Conformational Selection of a Tryptophan Side Chain Drives the Generalized Increase in Activity of PET Hydrolases Through a Ser/Ile Double Mutation

Abstract

Polyethylene terephthalate (PET) is the most common polyester plastic in the packaging industry, and a major source of environmental pollution due to its single use. Several enzymes, termed PET hydrolases (PETases), have been found to hydrolyze this polymer at different temperatures, with the enzyme from I. sakaiensis (IsPETase) having optimal catalytic activity at 40ºC. Crystal structures of IsPETase have revealed that the side chain of a conserved tryptophan residue within an active site loop (W185) shifts between 3 conformations to enable substrate binding and product release. This is facilitated by two residues unique to IsPETase, S214 and I218 (S/I). When these residues are inserted into other PETases in place of the otherwise strictly conserved His/Phe (H/F) residues found at their respective positions, they enhance activity and decrease Topt. Herein, we combine conventional molecular dynamics and well-tempered metadynamics simulations to investigate dynamic changes of the S/I and H/F variants of IsPETase, as well as three other mesophilic and thermophilic PETases, at their respective temperature and pH optima. Our simulations show that the S/I insertion both increases the flexibility of active site loop regions harboring key catalytic residues and the conserved Trp, as well as expanding the conformational plasticity of this Trp side chain, allowing the conformational transitions that allow for substrate binding and product release in IsPETase. The observed catalytic enhancement caused by this substitution in other PETases appears to be due to conformational selection, by capturing the conformational ensemble observed in IsPETase.