Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasteurianum ferredoxin as an example

Proteins: Structure, Function and Genetics

Volumn 29, Issue 3, 1997, Pages 348-358

  Bertini, Ivano ^a   Donaire, Antonio ^a   Luchinat, Claudio ^a   Rosato, Antonio ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

Author keywords

Ferredoxin; NMR; Paramagnetic; Relaxation; Solution structure

Indexed keywords

FERREDOXIN;

ARTICLE; CLOSTRIDIUM PASTEURIANUM; ELECTRON SPIN RESONANCE; MATHEMATICAL COMPUTING; METAL BINDING; NONHUMAN; PRIORITY JOURNAL; PROTEIN DETERMINATION; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

CLOSTRIDIUM; FERREDOXINS; MAGNETICS; MATHEMATICAL COMPUTING; PROTEIN CONFORMATION; SOLUTIONS;

EID: 0030733859     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199711)29:3<348::AID-PROT8>3.0.CO;2-6     Document Type: Article

References (41)

1. Wüthrich, K. "NMR of Proteins and Nucleic Acids." New York: Wiley, 1986.
2. 1H correlation spectroscopy as a probe of metal coordination environments in metalloproteins. J. Magn. Reson. 61:579-584, 1985.
3. 113Cd coupling. J. Am. Chem. Soc. 107:3043-3045, 1985.
4. Coleman, J.E. Cadmium-113 nuclear magnetic resonance applied to metalloproteins. Methods Enzymol. 227:16-43, 1993.
5. 6 binuclear cluster. Proc. Natl. Acad. Sci. U.S.A. 87:2077-2081, 1990.
6. Utschig, L.M., Bryson, J.W., O'Halloran, T.V. Mercury-199 NMR of the metal receptor site in MerR and its protein-DNA complex. Science 268:380-385, 1995.
7. Banci, L., Bertini, I., Luchinat, C. "Nuclear and Electron Relaxation: The Magnetic Nucleus-Unpaired Electron Coupling in Solution," Weinheim: VCH, 1991.
8. Banci, L., Bertini, I., Eltis, L.D., Felli, I.C., Kastrau, D.H.W., Luchinat, C., Piccioli, M., Pierattelli, R., Smith, M. The three-dimensional structure in solution of the paramagnetic protein high-potential iron-sulfur protein I from Ectothiorhodospira halophila through nuclear magnetic resonance. Eur. J. Biochem. 225:715-725, 1994.
9. Banci, L., Bertini, I., Dikiy, A., Kastrau, D.H.W., Luchinat, C., Sompornpisut, P. The tridimensional solution structure of the reduced high potential iron sulfur protein Chromatium vinosum through NMR. Biochemistry 34:206-219, 1995.
10. Bertini, I., Dikiy, A., Kastrau, D.H.W., Luchinat, C., Sompornpisut, P. The three dimensional solution structure of the oxidized HiPIP from Chromatium vinosum through NMR: comparative analysis with the solution structure of the reduced species. Biochemistry 34:9851-9858, 1995.
11. Bertini, I., Eltis, L.D., Felli, I.C., Kastrau, D.H.W., Luchinat, C., Piccioli, M. The solution structure of oxidized HiPIP I from Ectothiorhodospira halophila: can NMR probe rearrangements associated to electron transfer processes? Chem Eur J 1:598-607, 1995.
12. 4] ferredoxin from Clostridium pasteurianum. Eur. J. Biochem. 232:192-205, 1995.
13. Banci, L., Bertini, I., Bren, K.L., Gray, H.B., Sompornpisut, P., Turano, P. The three dimensional solution structure of the cyanide adduct of Saccharomyces cerevisiae Met80Ala-iso-1-cytochrome c. Identification of ligand-residue interactions in the distal heme cavity. Biochemistry 34:11385-11398, 1995.
14. 4 centers in ferredoxins studied through proton and carbon hyperfine coupling. Sequence specific assignments of cysteines in ferredoxins from Clostridium acidi urici and Clostridium pasteurianum. J. Am. Chem. Soc. 116:651-660, 1994.
15. Banci, L., Bertini, I., Bren, K.L., Cremonini, M.A., Gray, H.B., Luchinat, C., Turano, P. The use of pseudocontact shifts to refine the solution structures of paramagnetic metalloproteins: Met80Ala cyano-cyt c as an example. JBIC 1:117-126, 1996.
16. Solomon, I. Relaxation processes in a system of two spins. Phys. Rev. 99:559-565, 1955.
17. Yu, L., Meadows, R.P., Wagner, R., Fesik, S.W., NMR studies of the FK506 binding protein bound to a spin-labeled ascomycin analog. J. Magn. Reson. Ser. B 104:77-80, 1994.
