Uracil DNA glycosylase is a key enzyme that identifies and removes damaged bases from DNA in the base excision repair pathway. Experimentalists have identified the possibility of Cd(II) reducing the activity of human uracil DNA glycosylase (hUNG) by binding with the enzyme replacing the catalytic water molecule. The present study focus on the stability variation of the enzyme in the presence and absence of Cd(II) and confirms the reported results with the stability analysis done using molecular dynamic (MD) simulation trajectories. The CavityPlus web server identified seven cavities for the free enzyme as possible binding sites and a cavity containing the active site of the enzyme as the best binding cavity for a ligand. Based on the CavityPlus results and the previously reported work, a free hUNG system and two systems of the enzyme with Cd(II); one with Cd(II) replacing the catalytic water molecule in the active site of the enzyme and the other replacing a non-catalytic water molecule in the active site were generated for the simulation. The simulation trajectories were used for the structural stability analysis of the enzyme in all three systems. The binding free energy of the Cd(II) with the enzyme was calculated using molecular mechanics Poisson Boltzmann surface area method. The results showed that the enzyme achieves comparatively high stability with the removal of catalytic water of the enzyme by Cd(II). Therefore, this supports the previously reported idea that Cd(II) replaces catalytic water molecules and affects enzyme activity.
Keywords: CavityPlus web server; Human uracil DNA glycosylase; MMPBSA; molecular dynamic simulation; structural stability.