Investigation of a protein complex network

Article

Abstract.

The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal non-random features of the network we also compare it with a null model in which the complexes randomly select their proteins. Finally we propose a simple evolutionary model based on duplication and divergence of proteins.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    R. Albert, A.-L. Barabási, Rev. Mod. Phys. 74, 47 (2002)CrossRefMathSciNetGoogle Scholar
  2. 2.
    S.N. Dorogovtsev, J.F.F. Mendes, Evolution of Networks: From Biological Nets to the Internet and WWW (Oxford University Press, 2003)Google Scholar
  3. 3.
    M.E.J. Newman, SIAM Rev. 45, 167 (2003)MATHGoogle Scholar
  4. 4.
    D.J. Watts, S.H. Strogatz, Nature 393, 440 (1998)CrossRefGoogle Scholar
  5. 5.
    A. Barrat, M. Weigt, Eur. Phys. J. B 13, 547 (2000)CrossRefGoogle Scholar
  6. 6.
    L.A.N. Amaral, A. Scala, M. Barthélémy, H.E. Stanly, Proc. Natl. Acad. Sci USA 97, 11149 (2000)CrossRefGoogle Scholar
  7. 7.
    R. Monasson, Eur. Phys. J. B 12, 555 (1999)CrossRefGoogle Scholar
  8. 8.
    R. Albert, H. Jeong, A.-L. Barabási, Nature 406, 378 (2000)CrossRefGoogle Scholar
  9. 9.
    D.S. Callaway, M.E.J. Newman, S.H. Strogatz, D.J. Watts, Phys. Rev. Lett. 85, 5468 (2000)CrossRefGoogle Scholar
  10. 10.
    E. Almaas, R.V. Kulkarni, D. Stroud, Phys. Rev. E 68, 056105 (2003)CrossRefGoogle Scholar
  11. 11.
    M.E.J. Newman, Phys. Rev. Lett. 89, 208701 (2002)CrossRefGoogle Scholar
  12. 12.
    M.E.J. Newman, Phys. Rev. E 67, 026126 (2003)CrossRefGoogle Scholar
  13. 13.
    P. Uetz et al. , Nature 403, 623 (2000)CrossRefGoogle Scholar
  14. 14.
    T. Ito et al. , Proc. Natl. Acad. Sci. USA 98, 4569 (2001)CrossRefGoogle Scholar
  15. 15.
    A. Abbott, Nature 417, 895 (2002)Google Scholar
  16. 16.
    A. Wagner, Mol. Biol. Evol. 18, 1283 (2001)Google Scholar
  17. 17.
    R. Pastor-Satorras, E. Smith, R.V. Solé, J. Theoret. Biol. 222, 199 (2003)CrossRefMathSciNetGoogle Scholar
  18. 18.
    S. Maslov, K. Sneppen, Science 296, 910 (2002)CrossRefGoogle Scholar
  19. 19.
    A. Vázquez, A. Flammini, A. Maritan, A. Vespignani, ComPlex Us 1, 38 (2003)CrossRefGoogle Scholar
  20. 20.
    H. Jeong, S.P. Mason, A.-L. Barabási, Z.M. Oltvai, Nature 411, 41 (2001)CrossRefGoogle Scholar
  21. 21.
    A. Kumar, M. Snyder, Nature 415, 123 (2002)CrossRefGoogle Scholar
  22. 22.
    A.-C. Gavin et al. , Nature 415, 141 (2002)CrossRefPubMedGoogle Scholar
  23. 23.
    Y. Ho et al. , Nature 415, 180 (2002)CrossRefGoogle Scholar
  24. 24.
    G. Parisi, cond-mat/0205297Google Scholar
  25. 25.
    A. Edwards et al. , TRENDS in Genetics 18, 529 (2002)CrossRefGoogle Scholar
  26. 26.
    P. Erdös, A. Rényi, Publ. Math. Inst. Hung. Acad. Sci. 5, 17 (1960)Google Scholar
  27. 27.
    M.E.J. Newman, Phys. Rev. E 68, 026121 (2003)CrossRefGoogle Scholar
  28. 28.
    M.E.J. Newman, S.H. Strogatz, D.J. Watts, Phys. Rev. E 64, 026118 (2001)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin/Heidelberg 2004

Authors and Affiliations

  • A. R. Mashaghi
    • 1
    • 2
  • A. Ramezanpour
    • 3
  • V. Karimipour
    • 3
  1. 1.Institute of Biochemistry and BiophysicsTehranIran
  2. 2.School of MedicineTehran UniversityTehranIran
  3. 3.Department of PhysicsSharif University of TechnologyTehranIran

Personalised recommendations