Advertisement

Journal of Biomolecular NMR

, Volume 24, Issue 4, pp 277–289 | Cite as

Structure determination of a pseudotripeptide zinc complex with the COSMOS-NMR force field and DFT methods

  • Raiker Witter
  • Lydia Seyfart
  • Georg Greiner
  • Siegmund Reissmann
  • Jennie Weston
  • Ernst Anders
  • Ulrich Sternberg
Article

Abstract

A His-X-His pseudotripeptide zinc complex (X is a N-alkyl glycine derivative) similar to the catalytic center of the carbonic anhydrase was computer designed and experimentally synthesized. Using 2D-NMR techniques, all proton, carbon chemical shifts and nuclear overhauser effect signals were assigned. The three-dimensional structure of the complex was determined with the COSMOS (computer simulation of molecular structures) force field by applying 13C bond polarization theory chemical shift pseudo forces and restrictions for NOE distances. From molecular dynamics, simulated annealing simulations and geometry optimizations, the three best force field structures were taken for a final investigation by density functional theory calculations.

carboanhydrase carbonic anhydrase geometry optimization molecular dynamics peptide pseudo forces restrictions simulated annealing structure determination zinc complex 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

REFERENCES

  1. Alia, Matysik, J., Erkelens, C., Hulsbergen, F.B., Gast, P., Lugtenburg, J. and de Groot, H.J.M. (2000) Chem. Phys. Lett., 330, 325–330.Google Scholar
  2. Alsfasser, R., Ruf, M., Trofimenko, S. and Vahrenkamp, H. (1993) Chem. Ber., 126, 703.Google Scholar
  3. Basosi, R., Gaggelli, E., Gaggelli, N., Pogni, R. and Valensin (1998) Inorg. Chim. Acta, 275, 274–278.Google Scholar
  4. Becke, A.D. (1993) J. Chem. Phys., 98, 5648.Google Scholar
  5. Braun, S., Kalinowski, H.O. and Berger, S. (1998) 150 and More Basic NMR-Experiments, Wiley-VCH, New York, NY.Google Scholar
  6. Burns, G. (1964) J. Chem. Phys., 41, 1521.Google Scholar
  7. Del R. (1958) J. Chem. Soc., 4031.Google Scholar
  8. Förster, M., Brasack, I., Duhme, A.-K., Nolting, H.-F. and Vahrenkam, H. (1996) Chem. Ber., 129, 347.Google Scholar
  9. Gaussian 98 (1998) Revision A.5, Gaussian, Inc., Pittsburgh, PA.Google Scholar
  10. Gockel, P., Gelinsky, M., Vogler, R. and Vahrenkamp, H. (1998) Inorg. Chim. Acta, 272, 115.Google Scholar
  11. Greiner, G., Seyfarth, L., Poppitz, W., Witter, R., Sternberg, U. and Reißmann, S. (2000) Lett. Peptide Sci., 7, 133–141.Google Scholar
  12. Grotendorst, J. (2000) Modern Methods and Algorithms of Quantum Chemistry, NIC, 1.Google Scholar
  13. Herr, U., Spahl, W., Trojandt, G. Steglich, W., Thaler, F. and van Eldrik, R. (1999) Bioorg. Med. Chem., 7, 699.Google Scholar
  14. Karplus, M. (1959) J. Chem. Phys., 30, 11–15.Google Scholar
  15. Kimura, E. (1994) In Progress in Inorganic Chemistry, Vol. 41Google Scholar
  16. Karlin, K.D. (Ed.), Wiley, New York, NY, p. 443.Google Scholar
  17. Klug, A. and Rhodes, D. (1987) Trends. Biochem. Sci., 12, 464.Google Scholar
  18. Koch, F.T., Bräuer, M., Kunert, M., Sternberg, U. and Anders, E. (2001) J. Mol. Model., 7, 54–64.Google Scholar
