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 (tRNA Phe, tRNA Asp, tRNA fMet, and tRNA Lys). 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.

Original languageEnglish
Pages (from-to)236-244
Number of pages9
JournalBiochemistry (Moscow)
Volume76
Issue number2
DOIs
StatePublished - 1 Feb 2011

    Scopus subject areas

  • Biochemistry

    Research areas

  • coarse-grained structural model, Dynamic programming, folding nucleus, hydrogen bond, stacking and hydrophobic interactions, tRNA folding

ID: 45420199