Advertisement

Searching low-energy conformations of two elastin sequences

  • H. ArkínEmail author
Article

Abstract

The three-dimensional structures of two common repeat motifs Val1-Pro2-Gly3-Val4-Gly5 and Val1-Gly2-Val3-Pro4-Gly5-Val6-Gly7-Val8-Pro9 of tropoelastin are investigated by using the multicanonical simulation procedure. By minimizing the energy structures along the trajectory the thermodynamically most stable low-energy microstates of the molecule are determined. The structural predictions are in good agreement with X-ray diffraction experiments.

Keywords

Ramachandran Plot Conformational Search Energy Local Minimum Side Chain Dihedral Angle Nuclear Magnetic Resonance Time Scale 
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.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    M. Vásquez, G. Némethy, H.A. Scheraga, Chem. Rev. 94, 2183 (1994)CrossRefGoogle Scholar
  2. 2.
    U.H.E. Hansmann, Y. Okamoto, Ann. Rev. Comp. Phys. 5, 129 (1999)CrossRefGoogle Scholar
  3. 3.
    A. Mitsutake, Y. Sugita, Y. Okamoto, Biopolymers (Peptide Science) 60, 96 (2001)CrossRefGoogle Scholar
  4. 4.
    B.A. Berg, T. Çelik, Phys. Rev. Lett. 69, 2292 (1992); B.A. Berg, Fields Inst. Commun. 28, 1 (2000)ADSCrossRefGoogle Scholar
  5. 5.
    P.G. Wolynes, J. Onuchic, D. Thirumalai, Science 267, 1619 (1995)ADSCrossRefGoogle Scholar
  6. 6.
    L.T. Wille, U.H.E. Hansmann, Phys. Rev. Lett. 88, 068105 (2002)ADSCrossRefGoogle Scholar
  7. 7.
    H. Arkın, T. Çelik, Int. J. Mod. Phys. C 14, 985 (2003)ADSCrossRefGoogle Scholar
  8. 8.
    H. Arkın, T. Çelik, Int. J. Mod. Phys. C 14, 113 (2003); H. Arkın, T. Çelik, Int. J. Mod. Phys. C 14, 567 (2003)ADSCrossRefGoogle Scholar
  9. 9.
    A.M. Ferrenberg, R.H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988); A.M. Ferrenberg, R.H. Swendsen, Phys. Rev. Lett. 63, 1658 (1989)ADSCrossRefGoogle Scholar
  10. 10.
    H. Arkın, T. Çelik, Eur. Phys. J. B 30, 577 (2002)ADSCrossRefGoogle Scholar
  11. 11.
    Z. Li, H.A. Scheraga, Proc. Natl. Acad. Sci. USA 84, 6611 (1987); Z. Li, H.A. Scheraga, J. Mol. Struct. 179, 333 (1988)ADSCrossRefGoogle Scholar
  12. 12.
    W.J. Cook, H. Einspahr, T.L. Trapane, D.W. Urry, C.E. Bugg, J. Am. Chem. Soc. 102, 5502 (1980)CrossRefGoogle Scholar
  13. 13.
    D. Urry, M.M. Long, CRC Crit. Rev. Biochem. 4, 1 (1976)CrossRefGoogle Scholar
  14. 14.
    F.A. Momany, R.F. McGuire, A.W. Burgess, H.A. Scheraga, J. Phys. Chem. 79, 2361 (1975); M.J. Sippl, G. Némethy, H.A. Scheraga, J. Phys. Chem. 88, 6231 (1984)CrossRefGoogle Scholar
  15. 15.
    B. von Freyberg, T. Schaumann, W. Braun, FANTOM User’s Manual and Instructions: ETH Zürich, Zürich, 1993; B. von Freyberg, W. Braun, J. Comput. Chem. 14, 510 (1993)CrossRefGoogle Scholar
  16. 16.
    H. Meirovitch, E. Meirovitch, J. Comput. Chem. 18, 240 (1997)CrossRefGoogle Scholar
  17. 17.
    B. Li, D.O.V. Alonso, V. Daggett, J. Mol. Biol. 305, 581 (2001)CrossRefGoogle Scholar
  18. 18.
    V. Villani, A.M. Tamburro, J. Mol. Struc. (Theochem) 431, 205 (1998)CrossRefGoogle Scholar
  19. 19.
    A.M. Tamburro, V. Guantieri, L. Pandolfo, A. Scopa, Biopolymers, 29, 855 (1990)Google Scholar
  20. 20.
    D.W. Urry, J. Phys. Chem. B 101, 11007 (1997)CrossRefGoogle Scholar

Copyright information

© EDP Sciences, Società Italiana di Fisica, Springer-Verlag 2003

Authors and Affiliations

  1. 1.Department of PhysicsHacettepe UniversityAnkaraTurkey

Personalised recommendations