Investigating Structure-Dynamics-Function Differences Among Various Species of Proyl-tRNA Synthetase Using a Hybrid QM/MM Computational Technique

Abstract

All living organisms contain amino-acyl tRNA synthetases (AARSs) ‒ a family of enzymes critical for protein synthesis. They are responsible for the covalent ligation of proline to its specific tRNA molecule, called tRNAPro, using ATP. The structures of prolyl-tRNA synthetases (ProRSs) have been found to contain a number of domains. The “eukaryote-like” species of ProRS consist of a zinc-binding domain instead of the insertion domain (INS domain) present in “prokaryote-like” proteins. These domains are in constant motion and work in a concerted manner to facilitate the catalytic reaction step. Coupled domain dynamics have been found to be necessary for the catalysis. This calls into question the differences in structure and dynamics between the two non-catalytic domains and how it influences the catalytic steps. A comparative study of the structure-dynamic-function relationship among various species of ProRS is being investigated using molecular simulations. In parallel, a computational study of the sequence homology amongst various species of ProRS using the Dali server for the comparison of proteins is being performed. In order to further investigate the evolution of the ProRS protein family, the similarities and differences of different ProRS species are being studied. The preliminary results for this investigation will be presented.