Atomistic adsorption of PETase onto large-scale PET 3D-models that mimic reality

Abstract

Polyethylene terephthalate (PET) has been widely used in plastic products, leading to massive PET waste accumulation in ecosystems worldwide. The efforts to find greener processes for dealing with post-consumer PET waste led to the discovery of PET-degrading enzymes such as Ideonella sakaiensis PETase (IsPETase). In silico studies have provided valuable contributions to this field, shedding light on the catalytic mechanisms and substrate interactions in many PET hydrolase enzymes. However, most of these studies often rely on short PET oligomers, failing to replicate the catalytic-relevant interactions and the true substrate motions occurring during contact with a PET-degrading enzyme. A comprehensive atomistic study of PET in both its crystalline (cPET) and amorphous (aPET) states, along with the adsorption of a PET-degrading enzyme onto solid PET, would greatly advance our understanding of the mechanisms driving PET biodegradation. In this study, we developed large-scale computational models of cPET, comprising thousands of monomers, and conducted Molecular Dynamics simulations to follow the transformation of cPET into aPET. These models were validated by confrontation with experimentally determined data. We then studied the adsorption of IsPETase on the assembled PET models, discussed the main phenomena that differentiate the two adsorption processes, and explored them from a catalytic perspective. The results and the computational PET models provided herein are envisioned to aid in the development of innovative strategies for PET waste biodegradation.