Engineered enzyme interactions with polycyclic aromatic hydrocarbons: a theoretical approach

In this paper, the techniques of modelling, docking and molecular dynamics were used to study eight single amino acid mutations of the enzyme PhnI to optimise its enzymatic degradation capability. The eight mutants were first equilibrated to avoid deformations of the secondary and tertiary structure and to minimise alterations in the functionality of the chimera enzymes that were obtained. For this purpose, we monitored the potential energy of the systems and the fluctuations of the backbone of the enzymes. The structures of mutant enzymes, at equilibrium, were subjected to docking calculations with selected PAHs. The results indicated a significant increase in the PAH-enzyme interaction with respect to the wild-type protein. The considerable computing resources offered by the GRID computing system made it possible to perform calculations on the entire enzyme system, consisting of six protein subunits, as highlighted in the recent literature.