Theoretical study of the effects of cation on tRNA

Abstract

The effects of cation on tRNA have been theoretically investigated using the semiempirical potential energy functions. The binding of $Mg^{+2}$ to the model compound and the hydration scheme of the anticodon loop have been determined, and their stabilization energies produced by the introduction of magnesium pentahydrate and water molecules in the first hydration shell were calculated. The results indicate that magnesium pentahydrate is important for the decreasing the flexibility of the anticodon loop and satisfying the large Y37 base stereochemically during the protein synthesis. The effects of $Mg^{+2}$ on the hydration scheme were investigated too.