Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling

TL;DR

Scientists used computational models to understand why the FAST-PETase enzyme is better at breaking down PET plastic than other enzymes.

Contribution

The study reveals how a specific mutation in FAST-PETase enhances its catalytic efficiency through structural and energetic changes.

Findings

The acylation step in FAST-PETase has a lower free energy barrier (12.1 kcal/mol) compared to PETase (16.5 kcal/mol).

The N233K mutation reduces hydrogen bonding at Asp206, increasing its basic character and improving catalytic interactions.

Abstract

Polyethylene terephthalate (PET) is the most abundant
polyester
plastic, widely used in textiles and packaging, but, unfortunately,
it is also one of the most discarded plastics after one use. In the
last years, the enzymatic biodegradation of PET has sparked great
interest owing to the discovery and subsequent mutation of PETase-like
enzymes, able to depolymerize PET. FAST-PETase is one of the best
enzymes hitherto proposed to efficiently degrade PET, although the
origin of its efficiency is not completely clear. To understand the
molecular origin of its enhanced catalytic activity, we have carried
out a thorough computational study of PET degradation by the FAST-PETase
action by employing classical and hybrid (QM/MM) molecular dynamics
(MD) simulations. Our findings show that the rate-limiting reaction
step for FAST-PETase corresponds to the acylation stage with an estimated
free energy barrier of 12.1 kcal mol–1, which is
significantly smaller than that calculated for PETase (16.5 kcal mol–1) and, therefore, supports the enhanced catalytic
activity of FAST-PETase. The origin of this enhancement is mainly
attributed to the N233K mutation, which, although sited relatively
far from the active site, induces a chain folding where the Asp206
of the catalytic triad is located, impeding that this residue sets
effective H-bonds with its neighboring residues. This effect makes
Asp206 hold a more basic character compared to the wild-type PETase
and boosts the interaction with the protonated His237 of the catalytic
triad in the transition state of acylation, with the consequent decrease
of the catalytic barrier and acceleration of the PET degradation reaction.

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