Active-site electronic properties and conformational dynamics of pet-degrading enzymes

Polyethylene terephthalate (PET) is one of the most widely used plastic polymers in the world. PET waste leads to the creation of micro- and nanosized plastic particles that have been linked to cell damage and inflammation in humans. Despite this worldwide environmental and health threat, accumulation of PET waste increases yearly because the main PET recycling method (thermomechanical) results in loss of its desired mechanical properties, which limits recycling. Reports of PET-degrading enzymes converting PET polymer into its molecular building blocks fuel circular economy concepts and a need to optimize these enzymes to achieve higher turnover rates for industrial applications. Here, we study PETase and MHETase from I. sakaiensis using molecular dynamics simulations with the Drude polarizable force field (Drude-2019). Parameters were developed to describe electronic features of PET polymer and its derived monomers, allowing us to study both enzymes in their bound and unbound forms. We found that the overall active site architecture in both PETase and MHETase is sensitive to the presence of substrate, suggesting a possible optimization target. Network analysis of enzyme dynamics suggests key residues that maintain binding site architecture. Moreover, dipole-dipole responses of PETase and MHETase binding site residues were also analyzed as a function of substrate binding. In addition, electronic properties of PET monomers were studied in multiple solvents with different dielectric properties to better understand the substrate polarization when bound to the enzyme. Electric field calculations allowed us to show how PETase and MHETase organize a electric fields that facilitate to catalysis. Overall, these results elucidate the interplay between electronic properties of PET-degrading enzymes and their conformational dynamics, opening new avenues for enzyme engineering efforts.