Advertisement

Investigation into the Effects of an Individual Amino Acid on Protein Function by Means of a Resonant Recognition Model

  • Charalambos Chrysostomou
  • Huseyin Seker
  • Nizamettin Aydin
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6935)

Abstract

Upon identification of a new protein it is important to single out these amino acids responsible for the structural classification of the protein as well as the amino acids contributing to the protein’s specific biological characterisation. A novel approach is presented to identify and quantify this cause and effect relationship between amino acid and protein. This exploits the Common Frequency Peak (CFP) that it extracts from the Resonant Recognition Model (RRM). Applicability and robustness of the method are shown on a case study where five different protein families of the influenza A virus Neuraminidase (NA) genes are studied. They include H1N1, H1N2, H2N2, H3N2 and H5N1. The analyses identified five segments, namely three between H1N1 and H5N1 and two between H1N2, H2N2 and H3N2 and suggested that they play a key role in Influenza A NA gene functionality and can potentially be considered as target areas for future antiviral drugs and vaccines such as neuraminidase inhibitors.

Keywords

Resonant Recognition Model Effects of individual amino acids Discrete Fourier Transform Influenza A Virus Neuraminidase 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. Journal of Molecular Biology 215(3), 403–410 (1990)CrossRefGoogle Scholar
  2. 2.
    Bao, Y., Bolotov, P., Dernovoy, D., Kiryutin, B., Zaslavsky, L., Tatusova, T., Ostell, J., Lipman, D.: The influenza virus resource at the National Center for Biotechnology Information. Journal of Virology 82(2), 596 (2008)CrossRefGoogle Scholar
  3. 3.
    Cosic, I.: Macromolecular bioactivity: is it resonant interaction between macromolecules?Theory and applications. IEEE Transactions on Bio-Medical Engineering 41, 1101 (1994)CrossRefGoogle Scholar
  4. 4.
    Kawashima, S., Ogata, H., Kanehisa, M.: AAindex: amino acid index database. Nucleic Acids Research 27(1), 368 (1999)CrossRefGoogle Scholar
  5. 5.
    Li, Z.: Profeat: A web server for computing structural and physicochemical features of proteins and peptides from amino acid sequence. Nucleic Acids Res. 34, 32–37 (2006)CrossRefGoogle Scholar
  6. 6.
    Morens, D., Taubenberger, J., Fauci, A.: The persistent legacy of the 1918 influenza virus. The New England Journal of Medicine 361(3), 225 (2009)CrossRefGoogle Scholar
  7. 7.
    Moscona, A.: Neuraminidase inhibitors for influenza. New England Journal of Medicine 353(13), 1363 (2005)CrossRefGoogle Scholar
  8. 8.
    Pirogova, E.: Analysis of amino acid parameters in the resonant recognition model. In: Proceedings of the International Conference on Bioelectromagnetism, p. 71 (1998)Google Scholar
  9. 9.
    Veljkovic, V., Cosic, I., Dimitrijevic, B., LalovicC, D.: Is it possible to analyze DNA and protein sequences by the methods of digital signal processing? IEEE Transaction on Biomedical Engineering 32(5), 337–341 (1985)CrossRefGoogle Scholar
  10. 10.
    Veljkovic, V., Veljkovic, N., Este, J., Huther, A., Dietrich, U.: Application of the EIIP/ISM bioinformatics concept in development of new drugs. Current Medicinal Chemistry 14(4), 441–453 (2007)CrossRefGoogle Scholar
  11. 11.
    Veljkovic, V., Veljkovic, N., Muller, C., Muller, S., Glisic, S., Perovic, V., Kohler, H.: Characterization of conserved properties of hemagglutinin of h5n1 and human influenza viruses: possible consequences for therapy and infection control. BMC Structural Biology 9(1), 21 (2009)CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Charalambos Chrysostomou
    • 1
  • Huseyin Seker
    • 1
  • Nizamettin Aydin
    • 2
  1. 1.Bio-Health Informatics Research Group, Centre for Computational Intelligence, Department of Informatics, Faculty of TechnologyDe Montfort UniversityLeicesterUK
  2. 2.Department of Computer EngineeringYildiz Technical UniversityTurkey

Personalised recommendations