Interpretation of chemical shifts and coupling constants in macromolecules

Current Opinion in Structural Biology

Volumn 10, Issue 2, 2000, Pages 197-203

  Case, David A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEIC ACID; PROTEIN;

ANISOTROPY; HYDROGEN BOND; MOLECULAR INTERACTION; NUCLEIC ACID STRUCTURE; PRIORITY JOURNAL; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; QUANTUM THEORY; REVIEW;

EID: 0034031647     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(00)00068-3     Document Type: Review

References (79)

1. McWeeny R. Methods of Molecular Quantum Mechanics. 2:1989;Academic Press, San Diego.
2. Helgaker T., Jaszunski M., Ruud K. Ab initio methods for the calculation of NMR shielding and indirect spin-spin coupling constants. Chem Rev. 99:1999;293-352. A thorough review of the fundamental theories and practical applications of quantum chemistry to the calculation of NMR shielding and indirect spin-spin coupling constants.
3. Wishart D.S., Nip A.M. Protein chemical shift analysis: a practical guide. Biochem Cell Biol. 76:1998;153-163. A recent guide to chemical shift referencing and to the use of empirical models for their interpretation in proteins.
4. Bühl M., Kaupp M., Malkina O.L., Malkin V.G. The DFT route to NMR chemical shifts. J Comput Chem. 20:1998;91-105. An overview of one successful density functional theory based approach to chemical shifts. This method modifies 'pure' Kohn-Sham energy denominators in an ad hoc, but numerically useful, manner.
5. Wilson P.J., Amos R.D., Handy N.C. Density functional predictions for magnetizabilities and nuclear shielding constants. Mol Phys. 97:1999;757-768.
6. Adamo C., Barone V. Toward chemical accuracy in the computation of NMR shieldings: the PBE0 model. Chem Phys Lett. 298:1998;113-119.
7. Bienati M., Adamo C., Barone V. Performance of a new hybrid Hartree-Fock/Kohn-Sham model (B98) in predicting vibrational frequencies, polarisabilities and NMR chemical shifts. Chem Phys Lett. 311:1999;69-76.
8. 13C-NMR shielding values. J Comput Chem. 20:1999;1299-1303.
9. Baldridge K.K., Siegel J.S. Correlation of empirical δ(TMS) and absolute NMR chemical shifts predicted by ab initio computations. J Phys Chem A. 103:1999;4038-4042.
10. Sitkoff D., Case D.A. Density functional calculations of proton chemical shifts in model peptides. J Am Chem Soc. 119:1997;12262-12273.
11. 13C shifts in peptides.
12. 15N amide tensors.
13. 13C chemical shifts. J Am Chem Soc. 120:1998;4230-4231.
14. Dejaegere A.P., Case D.A. Density functional study of ribose and deoxyribose chemical shifts. J Phys Chem A. 102:1998;5280-5289.
15. Malkina O.L., Salahub D.R., Malkin V.G. Nuclear magnetic resonance spin-spin coupling constants from density functional theory: problems and results. J Chem Phys. 105:1996;8793-8800.
16. 13C spin coupling behavior in aldofuranosyl rings from density functional theory. J Phys Chem A. 103:1999;3783-3795.
17. Case D.A. The use of chemical shifts and their anisotropies in biomolecular structure determination. Curr Opin Struct Biol. 8:1998;624-630.
18. Cornilescu G., Delaglio F., Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J Biomol NMR. 13:1999;289-302. The authors discuss how searching a database for shift patterns among several adjacent residues provides useful information about backbone dihedral angles.
19. 1H chemical shift calculations for use in structure refinement. J Biomol NMR. 10:1997;337-350.
20. Dejaegere A., Bryce R.A., Case D.A. An empirical analysis of proton chemical shifts in nucleic acids. Facelli J.C., de Dios A.C. Modeling NMR Chemical Shifts. Gaining Insights into Structure and Environment. 1999;194-206 American Chemical Society, Washington DC.
21. Werbelow L.G. Relaxation processes: cross correlation and interference terms. Grant D.M., Harris R.K. Encyclopedia of Nuclear Magnetic Resonance. 1996;4072-4078 John Wiley, London.
22. 2 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. 94:1997;12366-12371.
23. 15N chemical shift anisotropy from quantitative measurement of relaxation interference kinetics. J Am Chem Soc. 118:1996;6986-6991.
24. ••]).
25. 15N chemical shift anisotropy values. Implications for the extraction of order parameters and other dynamical information are discussed.
