New applications of paramagnetic NMR in chemical biology

Current Opinion in Chemical Biology

Volumn 3, Issue 2, 1999, Pages 145-151

  Bertini, Ivano ^a   Luchinat, Claudio ^a  

^a UNIVERSITY OF FLORENCE   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ANISOTROPY; ELECTRON TRANSPORT; MAGNETIC FIELD; METHODOLOGY; NUCLEAR MAGNETIC RESONANCE; OXIDATION REDUCTION REACTION; PROTEIN FOLDING; PROTEIN STABILITY; REVIEW;

EID: 0033120479     PISSN: 13675931     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1367-5931(99)80026-X     Document Type: Article

References (68)

1. Bertini I, Luchinat C: Coordination Chemisry Reviews, vol 150. Edited by ABP Lever. Amsterdam: Elsevier Science Ltd; 1996.
2. McConnell HM, Chesnut DB: Theory of isotropic hyperfine interactions in π-electron radicals. J Chem Phys 1958, 28:107-117.
3. Karplus M: Contact electron-spin coupling of nuclear magnetic moments. J Chem Phys 1959, 30:11-15.
4. 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 1994, 116:651-660.
5. Barry CD, Glasel JA, Williams RJP, Xavier AV: Quantitative determination of conformations of flexible molecules in solution using lanthanide ions as nuclear magnetic resonance probes: Application to adenosine-5′-monophosphate. J Mol Biol 1974, 84:471-490.
6. Banci L, Bertini I, Bren KL, Cremonini MA, Gray HB, Luchinat C, Turano P: The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome c as an example. J Biol Inorg Chem 1996, 1:117-126.
7. Cohn M, Mildvan AS: Aspects of enzyme mechanisms studied by spin relaxation induced by paramagnetic probes. Adv Enzymol 1970, 33:1-12
8. 15N signals of reduced Clostridium pasteurianum rubredoxin: Oxidation state-dependent changes in chemical shifts and relaxation rates. J Biomol NMR 1997, 10:411-412.
9. Bertini I, Donaire A, Luchinat C, Rosato A: Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasterianum ferredoxin as an example. Proteins Struct Funct Genet 1997, 29:348-358. The possibility of using nuclear relaxation enhancements caused by hyperfine coupling is assessed. The leveling effects of cross-relaxation are evaluated through a relaxation matrix analysis. The structure of ferredoxin is sensibly improved.
10. Bothner-By AA, Domaille JP, Gayathri C: Ultra high-field NMR spectroscopy: Observation of proton-proton dipolar coupling in paramagnetic bis[tolyltris(pyrazolyl)borato]cobalt(II). J Am Chem Soc 1981, 103:5602-5603.
11. zz with paramagnetic ions. J Am Chem Soc 1996, 118:269-270.
12. Giacometti G, Nordio PL, Rigatti G, Segre U: Theory of nuclear magnetic resonance paramagnetic shifts in liquid crystalline solvents. J Chem Soc Faraday Trans 1973, 69:1815-1820.
13. Banci L, Bertini I, Huber JG, Spyroulias GA, Turano P: Solution structure of reduced horse heart cytochrome c. J Biol Inorg Chem 1999, in press.
14. Banci L, Bertini I, Bren KL, Gray HB, Sompornpisut P, Turano P: Solution structure of oxidized Saccharomyces cerevisiae Iso-1-cytochrome c. Biochemistry 1997, 36:8992-9001. This structure of this enzyme is obtained using both nuclear Overhausen effects and pseudocontact shift analysis. The approach is such that iron is at the origin of the χ-tensor axes (see Equation 1 ); a single average χ-tensor is obtained by the family of conformers. The PCSHIFT module of AMBER [43•] was used. The structure is well refined using only protons.
15. Banci L, Bertini I, Gray HB, Luchinat C, Reddig T, Rosato A, Turano P: Solution structure of oxidized horse heart cytochrome c. Biochemistry 1997, 36:9867-9877. This structure, obtained through nuclear Overhausen effects and pseudo-contact shifts (pcs), leaves the iron free to find its position in each conformer, its structural constraints being defined by pcs. The pcs are also used in energy minimization. The quality of the structure is satisfactory.
16. Baistrocchi P, Banci L, Bertini I, Turano P, Bren KL, Gray HB: Three-dimensional solution structure of Saccharomyces cerevisiae reduced iso-1-cytochrome c. Biochemistry 1996, 35:13788-13796.
17. 6 the from green alga Monoraphidium braunii. J Biol Inorg Chem 1996, 1:330-340.
18. 6 from the green alga Monoraphidium braunii. Biochemistry 1998, 37:4831-4343.
19. 5 is described here using a classical procedure involving both nuclear Overhausen effects and pseudocontact shifts. The structure is well-resolved and permits a meaningful comparison with the reduced structure.
20. 5. Eur J Biochem 1997, 249:270-279.
21. Banci L, Bertini I, Eltis LD, Felli IC, Kastrau DHW, 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 hatophila through nuclear magnetic resonance. Eur J Biochem 1994, 225:715-725.