  19. Koch, F.-T., Losso, P. and Sternberg, U., COSMOS: Computer Simulation of Molecular Structures, www.cosmos-software.de 289Google Scholar
  20. Koch, F.T., Möllhoff, M. and Sternberg, U. (1994) J. Comp. Chem., 15, 524.Google Scholar
  21. Krizek, B.A., Amann, B.T., Kilfoil, V.J., Merkle, D.L. and Berg, J.M. (1991) J. Am. Chem. Soc., 113, 4518.Google Scholar
  22. Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559.Google Scholar
  23. Luisis, B.F., Xu, W.X., Otwinowsky, Z., Freedman, L.P., Yamamoto, K.R. and Sigler, P.B. (1991) Nature, 352, 497.Google Scholar
  24. Magafa, V., Stavropoulos, G. and Tsiveriotis, P. (1998) Inorg. Chim. Acta, 272, 7–17.Google Scholar
  25. Magonet E., Hayen, D., Delforge, D., Delaire, F. and Remacle, J. (1992) Biochem J., 287, 361 and references therein.Google Scholar
  26. Malrieu, J.-P. (1977) Mod. Theor. Chem., 7, 69.Google Scholar
  27. Marmorstein, R., Carey, M., Ptashne, M. and Harrison, S.C. (1992) Nature, 356, 408.Google Scholar
  28. Mauksch, M., Bräuer, M., Weston, J. and Anders, E. (2001) Chem. Biochem., 2, 190–198.Google Scholar
  29. Möllhoff, M. and Sternberg, U. (2001) J. Mol. Model., 7, 90–120.Google Scholar
  30. O'Keefe, M. and Brese, N.E. (1991) J. Am. Chem. Soc., 113, 3226–3229.Google Scholar
  31. Priess, W. and Sternberg, U. (2001) J. Mol. Struct: Theochem., 544 (1–3), 181–190.Google Scholar
  32. Slater, J.C. (1930) Phys. Rev., 36, 57.Google Scholar
  33. Spoel, D. (1996) Structure and Dynamics of Peptides: Theoretical Aspects of Protein Folding, Thesis, University Groningen, 23–28.Google Scholar
  34. Sternberg, U. (1988) J. Mol. Phys., 63, 249.Google Scholar
  35. Sternberg, U. and Priess, W. (1997) J. Magn. Reson., 125, 8–19.Google Scholar
  36. Stillman, M.J., Shaw, C.F. and Suzuki, K.T. (1992) Methallothioneins, VCH, Weinheim.Google Scholar
  37. Tsiveriotis, P., Hadjiliadis, N. and Stavropoulos, G. (1997) Inorg. Chim. Acta, 261, 83–92.Google Scholar
  38. Vallee, B.L., Coleman, J.E. and Auld, D.S. (1991) Proc. Natl. Acad. Sci. USA, 88, 999.Google Scholar
  39. van Eldrik, R. (1999) Coord. Chem. Rev., 182, 373.Google Scholar
  40. Veeman, W.S. (1984) Progr. NMR Spectrosc., 20, 193–235.Google Scholar
  41. Vuister, G.W., Delaglio, F. and Bax, A. (1992) J. Am. Chem. Soc., 114, 9674–9675.Google Scholar
  42. Williamson, M.P. (1993) Nat. Prod. Rep., 207–232.Google Scholar
  43. Witter, R., Prieß, W. and Sternberg, U. (2002) J. Comp. Chem., 23, 298–305.Google Scholar
  44. Wolinski, K., Hilton, J.F. and Pulay, P. (1990) J. Am. Chem. Soc., 112, 8251.Google Scholar
  45. Zhang, X., Hubbard, C.D. and van Eldrik, R. (1996) J. Phys. Chem., 100, 9161.Google Scholar

Copyright information

© Kluwer Academic Publishers 2002

Authors and Affiliations

  • Raiker Witter
    • 1
  • Lydia Seyfart
    • 2
  • Georg Greiner
    • 2
  • Siegmund Reissmann
    • 2
  • Jennie Weston
    • 3
  • Ernst Anders
    • 3
  • Ulrich Sternberg
    • 1
  1. 1.PAF / IOQ / HFFriedrich-Schiller-Universität JenaJenaGermany
  2. 2.Institute of Biochemistry and BiophysicsFriedrich-Schiller-Universität JenaJenaGermany
  3. 3.Institute of Organic Chemistry and Macromolecular ChemistryFriedrich-Schiller-Universität JenaJenaGermany

Personalised recommendations