Advertisement

Biochemistry (Moscow)

, Volume 76, Issue 2, pp 236–244 | Cite as

Prediction of folding nuclei in tRNA molecules

  • L. B. Pereyaslavets
  • M. V. Baranov
  • E. I. Leonova
  • O. V. Galzitskaya
Article

Abstract

Prediction of folding nuclei in RNA molecules allows one to look in a new way at the problem of possible RNA base sequence folding and at problems associated with incorrect RNA folding, as well as at RNA structure stability. We have chosen a model and energy parameters for description of RNA structure. The algorithm for studying processes including protein folding/unfolding was successfully applied to calculations on tRNA. Four tRNA molecules were considered whose structures were obtained in the free state (tRNAPhe, tRNAAsp, tRNAfMet, and tRNALys). The calculated Φ-values for tRNA molecules correlate with experimental data showing that nucleotide residues in the D and T hairpin regions are involved in tRNA structure last, or more exactly, they are not included in the tRNA folding nucleus. High Φ-values in the anticodon hairpin region show that the nucleus of tRNA folding is localized just in that place.

Key words

dynamic programming folding nucleus hydrogen bond stacking and hydrophobic interactions coarse-grained structural model tRNA folding 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Woodson, S. A. (2010) Annu. Rev. Biophys., 39, 61–77.PubMedCrossRefGoogle Scholar
  2. 2.
    Lee, M. K., Gal, M., Frydman, L., and Varani, G. (2010) Proc. Natl. Acad. Sci. USA, 107, 9192–9197.PubMedCrossRefGoogle Scholar
  3. 3.
    Levinthal, C. (1968) J. Chem. Phys., 65, 44–45.Google Scholar
  4. 4.
    Spirin, A. S. (2005) Mol. Biol. (Moscow), 35, 550–556.Google Scholar
  5. 5.
    Maglott, E. J., Goodwin, J. T., and Glick, G. D. (1999) J. Am. Chem. Soc., 121, 7461–7462.CrossRefGoogle Scholar
  6. 6.
    Matouschek, J. T., Kellis, Jr., Serrano, L., and Fersht, A. R. (1989) Nature, 340, 122–126.PubMedCrossRefGoogle Scholar
  7. 7.
    Matouschek, J. T., Kellis, Jr., Serrano, L., Bycroft, M., and Fersht, A. R. (1990) Nature, 346, 440–445.PubMedCrossRefGoogle Scholar
  8. 8.
    Wilkinson, K. A., Merito, E. J., and Weeks, K. M. (2005) J. Am. Chem. Soc., 127, 4659–4667.PubMedCrossRefGoogle Scholar
  9. 9.
    Taketomi, H., Ueda, Y., and Go, N. (1975) Int. J. Pept. Protein Res., 7, 445–459.PubMedCrossRefGoogle Scholar
  10. 10.
    Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E., and Dokholyan, N. V. (2008) RNA, 14, 1164–1173.PubMedCrossRefGoogle Scholar
  11. 11.
    Saenger, W. (1987) Principles of Nucleic Acid Structure [Russian translation], Mir, Moscow, pp. 334–374.Google Scholar
  12. 12.
    Finkelstein, A. V., and Badretdinov, A. Ya. (1997) Mol. Biol. (Moscow), 31, 469–477.Google Scholar
  13. 13.
    Galzitskaya, O. V., and Finkelstein, A. V. (1999) Proc. Natl. Acad. Sci. USA, 96, 11299–11304.PubMedCrossRefGoogle Scholar
  14. 14.
    Caliskan, G., Hyeon, C., Perez-Salas, U., Briber, R. M., Woodson, S. A., and Thirumalai, D. (2005) Phys. Rev. Lett., 95, 268–303.CrossRefGoogle Scholar
  15. 15.
    Bernstein, F. C., Koetzte, T. F., Williams, G. J. B., Meyer, E. F., Brice, M., Rogers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) Eur. J. Biochem., 80, 319–324.PubMedCrossRefGoogle Scholar
  16. 16.
    Landsberg, P. T. (1971) Problems in Thermodynamics and Statistical Physics, PION, London.Google Scholar

Copyright information

© Pleiades Publishing, Ltd. 2011

Authors and Affiliations

  • L. B. Pereyaslavets
    • 1
  • M. V. Baranov
    • 1
    • 2
  • E. I. Leonova
    • 1
  • O. V. Galzitskaya
    • 1
  1. 1.Institute of Protein ResearchRussian Academy of SciencesPushchino, Moscow RegionRussia
  2. 2.Biological FacultyLomonosov Moscow State UniversityMoscowRussia

Personalised recommendations