title: Prediction of folding nuclei in tRNA molecules.
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 (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.
authors.affiliation: Institute of Protein Research, Russian Academy of Sciences, Pushchino, Moscow Region, Russia.
authors.forename: L B
authors.initials: LB
authors.lastname: Pereyaslavets
authors.forename: M V
authors.initials: MV
authors.lastname: Baranov
authors.forename: E I
authors.initials: EI
authors.lastname: Leonova
authors.forename: O V
authors.initials: OV
authors.lastname: Galzitskaya
mesh_terms: D000465:Algorithms; D000926:Anticodon; D020029:Base Pairing / Q000502:physiology; D001483:Base Sequence; D057927:Hydrophobic and Hydrophilic Interactions; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry*
chemical_list: D000926:Anticodon; D012346:RNA, Transfer, Amino Acyl