Ab Initio molecular orbital study on the thermostability of the extreme thermophile tRNA: Role of the base stacking

Abstract

In extremely thermophilic tRNA, ribosylthymine is replaced by 2-thioribosylthymine at the key site in tRNA. By means of the ab initio molecular orbital (MO) calculation using the 4–31G basis set, we evaluate how this replacement brings about an increment of stacking energy, and how this increment in stacking energy is responsible for the stability of the thermophile tRNA. Calculated stacking energy for G : s 2 T : Ψ is larger by 4·85 kJ/mol (1·16 kcal/mol) than that for G : T : Ψ. Taking account of the thermodynamical data of yeast tRNAs by Privalov & Filimonov (1978), such an increment in stacking energy seems to considerably contribute to the increase of the midpoint melting temperature ( T m ) in the thermophile tRNA, although other factors such as hydrogen bonding, ribose puckering and magnesium ions can not be excluded. It is found that the dispersion force mainly contributes to the stacking energies for G : T : Ψ and G : s 2 T : Ψ, especially for the latter. From the decomposition of the SCF energy, electrostatic and charge transfer energies are found to contribute to the stabilization of the thermophile tRNA, though the contribution of the former is larger than the latter.