement. J. Biomol. NMR, 5: 161-172.
8. de Dios, A.C., Pearson, J.G., and Oldfield, E. 1993. Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach. Science (Washington, D.C.), 260: 1491-1496.
9. Dalgarno, D.C., Levine, B.A., and Williams, R.J.P. 1983. Structural information from NMR secondary chemical shifts of peptide αC-H protons in proteins. Biosci. Rep. 3: 443-452.
10. DeMarco, A. 1977. pH dependence of internal references. J. Magn. Reson. 26: 527-528.
11. 15N chemical shifts of backbone amides in bovine pancreatic trypsin inhibitor and apamin. J. Am. Chem. Soc. 111: 7716-7722.
12. 13C chemical shifts. J. Biomol. NMR, 4: 455-458.
13. Gronwald, W., Boyko, R.F., Sonnichsen, F.D., Wishart, D.S., and Sykes, B.D. 1997. ORB, a homology based program for the prediction of NMR chemical shifts. J. Biomol. NMR, 10: 165-179.
14. 15N-enriched proteins. J. Biomol NMR, 3: 185-204.
15. Herranz, J., Gonzalez, C., Rico, M., Nieto, J.L., Santoro, J., Jimenez, M.A., Bruix, M., Neira, J.L., and Blanco, F.J. 1992. Peptide group chemical shift computation. Magn. Reson. Chem. 30: 1012-1018.
16. 15N spectra of proteins: heteronuclear triple-resonance three-dimensional NMR spectroscopy. Application to calmodulin. Biochemistry, 29: 4659-4667.
17. 13C chemical shifts in the model peptide N-acetyl-N′methylglycinamide. J. Am. Chem. Soc. 115: 10883-10887.
18. Jimenez, M.A., Blanco, F.J., Rico, M., Santoro, J., Herranz, J., and Nieto, J.L. 1992. Periodic properties of proton conformational shifts in isolated protein helices. Eur. J. Biochem. 207: 39-49.
19. 13Cα and 13Cβ chemical shifts on protein structure determination by NMR. J. Magn. Reson. Ser. B, 106: 92-96.
20. 13Cβ chemical shifts on protein structure determination by NMR. J. Magn. Reson. Ser. B, 107: 293-297.
21. Laws, D.D., de Dios, A.C., and Oldfield, E. 1993. NMR chemical shifts and structure refinement in proteins. J. Biomol. NMR, 3: 607-612.
22. 15N NMR. J. Magn. Reson. Ser. B, 108: 274-275.
23. 15N NMR chemical shifts in protein and secondary structure. J. Biomol. NMR, 4: 341-348.
24. Le, H., Pearson, J.G., de Dios, A.C., and Oldfield, E. 1995. Protein structure refinement and prediction via NMR chemical shifts and quantum chemistry. J. Am. Chem. Soc. 117: 3800-3807.
25. 15N NMR study of gramicidin S in water and organic solvents. J. Am Chem. Soc. 106: 1939-1943.
26. 19F spectra. J. Magn. Reson. Ser. B, 113: 177-178.
27. 1H chemical shifts obtained as a function of temperature and trifluoroethanol concentration for the peptide series GGXGG. J. Biomol. NMR, 5: 14-24.
28. 15N NMR assignments and global folding pattern. Biochemistry, 32: 13818-13829.
29. Oldfield, E. 1995. Chemical shifts and three-dimensional protein structures. J. Biomol. NMR, 5: 217-225.
30. Osapay, K., and Case, D.A. 1991. A new analysis of proton chemical shifts in proteins. J. Am. Chem. Soc. 113: 9436-9444.
31. Osapay, K., and Case, D.A. 1994. Analysis of proton chemical shifts in regular secondary structure of proteins. J. Biomol. NMR, 4: 215-230.
32. Osapay, K., Theriault, Y., Wright, P.E., and Case, D.A. 1994. Solution structure of carbonmonoxy myoglobin determined from nuclear magnetic resonance distance and chemical shift contstraints. J. Mol. Biol. 244: 183-197.
