On the Role of Temperature in the Depolymerization of PET by FAST‐PETase: An Atomistic Point of View on Possible Active Site Pre‐Organization and Substrate‐Destabilization Effects

Abstract

Enzyme FAST‐PETase, recently obtained by machine learning approach, can depolymerize polyethylene terephthalate (PET), a synthetic resin employed in plastics and in clothing fibers. Therefore it represents a promising solution for the recycling of PET‐based materials. In the present study, a model of PET was adopted to describe the substrate, and all‐atoms classical molecular dynamics (MD) simulations on apo‐ and substrate bound‐ FAST‐PETase were carried out at 30°C and 50°C, to provide atomistic details on the binding step of the catalytic cycle. Comparative analysis sheds light on the interactions occurring between the FAST‐PETase and 4PET at 50 °C, the optimal working condition of the enzyme. Pre‐organization of the enzyme active and binding sites has been highlighted while MD of FAST‐PETase:4PET pointed out on the occurrence of solvent‐inaccessible conformations of the substrate promoted by the enzyme. Indeed, neither of these conformations were observed during MD of substrate alone in solution performed at 30 °C, 50 °C and 150 °C. The analysis led us to propose that, at 50 °C, the FAST‐PETase is pre‐organized to bind the PET and that the interactions occurring in the binding site can promote more reactive conformation of PET substrate, thus enhancing the catalytic activity of the enzyme.

From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets

“…This is supported by recent studies suggesting that a 'wrapped' PET conformation is energetically favored in solution, while a 'W-shaped' extended conformation, which is crucial for productive binding poses, is observed in association with the enzyme at elevated temperatures. 68 Such conformational changes, and thus the associated energy barrier, could be influenced by PET-PET and residue-PET interactions, which is investigated next by analyzing intramolecular PET interactions and intermolecular PET-enzyme interactions during productive PET entries.…”