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From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets
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Researchers used computational and structural analyses to decode how PET polymer chains enter and bind within the active sites of plastic-degrading hydrolase enzymes, providing mechanistic insights that could guide engineering of more efficient PETase variants for industrial recycling applications.
Plastic-degrading enzymes facilitate the biocatalytic recycling of poly(ethylene terephthalate) (PET), a significant synthetic polymer, and substantial progress has been made in utilizing PET hydrolases for industrial applications. To fully exploit the potential of these enzymes, a deeper mechanistic understanding followed by targeted protein engineering is essential. Through advanced molecular dynamics simulations and free energy analysis methods, we elucidated the complete pathway from the initial binding of two PET hydrolases-the thermophilic leaf-branch compost cutinase (LCC) and polyester hydrolase 1 (PES-H1)-to an amorphous PET substrate, ultimately leading to a PET chain entering the active site in a hydrolyzable conformation. Our findings indicate that initial PET binding is nonspecific and driven by polar and hydrophobic interactions. We demonstrate that the subsequent entry of PET into the active site can occur via one of three key pathways, identifying barriers related to both PET-PET and PET-enzyme interactions, as well as specific residues highlighted through in silico and in vitro mutagenesis. These insights not only enhance our understanding of the mechanisms underlying PET degradation and facilitate the development of targeted enzyme enhancement strategies but also provide a novel framework applicable to enzyme studies across various disciplines.
More Papers Like This
From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets
AI summary Read the abstract
Researchers used molecular dynamics simulations and free energy analysis to decode the complete pathway by which PET polymer chains enter the binding pockets of plastic-degrading hydrolase enzymes at the atomic level. The study aims to deepen mechanistic understanding needed to guide protein engineering of PET hydrolases toward sufficient activity for industrial biocatalytic recycling.
Probing Enzymatic PET Degradation: Molecular Dynamics Analysis of Cutinase Adsorption and Stability
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This study used all-atom molecular dynamics simulations to reveal that the LCC-ICCG cutinase enzyme binds to PET plastic surfaces primarily through hydrophobic and aromatic interactions, with minimal structural changes to the enzyme and a 24% reduction in enzyme-water hydrogen bonds upon adsorption, clarifying key initial steps of enzymatic PET degradation.
Atomistic-Level Insights into the Role of Mutations in the Engineering of PET Hydrolases: A Systematic Review
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This systematic review examined the role of mutations in engineering PET-degrading enzymes including TfCut2, IsPETase, and LCC across 20 studies, integrating molecular dynamics simulations with experimental findings. The review identifies key residue hotspots enhancing catalytic performance and thermostability, demonstrating MD simulations as powerful tools guiding targeted mutation strategies for enzymatic plastic degradation.
Insights into the Enhancement of the Poly(ethylene terephthalate) Degradation by FAST-PETase from Computational Modeling
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"Researchers used classical and quantum mechanical/molecular mechanics simulations to reveal why the engineered enzyme FAST-PETase degrades PET plastic far more efficiently than its parent enzyme PETase, tracing the enhancement to a single N233K mutation that increases the basicity of a catalytic residue and lowers the energy barrier for the rate-limiting acylation step by over 4 kcal/mol. These findings provide molecular-level design principles for engineering even more effective plastic-degrading enzymes."
Dynamic shift of internal electric field accelerates enzymatic polyethylene terephthalate depolymerization
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Quantum mechanics/molecular mechanics simulations reveal that PET depolymerization by the hydrolase LCCICCG is controlled by a dynamically shifting internal electric field that stabilizes transition states, lowering the rate-determining energy barrier to 20.4 kcal/mol. These mechanistic insights into how enzyme internal electric fields drive plastic hydrolysis provide a rational engineering framework for designing more efficient PET-degrading enzymes, directly advancing enzymatic approaches to eliminating PET microplastic pollution.
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