QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate

The environmental problems derived from the generalized plastic consumption and disposal could find a friendly solution in enzymatic biodegradation. Recently, two hydrolases from Ideonella sakaiensis 201-F6 and the metagenome-derived leaf-branch compost cutinase (LCC), more specially the improved ICCG variant, have revealed degradation activity toward poly ethylene terephthalate (PET). In the present study, the reaction mechanism of this polymer breakage is studied at an atomic level by multiscale QM/MM molecular dynamics simulations, using semiempirical and DFT Hamiltonians to describe the QM region. The obtained free energy surfaces confirmed a characteristic four-step path for both systems, with activation energies in agreement with the experimental observations. Structural analysis of the evolution of the active site along the reaction progress and the study of electrostatic effects generated by the proteins reveal the similarity in the behavior of the active site of these two enzymes. The origin of the apparent better performance of the LCC-ICCG protein over PETase must be due to its capabilities of working at higher temperature and its intrinsic relationship with the crystallinity grade of the polymer. Our results may be useful for the development of more efficient enzymes in the biodegradation of PET.

Automated summary

This study investigated the enzymatic biodegradation of PET at an atomic level using molecular dynamics simulations. Two hydrolases, Ideonella sakaiensis 201-F6 and leaf-branch compost cutinase, showed degradation activity towards PET. The study revealed a characteristic four-step degradation pathway for both enzymes, with LCC-ICCG variant outperforming PETase possibly due to its ability to work at higher temperatures and its intrinsic relationship with the crystallinity grade of the polymer.