Machine Learning Prediction of Amino Acid Patterns in Protein N-myristoylation

  • Ryo Okada
  • Manabu Sugii
  • Hiroshi Matsuno
  • Satoru Miyano
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4146)


Protein N-myristoylation is the lipid modification in which the 14-carbon saturated fatty acid binds covalently to N-terminal of virus-based and eukaryotic protein. In this study, we suggest an approach to predict the pattern of N-myristoylation signal using the machine learning system BONSAI. BONSAI finds rules in combination of an alphabet indexings and decision trees. Computational experiments with BONSAI classified amino acid residues depending on effect for N-myristoylation and found rules of the alphabet indexing. In addition, BONSAI suggested new requirements for the position of an amino acid in N-myristoylation signal.


Amino Acid Residue Amino Acid Requirement Amino Acid Pattern Acid Indexing Amino Alphabet Indexing 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. 1.
    Maurer-Stroh, S., Eisenhaber, B., Eisenhaber, F.: N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. J. Mol. Biol. 317, 523–540 (2002)CrossRefGoogle Scholar
  2. 2.
    Utsumi, T., Nakano, K., Funakoshi, T., Kayano, Y., Nakao, S., Sakurai, N., Iwata, H., Ishisaka, R.: Vertical-scanning mutagenesis of amino acid in a model N-myristoylation motif reveals the major amino-terminal sequence requirements for protein N-myristoylation. Eur. J. Mol. Biochem. 271, 863–874 (2004)CrossRefGoogle Scholar
  3. 3.
    Utsumi, T., Sato, M., Nakano, K., Takemura, D., Iwata, H., Ishisaka, R.: Amino Acid Residue Penultimate to Amino-terminal Gly Residue Strongly Affects Two Cotranslational Protein Modifications, N-Myristoylation and N-Acetylation. J. Biol. Chem. 276, 10505–10513 (2001)CrossRefGoogle Scholar
  4. 4.
    Shimozono, S., Shinohara, A., Shinohara, T., Miyano, S., Kuhara, S., Arikawa, S.: Knowledge Acquisition from Amino Acid Sequences by Machine Learning System BONSAI. Trans. Inform. Process. Soc. Japan 35, 2009–2018 (1994)Google Scholar
  5. 5.
    Farazi, T.A., Waksman, G., Gordon, J.I.: The biology and enzymology of protein N-myristoylation. J. Biol. Chem. 276, 39501–39504 (2001)CrossRefGoogle Scholar
  6. 6.
    Resh, M.D.: Fatty acylation of proteins: new insights into membrane targeting of myristoylated and palmitoylated proteins. Biochim. Biophys. Acta 1451, 1–16 (1999)CrossRefGoogle Scholar
  7. 7.
    Zha, J., Weiler, S., Oh, K.J., Wei, M.C., Korsmeyer, S.J.: Posttranslational N-myristoylation of BID as a molecular switch for targeting mitochondria and apoptosis. Science 290, 1761–1765 (2000)CrossRefGoogle Scholar
  8. 8.
    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
  9. 9.
    Towler, D.A., Adams, S.P., Eubanks, S.R., Towery, D.S., Jackson-Machelski, E., Glaser, L., Gordon, J.I.: Purification and characterization of yeast myristoyl CoA: protein N-myristoyltransferase. Proc. Natl. Acad. Sci. USA 84, 2708–2712 (1987)CrossRefGoogle Scholar
  10. 10.
    Rocque, W.J., McWherter, C.A., Wood, D.C., Gordon, J.I.: A comparative analysis of the kinetic mechanism and peptide substrate specificity of human and Saccharomyces cerevisiae myristoyl-CoA: protein N-myristoyltransferase. J. Biol. Chem. 268, 9964–9971 (1993)Google Scholar
  11. 11.

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Ryo Okada
    • 1
  • Manabu Sugii
    • 2
  • Hiroshi Matsuno
    • 1
  • Satoru Miyano
    • 3
  1. 1.Graduate School of Science and Engineering 
  2. 2.Media and Information Technology CenterYamaguchi UniversityYamaguchiJapan
  3. 3.Human Genome CenterUniversity of TokyoTokyoJapan

Personalised recommendations