Solution Structures Of Proteins Containing Paramagnetic Metal Ions

  • Ivano Bertini
  • Antonio Rosato
Part of the NATO ASI Series book series (ASHT, volume 41)


Metal ions containing unpaired electrons (i.e. paramagnetic) are rather common in biological systems. In particular, electron transfer metalloproteins must have at least one redox state with unpaired electrons. The quantum-mechanical treatment of these systems is cumbersome and the results are uncertain [1,2], although the density functional approach has provided some interesting data [3].


Nuclear Relaxation Clostridium Pasteurianum Density Functional Approach Pseudocontact Shift Contact Shift 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Davis, M.E. and McCanunon, J.A. (1990) Electrostatics in Biomolecular Structure and Dynamics, Chem. Rev. 90, 509–521.CrossRefGoogle Scholar
  2. 2.
    Comba, P. and Hambley, T.W. (1995) Molecular Modeling of Inorganic Compounds, VCH, Weinheim, D.Google Scholar
  3. 3.
    Mouesca, J.M., Chen, J.L., Noodleman, L., Bashford, D. and Case, D.A. (1994) Density Functional/Poisson-Boltzmann Calculations of Redox Potentials for Iron-Sulfur Clusters, J. Am. Chem. Soc. 116, 11898–11914.CrossRefGoogle Scholar
  4. 4.
    Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York.Google Scholar
  5. 5.
    Wüthrich, K. (1989) The development of nuclear magnetic resonance spectroscopy as a technique for protein structure determination, Acc. Chem. Res. 22, 36–44.CrossRefGoogle Scholar
  6. 6.
    NMR of Paramagnetic Molecules,Academic Press, New York.Google Scholar
  7. 7.
    Bertin, I. and Luchinat, C. (1986) NMI? of paramagnetic molecules in biological systems, Benjamin/Cummings, Menlo Park, CA. 15Google Scholar
  8. 8.
    Biological Magnetic Resonance, Vol. 12: NMR of Paramagnetic Molecules,Plenum Press, New york.Google Scholar
  9. 9.
    Bertini, I. and Luchinat, C. (1996) NMR of paramagnetic substances, Coord.Chem.Rev. 150, Elsevier, Amsterdam.Google Scholar
  10. 10.
    Solomon, I. (1955) Relaxation Processes in a System of Two Spins, Phys. Rev. 99, 559–565.CrossRefGoogle Scholar
  11. 11.
    Solomon, I. and Bloembergen, N. (1956) Nuclear Magnetic Interactions in the HF Molecule, J. Chem. Phys. 25, 261–266.CrossRefGoogle Scholar
  12. 12.
    Guéron, M. (1975) Nuclear Relaxation in Macromolecules by Paramagnetic Ions: A Novel Mechanism, J. Magn. Reson. 19, 58–66.Google Scholar
  13. 13.
    Vega, A.J. and Fiat, D. (1976) Nuclear Relaxation Processes of Paramagnetic Complexes. The Slow Motion Case, Mol. Phys. 31, 347–362.CrossRefGoogle Scholar
  14. 14.
    Bertini, I., Jonsson, B.-H., Luchinat, C., Pierattelli, R. and Vila, A.J. (1994) Strategies of signal assignments in paramagnetic metalloproteins. An NMR investigation of the thiocyanate adduct of the cobalt(II)-substituted human carbonic anhydrase II, J. Magn. Reson. Ser. B 104, 230–239.CrossRefGoogle Scholar
  15. 15.
    Abragam, A. (1961) The Principles of Nuclear Magnetism, Oxford University Press, Oxford.Google Scholar
  16. 16.
    Bax, A. (1982) Two dimensional nuclear magnetic resonance in liquids, Reidel, Dordrecht.Google Scholar
  17. 17.
    Shriver, J. (1992) Product operators and coherence transfer in multiple-pulse NMR experiments, Concepts Magn. Reson. 4, 1–34.CrossRefGoogle Scholar
  18. 18.
    Banci, L., Bertini, I., Eltis, L.D., Felli, I.C., Kastrau, D.H.W., Luchinat, C., Piccioli, M., Pierattelli, R. and Smith, M. (1994) 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.CrossRefGoogle Scholar
  19. 19.
    Banci, L., Bertini, I., Bren, K.L., Gray, H.B., Sompornpisut, P. and Turano, P. (1995) The three dimensional solution structure of the cyanide adduct of Saccharomyces cerevisiae Met80Ala-iso-l-cytochrome c. Identification of ligand-residue interactions in the distal heme cavity, Biochemistry 34, 11385–11398.CrossRefGoogle Scholar
  20. 20.
    Bertini, I., Luchinat, C. and Rosato, A. (1996) The solution structure of paramagnetic metalloproteins, Prog. Biophys. Mol. Biol. 66, 43–80.CrossRefGoogle Scholar
  21. 21.
    Banci, L., Bertini, I. and Luchinat, C. (1991) Nuclear and electron relaxation. The magnetic nucleus-unpaired electron coupling in solution, VCH, Weinheim. 16Google Scholar
