Rational Redesign of Enzyme via the Combination of Quantum Mechanics/Molecular Mechanics, Molecular Dynamics, and Structural Biology Study

Hong Yan Lin, Xi Chen, Jin Dong, Jing Fang Yang, Han Xiao, Ying Ye, Lin Hui Li, Chang Guo Zhan, Wen Chao Yang, Guang Fu Yang

Research output: Contribution to journalArticlepeer-review

14 Scopus citations


Increasing demands for efficient and versatile chemical reactions have prompted innovations in enzyme engineering. A major challenge in engineering α-ketoglutarate-dependent oxygenases is to develop a rational strategy which can be widely used for directly evolving the desired mutant to generate new products. Herein, we report a strategy for rational redesign of a model enzyme, 4-hydroxyphenylpyruvate dioxygenase (HPPD), based on quantum mechanics/molecular mechanics (QM/MM) calculation and molecular dynamic simulations. This strategy enriched our understanding of the HPPD catalytic reaction pathway and led to the discovery of a series of HPPD mutants producing hydroxyphenylacetate (HPA) as the alternative product other than the native product homogentisate. The predicted HPPD-Fe(IV)═O-HPA intermediate was further confirmed by the crystal structure of Arabidopsis thaliana HPPD/S267W complexed with HPA. These findings not only provide a good understanding of the structure-function relationship of HPPD but also demonstrate a generally applicable platform for the development of biocatalysts.

Original languageEnglish
Pages (from-to)15674-15687
Number of pages14
JournalJournal of the American Chemical Society
Issue number38
StatePublished - Sep 29 2021

Bibliographical note

Funding Information:
This work was funded in part by the National Key Research and Development Program of China (No. 2017YFD0200500), National Natural Science Foundation of China (Nos. 21837001, 22007035, U20A2038, and 21273089), Hubei Province Natural Science Foundation (Nos. 2020BHB027 and 2020CFB487), and Fundamental Research Funds for the South-Central University for Nationalities (No. CZW20020). We thank the Shanghai Synchrotron Radiation Facility BL17U for providing the facility support and Prof. Jun-Jun Liu at Tongji Medical College of Huazhong University of Science & Technology for offering valuable advice on QM/MM calculations. Dedicated to the 100th anniversary of Chemistry at Nankai University.

Publisher Copyright:
© 2021 American Chemical Society.

ASJC Scopus subject areas

  • Catalysis
  • Chemistry (all)
  • Biochemistry
  • Colloid and Surface Chemistry


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