18. Kosen, P.A. Spin labeling of proteins. Methods Enzymol. 177:86-121, 1989.
19. Frederick, A.F., Kay, L.E., Prestegard, J.H. Localization of divalent ion sites in acyl carrier protein using relaxation perturbed 2D NMR. FEBS Lett. 238:43-48, 1988.
20. + from combined paramagnetic and diamagnetic NMR constraints with molecular modeling. J. Am. Chem. Soc. 107:10702-10712, 1995.
21. Granot, J. Paramagnetic relaxation in dipolar-coupled homonuclear spin systems. J. Magn. Reson. 49:257-270, 1982.
22. La Mar, G.N. and de Ropp, J.S. NMR Methodology for Paramagnetic Proteins. In: "Biological Magnetic Resonance," Vol. 12. Berliner, L.J., Reuben, J. (eds.) New York: Plenum, 1993:1-78.
23. 1 Relaxation measurements by two-dimensional NMR spectroscopy. J. Magn. Reson. 70:427-435, 1986.
24. Kay, L.E., Prestegard, J.H. Spin-lattice relaxation rates of coupled spins from 2D accordion spectroscopy. J. Magn. Reson. 77:599-605, 1988.
25. Bremer, J., Mendz, G.L., Moore, W.J. Skewed Exchange spectroscopy: two-dimensional method for the measurment of cross relaxation in 1H NMR spectroscopy. J. Am. Chem. Soc. 106:4691-4696, 1984.
26. Zhu, L., Reid, B.R. An improved NOESY simulation program for partially relaxed spectra: BIRDER. J. Magn. Reson. Ser. B 106:227-235, 1995.
27. Bertini, I., Felli, I.C., Luchinat, C., Rosato, A. A complete relaxation matrix refinement of the solution structure of a paramagnetic metalloprotein: reduced HiPIP I from E. halophila. Proteins 24:158-164, 1996.
28. 1H NMR investigation of the paramagnetic cluster environment in Pyrococcus furiosus three-iron ferredoxin: sequence-specific assignment of ligated cysteines independent of tertiary structure. Biochemistry 34:600-610, 1995.
29. 1H NMR investigation of the secondary structure, tertiary contacts and cluster environment of the four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis. J. Biomol. NMR 7:35-47, 1996.
30. Oh, B.-H., Markley, J.L. Multinuclear magnetic resonance studies of the 2Fe-2S* ferredoxin from Anabaena species strain PCC 7210. 3. Detection and characterization of hyperfine-shifted nitrogen-15 and hydrogen-1 resonances of the oxidized form. Biochemistry 29:4012-4017, 1990.
31. Güntert, P., Braun, W., Wüthrich, K. Efficient computation of three-dimensional protein structures in solution from Nuclear Magnetic Resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA. J. Mol. Biol. 217:517-530, 1991.
32. Eccles, C., Güntert, P., Billeter, M., Wüthrich, K. Efficient analysis of protein 2D NMR spectra using the software package EASY. J. Biomol. NMR 1:111-130, 1991.
33. Ernst, R.R., Bodenhausen, G., Wokaun, A. "Principles of Nuclear Magnetic Resonance in One and Two Dimensions," London: Oxford University Press, 1987.
34. Neuhaus, D., Williamson, M. "The Nuclear Overhauser Effect in Structural and Conformational Analysis." New York: VCH, 1989.
35. Keepers, J.W., James, T.L. A theoretical study of distance determinations from NMR. Two-dimensional nuclear Overhauser effect spectra. J. Magn. Reson. 57:404-426, 1984.
36. Noggle, J.H., Schirmer, R.E. "The Nuclear Overhauser Effect." New York: Academic Press, 1971.
37. Tanford, C. "Physical Chemistry of Macromolecules." New York: 1985.
38. Ishima, R., Shibata, S., Akasaka, A. General features of proton longitudinal relaxation in proteins in solution. J. Magn. Reson. 91:455-465, 1991.
39. Boelens, R., Koning, T.M.G., Van der Marel, G.A., Van Boom, J.H., Kaptein, R. Iterative procedure for structure determination from proton-proton NOEs using a full relaxation matrix approach: application to a DNA octamer. J. Magn. Reson. 82:290-308, 1989.
40. Chen, W., Zhu, X.-H., Avison, J.A., Shulman, R.G. Nuclear magnetic resonance relaxation of glycogen H1 in solution. Biochemistry 32:9417-9422, 1993.
41. 1H NMR of high potential iron-sulfur protein from the purple non-sulfur bacterium Rhodoferax fermentans. Eur. J. Biochem. 236:405-411, 1996.