Dynamics of transfer RNAs analyzed by normal mode calculation

Abstract

Normal mode calculation is applied to tRNAPhe and tRNAAsp, and their structural and vibrational aspects are analyzed. Dihedral angles along the phosphate-ribose backbone (alpha, beta, gamma, epsilon, zeta) and dihedral angles of glycosyl bonds (chi) are selected as movable parameters. The calculated displacement of each atom agrees with experimental data. In modes with frequencies higher than 130 cm-1, the motions are localized around each stem and the elbow region of the L-shape. On the other hand, collective motions such as bending or twisting of arms are seen in modes with lower frequencies. Hinge axes and bend angles are calculated without prior knowledge. Movements in modes with very low frequencies are combinations of hinge bending motions with various hinge axes and bend angles. The thermal fluctuations of dihedral angles well reflect the structural characters of transfer RNAs. There are some dihedral angles of nucleotides located around the elbow region of L-shape, which fluctuate about five to six times more than the average value. Nucleotides in the position seem to be influential in the dynamics of the entire structure. The normal mode calculation seems to provide much information for the study of conformational changes of transfer RNAs induced by aminoacyl-tRNA synthetase or codon during molecular recognition.