Molecular Engineering

, Volume 5, Issue 1–3, pp 107–119 | Cite as

Dynamic domains: A simple method of analysing structural movements in proteins

  • Krystyna Zakrzewska
Article

Abstract

A method is presented to analyse conformational changes in enzymes upon coenzyme and/or substrate binding. The method is based on a rigid body approximation for secondary structures and defines a dynamic domain as a collection of secondary structures which move together. The technique has been tested on a number of enzymes for which the conformation transition is well characterised. It was then applied to the analysis of two theoretically derived transition pathways for citrate synthase.

Key words

Enzymes transition pathways conformational analysis protein domains 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    J. Janin and S.J. Wodak:Prog. Biophys. Molec. Biol. 42, 21 (1983).Google Scholar
  2. 2.
    W. S. Bennett, Jr. and R. Huber:CRC Crit. Rev. Biochem. 15, 291 (1984).Google Scholar
  3. 3.
    A. M. Lesk and C. Chothia:J. Mol. Biol. 174, 175 (1984).Google Scholar
  4. 4.
    C. Chothia and A. M. Lesk:Trends Biol. Sci. 10, 116 (1985).Google Scholar
  5. 5.
    M. A. Ech-Cherif El-Kettani and J. Durup:Biopolymers 32, 561 (1989).Google Scholar
  6. 6.
    J. Durup:J. Phys. Chem. 95, 1817 (1991).Google Scholar
  7. 7.
    M. A. Ech-Cherif El-Kettani, K. Zakrzewska, J. Durup, and R. Lavery:Proteins: Structure, Function, and Genetics 16, 393 (1993).Google Scholar
  8. 8.
    H. Sklenar, C. Etchebest, and R. Lavery:Protein: Structure, Function and Genetics 6, 46 (1989).Google Scholar
  9. 9.
    K. Zakrzewska and R. Lavery: inModelling of Molecular Structures and Properties, J.-L. Rivail (Ed.), Studies in Physical and Theoretical Chemistry, Elsevier, Amsterdam, Vol. 71, p. 81 (1990).Google Scholar
  10. 10.
    A.D. McLachlan:J. Mol. Biol. 128, 49 (1978).Google Scholar
  11. 11.
    F. C. Bernstein, T. F. Koetzle, G. J. B. Williams, E. F. Meyer, M. D. Brice, J. R. Rodgers, O. Kennard, T. Shimanouchi, and M. Tasumi:J. Mol. Biol. 112, 535 (1977).Google Scholar
  12. 12.
    P. J. Kraulis:J. Appl. Crystallogr. 24, 946 (1991).Google Scholar
  13. 13.
    F. Colonna-Cesari, D. Perahia, M. Karplus, H. Eklund, C. I. Branden, and O. Tapia:J. Biol. Chem. 261, 15273 (1986.)Google Scholar
  14. 14.
    A. G. W. Leslie and A. J. Wonacott:J. Mol. Biol. 178, 743 (1984).Google Scholar
  15. 15.
    T. Skarzynski and A. Wonacott:J. Mol. Biol. 203, 1097 (1988).Google Scholar
  16. 16.
    Ch. M. Anderson, R. E. Stenkamp, and T. A. Steitz:J. Mol. Biol. 123, 15 (1978).Google Scholar
  17. 17.
    W. S. Bennett, Jr. and T. A. Steitz:J. Mol. Biol. 140, 211 (1980).Google Scholar
  18. 18.
    G. Wiegand and S. Remington:Ann. Rev. Biophys. Biophys. Chem. 15, 97 (1986).Google Scholar
  19. 19.
    S. Remington, G. Wiegand, and R. Huber:J. Mol. Biol. 158, 111 (1982).Google Scholar
  20. 20.
    G. Wiegand, S. Remington, J. Deisenhoffer, and R. Huber:J. Mol. Biol. 174, 205 (1984).Google Scholar
  21. 21.
    M. Karpusas, B. Branchaud, and S. J. Remington:Biochemistry 29, 2213 (1990).Google Scholar

Copyright information

© Kluwer Academic Publishers 1995

Authors and Affiliations

  • Krystyna Zakrzewska
    • 1
  1. 1.Laboratoire de Biochimie Théorique (URA77 CNRS)Institut de Biologie Physico-ChimiqueParisFrance

Personalised recommendations