26. Boyd J., Redfield C. Characterization of the N-15 chemical shift anisotropy from orientation-dependent changes to N-15 chemical shifts in dilute bicelle solutions. J Am Chem Soc. 121:1999;7441-7442. Chemical shift changes for lysozyme in partially oriented samples appear to be consistent with a fairly uniform chemical shift anisotropy (CSA) tensor for individual amides; however, more extensive data would be needed to extract CSA parameters for individual residues.
27. 15N dipolar interaction: correlation with secondary structure. J Am Chem Soc. 119:1997;8985-8990.
28. 15N-enriched proteins. Correlation with hydrogen bond length. J Am Chem Soc. 119:1997;8076-8082.
29. 2H dipolar NMR study of the water molecule in crystalline hydrates. J Am Chem Soc. 120:1998;13187-13193.
30. Sitkoff D., Case D.A. Theories of chemical shift anisotropies in proteins and nucleic acids. Prog NMR Spectrosc. 32:1998;165-190.
31. α chemical shift anisotropies in proteins correlate with secondary structure. J Am Chem Soc. 119:1997;9576-9577.
32. Fischer M.W., Zeng L., Majumdar A., Zuiderweg E.R. Characterizing semilocal motions in proteins by NMR relaxation studies. Proc Natl Acad Sci USA. 95:1998;8016-8019.
33. Pang Y., Wang L., Pellecchia M., Kurochkin A.V., Zuiderweg E.R.P. Evidence for extensive anisotropic local motions in a small enzyme using a new method to determine NMR cross-correlated relaxation rates in the absence of resolved scalar couplings. J Biomol NMR. 14:1999;297-306.
34. Norwood T., Tillett M., Lian L. Influence of cross-correlation between the chemical shift anisotropies of pairs of nuclei on multiple-quantum relaxation rates in macromolecules. Chem Phys Lett. 300:1999;429-434.
35. Cornilescu G., Marquardt J.L., Ottiger M., Bax A. Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase. J Am Chem Soc. 120:1998;6836-6837.
36. 13CO chemical shift anisotropy relaxation mechanisms by multiple quantum NMR. J Am Chem Soc. 121:1999;9165-9170.
37. 13C-labeled DNA duplex. J Magn Reson. 136:1999;169-175.
38. 13C anisotropies in the bases are smaller than in benzene.
39. Damberg P., Jarvet J., Allard P., Grslund A. Quantitative estimation of the magnitude and orientation of the CSA tensor from field dependence of longitudinal NMR relaxation rates. J Biomol NMR. 15:1999;27-37.
40. Bertini I., Turano P., Vila A.J. Nuclear magnetic resonance of paramagnetic metalloproteins. Chem Rev. 93:1993;2833-2932.
41. Gueron M. Nuclear relaxation in macromolecules by paramagnetic ions: a novel mechanism. J Magn Reson. 19:1975;58-66.
42. Bertini I., Luchinat C., Tarchi D. Are true scalar proton-proton connectivities ever measured in COSY spectra of paramagnetic molecules? Chem Phys Lett. 203:1993;445-449.
43. Ghose R., Prestegard J.H. Electron spin-nuclear spin cross-correlation effects on multiplet splittings in paramagnetic proteins. J Magn Reson. 128:1997;138-143.
44. McConnell H.M. Theory of nuclear magnetic shielding in molecules. I. Long-range dipolar shielding of protons. J Chem Phys. 27:1957;226-229.
45. Banci L., Bertini I., Gori Savellini G., Romagnoli A., Turano P., Cremonini M.A., Luchinat C., Gray H.B. Pseudocontact shifts as constraints for energy minimization and molecular dynamics calculations on solution structures of paramagnetic metalloproteins. Proteins. 29:1997;68-76.
46. Tu K., Gochin M. Structure determination by restrained molecular dynamics using NMR pseudocontact shifts as experimentally determined constraints. J Am Chem Soc. 121:1999;9276-9285.
47. Volkman B.F., Wilkens S.J., Lee A.L., Xia B., Westler W.M., Beger R., Markley J.L. Redox-dependent magnetic alignment of Clostridium pasteurianum rubredoxin: measurement of magnetic susceptibility anisotropy and prediction of pseudocontact shift contributions. J Am Chem Soc. 121:1999;4677-4683.
48. 15N labeled biomolecules characterized through cross-correlation rates: applications to paramagnetic proteins. J Biomol NMR. 12:1998;509-521.
49. Boisbouvier J., Gans P., Blackledge M., Brutscher B., Marion D. Long range structural information in NMR studies of paramagnetic molecules from electron spin-nuclear spin cross-correlated relaxation. J Am Chem Soc. 121:1999;7700-7701. Comparisons of cross-correlated relaxation in paramagnetic and diamagnetic forms of cytochrome c′ were used to extract long-range structural information. Unlike the analysis of pseudocontact shifts, the effect does not require an anisotropic metal center.
