Journal of Protein Chemistry

, Volume 22, Issue 2, pp 109–113 | Cite as

Palindromes in Proteins

  • Malgorzata Giel-Pietraszuk
  • Marcin Hoffmann
  • Sylwia Dolecka
  • Jacek Rychlewski
  • Jan Barciszewski
Article

Abstract

Palindromes in DNA consist of nucleotides sequences that read the same from the 5′-end to the 3′-end, and its double helix is related by twofold axis. They occur in genomes of all organisms and have various functions. For example, restriction enzymes often recognize palindromic sequences of DNA. Palindromes in telomeres are crucial for initiation of replication. One can ask the questions, Do palindromes occur in protein, and if so, what function they play? We have searched the protein SWISSPROT database for palindromic sequences. A great number (26%) of different protein palindromes were found. One example of such protein is systemin, an 18-amino-acid-long peptide. It contains palindrome in its β-sheet domain that interacts with palindromic fragment of DNA. The other palindrome containing protein is cellular human tumor suppressor p53. Oligonucleotide LTIITL has been observed in the crystal structure and is located close to a DNA recognizing domain. As the number of possible palindromic sequences of a given length is far much greater for proteins (20N) than for nucleic acids (4N), the study on their role seems to be an exciting challenge. Our results have clearly showed that palindromes are frequently occurring motives in proteins. Moreover, even very few examples that we have examined so far indicate the importance of further studies on protein palindromes.

Protein palindromes palindrome-like protein domain aminoacyl-tRNA synthetase systemin 

REFERENCES

  1. Baroudy, B. M., Venkatesan, S., and Moss, B. (1982). Cell 28: 315–324.Google Scholar
  2. Bourguignon, G. J., Tattersall, P. J., and Ward, D. C. (1976). J. Virol. 20: 290–306.Google Scholar
  3. Butler, D. K., Yasuda, L. E., and Yao, M. C. (1996). Cell 87: 1115–1122.Google Scholar
  4. Cain, D., Erlwein, O., Grigg, A., Russell, R. A., and McClure, M. O. (2001). J. Virol. 75: 3731–3739.Google Scholar
  5. Cavarelli, J., Rees, B., Thierry, J. C., and Moras, D. (1993). Biochimie 75: 1117–1123.Google Scholar
  6. Cho, Y., Gorina, S., Jeffrey, P. D., and Pavletich, N. P. (1994). Science 265: 346–355.Google Scholar
  7. Chu, W. M., Ballard, R. E., and Schmidt, C. W. (1997). Nucleic Acid Res. 25: 2077–2082.Google Scholar
  8. Constabel, C. P., Bergey, D. R., and Ryan, C. A. (1995). Proc. Natl. Acad. Sci. USA 92: 407–411.Google Scholar
  9. Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V., and Huber, R. (1999). EMBO J. 18: 5805–5816.Google Scholar
  10. Ford, M., and Fried, M. (1986). Cell 45: 425–430.Google Scholar
  11. Fried, M., Feo, S., and Heard, E. (1991). Biochim. Biophys. Acta 1090: 143–155.Google Scholar
  12. Gelfand, M., and Koonin, E. V. (1997). Nucleic Acids Res. 25: 2430–2439.Google Scholar
  13. Geshelin, P., and Berns, K. I. (1974). J. Mol. Biol. 88: 785–796.Google Scholar
  14. Giel-Pietraszuk, M., Szymanski, M., Slósarek, G., Specht, T., Erdmann, V. A., Mucha, P., et al. (1997). In: Legocki, A. B., and Soda, K., (eds.), Trends in Protein Research, Poznan, pp. 141–148.Google Scholar
  15. Hainaut, P., Soussi, T., Shomer, B., Hollstein, M., Greenblatt, M., Hovig, E., et al. (1997). Nucleic Acids Res. 25: 151–157.Google Scholar
  16. Hauswirth, W. W., and Berns, K. I. (1979). Virology 93: 57–68.Google Scholar
  17. Hoffmann, M., and Rychlewski, J. (1999). Comput. Methods Sci. Technol. 5: 21–24.Google Scholar
  18. Korn, L. J., and Brown, D. D. (1978). Cell 24: 261–270.Google Scholar
  19. Lacroix, E., Viguera, A. R., and Serrano, L. (1998). Fold. Des. 3: 79–85.Google Scholar
  20. Lewis, S., Akgun, E., and Jasin, M. (1999). Ann. N. Y. Acad. Sci. 870: 45–57.Google Scholar
  21. Marmorstein, R., Carey, M., Ptashne, M., and Harrison, S. C. (1992). Nature 356: 408–414.Google Scholar
  22. McClarin, J. A., Frederick, C. A., Wang, B. C., Greene, P., Boyer, H. W., Grable, J., et al. (1986). Science 234: 1526–1541.Google Scholar
  23. McGurl, B., Pearce, G., Orozco-Cardenas, M., and Ryan, C. A. (1992). Science 255: 1570–1573.Google Scholar
  24. Ogata, H., Audic, S., Abergel, Ch., Fournier, P. E., and Claverie, J. M. (2002). Genome Res. 12: 808–816.Google Scholar
  25. Olszewski, K. A., Kolinski, A., and Skolnick, J. (1996). Protein Eng. 9: 5–14.Google Scholar
  26. Park, J., Dietmann, S., Heger, A., and Holm, L. (2000). Bioinformatics 16: 978–987.Google Scholar
  27. Slósarek, G., Kalbitzer, H. R., Mucha, P., Rekowski, P., Kupryszewski, G., Giel-Pietraszuk, M., et al. (1995). J. Struct. Biol. 115: 30–36.Google Scholar
  28. Suzuki, M. (1992). Proc. Natl. Acad. Sci. USA 89: 8726–8730.Google Scholar
  29. Szymanski, M., Deniziak, M. A., and Barciszewski, J. (2001). Nucleic Acids Res. 29: 288–290.Google Scholar
  30. Ullu, E., and Weiner, A. M. (1984). EMBO J. 3: 3303–3310.Google Scholar
  31. Willwand, K., Mumtsidu, E., Kuntz-Simon, G., and Rommelaere, J. (1998). J. Biol. Chem. 273: 1165–1174.Google Scholar
  32. Wingate, V. P., and Ryan, C. A. (1991). J. Biol. Chem. 266: 5814–8518.Google Scholar

Copyright information

© Plenum Publishing Corporation 2003

Authors and Affiliations

  • Malgorzata Giel-Pietraszuk
    • 1
  • Marcin Hoffmann
    • 2
  • Sylwia Dolecka
    • 1
  • Jacek Rychlewski
    • 1
  • Jan Barciszewski
    • 1
  1. 1.Polish Academy of SciencesInstitute for Bioorganic ChemistryPoznanPoland
  2. 2.Quantum Chemistry Group, Faculty of ChemistryA. Mickiewicz UniversityPoznanPoland

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