15N-1H residual dipolar coupling analysis of native and alkaline-K79A Saccharomyces cerevisiae cytochrome c

Biophysical Journal

Volumn 84, Issue 6, 2003, Pages 3917-3923

  Assfalg, Michael ^a   Bertini, Ivano ^a   Turano, Paola ^a   Mauk, A Grant ^b   Winkler, Jay R ^c   Gray, Harry B ^c  

^a UNIVERSITY OF FLORENCE   (Italy)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C; HYDROGEN; IRON; METAL ION; NITROGEN 15; NITROGEN; PROTON; SACCHAROMYCES CEREVISIAE PROTEIN;

ALKALINITY; ANISOTROPY; ARTICLE; DIPOLE; ENZYME ANALYSIS; MAGNETIC FIELD; MAGNETISM; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; OXIDATION REDUCTION STATE; PH; PROTEIN SECONDARY STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE; SACCHAROMYCES CEREVISIAE; CHEMICAL STRUCTURE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; COMPUTER SIMULATION; EVALUATION; METHODOLOGY; MUTATION; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; OXIDATION REDUCTION REACTION; PROTEIN CONFORMATION; PROTEIN FOLDING; STRUCTURE ACTIVITY RELATION;

SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

ANISOTROPY; COMPUTER SIMULATION; CYTOCHROMES C; HYDROGEN-ION CONCENTRATION; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MUTATION; NITROGEN ISOTOPES; OXIDATION-REDUCTION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTONS; SACCHAROMYCES CEREVISIAE PROTEINS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 0038101545     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(03)75119-4     Document Type: Article

References (48)

