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From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets
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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.
Abstract Plastic-degrading enzymes hold promise for biocatalytic recycling of poly(ethylene terephthalate) (PET), a key synthetic polymer. Despite their potential, the current activity of PET hydrolases is not sufficient for industrial use. To unlock their full potential, a deep mechanistic understanding followed by protein engineering is required. Using cuttingedge molecular dynamics simulations and free energy analysis methods, we uncover the entire 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 material to a PET chain entering the active site and adopting a hydrolyzable geometry. Our results reveal the initial PET binding and elucidate its non-specific nature driven by electrostatic and hydrophobic forces. Upon PET entry into the active site, we uncover that this process can occur via one of three key pathways and detect barriers to it arising from both PET–PET and PET–enzyme interactions, with specific residues identified by in silico and in vitro mutagenesis. These insights not only advance our understanding of PET degradation mechanisms and pave the way for targeted enzyme enhancement strategies, but also offer an innovative approach applicable to enzyme studies across 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 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.
On the Role of Temperature in the Depolymerization of PET by FAST‐PETase: An Atomistic Point of View on Possible Active Site Pre‐Organization and Substrate‐Destabilization Effects
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Researchers used molecular simulations to understand why the plastic-degrading enzyme FAST-PETase works better at 50°C than at lower temperatures when breaking down PET plastic. They found that at the optimal temperature the enzyme's active site pre-organizes itself to bind PET more efficiently, and the enzyme forces the plastic into a more reactive shape. Understanding these mechanisms can guide the engineering of even more effective enzymes for breaking down PET microplastics and plastic waste at practical scales.
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.
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.
Rational redesigning the Acinetobacter haemolyticus lipase KV1 for improved polyethylene terephthalate degradation via molecular docking and dynamics simulations
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This study evaluated engineered variants of lipase KV1 for improved PET degradation, using binding mode analysis and molecular simulations to understand enzymatic PET hydrolysis mechanisms. Optimized variants demonstrated improved degradation efficiency, contributing to biotechnological solutions for plastic waste.
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