Evolutionary clade-guided consensus redesign of IsPETase: A computational framework for enhancing thermodynamic
Nima Ghahremani Nezhad1, Shilan S Saleem2, Oluwasola Michael Akinola3
1Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 UKM Bangi, Selangor, Malaysia.
Computational Biology and Chemistry
|May 30, 2026
Summary
Engineered PETase shows enhanced thermostability and PET binding, offering a promising solution for plastic waste. This improved enzyme facilitates more efficient polyethylene terephthalate (PET) degradation.
Area of Science:
- Biotechnology
- Environmental Science
- Biochemistry
Background:
- Global accumulation of polyethylene terephthalate (PET) poses environmental challenges.
- Development of thermostable PET-degrading enzymes is crucial for industrial applications.
- Existing enzymes often lack the stability required for large-scale PET recycling.
Purpose of the Study:
- To engineer a thermostable PETase using a clade-informed consensus design approach.
- To analyze the structural, catalytic, and thermodynamic properties of the engineered enzyme.
- To evaluate the potential of the engineered PETase for enhanced PET degradation.
Main Methods:
- Clade-informed consensus design for enzyme engineering.
- Computational techniques including molecular docking and molecular dynamics simulations.
- Analysis of catalytic pocket volume, binding affinity, and thermodynamic stability (RMSD, SASA, Rg).
Main Results:
- Engineered Con PETase exhibits an enlarged catalytic pocket (496 ų) compared to WT IsPETase (427 ų).
- Con PETase shows increased PET binding affinity (-5.2 kcal/mol) with strengthened catalytic triad interactions.
- Molecular dynamics simulations reveal superior thermodynamic stability for Con PETase, with a ~40°C wider stability window.
Conclusions:
- Consensus ensemble reconstruction successfully reconfigured PETase for enhanced thermal stability.
- The engineered PETase demonstrates improved structural robustness and catalytic efficiency for PET degradation.
- This work provides a pathway for developing highly stable enzymes for effective plastic recycling.
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