  22. 22.
    Granot, J. (1982) Paramagnetic Relaxation in Dipolar-Coupled Homonuclear Spin Systems, J. Magn. Reson. 49, 257–270.Google Scholar
  23. 23.
    La Mar, G.N. and de Ropp, J.S (1993) NMR Methodology for Paramagnetic Proteins, in Berliner, L.J. and Reuben, J. (eds) Biological Magnetic Resonance, Vol. 12, Plenum Press, New York, pp. 1–78.Google Scholar
  24. 24.
    Bertini, I., Couture, M.M.J., Donaire, A., Eltis, L.D., Felli, I.C., Luchinat, C., Piccioli, M. and Rosato, A. (1996) The Solution Structure Refinement of the Paramagnetic Reduced HiPIP I from Ectothiorhodospira halophila by Using Stable Isotope Labeling and Nuclear Relaxation, Eur. J. Biochem. 241, 440–452.CrossRefGoogle Scholar
  25. 25.
    Huber, J.G., Moulis, J.-M. and Gaillard, J. (1996) Use of 1H Longitudinal Relaxation Times in the Solution Structure of Paramagnetic Proteins. Application to [4Fe-4S] Proteins, Biochemistry 35, 12705–12711.CrossRefGoogle Scholar
  26. 26.
    Bertini, I., Donaire, A., Luchinat, C. and Rosato, A. (1997) Paramagnetic relaxation as a tool for solution structure determination: Clostridium pasterianum ferredoxin as an example, Proteins: Structure,Function,and Genetics in pressGoogle Scholar
  27. 27.
    Ciurli, S., Cremonini, M.A., Kofod, P. and Luchinat, C. (1996) 111 NMR of high potential iron-sulfur protein from the purple non-sulfur bacterium Rhodoferax fermentas, Eur. J. Biochem. 236, 405–411.Google Scholar
  28. 28.
    McConnell, H.M. and Chesnut, D.B. (1958) Theory of isotropic hyperfine interactions in p-electron radicals, J. Chem. Phys. 28, 107–117.CrossRefGoogle Scholar
  29. 29.
    Kurland, R.J. and McGarvey, B.R. (1970) Isotropic NMR shifts in transition metal complexes: calculation of the Fermi contact and pseudocontact terms, J. Magn. Reson. 2, 286–301.Google Scholar
  30. 30.
    Lee, L. and Sykes, B.D. (1983) Use of lanthanide-induced nuclear magnetic resonance shifts for determination of protein in solution: EF calcium binding site of Carp Parvalbumin, Biochemistry 22, 4366–4373.CrossRefGoogle Scholar
  31. 31.
    Shelling, J.G., Bjorson, M.E., Hodges, R.S., Taneja, A.K. and Sykes, B.D. (1984) Contact and dipolar contributions to lanthanide-induced NMR shifts of amino acid and peptide models for calcium binding sites in proteins, J. Magn. Reson. 57, 99–114.Google Scholar
  32. 32.
    Bertini, I., Luchinat, C. and Scozzafava, A. (1977) Interaction of cobalt(lI) bovine carbonic anhydrase with aniline, benzoate and anthranilate, J. Am. Chem. Soc. 99, 581–584. 17Google Scholar
  33. 33.
    Banci, L., Dugad, L.B., La Mar, G.N., Keating, K.A., Luchinat, C. and Pierattelli, R. (1992) 1H Nuclear Magnetic Resonance investigation of cobalt(II) substituted carbonic anhydrase, Biophys. J. 63, 530–543.CrossRefGoogle Scholar
  34. 34.
    Auld, D.S., Bertin, I., Donaire, A., Messori, L. and Moratal Mascarell, J.M. (1992) The pH dependent properties of cobalt(II) carboxypeptidase A inhibitor complexes, Biochemistry 31, 3840–3846.CrossRefGoogle Scholar
  35. 35.
    Williams, G., Clayden, N.J., Moore, G.R. and Williams, R.J.P. (1985) Comparison of the solution and crystal structures of mitochondrial cytochrome c. Amalysis of paramagnetic shifts in the nuclear magnetic resonance spectrum of ferricytochrome c, J. Mol. Biol. 183, 447–460.CrossRefGoogle Scholar
  36. 36.
    Feng, Y.Q., Roder, H. and Englander, S.W. (1990) Redox dependent structure change and hyperfine nuclear magnetic resonance shifts in cytochrome c, Biochemistry 29, 3494–3504.CrossRefGoogle Scholar
  37. 37.
    Gao, Y., Boyd, J., Pielak, G.J. and Williams, R.J.P. (1991) Comparison of reduced and oxidized yeast iso-l-cytochrome c using proton paramagnetic shifts, Biochemistry 30, 1928–1934.CrossRefGoogle Scholar
  38. 38.
    Emerson, S.D. and La Mar, G.N. (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.CrossRefGoogle Scholar
  39. 39.
    Rajarathnam, K., La Mar, G.N., Chiu, M.L. and Sligar, S.G. (1992) Determination of the orientation of the magnetic axes of the cyano-metMb complexes of point mutants of myoglobin by solution 1H NMR: influence of HisE7-Gly and Arg CD3-Gly substitutions, J. Am. Chem. Soc. 114, 9048–9058.CrossRefGoogle Scholar