1. 562. Biochemistry. 38:8657-8670.
2. 5. Biochemistry. 37:173-184.
3. 562 as source of constraints for solution structure determination. J. Biomol, NMR. 17:295-304.
4. Assfalg, M., I. Bertini, A. Dolfi, P. Turano, A. G. Mauk, F. I. Rosell, and H. B. Gray. 2003. Structural model for an alkaline form of ferricytochrome c. J. Am. Chem. Soc. 125:2913-2922.
5. Baistrocchi, P., L. Banci, I. Bertini, P. Turano, K. L. Bren, and H. B. Gray. 1996. Three-dimensional solution structure of Saccharomyces cerevisiae reduced iso-1-cytochrome c. Biochemistry. 35:13788-13796.
6. Banci, L., I. Bertini, K. L. Bren, M. A. Cremonini, H. B. Gray, C. Luchinat, and P. Turano. 1996. The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example. J. Biol. Inorg. Chem. 1:117-126.
7. Banci, L., I. Bertini, K. L. Bren, H. B. Gray, P. Sompompisut, and P. Turano. 1997a. Solution structure of oxidized Saccharomyces cerevisiae Iso-1-cytochrome c. Biochemistry. 36:8992-9001.
8. Banci, L., I. Bertini, H. B. Gray, C. Luchinat, T. Reddig, A. Rosato, and P. Turano. 1997b. Solution structure of oxidized horse heart cytochrome c. Biochemistry. 36:9867-9877.
9. 5 at high magnetic fields: magnetic susceptibility anisotropy contributions and consequences for protein solution structure determination. J. Am. Chem. Soc. 120:12903-12909.
10. Banci, L., I. Bertini, R. Pierattelli, M. Tien, and A. J. Vila. 1995. Factoring of the hyperfine shifts in the cyanide adduct of lignin peroxidase from P. chrysosporium. J. Am. Chem. Soc. 117:8659-8667.
11. 1H Nuclear Magnetic Resonance investigation of cobalt(II) substituted carbonic anhydrase. Biophys. J. 63:530-543.
12. 15N relaxation using inverse detected two-dimensional NMR spectroscopy; the central helix is flexible. Biochemistry. 31:5269-5278.
13. Barbieri, R., I. Bertini, G. Cavallaro, Y. M. Lee, C. Luchinat, and A. Rosato. 2002. Paramagnetically induced residual dipolar couplings for solution structure determination of lanthanide-binding proteins. J. Am. Chem. Soc. 124:5581-5587.
14. Barker, P. B., I. Bertini, R. Del Conte, S. J. Ferguson, P. Hajieva, E. J. Tomlinson, P. Turano, and M. S. Viezzoli. 2001. A further clue to understanding the mobility of mitochondrial yeast cytochrome c: a 15N T1p investigation of the oxidized and reduced species. Eur. J. Biochem. 268:4468-4476.
15. Bax, A., and N. Tjandra. 1997. Are proteins even floppier than we thought? Nat. Struct. Biol. 4:254-256.
16. 1H NMR. Biochemisny. 36:11605-11618.
17. Berghuis, A. M., and G. D. Brayer. 1992. Oxidation state-dependent conformational changes in cytochrome c. J. Mol. Biol. 223:959-976.
18. Bertini. I., M. B. L. Janik, Y.-M. Lee, C. Luchinat, and A. Rosato. 2001a. Magnetic susceptibility tensor anisotropies for a lanthanide ion series in a fixed protein matrix. J. Am. Chem. Soc. 123:4181-4188.
19. Bertini, I., M. B. L. Janik, G. Liu, C. Luchinat, and A. Rosato. 2001b. Solution structure calculations through self-orientation in a magnetic field of cerium (III) substituted calcium-binding protein. J. Magn. Reson. 148:23-30.
20. Bertini, I., C. Luchinat, and G. Parigi. 2002. Magnetic susceptibility in paramagnetic NMR. Progr. NMR Spectr. 40:249-273.
21. Bothner-By, A. A. 1996. Magnetic field induced alignment of molecules. In Encyclopedia of Nuclear Magnetic Resonance. D. M. Grant, and R. K. Harris, editors. John Wiley and Sons, Chichester, UK. pp. 2932-2938.
22. Bothner-By, A. A., J. P. Domaille, and C. Gayathri. 1981. Ultra high-field NMR spectroscopy: observation of proton-proton dipolar coupling in paramagnetic bis[tolyltris(pyrazolyl)borato]cobalt(II). J. Am. Chem. Soc. 103:5602-5603.
23. Bothner-By, A. A., C. Gayathri, P. C. M. Van Zijl, and C. Maclean. 1984. Anisotropy of the diamagnetic susceptibility of benzene. Determination by high-field deuterium NMR. J. Magn. Reson. 56:456-462.
24. Bothner-By, A. A., C. Gayathri, P. C. M. Van Zijl, C. Maclean, J.-J. Lai, and K. M. Smith. 1985. High-field orientation effects in the high-resolution proton NMR spectra of diverse porphyrins. Magn. Reson. Chem. 23:935-938.
25. Clore, G. M., A. M. Gronenborn, and N. Tjandra. 1998. Direct structure refinement against residual dipolar couplings in the presence of rhombicity of unknown magnitude. J. Magn. Reson. 131:159-162.
