Skip to main content
SpringerLink
Log in

Molecular dynamics study of a monomeric heme undecapeptide of cytochromec

  • Research Papers
  • Published:
Journal of Computer-Aided Materials Design

Summary

Molecular dynamics simulations were performed to predict the structure of the monomeric heme-containing peptide microperoxidase-11 (MP-11). The simulations were carried out both in vacuo and in water solvent, taking as starting coordinates those of the corresponding amino acid sequence in the crystal structure of cytochrome c, since the crystallographic structure of MP-11 is not known. The structural data, including the H-bond network, are reported and visualised with the aid of graphical tools. The structure predicted is consistent with what is known experimentally on MP-11. This agreement suggests that molecular dynamics simulations might be useful in the prediction of the catalytic activity or reactivity of microperoxidases.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  1. Ehrenberg, A. and Theorell, H., Nature, 176 (1955) 158.

    Google Scholar 

  2. Peterson, J., Silver, J., Wilson, M.T. and Morrison, I.E.G., J. Inorg. Biochem., 13 (1980) 75.

    Google Scholar 

  3. Paleus, S., Ehrenberg, A. and Tuppy, H., Acta Chem. Scand., 9 (1955) 365.

    Google Scholar 

  4. Harbury, H.A. and Loach, P.A., J. Biol. Chem., 235 (1960) 2646.

    Google Scholar 

  5. Plattner, H., Wolfrem, D., Bachmann, L. and Wachter, E., Histochemistry, 45 (1970) 1.

    Google Scholar 

  6. Feder, N., J. Histochem. Cytochem., 18 (1970) 911.

    Google Scholar 

  7. Baldwin, D.A., Marques, H.M. and Pratt, J.M., J. Inorg. Biochem., 30 (1987) 203.

    Google Scholar 

  8. Sharma, V.S., Schmidt, M.R. and Ramey, H.M., J. Biol. Chem., 251 (1976) 4267.

    Google Scholar 

  9. Eglinton, D.G., Hill, B.C., Greenwood, C. and Thomson, A.J., J. Inorg. Biochem., 21 (1984) 1.

    Google Scholar 

  10. Peterson, J., Saleem, M.M.M., Silver, J. and Wilson, M.T., J. Inorg. Biochem., 19 (1983) 165.

    Google Scholar 

  11. Adams, P.A., Bylield, M.P., Milton, R.C. de L. and Pratt, J.M., J. Inorg. Biochem., 34 (1988) 167.

    Google Scholar 

  12. Kimura, K., Peterson, J., Wilson, M., Cookson, D.J. and Williams, R.J.P., J. Inorg. Biochem., 15 (1981) 11.

    Google Scholar 

  13. Urry, D.W. and Pettegrew, J.W., J. Am. Chem. Soc., 89 (1967) 5276.

    Google Scholar 

  14. Wilson, M.T., Ranson, R.J., Masiakowski, P., Czarnecka, E. and Brunori, M., Eur. J. Biochem., 77 (1977) 193.

    Google Scholar 

  15. Othman, S., Le Lirzin, A. and Desbois, A., Biochemistry, 32 (1993) 9781.

    Google Scholar 

  16. Brooks III, C.L., Karplus, M. and Pettitt, B.M., Proteins: A Theoretical Perspective of Dynamics, Structure and Thermodynamics, Adv. Chem. Phys., Vol. 61, Wiley, New York, NY, 1988.

    Google Scholar 

  17. Van Gunsteren, W.E., In Van Gunsteren, W.R., Weiner, P.K. and Wilkinson, A.J. (Eds.) Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Vol. 2, ESCOM, Leiden, 1993, pp. 3–36.

    Google Scholar 

  18. Berendsen, H.J.C., In Van Gunsteren, W.E., Weiner, P.K. and Wilkinson, A.J. (Eds.) Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications, Vol. 2, ESCOM, Leiden, 1993, pp. 161–181.

    Google Scholar 

  19. Tanaka, N., Yamane, T., Tsukihara, T., Ashida, T. and Kakudo, M., J. Biochem., 77 (1975) 147.

    Google Scholar 

  20. Van Gunsteren, W.F. and Berendsen, H.J.C., Groningen Molecular Simulation (GROMOS) Library Manual, Biomos, Groningen, 1987.

    Google Scholar 

  21. Lifson, S., Hagler, A.T. and Dauber, P., J. Am. Chem. Soc., 101 (1979) 511.

    Google Scholar 

  22. Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F. and Hermans, J., In Pullmann, B. (Ed.) Intermolecular Forces, Reidel, Dordrecht, 1981, pp. 331–342.

    Google Scholar 

  23. Ryckaert, J.P., Ciccotti, G. and Berendsen, H.J.C., J. Comput. Phys., 23 (1977) 327.

    Google Scholar 

  24. Karplus, M. and Van Gunsteren, WE, Macromolecules, 15 (1982) 1528.

    Google Scholar 

  25. Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, WE, DiNola, A. and Haak, J.R., J. Chem. Phys., 81 (1984) 3684.

    Google Scholar 

  26. Iori, G., Marinari, E. and Parisi, G., J. Phys. A, Math. Gen., 24 (1991) 5349.

    Google Scholar 

  27. Lopez, M.A. and Kollman, P.A., J. Am. Chem. Soc., 111 (1989) 6212.

    Google Scholar 

  28. Takano, T., J. Mol. Biol., 110 (1977) 537.

    Google Scholar 

  29. Bolognesi, M., Onesti, S., Gatti, G., Coda, A., Ascenzi, P. and Brunori, M., J. Mol. Biol., 105 (1989) 529.

    Google Scholar 

  30. Jeffrey, G.A. and Saenger, W., Hydrogen Bonding in Biological Structures, Springer, Berlin, 1991, pp. 15–48.

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Chimica, Universita' degli Studi di Roma ‘La Sapienza’, Piazzale A. Moro 5, I-00185, Rome, Italy

    Simone Melchionna & Mario Barteri

  2. Dipartimento di Fisica, Universita' degli Studi di Roma ‘La Sapienza’, I-00185, Rome, Italy

    Giovanni Ciccotti

  3. Centre Européen de Calcul Atomique et Moléculaire, ENS-Lyon, F-69364, Lyon Cedex 07, France

    Giovanni Ciccotti

Authors
  1. Simone Melchionna
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Mario Barteri
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Giovanni Ciccotti
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Melchionna, S., Barteri, M. & Ciccotti, G. Molecular dynamics study of a monomeric heme undecapeptide of cytochromec . J Computer-Aided Mater Des 2, 9–22 (1995). https://doi.org/10.1007/BF00701678

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00701678

Keywords

Search

Navigation