Fig. 1: Structural characteristics of amorphous PET polymer, catalytic mechanism of PET hydrolase, and computational model for the redesign of PET hydrolase.
From: Computational loop reconstruction based design of efficient PET hydrolases
a Structural characteristics of amorphous PET polymer and the potential energy variations of each torsion angle in the PET polymer chain. The molecular simulation results were obtained from Boyd et al.16. Type I bond (CA-CD-O-C) linking ethylene glycol and the ester, its minimum potential energy angle lies at 180°; type II bond (OD-CD-CA-CA) linking phenyl and the ester, its minimum potential energy angle lies at 0° or 180°; type III bond (O-C-C-O), the ethylenic bond, its minimum potential energy angle lies at ±60° or 180°; type IV bond (CD-O-C-C), the glycol bond, its low potential energy angle lies in the range of 100°–260°. b Catalytic mechanism of PET hydrolase. The reaction initiates with a nucleophilic attack by serine on the polymer’s ester bond, forming the first tetrahedral intermediate (TI1). Then the first reaction product (MHET or an oligomer) was released, forming an acyl-enzyme intermediate (AI). Subsequently, a water molecule attacks the new ester bond in AI, resulting in deacylation and the formation of a second tetrahedral intermediate (TI2), ultimately releasing the PET fragment. The red arrows indicate the electron transfer pathways. c Computational enzyme design model and the catalytic geometric constraints. The PET model substrate is marked in blue, while the catalytic triad and oxyanion hole residues are shown in black. d2 represents the hydrogen bond distance constraint between the donor atom and the acceptor atom (2.6–3.2 Å). θ2 represents the hydrogen bond angle constraint between the donor, the hydrogen atom, and the acceptor (120–180°). d1 represents the nucleophilic attack distance constraint of the hydroxyl oxygen of serine and the central carbon atom of the substrate ((Ser) OG-C12 (PET), 1.4–1.7 Å)).
