Initiator and elongator tRNA recognition mechanism in Mycobacterium tuberculosis methionyl-tRNA synthetase

Protein synthesis is an essential target for anti-tubercular drug design. Methionyl-tRNA synthetase (MetRS) plays a crucial role in both the initiation and elongation phases of protein synthesis. Molecular recognition of the CAU anticodon of tRNA by MetRS during these two processes is a key step. To date, no experimental structures from Mycobacterium tuberculosis (Mtb) have revealed this binding. Therefore, we modeled the Mtb MetRS complexes with initiator and elongator tRNAs to find their differential binding mechanisms during molecular dynamics simulations of 9 microseconds. We found that the elongator tRNA formed a stable complex with the protein, whereas the initiator tRNA bound transiently. Nevertheless, major intra-tRNA interactions were maintained in both. This may reflect the rapid charging of the initiator tRNA, in contrast to the elongator tRNA, which may require more time for aminoacylation. tRNA interacts with both the active site and the anticodon-binding domain. Electrostatic attractions between tRNA and the protein's catalytic domain likely facilitate its charging with methionine. Meanwhile, a combination of repulsive and attractive forces between the tRNA and the protein's connective peptide domain and KMSKS loop triggered opening of the binding pocket, promoting the reaction and subsequent product release. Concurrently, strong tRNA binding to the anticodon domain supported this process. These findings suggest a possible pathway of tRNA charging. The tRNA formed salt-bridges with positively charged Arg and Lys, whereas negatively charged Asp and Glu caused repulsive binding. In brief, this study provides a plausible mechanism for the differential recognition of initiator and elongator tRNA by Mtb MetRS.