33. Pardi, A., Wagner, G., and Wuthrich, K. 1983. Protein conformation and proton nuclear magnetic resonance chemical shifts. Eur. J. Biochem. 137: 445-454.
34. Pastore, A., and Saudek, V. 1990. The relationship between chemical shift and secondary structure in proteins. J. Magn. Reson. 90: 165-176.
35. Pearson, J.T., Le, H., Sanders, L.K., Godbout, N., Havlin, R.H., and Oldfield, E. 1997. Predicting chemical shifts in proteins: structure refinement of valine residues by using ab initio and empirical geometry optimizations. J. Am. Chem. Soc. 119: 11941-11950.
36. Plaxco, K.W., Morton, C.J., Grimshaw, S.B., Jones, J.A., Pitkeathly, M., and Campbell, I.D., and Dobson, C.M. 1997. The effects of guanidine hydrochloride on the random coil conformations and NMR chemical shifts of the peptide series GGXGG. J. Biomol. NMR, 10: 221-230.
37. 15N resonance assignment of Fusarium solani pisi cutinase and preliminary features of the structure in solution. Protein Sci. 6: 2375-2384.
38. Richarz, R., and Wuthrich, K. 1978. Carbon-13 NMR chemical shifts of the common amino acid residues measured in aqueous solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH. Biopolymers, 17: 2133-2141.
39. 13C nuclear magnetic resonance chemical shifts. J. Am. Chem. Soc. 113: 5490-5492.
40. Sternlicht, H., and Wilson, D. 1967. Magnetic resonance studies of macromolecules. 1. Aromatic-methyl interactions and helical structure effects in lysozyme. Biochemistry, 6: 2881-2892.
41. Szilagyi, L. 1995. Chemical shifts in proteins come of age. Prog. Nucl. Magn. Reson. Spectrosc. 27: 325-443.
42. Taylor, D.A., Sack, J.S., Maune, J.F., Beckingham, K., and Quiocho, F.A. 1991. Structure of a recombinant calmodulin from Drosophila melanogaster refined at 2.2-Å resolution. J. Biol. Chem. 266: 21375-21380.
43. 13C chemical shifts of amino acids in aqueous solution containing organic solvents: application to the seconday structure characterization of peptides in aqueous trifluorethanol solution. J. Biomol. NMR, 4: 47-59.
44. 13Ca chemical shift anisotropy in proteins correlate with secondary structure. J. Am. Chem. Soc. 119: 9576-9577.
45. Williamson, M.P., and Asakura, T. 1997. Protein chemical shifts. Methods Mol. Biol. 60: 53-59.
46. Williamson, M.P., Asakura, T., Nakamura, E., and Demura, M. 1992. A method for the calculation of protein α-CH chemical shifts. J. Biomol. NMR, 2: 93-98.
47. 1H NMR chemical shifts to measure the quality of protein structures. J. Mol. Biol. 247: 541-546.
48. Wishart, D.S., and Sykes, B.D. 1994a. Chemcal shifts as a tool for structure determination. Methods Enzymol. 239: 363-392.
49. 13C chemical-shift data. J. Biomol. NMR, 4: 171-180.
50. Wishart, D.S., Sykes, B.D., and Richards, F.M. 1991a. Relationship betweeen nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222: 311-333.
51. 1H NMR spectroscopy. FEBS Lett. 293: 72-80.
52. Wishart, D.S., Sykes, B.D., and Richards, F.M. 1992. The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy. Biochemistry, 31: 1647-1651.
53. 15N chemical shift referencing in biomolecular NMR. J. Biomol. NMR, 6: 135-140.
54. 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects. J. Biomol. NMR, 5: 67-81.
55. 13C chemical shift prediction using the BioMagResBank. J. Biomol. NMR, 10: 329-336.
56. Witanowski, M., Stefaniuk, L., and Webb, G.A. 1993. Nitrogen NMR spectroscopy. Annu. Rep. NMR Spectrosc. 25: 1-480.
57. Wuthrich, K. 1986. NMR of proteins and nucleic acids. John Wiley & Sons, Inc., New York.