Harnessing protein language model for structure-based discovery of highly efficient and robust PET hydrolases

Banghao Wu, Bozitao Zhong, Lirong Zheng (), Runye Huang, Shifeng Jiang, Mingchen Li, Liang Hong () and Pan Tan ()
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Banghao Wu: Shanghai Jiao Tong University
Bozitao Zhong: Shanghai Jiao Tong University
Lirong Zheng: Shanghai Jiao Tong University
Runye Huang: Shanghai Jiao Tong University
Shifeng Jiang: Shanghai Jiao Tong University
Mingchen Li: Shanghai Jiao Tong University
Liang Hong: Shanghai Jiao Tong University
Pan Tan: Shanghai Jiao Tong University

Nature Communications, 2025, vol. 16, issue 1, 1-12

Abstract: Abstract Plastic waste, particularly polyethylene terephthalate (PET), presents significant environmental challenges, driving extensive research into enzymatic biodegradation. However, existing PET hydrolases (PETases) are limited by narrow sequence diversity and suboptimal performance. This study introduces VenusMine, a protein discovery pipeline that integrates protein language models (PLMs) with a representation tree to identify PETases based on structural similarity using sequence information. Using the crystal structure of IsPETase as a template, VenusMine identifies and clusters target proteins. Candidates are further screened using PLM-based assessments of solubility and thermostability, leading to the selection of 34 proteins for biochemical validation. Results reveal that 14 candidates exhibit PET degradation activity across 30–60 °C. Notably, a PET hydrolase from Kibdelosporangium banguiense (KbPETase) demonstrates a melting temperature (Tm) 32 °C higher than IsPETase and exhibits the highest PET degradation activity within 30 – 65 °C among wild-type PETases. KbPETase also surpasses FastPETase and LCC in catalytic efficiency. X-ray crystallography and molecular dynamics simulations show that KbPETase possesses a conserved catalytic domain and enhanced intramolecular interactions, underpinning its improved functionality and thermostability. This work demonstrates a novel deep learning approach for discovering natural PETases with enhanced properties.

Date: 2025
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DOI: 10.1038/s41467-025-61599-z

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