50. Altona C. Vicinal coupling constants & conformation of biomolecules. Grant D.M., Harris .K.R Encyclopedia of Nuclear Magnetic Resonance. 1996;4909-4922 John Wiley, London.
51. 31P) can be used in RNA structure determination.
52. 13C three-bond J couplings measured by three-dimensional heteronuclear NMR. How planar is the peptide bond? J Am Chem Soc. 119:1997;6360-6368.
53. 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles. J Biomol NMR. 14:1999;1-12. This paper, together with [52], provides empirical Karplus curves for all six three-bond couplings about φ on the basis of data from ubiquitin and ferredoxin.
54. Brüschweiler R., Case D.A. Adding harmonic motion to the Karplus relation for spin-spin couplings. J Am Chem Soc. 116:1994;11199-11200.
55. Theis K., Dingley A.J., Hoffmann A., Omichinski J.G., Grzesiek S. Determination of backbone nitrogen-nitrogen J correlations in proteins. J Biomol NMR. 10:1997;403-408.
56. 15N-enriched human ubiquitin. J Am Chem Soc. 117:1995;1810-1813.
57. 15N labeled proteins: application to the photoactive yellow protein. J Biomol NMR. 10:1997;301-306.
58. 13C-labeled proteins. J Am Chem Soc. 120:1998;6824-6825.
59. NCγ couplings. J Am Chem Soc. 119:1997;1803-1804.
60. 1 torsion angle preferences. J Mol Biol. 280:1998;867-878.
61. 15N NMR spectroscopy. J Mol Biol. 288:1999;705-724. This paper shows how coupling constants can be used to gain novel conformational information on unfolded or partially folded proteins.
62. Tjandra N., Bax A. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 278:1997;1111-1114.
63. α coupling constants as restraints in MD simulations. J Am Chem Soc. 114:1992;8283-8284.
64. CαHβ coupling constants as a probe for protein backbone conformation. J Biomol NMR. 3:1993;67-80.
65. β couplings in polypeptides correlate with backbone conformation. J Am Chem Soc. 2000;. in press.
66. NC' scalar couplings. J Am Chem Soc. 121:1999;1601-1602.
67. HC' in a perdeuterated protein. J Magn Reson. 140:1999;510-512.
68. NC' connectivities across hydrogen bonds in a 30 kDa protein. J Biomol NMR. 14:1999;181-184.
69. Cornilescu G., Hu J., Bax A. Identification of the hydrogen bonding network in a protein by scalar couplings. J Am Chem Soc. 121:1999;2949-2950.
70. NC' and hydrogen bond length in proteins. J Am Chem Soc. 121:1999;6275-6279.
71. Scheurer C., Brüschweiler R. Quantum-chemical characterization of nuclear spin - spin couplings across hydrogen bonds. J Am Chem Soc. 121:1999;8661-8662. Density functional calculations were used to map out the expected distance and angle dependence of spin-spin couplings across a hydrogen bond.
72. NN couplings. J Am Chem Soc. 120:1998;8293-8297.
73. Pervushin K., Ono A., Wüthrich K. NMR scalar couplings across Watson-Crick base pair hydrogen bonds in DNA observed by transverse relaxation-optimized spectroscopy. Proc Natl Acad Sci USA. 95:1998;14147-14151.
74. Wöhnert J., Dingley A., Stoldt M., Görlach M., Grzesiek S., Brown L. Direct identification of NH.N hydrogen bonds in non-canonical base pairs of RNA by NMR spectroscopy. Nucleic Acids Res. 27:1999;3104.
75. 15N nuclei with widely separated chemical shifts. J Biomol NMR. 14:1999;67-70.
76. Dingley A.J., Masse J.E., Peterson R.D., Barfield M., Feigon J., Grzesiek S. Internucleotide scalar couplings across hydrogen bonds in Watson-Crick and Hoogsteen base pairs of a DNA triplex. J Am Chem Soc. 121:1999;6019-6027. This paper includes quantum calculations in good agreement with observed couplings across hydrogen bonds.
77. Rüdisser S., Pelton J.G., Tinoco I. Jr. Assignment of cytosine N3 resonances in nucleic acids via intrabase three-bond coupling to amino proteins. J Biomol NMR. 15:1999;173-176.
78. Majumdar A., Kettani A., Skripkin E., Patel D.J. Observation of internucleotide NH-H hydrogen bonds in the absence of directly detectable protons. J Biomol NMR. 15:1999;207-211.
79. Griesinger C., Hennig M., Marino J.P., Reif B., Richter C., Schwalbe H. Methods for the determination of torsion angle restraints in biomacromolecules. Krishna R.R., Berliner L.J. Biological Magnetic Resonance, Volume 16: Modern Techniques in Protein NMR. 1999;259-367 Kluwer Academic, New York.