Dynamics of tRNA: Experimental Neutron Spectra Compared with a Normal Mode Analysis

Abstract

AbstractA comparison is made of experimental inelastic neutron scattering spectra from tRNA with spectra calculated from a normal mode analysis of the molecule. The experimental data indicate that a dynamic transition occurs with temperature, as is seen in proteins. At low temperatures a broad peak is seen in the dynamic structure factor, due to the lowest frequency collective modes. This peak is centered at ˜40 cm−1, somewhat higher in frequency than that observed in small globular proteins. The vibrational frequency distribution calculated from the normal mode analysis rises to a broad maximum at 50 cm−1, in general accord with the experiment. However, the lowest frequency vibrations in the harmonic model (<40 cm−1) are not present in the experimental sample. Possible reasons for this are discussed.