Molecular modeling annual

, Volume 5, Issue 6, pp 103–115

Latent Periodicity of Protein Sequences

  • Maria A. Korotkova
  • Eugene V. Korotkov
  • Valentina M. Rudenko
Full Paper

DOI: 10.1007/s008940050122

Cite this article as:
Korotkova, M., Korotkov, E. & Rudenko, V. J Mol Model (1999) 5: 103. doi:10.1007/s008940050122

Abstract

This article is in the area of protein sequence investigation. It studies protein sequence periodicity. The notion of latent periodicity is introduced. A mathematical method for searching for latent periodicity in protein sequences is developed. Implementation of the method developed for known cases of perfect and imperfect periodicity is demonstrated. Latent periodicity of many protein sequences from the SWISS-PROT data bank is revealed by the method and examples of latent periodicity of amino acid sequences are demonstrated for: the translation initiation factor EIF-2B (epsilon subunit) of Saccharomyces cerevisiae from the E2BE_YEAST sequence; the E.coli ferrienterochelin receptor from the FEPA_ECOLI sequence; the lysozyme of Bacteriophage SF6 from the LY_BPSF6 sequence; lipoamide dehydrogenase of Azotobacter vinelandii from the DLDH_AZOVI sequence. These protein sequences have latent periods equal to six, two, seven and 19 amino acids, respectively. We propose that a possible purpose of the amino acid sequence latent periodicity is to determine certain protein structures.

Keywords Latent periodicity, Protein sequences, Mutual information

Copyright information

© Springer-Verlag Heidelberg 1999

Authors and Affiliations

  • Maria A. Korotkova
    • 1
  • Eugene V. Korotkov
    • 2
  • Valentina M. Rudenko
    • 2
  1. 1.Department of Cybernetics, Moscow Physical Engineering Institute, Kashirskoe shosse 31, 115409, Moscow, Russia.RU
  2. 2.Center of Bioengineering, Russian Academy of Sciences, Prospect 60-tya Oktyabrya, 7/1, 117312, Moscow, Russia. Tel:   +7-095-430-32-70; Fax: +7-095-135-05-71. E-mail: katrin2@biengi.ac.ruRU