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Prediction of Folding Nuclei in tRNA Molecules

L. B. Pereyaslavets1, M. V. Baranov1,2, E. I. Leonova1, and O. V. Galzitskaya1*

1Institute of Protein Research, Russian Academy of Sciences, Institutskaya ul. 4, 142290 Pushchino, Moscow Region, Russia; fax: (4967) 318-435; E-mail: ogalzit@vega.protres.ru

2Biological Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia

* To whom correspondence should be addressed.

Received June 2, 2010; Revision received September 16, 2010
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

DOI: 10.1134/S0006297911020106