QM/MM Investigation to Identify the Hallmarks of Superior PET Biodegradation Activity of PETase over Cutinase

Abstract

Polyethylene terephthalate (PET), the most extensively used plastic, is one of the significant contributors to global plastic pollution. Enzymatic biodegradation of PET using different hydrolases has been previously reported as a promising biodegradation strategy for closed-loop recycling. Among the different hydrolases known to depolymerize PET to its soluble building blocks, the PETase and cutinase family of enzymes have notable PET biodegradation activities. In fact, they exhibit different thermostabilities and efficiencies in hydrolyzing PET polyesters despite sharing high structural similarities. Herein, we employed quantum mechanics/molecular mechanics calculations to identify the key factors necessary for efficient PET hydrolysis. Our results show that in both PETase and cutinase (Tfcut2 as a model system), the PET hydrolysis reaction pathway proceeds through a multi-step process with rate-limiting steps having energy barriers of ∼18.0 and ∼20 kcal/mol for PETase and TfCut2, respectively, which agrees well with the experimental data. A deeper inspection of the structural complexes revealed that the bent conformation adopted by PET and the tighter H-bond interaction between the catalytic triad residues, mediated by the unique disulfide bridge, contribute to the lower barrier (i.e., better catalytic performance) of PETase. The intrinsic molecular features identified in this work will also be useful for rational engineering of more efficient cutinases for PET hydrolysis.

Computational Chemistry as Applied in Environmental Research: Opportunities and Challenges

“…QM/MM has been applied to enzymatic biodegradation processes in environmentally related applications such as the biodegradation of polyethylene terephthalate (PET) by various hydrolases and depolymerases. − Biodegradation has emerged as an environmentally conscious way of converting PET to its building blocks. Comparative studies have elucidated a four-step catalytic process for PET degradation by measuring the evolution of the active site and the electronic effects of the enzymes along the reaction pathway using an ONIOM approach (Figure a).…”

Synthesis and characterization of novel Ru(III) complexes of 2‐aminopyrazine: Interaction with biomolecules, antineoplastic activity, and computational investigation

“…DFT implemented in Gaussian16 software 29 was successfully used to fully characterize the most stable geometries for the two studied complexes. Becke, 3-parameter, Lee-Yang-Parr (B3LYP) functional, [30][31][32][33] which has been extensively used to study various chemical systems, [34][35][36][37][38] in conjunction with 6-311++G(3df,3pd) basis set was used to treat all atoms except Au which was treated based on Los Alamos National Laboratory 2 Double-Zeta (LANL2DZ) basis set. This combination of functional and basis sets has been used extensively to describe various chemical systems.…”

Improving plastic degrading enzymes via directed evolution

“…Notably, caution must be taken in interpreting the results of docking studies as the structures of short substrates bound to PETases do not represent the interaction of PETases with an extended PET chain and molecular dynamic simulations continue to give further insights in the molecular mechanism ( Aboelnga and Kalyaanamoorthy 2022 , Falkenstein et al. 2023 ).…”