  40. 40.
    La Mar, G.N., Chen, Z.G., Vyas, K. and McPherson, A.D. (1995) An interpretative basis of the hyperfine shifts in cyanide-inhibited horseradish peroxidase on the magnetic axes and ligand tilt. Influence of substrate binding and extension to other peroxidases, J. Am. Chem. Soc. 117, 411–419.CrossRefGoogle Scholar
  41. 41.
    Banci, L., Bertin, I., Pierattelli, R., Tien, M. and Vila, A.J. (1995) Factoring of the hyperfine shifts in the cyanide adduct of lignin peroxidase from P. chrysosporium, J. Am. Chem. Soc. 117, 8659–8667. 18Google Scholar
  42. 42.
    Gochin, M. and Roder, H. (1995) Protein Structure Refinement based on Paramagnetic NMR shifts. Applications to Wild-Type and mutants forms of Cytochrome c, Protein Sci. 4, 296–305.CrossRefGoogle Scholar
  43. 43.
    Banci, L., Bertini, I., Cremonini, M.A., Gori Savellini, G., Gtlntert, P. and Luchinat, C. (1997) The pseudocontact shifts as structural constraints for solution structure determination of paramagnetic metalloproteins: a protocol for the Distance Geometry approach,submitted.Google Scholar
  44. 44.
    Banci, L., Bertin, I., Bren, K.L., Cremonini, M.A., Gray, H.B., Luchinat, C. and Turano, P. (1996) The use of pseudocontact shifts to refine solution structures of paramagnetic metalloproteins: Met80Ala cyano-cytochrome cas an example, JBIC 1, 117–126.CrossRefGoogle Scholar
  45. 45.
    Banci, L., Bertini, I., Gori Savellini, G., Romagnoli, A., Turano, P., Cremonini, M.A., Luchinat, C. and Gray, H.B. (1997) The pseudocontact shifts as constraints for energy minimization and molecular dynamic calculations on solution structures of paramagnetic metalloproteins, Proteins: Structure,Function,and Genetics in pressGoogle Scholar
  46. 46.
    Banci, L., Bertini, I., Gray, H.B., Luchinat, C., Reddig, T., Rosato, A. and Turano, P. (1998) Solution structure of oxidized horse heart cytochrome c,Biochemistry in pressGoogle Scholar
  47. 47.
    Gilntert, P., Mumenthaler, C. and Wiüthrich, K. (1996) DYANA: torsion angle dynamics for structure calculation and automatic assignment of NOESY spectra, XVIIth International Conference on Magnetic Resonance in Biological systems (Abstract)Google Scholar
  48. 48.
    Pearlman, D.A. and Case, D.A. (1991) SANDER: University of California,San Francisco Google Scholar
  49. 49.
    Pearlman, D.A., Case, D.A., Caldwell, J.W., Ross, W.S., Cheatham, T.E., Ferguson, D.M., Seibel, G.L., Singh, U.C., Weiner, P.K. and Kollman, P.A. (1995) AMBER 4.1, University of California, San Francisco.Google Scholar
  50. 50.
    Quaegebeur, J.P., Chachaty, C. and Yasukawa, T. (1979) Hyperfine couplings and 13C relaxation in alkylamines coordinated to Ni(11) acetylacetonate, Mol. Phys. 37, 409–424.CrossRefGoogle Scholar
  51. 51.
    Bertin, I., Capozzi, F., Luchinat, C., Piccioli, M. and Vila, A.J. (1994) The Fe4S4 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. 19Google Scholar
  52. 52.
    Bertini, I., Ciurli, S. and Luchinat, C. (1995) The electronic structure of FeS centers in protein and models. A contribution to the understanding of their electron transfer properties, in Structure and Bonding, Springer-Verlag, Vol. 83, Berlin Heidelberg, pp. 1–54.Google Scholar
  53. 53.
    Bertin, I., Donaire, A., Feinberg, B.A., Luchinat, C., Piccioli, M. and Yuan, H. (1995) Solution structure of the oxidized 2[Fe4S4] ferredoxin from Clostridium pasteurianum, Eur. J. Biochem. 232, 192–205.CrossRefGoogle Scholar
  54. 54.
    Wang, P.L., Donaire, A., Zhou, Z.H., Adams, M.W.W. and La Mar, G.N. (1996) Molecular model of the solution structure for the paramagnetic four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis, Biochemistry 35, 11319–11328.CrossRefGoogle Scholar
  55. 55.
    Bentrop, D., Bertini, I., Cremonini, M.A., Forsén, S., Luchinat, C. and Malmendal, A. (1998) The solution structure of the paramagnetic complex of the N-terminal domain of calmodulin with two Ce3+ions by 1 H N111R,submitted.Google Scholar

Copyright information

© Springer Science+Business Media Dordrecht 1997

Authors and Affiliations

  • Ivano Bertini
    • 1
  • Antonio Rosato
    • 1
  1. 1.Department of ChemistryUniversity of FlorenceFlorenceItaly

Personalised recommendations