Reaction Mechanisms of Editing (Proofreading) by Leucyl-tRNA Synthetase Revealed by QM/MM Molecular Dynamics Simulations

Abstract

Aminoacyl-tRNA synthetases (aaRS's) play a critical role in decoding genetic information located on genome DNA sequence, through catalyzing attachment of their cognate amino acid to 3′-end of the specific tRNA. The fidelity of translation is assured by their strict discrimination of the cognate amino acids from non-cognate ones. However, in the case of valine, isoleucine, and leucine systems, it is difficult for the cognate enzymes to discriminate their specific amino acid; thus, the synthetases produce mis-aminoacylated tRNAs, such as Ile-tRNALeu. However, the mis-products are hydrolyzed through the “editing” reaction by the aaRS's.In this study, we performed molecular docking simulations of the LeuRS•tRNALeu complex and an incognate amino acid (Val), using a novel algorithm referred to as the Fully Solvated Dynamical Docking (FSDD) scheme which is developed by our group (see the presentation by Hagiwara, Y., et al.). Thus, we have successfully identified ordered water molecules in its active site, and also, one of such waters has been found to be located at the appropriate position as the nucleophile.Then, for the modeled structure of the LeuRS•Val-tRNALeu complex, we performed QM/MM calculations using our new interface program connecting QM (gamess) and MM (amber) engines, which has also been developed by us. Thereby, it has been found that LUMO is located on the reaction point on the substrate, suggesting that the water identified actually attacks the orbital as the nucleophile. In fact, as the distance between the substrate and the water (O atom) is decreased, the orbital energies of 2p electrons of the oxygen atom is elevated toward the energy level of HOMO. In the presentation, we will show recent results of our QM/MM-MD simulations performed to elucidate detailed reaction mechanisms of the editing.