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.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
REFERENCES
Baroudy, B. M., Venkatesan, S., and Moss, B. (1982). Cell 28: 315–324.
Bourguignon, G. J., Tattersall, P. J., and Ward, D. C. (1976). J. Virol. 20: 290–306.
Butler, D. K., Yasuda, L. E., and Yao, M. C. (1996). Cell 87: 1115–1122.
Cain, D., Erlwein, O., Grigg, A., Russell, R. A., and McClure, M. O. (2001). J. Virol. 75: 3731–3739.
Cavarelli, J., Rees, B., Thierry, J. C., and Moras, D. (1993). Biochimie 75: 1117–1123.
Cho, Y., Gorina, S., Jeffrey, P. D., and Pavletich, N. P. (1994). Science 265: 346–355.
Chu, W. M., Ballard, R. E., and Schmidt, C. W. (1997). Nucleic Acid Res. 25: 2077–2082.
Constabel, C. P., Bergey, D. R., and Ryan, C. A. (1995). Proc. Natl. Acad. Sci. USA 92: 407–411.
Deibert, M., Grazulis, S., Janulaitis, A., Siksnys, V., and Huber, R. (1999). EMBO J. 18: 5805–5816.
Ford, M., and Fried, M. (1986). Cell 45: 425–430.
Fried, M., Feo, S., and Heard, E. (1991). Biochim. Biophys. Acta 1090: 143–155.
Gelfand, M., and Koonin, E. V. (1997). Nucleic Acids Res. 25: 2430–2439.
Geshelin, P., and Berns, K. I. (1974). J. Mol. Biol. 88: 785–796.
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.
Hainaut, P., Soussi, T., Shomer, B., Hollstein, M., Greenblatt, M., Hovig, E., et al. (1997). Nucleic Acids Res. 25: 151–157.
Hauswirth, W. W., and Berns, K. I. (1979). Virology 93: 57–68.
Hoffmann, M., and Rychlewski, J. (1999). Comput. Methods Sci. Technol. 5: 21–24.
Korn, L. J., and Brown, D. D. (1978). Cell 24: 261–270.
Lacroix, E., Viguera, A. R., and Serrano, L. (1998). Fold. Des. 3: 79–85.
Lewis, S., Akgun, E., and Jasin, M. (1999). Ann. N. Y. Acad. Sci. 870: 45–57.
Marmorstein, R., Carey, M., Ptashne, M., and Harrison, S. C. (1992). Nature 356: 408–414.
McClarin, J. A., Frederick, C. A., Wang, B. C., Greene, P., Boyer, H. W., Grable, J., et al. (1986). Science 234: 1526–1541.
McGurl, B., Pearce, G., Orozco-Cardenas, M., and Ryan, C. A. (1992). Science 255: 1570–1573.
Ogata, H., Audic, S., Abergel, Ch., Fournier, P. E., and Claverie, J. M. (2002). Genome Res. 12: 808–816.
Olszewski, K. A., Kolinski, A., and Skolnick, J. (1996). Protein Eng. 9: 5–14.
Park, J., Dietmann, S., Heger, A., and Holm, L. (2000). Bioinformatics 16: 978–987.
Slósarek, G., Kalbitzer, H. R., Mucha, P., Rekowski, P., Kupryszewski, G., Giel-Pietraszuk, M., et al. (1995). J. Struct. Biol. 115: 30–36.
Suzuki, M. (1992). Proc. Natl. Acad. Sci. USA 89: 8726–8730.
Szymanski, M., Deniziak, M. A., and Barciszewski, J. (2001). Nucleic Acids Res. 29: 288–290.
Ullu, E., and Weiner, A. M. (1984). EMBO J. 3: 3303–3310.
Willwand, K., Mumtsidu, E., Kuntz-Simon, G., and Rommelaere, J. (1998). J. Biol. Chem. 273: 1165–1174.
Wingate, V. P., and Ryan, C. A. (1991). J. Biol. Chem. 266: 5814–8518.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Giel-Pietraszuk, M., Hoffmann, M., Dolecka, S. et al. Palindromes in Proteins. J Protein Chem 22, 109–113 (2003). https://doi.org/10.1023/A:1023454111924
Published:
Issue Date:
DOI: https://doi.org/10.1023/A:1023454111924