Human Glycinamide ribonucleotide transformylase (GAR Tfase) is a regulatory enzyme in de novo purine biosynthesis pathway. Inhibition of the GAR Tfase enzyme can control purine formation which can inhibit uncontrolled cell division. Hence, GAR Tfase is considered as an anti-cancer target. Extensive research is being done to optimize the enzyme-inhibitor binding. Knowledge of the catalytic mechanism would help in designing an efficient inhibitor. We choose to study E.coli GAR Tfase because it is a well-studied system and most of the functional residues are the same in human and E.coli GAR Tfase. E.coli GAR Tfase exhibits pH-dependent conformational changes and the catalytic activity. E.coli GAR Tfase is catalytically active between pH 6 to 10 and the pH-activity curve adopts bell-shaped curve. In an experimentally proposed mechanism for E.coli GAR Tfase, His108 is considered as a general acid catalyst because this residue is present at hydrogen bonding distance with the carbonyl group of the ligand. Catalytic water near Asp144, which transfers a proton between ligands, is not in hydrogen bonding distance with ligands. So, the mechanism of proton transfer is unclear. We have addressed these issues and probed this problem through pH-replica exchange molecular dynamics (pH-REMD) simulation. From simulation analyses, we propose that Asp144 is the residue which acts as the general acid catalyst, not His108. Furthermore, a new position for catalytic water has been proposed which is within hydrogen bonding distance with the ligand and remains in the vicinity throughout the simulation. In the future, we will show that the mechanism we propose has lower free energy barrier than the previously proposed mechanism.

Improvised catalytic mechanism of E. coli glycinamide ribonucleotide transformylase: A computational study

255th National Meeting (2018)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.