22. Bertini I, Eltis LD, Felli IC, Kastrau DHW, Luchinat C, Piccioli M: The solution structure of oxidized HiPIP I from Ectothiorhodospira halophila, can NMR probe rearrangements associated to electron transfer processes? Chemistry - Eur J 1995, 1:598-607.
23. Bertini I, Dikiy A, Kastrau DHW, 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 1995, 34:9851-9858.
24. Banci L, Bertini I, Dikiy A, Kastrau DHW, Luchinat C, Sompornpisut P: The three-dimensional solution structure of the reduced high potential iron sulfur protein Chromatium vinosum through NMR. Biochemistry 1995, 34:206-219.
25. Berghuis AM, Brayer GD: Oxidation state-dependent conformational changes in cytochrome c. J Mol Biol 1992, 223:959-976.
26. Malmström BG: Cytochrome oxidase: Pathways for electron tunneling and proton transfer. J Biol Inorg Chem 1998, 3:339-343.
27. Walker FA, Emrick D, Rivera JE, Hanquet BJ, Buttlaire DH: Effect of heme orientation on the reduction potential of cytochrome b5. J Am Chem Soc 1988, 110:6234-6240.
28. 15N rotating frame NMR relaxation measurements: Biological implications. Biochemistry 1999, in press
29. 1p shows evidence of chemical exchange.
30. Bai YW, Sosnick TR, Mayne L, Englander SW: Protein folding intermediates: Native-state hydrogen exchange. Science 1995, 269:192-197.
31. Winkler JR, Wittung P, Leckner J, Malmström BG, Gray HB: Effects of folding on metalloprotein active sites. Proc Natl Acad Sci USA 1997, 94:4246-4249.
32. Louie GV, Brayer GD: High-resolution refinement of yeast iso-1-cytochrome c and comparison with other eukaryotic cytochromes. J Mol Biol 1990, 214:527-555.
33. Pelletier H, Kraut J: Crystal structure of a complex between electron transfer partners, cytochrome c peroxidase and cytochrome c. Science 1992, 258:1748-1755.
34. A site in cytochrome c oxidase. FEBS Lett 1990, 268:274-276.
35. Iwata S, Ostermeier C, Ludwig B, Michel H: Structure at 2.8 Å resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 1995, 376:660-669.
36. 3: An NMR investigation of the paramagnetic protein. J Am Chem Soc 1996, 46:11658-11659.
37. A center of cytochrome oxidase. FEBS Lett 1996, 394:340-344.
38. 2H NMR spectroscopy is discussed. The reasons for short electronic relaxation times are discussed, as well as the peculiar electronic structure seen.
39. A site within the thermal bath.
40. McConnell HM, Robertson RE: Isotropic nuclear resonance shifts. J Chem Phys 1958, 29:1361-1365.
41. Kurland RJ, McGarvey BR: Isotropic NMR shifts in transition metal complexes: Calculation of the Fermi contact and pseudocontact terms. J Magn Reson 1970, 2:286-301.
42. Banci L, Bertini I, Cremonini MA, Gori Savellini G, Güntert P, Luchinat C, Wüthrich K: Pseudocontact shifts in paramagnetic metalloproteins as structural constraints for NMR structure calculations using torsion angle dynamics. J Biomol NMR 1998, 12:553-557. The rationale for the use of pseudocontact shifts in structural determinations is discussed and incorporated into the torsion angle dynamics DYANA package.
43. Banci L, Bertini I, Gori Savellini G, Romagnoli A, Turano P, Cremonini MA, Luchinat C, Gray HB: The pseudocontact shifts as constraints for energy minimization and molecular dynamic calculations on solution structures of paramagnetic metalloproteins. Proteins Struct Funct Genet 1997, 29:68-76. A module within the AMBER program was developed and tested in order to perform energy minimization by keeping pseudocontact shifts as constraints.
44. Güntert P, Mumenthaler C. Wüthrich K: Torsion angle dynamics for NMR structure calculation with the new program DYANA. J Mol Biol 1997, 273:283-298.
45. Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE, Ferguson DM, Seibel GL, Singh UC, Weiner PK, Kollman PA: AMBER 5.0. San Francisco: University of California; 1997.
46. Gochin M: Nuclear magnetic resonance characterization of a paramagnetic DNA-drug complex with high spin cobalt; assignment of the 1H and 31P NMR spectra, and determination of electronic, spectroscopic and molecular properties. J Biomol NMR 1998, 12:243-257.
47. Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH: Nuclear magnetic dipole interactions in field-oriented proteins: Information for structure determination in solution. Proc Natl Acad Sci USA 1995, 92:9279-9283.
48. 13C couplings in the structure determination of magnetically oriented macromolecules in solution. Nat Struct Biol 1997, 4:732-738.
49. Tjandra N, Bax A: Direct measurement of distances and angles in biomolecules by NMR in a diluite liquid crystalline medium. Science 1997, 278:1111-1114.
