Exploring the Reaction Mechanism of Polyethylene Terephthalate Biodegradation through QM/MM Approach

The enzyme PETase
fromIdeonella sakaiensis (IsPETase) strain 201-F6 can catalyze the hydrolysis
of polyethylene terephthalate (PET), mainly converting it into mono(2-hydroxyethyl)
terephthalic acid (MHET). In this study, we used quantum mechanics/molecular
mechanics (QM/MM) simulations to explore the molecular details of
the catalytic reaction mechanism of IsPETase in the
formation of MHET. The QM region was described with AM1d/PhoT and
M06-2X/6-31+G(d,p) potential. QM/MM simulations unveil
the complete enzymatic PET hydrolysis mechanism and identify two possible
reaction pathways for acylation and deacylation steps. The barrier
obtained at M06-2X/6-31+G(d,p)/MM potential for the
deacylation step corresponds to 20.4 kcal/mol, aligning with the experimental
value of 18 kcal/mol. Our findings indicate that deacylation is the
rate-limiting step of the process. Furthermore, per-residue interaction
energy contributions revealed unfavorable contributions to the transition
state of amino acids located at positions 200–230, suggesting
potential sites for targeted mutations. These results can contribute
to the development of more active and selective enzymes for PET depolymerization.