26. Déméné, H., P. Tsan, P. Gans, and D. Marion. 2000. NMR determination of the magnetic susceptibility anisotropy of cytochrome c' of Rhodobacter capsulatus by IJHN dipolar coupling constants measurement: characterization of its monomeric state in solution. J. Phys. Chem. B. 104:2559-2569.
27. Dickerson, R. E., T. Takano, D. Eisenberg, O. B. Kallai, L. Samson, A. Cooper, and E. Margoliash. 1971. Ferricytochrome c. I. General features of the horse and bonito proteins at 2.8 Å resolution. J. Biol. Chem. 246:1511-1535.
28. Domaille, J. P. 1980. Direct measurement of the electron susceptibility anisotropy in paramagnetic complexes using high-field deuterium NMR. J. Am. Chem. Soc. 102:5392-5393.
29. Emerson, S. D., and G. N. La Mar. 1990. NMR determination of the orientation of the magnetic susceptibility tensor in cyanometmyoglobin: a new probe of steric tilt of bound ligand. Biochemistry. 29:1556-1566.
30. 15N relaxation measurements for oxidized and reduced iso-1-cytochrome c. Biochemistry. 38:4480-4492.
31. 2O in protein NMR. Application to sensitivity enhancement and NOE measurements. J. Am. Chem. Soc. 115:12593-12594.
32. 2 values in proteins. J. Magn. Reson. 97:359-375.
33. 2H NMR spectra. Chem. Phys. Lett. 58:483-486.
34. Meiler, J., N. Blomberg, M. Nilges, and C. Griesinger. 2000. A new approach for applying residual dipolar couplings as restraints in structure elucidation. J. Biomol. NMR. 16:245-252.
35. Meiler, J., J. J. Prompers, W. Peti, C. Griesinger, and R. Bruschweiler. 2001. Model-free approach to the dynamic interpretation of residual dipolar couplings in globular proteins. J. Am. Chem. Soc. 123:6098-6107.
36. Moore, G. R., and G. W. Pettigrew. 1990. Cytochromes c; Evolutionary, Structural and Physicochemical Aspects. Springer-Verlag, Berlin.
37. Palmer III, A. G., N. J. Skelton, W. J. Chazin, P. E. Wright, and M. Rance. 1992. Suppression of the effects of cross-correlation between dipolar and anisotropic chemical shift relaxation mechanisms in the measurements of spin-spin relaxation rates. Mol. Phys. 75:699-711.
38. Peng, J. W., and G. Wagner. 1992. Mapping of spectral density function using heteronuclear NMR relaxation measurements. J. Magn. Reson. 98:308-332.
39. Sass, H. J., G. Musco, S. J. Stahl, P. T. Wingfield, and S. Grzesiek. 2000. Solution NMR of proteins within polyacrylamide gels: diffusional properties and residual alignment by mechanical stress or embedding of oriented purple membranes. J. Biomol. NMR. 18:303-309.
40. Scott, R. A., and A. G. Mauk. 1996. Cytochrome c. A Multidisciplinary Approach. University Science Books, Sausalito, California.
41. Tjandra, N., and A. Bax. 1997. Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. Science. 278:1111-1114.
42. Tjandra, N., S. Grzesiek, and A. Bax. 1996. Magnetic field dependence of nitrogen-proton J splittings in 15N-enriched human Ubiquitin resulting from relaxation interference and residual dipolar coupling. J. Am. Chem. Soc. 118:6264-6272.
43. 13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat. Struct. Biol. 4:732-738.
44. Tolman, J. R., J. M. Flanagan, M. A. Kennedy, and J. H. Prestegard. 1995. Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution. Proc. Natl. Acad. Sci. USA. 92:9279-9283.
45. Tolman, J. R., J. M. Flanagan, M. A. Kennedy, and J. H. Prestegard. 1997. NMR evidence for slow collective motions in cyanometmyoglobin. Nat. Struct. Biol. 4:292-297.
46. Van Zijl, P. C. M., B. H. Ruessink, J. Bulthuis, and C. Maclean. 1984. NMR of partially aligned liquids: magnetic susceptibility anisotropies and dielectric properties. Acct. Chem. Res. 17:172-180.
47. Williams, G., N. J. Clayden, G. R. Moore, and R. J. P. Williams. 1985. Comparison of the solution and crystal structures of mitochondrial cytochrome c. Analysis of paramagnetic shifts in the nuclear magnetic resonance spectrum of ferricytochrome c. J. Mol. Biol. 183:447-460.
48. Wilson, M. T., and C. Greenwood. 1996. The alkaline transition in ferricytochrome c. In Cytochrome c. A Multidisciplinary Approach. R. A. Scott, and A. G. Mauk, editors. University Science Books, Sausalito, California. pp. 611-634.