50. 5. The partial orientation of this protein is relatively large because of the large magnetic susceptibility anisotropy. For the first time, rhombic anisotropy is included in the calculation. A molecular magnetic susceptibility tensor is defined as different from the paramagnetic susceptibility tensor due to the metal ion and is related to the pseudocontact shifts. The tensorial difference between the two tensors is the diamagnetic susceptibility tensor, which is also found experimentally by monitoring the residual dipolar couplings of the reduced diamagnetic protein.
51. Vold RR, Prosser PS: Magnetically oriented phospholipid bilayered micelles for structural studies of polypeptides. Does the ideal bicelle exist? J Magn Reson Ser B 1996, 113:267-271.
52. Bax A, Tjandra N: High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium. J Biomol NMR 1997, 10:289-292.
53. Sitkoff D, Case DA: Theories of chemical shift anisotropies in proteins and nucleic acids. Progr NMR Spectrosc 1998, 32:165-190.
54. 1p analyses were performed to relate structure and dynamics with the partial unfolding. A role of the polymetallic center in the folding stability is evident.
55. 4 protein: The role of the cofactor in protein folding. Biochemistry 1999, in press.
56. Taler G, Schejter A, Navon G, Vig I, Margoliash E: The nature of the thermal equilibrium affecting the iron coordination of ferric cytochrome c. Biochemistry 1995, 34:14209-14212.
57. 3 and at high temperature. Eur J Inorg Chem 1998:583-591.
58. Banci L, Berners-Price S, Bertini I, Clementi, V, Luchinat C, Spyroulias GA, Turano P: Water-protein interaction in native and partially unfolded equine cytochrome c. (Dedicated to Prof R Ernst). Mol Phys 1998, 95:797-808. The partially unfolded horse heart cytochrome c in 2 M guanidinium chloride is investigated here by means of nuclear Overhausen effect spectroscopy (NOESY) maps and water proton relaxation. The latter is related to the number of exchanging NH protons. A relaxation matrix analysis allows us to count the exchanging NH protons that disappear from the NOESY map.
59. Pascher T, Chesick JP, Winkler JR, Gray HB: Protein folding triggered by electron transfer. Science 1996, 271:1558-1560.
60. 5 in the presence of 2 M guanidinium chloride: Monitoring the early steps in protein unfolding. Biochemistry 1998, 37:17082-17092. This paper describes the average structure of a paramagnetic protein after initiation of unfolding in the presence of 2.8 M guanidinium chloride.
61. 1H NMR study of the electronic structure and magnetic properties of high-spin ferrous or deoxy myoglobins. J Am Chem Soc 1998, 120:2113-2123.
62. Bertini I, Felli IC, Luchinat C: High magnetic field consequences on the NMR hyperfine shifts in solution. J Magn Reson 1998, 134:360-364. At high magnetic field, the difference in population of the electronic Zeeman levels is not linear with the external magnetic field. A dependence of the hypertine shifts on the field is expected and found.
63. 13C isotropic shifts of horse heart ferricytochrome c: Explanation of Curie and anti-Curie temperature dependence and nonlinear pseudocontact shifts in a two-level framework. J Am Chem Soc 1998, 120:8472-8479.
64. Ubbink M, Ejdebaeck M, Karlsson BG, Bendall DS: The structure of the complex of plastocyanin and cytochrome f, determined by paramagnetic NMR and restrained rigid-body molecular dynamics. Structure 1998, 6:323-335. The combined use of diamagnetic and paramagnetic chemical shift changes makes it possible to obtain detailed information about the structure of a transient complex of redox proteins. The structure suggests that the electrostatic interactions 'guide' the partners into a position that is optimal for electron transfer, and which may be stabilized by short-range interactions.
65. Ubbink M, Bendall DS: Complex of plastocyanin and cytochrome c characterized by NMR chemical shift analysis. Biochemistry 1997, 36:6326-6335.
66. 1H NMR. Biochemistry 1997, 36:11605-11618. Pseudocontact shifts from the two cerium(III) ions substituted for calcium permitted their use to refine the structure of the protein and also identification of the precise location of the metals in the protein structure. Direct information on the metal coordinates would not have been available using conventional NMR constraints.
67. 1 measurements, yield a reliable structural model for the long-range bending of the DNA duplex that would have been difficult or impossible to obtain from only short-range nuclear Overhausen effect information.
68. Ramos A, Varani G: A new method to detect long-range protein-RNA contacts: NMR detection of electron-proton relaxation induced by nitroxide spin-labeled RNA. J Am Chem Soc 1998, 120:10992-10993. The spin label wipes out some of the protein resonances and broadens some others. From the broadened resonances, the position of the spin label and, hence, of the RNA with respect to the protein, could be determined.