Advertisement

Chinese Science Bulletin

, 50:536 | Cite as

A symmetry-related sequence-structure relation of proteins

  • Ruizhen Xu
  • Mingfen Li
  • Hanlin Chen
  • Yanzhao Huang
  • Yi Xiao
Articles

Abstract

Proteins have regular tertiary structures but irregular amino acid sequences. This made it very difficult to decode the structural information in the protein sequences. Here we demonstrate that many small α protein domains have hidden sequence symmetries characteristic of their pseudo-symmetric tertiary structures. We also present a modified method of recurrent plot to reveal this kind of the hidden sequence symmetry. The results may enable us to understand part of the relations between protein sequences and their tertiary structures.

Keywords

protein symmetry sequence-structure relation recurrence quantification analysis 

References

  1. 1.
    Baker, D., A surprising simplicity to protein folding, Nature, 2000, 405: 39–42.PubMedCrossRefGoogle Scholar
  2. 2.
    Wolynes, P. G., Onuchic, J. N., Thirumalai, D., Navigating the folding routes, Science, 1995, 267: 1619–1920.PubMedCrossRefGoogle Scholar
  3. 3.
    Sali, A., Shakhnovich, E., Karplus, M., How does a protein fold? Nature, 1994, 369: 248–251.PubMedCrossRefGoogle Scholar
  4. 4.
    White, S. T., Jacob, R. E., Statistical distribution of hydrophobic residues along the length of protein chains, Implications for protein folding and evolution, Biophys. J., 1990, 57: 911–921.PubMedCrossRefGoogle Scholar
  5. 5.
    Pande, V. S., Grosberg, A. Y., Tanaka, T., Nonrandomness in protein sequences: Evidence for a physically driven stage of evolution? Proc. Natl. Acad. Sci. USA, 1994, 91: 12972–12975.PubMedCrossRefGoogle Scholar
  6. 6.
    Irbäck, A., Sandelin, E., On hydrophobicity correlations in protein chains, Biophys. J., 2000, 79: 2252–2258.PubMedGoogle Scholar
  7. 7.
    Szklarczyk, R., Heringa, J., Tracking repeats using significance and transitivity, Bioinformatics, 2004, 20(Suppl 1): 1311–1317.CrossRefGoogle Scholar
  8. 8.
    Rackovsky, S., “Hidden” sequence periodicities and protein architecture, Proc. Natl. Acad. Sci. USA, 1998, 95(15): 8580–8584.PubMedCrossRefGoogle Scholar
  9. 9.
    Needleman, S. B., Wunsch, C. D., A general method applicable to the search for similarities in the amino acid sequences of two proteins, J. Mol. Biol., 1970, 48: 443–453.PubMedCrossRefGoogle Scholar
  10. 10.
    Smith, T. F., Waterman, M. S., Identification of common molecular subsequences, J. Mol. Biol., 1981, 147: 195–197.PubMedCrossRefGoogle Scholar
  11. 11.
    Mount, D. W., Bioinformatics: Sequences and Genome Analysis, New York: Cold Spring Harbor Laboratory Press, 2001, 428.Google Scholar
  12. 12.
    Eckmann, J. P., Kamphorst, S. O., Ruelle, D., Recurrence plots of dynamical systems, Europhys. Lett., 1987, 4: 973–977.CrossRefGoogle Scholar
  13. 13.
    Zbilut, J. P., Sirabella, P., Giuliani, A. et al., Review of nonlinear analysis of proteins through recurrence quantification, Cell Biochem. Biophys., 2002, 36: 67–87.PubMedCrossRefGoogle Scholar

Copyright information

© Science in China Press 2005

Authors and Affiliations

  • Ruizhen Xu
    • 1
  • Mingfen Li
    • 1
  • Hanlin Chen
    • 1
  • Yanzhao Huang
    • 1
  • Yi Xiao
    • 1
  1. 1.Biomolecular Physics and Modeling Group, Department of PhysicsHuazhong University of Science and TechnologyWuhanChina

Personalised recommendations