[A method of conformation calculations of large nucleic acid fragments. V. Conformation rearrangements of the modified T psi C-loop of phenylalanyl tRNA].

A development of our method of group-group interactions for conformational calculations of large polynucleotide chains is described. The method takes into account the base-base interactions by means of H-bonds which form Watson-Crick, Hoogsteen and reverse Hoogsteen base-pairs. A variation of the dielectric constant on microscopic distances is considered. Calculations of conformational possibilities of the T psi C-loop in rabbit liver tRNAVal, which, in contrast to tRNAPhe, contains two adenosine A59 and A60 opposite to U54 and psi 55 is performed. In T psi C-loop of tRNAVal energetically favourable conformational rearrangements are possible. The T psi C-stem is extended by an additional A60 X U54 and A59 X psi55 Watson-Crick pair, and 3 nucleotides are present in the loop. There are 3 conformations of the T psi C-loop of tRNAVal with a long stem, which have various conformations of the 3 non-paired nucleotides. The relative energy of various conformations are defined to a considerable extent by screening the electrostatic interactions of phosphate groups. The agreement of conformational rearrangement calculations with experimental data is discussed.