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Estimation of Evolutionary Average Hydrophobicity Profile from a Family of Protein Sequences

  • Said Hassan Ahmed
  • Tor Flå
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4774)

Abstract

Hydrophobicity has long been considered as one of the primary driving forces in the folding of proteins. We discuss here the evolutionary average of the hydrophobicity profile in an aligned family of proteins and found a patchy mean hydrophobicity profile. This is in contrast to Bastolla et al (2005b) results for the large superfamily of globular proteins. The idea is to use singular value decomposition and cavity filtering in order to remove the eigensequences burried in the evolutionary noise

Keywords

Singular Value Decomposition Scree Plot Boltzmann Lattice Residue Number Amino Acid Type 
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.

References

  1. 1.
    Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M.: The principal eigenvector of contact matrices and hydrophobicity profiles in proteins. Proteins 58, 22–30 (2005a)CrossRefGoogle Scholar
  2. 2.
    Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M.: Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution. J. Mol. Evol. 56, 243–254 (2003)CrossRefGoogle Scholar
  3. 3.
    Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M.: Lack of self-averaging in neutral evolution of proteins. Phys. Rev. Lett. 89, 208101/1–208101/4 (2002)CrossRefGoogle Scholar
  4. 4.
    Bastolla, U., Porto, M., Roman, H.E., Vendruscolo, M.: Statistical properties of neutral evolution. J. Mol. Evol. 57, S103–S119 (2003)CrossRefGoogle Scholar
  5. 5.
    Branden, C., Tooze, J.: Introduction to Protein Structure, 2nd edn. Garland publishing, New York (1999)Google Scholar
  6. 6.
    Johnstone, R.A., Wichern, D.W.: Applied Multivariate Statistical Analysis, 5th edn. Prentice Hall, Englewood Cliffs (2002)Google Scholar
  7. 7.
    Kyte, J., Doolittle, R.F.: A Simple Method for Displaying the Hydropathic character of a Protein. J. Mol. Biol. 157, 105–132 (1982)CrossRefGoogle Scholar
  8. 8.
    Lindeberg, T.: Scale-Space Theory in Computer Vision. The Kluwer International Series in Engineering and Computer Science. Kluwer Academic Publishers, Dordrecht (1994)Google Scholar
  9. 9.
    Miyazawa, S., Jernigan, R.L.: Self-consistent estimation of inter-residue protein contact energies based on an equillibrium mixture approximation of residues. Proteins: Structure and Molecular Principles 34, 49–68 (1999)Google Scholar
  10. 10.
    Opper, M., Winther, O.: From Naive Mean Field Theory to the TAP Equations. The MIT Press, Cambridge, Massachusetts London, England (2002)Google Scholar
  11. 11.
    Porto, M., Roman, H.E., Vendruscolo, M., Bastolla, U.: Prediction of site-specific amino acid distributions and limits of divergent evolutionary changes in protein sequences. Mol. Biol. Evol. 22, 630–638 (2005)CrossRefGoogle Scholar
  12. 12.
    Fornasari, M.S., Parisi, G., Echave, J.: Site-specific amino acid replacement matrices from structurally constrained protein evolutioin. Mol. Biol. 19, 352–356 (2002)Google Scholar
  13. 13.
    Thorvaldsen, S., Flå, T., Willassen, N.P.: Extracting molecular diversity between populations through sequence alignments. In: Oliveira, J.L., Maojo, V., Martín-Sánchez, F., Pereira, A.S. (eds.) ISBMDA 2005. LNCS (LNBI), vol. 3745, pp. 317–328. Springer, Heidelberg (2005)CrossRefGoogle Scholar
  14. 14.
    Wall, M.E., Rechtsteiner, A., Rocha, L.M.: Singular Value Decomposition and Principal Component Analysis. In: Berrar, D.P., Dubitzky, W., Granzow, M. (eds.) A Practical Approach to Microarray Data Analysis, pp. 91–109. Kluwer, Norwell, MA (2003)CrossRefGoogle Scholar
  15. 15.
    Tang, C.: Simple Models of the Protein Folding problem. Physica A 31, 288 (2000)Google Scholar
  16. 16.
    Moelbert, S., Emberly, E., Tang, C.: Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins. Protein Science 13, 752–762 (2004)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Said Hassan Ahmed
    • 1
  • Tor Flå
    • 1
  1. 1.Dept of Mathematics and Statistics, University of Tromsø, 9037 TromsøNorway

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