Structural modelling of the complex of leucyl-tRNA synthetase and mis-aminoacylated tRNALeu

To assure fidelity of translation, class Ia aminoacyl-tRNA synthetases (aaRSs) edit mis-aminoacylated tRNAs. Mis-attached amino acids and structural water molecules are not included simultaneously in the current crystal structures of the aaRS•tRNA complexes, where the 3′-ends (adenine 76; A76) are bound to the editing sites. A structural model of the completely solvated leucyl-tRNA synthetase complexed with valyl-tRNALeu was constructed by exploiting molecular dynamics simulations modified for the present modelling. The results showed that the ribose conformation of A76 is distinct from those observed in the above-mentioned crystal structures, which could be derived from structural constraints in a sandwiched manner induced by the mis-attached valine and tRNALeu.