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.
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References
Woodson, S. A. (2010) Annu. Rev. Biophys., 39, 61–77.
Lee, M. K., Gal, M., Frydman, L., and Varani, G. (2010) Proc. Natl. Acad. Sci. USA, 107, 9192–9197.
Levinthal, C. (1968) J. Chem. Phys., 65, 44–45.
Spirin, A. S. (2005) Mol. Biol. (Moscow), 35, 550–556.
Maglott, E. J., Goodwin, J. T., and Glick, G. D. (1999) J. Am. Chem. Soc., 121, 7461–7462.
Matouschek, J. T., Kellis, Jr., Serrano, L., and Fersht, A. R. (1989) Nature, 340, 122–126.
Matouschek, J. T., Kellis, Jr., Serrano, L., Bycroft, M., and Fersht, A. R. (1990) Nature, 346, 440–445.
Wilkinson, K. A., Merito, E. J., and Weeks, K. M. (2005) J. Am. Chem. Soc., 127, 4659–4667.
Taketomi, H., Ueda, Y., and Go, N. (1975) Int. J. Pept. Protein Res., 7, 445–459.
Ding, F., Sharma, S., Chalasani, P., Demidov, V. V., Broude, N. E., and Dokholyan, N. V. (2008) RNA, 14, 1164–1173.
Saenger, W. (1987) Principles of Nucleic Acid Structure [Russian translation], Mir, Moscow, pp. 334–374.
Finkelstein, A. V., and Badretdinov, A. Ya. (1997) Mol. Biol. (Moscow), 31, 469–477.
Galzitskaya, O. V., and Finkelstein, A. V. (1999) Proc. Natl. Acad. Sci. USA, 96, 11299–11304.
Caliskan, G., Hyeon, C., Perez-Salas, U., Briber, R. M., Woodson, S. A., and Thirumalai, D. (2005) Phys. Rev. Lett., 95, 268–303.
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.
Landsberg, P. T. (1971) Problems in Thermodynamics and Statistical Physics, PION, London.
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Original Russian Text © L. B. Pereyaslavets, M. V. Baranov, E. I. Leonova, O. V. Galzitskaya, 2011, published in Biokhimiya, 2011, Vol. 76, No. 2, pp. 287–296.
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Pereyaslavets, L.B., Baranov, M.V., Leonova, E.I. et al. Prediction of folding nuclei in tRNA molecules. Biochemistry Moscow 76, 236–244 (2011). https://doi.org/10.1134/S0006297911020106
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DOI: https://doi.org/10.1134/S0006297911020106