Type of Proposal
24-3-2015 2:00 PM
24-3-2015 2:50 PM
Faculty of Science
Importance of the Project
Aminoacyl-tRNA synthetases (aaRS's) are ubiquitous ancient enzymes that have central roles in a range of biological processes including viral assembly, inflammation and cell death. Through elucidating the mechanism of glutamyl tRNA synthetase, key developments can be made in both pharmaceutical development and genetic engineering. As of right now, the mechanism of activation for glutamyl-tRNA synthetase is unclear.
Existing State of Knowledge
Aminoacyl-tRNA synthetases are, perhaps, most well known for their role in protein synthesis. However, glutamyl-tRNA synthetase is unique in that it also plays a critical role in the biosynthesis of chlorophyll. More specifically, it catalyses the aminoacylation of its cognate tRNA via two half-reactions. In the first glutamate is activated by reacting with ATP to give the aminoacyl-adenylate. In the second half-reaction the latter is then reacted with its cognate tRNA, resulting in transfer of the aminoacyl fragment onto the tRNA moiety. This overall process is further complicated by the fact that it appears that all 3 reactants, ATP, glutamate and the cognate tRNA are required for the first half-reaction. Glutamyl-tRNA synthetase has been previously explored, which has lead to the suggestion that tRNA may act as a cofactor during the activation step.
The reaction of ATP with glutamate, within the enzymes active site, can not occur without tRNA also being present. How the tRNA may modify the enzyme, or participate in the reaction is unclear.
A quantum mechanical chemical (QM cluster)-based computational approach to exploring the active site of glutamyl-tRNA synthetase has been used. Previous studies have proven this to be a powerful way to study different catalytic mechanisms. Specifically, it is able to precisely represent the active site residues as well as the substrates. A study by Seigbahn, P. and Himo, F. has shown QM clusters as an effective way to study enzyme's catalytic mechanisms.
Using computational chemistry, we have modeled the activation of glutamate by glutamyl-tRNA synthetase, with and without the presence of the tRNA moiety. Particularly, atomistic-level insights have been gained using a quantum mechanical-chemical (QM cluster)-based computational approach. Current findings suggest, with proper substrate stabilization and orientation, that the activation step can occur. This has lead to the exploration of tRNA's involvement in the mechanism.
The Catalytic Mechanism of Activation by Glutamyl-tRNA Synthetase; A QM-Cluster Study.