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Biodegradation of anionic polyacrylamide by manganese peroxidase: docking, virtual mutation based on affinity, QM/MM calculation and molecular dynamics simulation

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Abstract

Manganese peroxidase (Mn P) is capable of effectively degrading anionic polyacrylamide (HPAM). However, the interaction of Mn P with HPAM at molecular level is lacking until now. Here, the HPAM model compounds, HPAM-2, HPAM-3, HPAM-4, and HPAM-5, were selected to reveal their binding mechanisms with Mn P. The results showed that the most suitable substrate for Mn P was HPAM-5, and the main reason for MnP-HPAM-5 with maximal affinity was strong hydrogen bond. LYS96 was the important key residue in all complexes, and the number of key residue was largest in MnP-HPAM-5. The optimal THR27ILE mutant may enhance the affinity of Mn P to HPAM-4. The stability of Mn P binding to HPAM-4 was the optimal. These results were helpful in designing highly efficient Mn P against HPAM to protect the ecological environment.

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Acknowledgements

The financial supports for this work from the National Natural Science Foundation of China under Grant No. 51274012, the National Natural Science Foundation of China under Grant No. 31601465, and the Stable Talent Fund of Huainan Normal University (BSKYQDJ) are gratefully acknowledged.

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Authors and Affiliations

  1. School of Material Science and Engineering, Anhui University of Science and Technology, Huainan, 232001, China

    Fanglue Wang & Dongchen Zhang

  2. School of Mechanical and Electrical Engineering, Huainan Normal University, Huainan, 232001, China

    Liwen Zhang

  3. School of Food and Bioengineering, Hefei University of Technology, Hefei, 230009, China

    Xuefeng Wu, Shengsong Deng & Xinyu Yuan

Authors
  1. Fanglue Wang
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  2. Dongchen Zhang
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  3. Liwen Zhang
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  4. Xuefeng Wu
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  5. Shengsong Deng
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  6. Xinyu Yuan
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Contributions

Designed and performed the experiments, analyzed the data, and wrote the paper: Fanglue Wang. Provided funding and guidance: Dongchen Zhang. Modified grammar, and drew parts of figures and tables: Liwen Zhang. Contributed simulation software (Discovery Studio 2020) and provided helpful discussion: Xuefeng Wu and Shengsong Deng. Performed part experiments: Xinyu Yuan.

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Correspondence to Fanglue Wang.

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Wang, F., Zhang, D., Zhang, L. et al. Biodegradation of anionic polyacrylamide by manganese peroxidase: docking, virtual mutation based on affinity, QM/MM calculation and molecular dynamics simulation. Bioprocess Biosyst Eng 45, 1349–1358 (2022). https://doi.org/10.1007/s00449-022-02750-8

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  • DOI: https://doi.org/10.1007/s00449-022-02750-8

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