Food and Fermentation Industries >

2024 , Vol. 50 >Issue 11: 85 - 94

DOI: https://doi.org/10.13995/j.cnki.11-1802/ts.036354

Interaction mechanism between polyphenols with different degree of polymerization and trimethylamine-N-oxide demethylase based on molecular simulation study

  • ZENG Xiangquan ,
  • CAO Rui ,
  • YU Meihong ,
  • ZHAO Jinling ,
  • CHENG Jieyi ,
  • LI Jian
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  • 1(Key Laboratory of Green and Low-carbon Processing Technology for Plant-based Food of China National Light Industry Council, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China)
    2(Beijing Engineering and Technology Research Center of Food Additives, School of Food and Health, Beijing Technology and Business University, Beijing 100048, China)

Received date: 2023-06-03

  Revised date: 2023-07-06

  Online published: 2024-07-12

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Abstract

Endogenous formaldehyde is a common factor that affects the quality and safety of seafood.Trimethylamine N-oxide demethylase (TMAOase) has been demonstrated to play a significant role in the formation of endogenous formaldehyde.Therefore, the formation of endogenous formaldehyde in seafood can be effectively controlled by inhibiting the activity of TMAOase.The results of previous studies have shown that plant polyphenols can significantly inhibit the activity of TMAOase, while researchers mainly focused on the non-covalent interactions between polyphenols and TMAOase basing on inhibition kinetics and spectroscopic analysis.However, few teams attempted to elucidate their key binding sites and structure-activity relationships by molecular simulation techniques.Hence, the present study aims to investigate the interaction between polyphenols with different degrees of polymerization and TMAOase using molecular docking and molecular dynamics simulation studies.Also, the binding stability of the complexes and effects of polyphenols on the structure of TMAOase were analyzed.The data of molecular docking studies showed that four polyphenols with different degrees of polymerization were able to form complexes with TMAOase, which were mainly combined by hydrophobic interactions and hydrogen bonds.The binding capacity of procyanidin B2 with TMAOase was the strongest, which could bind with TMAOase by hydrophobic residues (His-89, Phe-169, Gly-195, Gly-198, Gly-243, Phe-244) and hydrogen bonding sites (Thr-199 and Asn-438).The molecular dynamics simulation study indicated four polyphenols increased the surface hydrophobicity of TMAOase, while the number of intramolecular hydrogen bonds greatly decreased.Nevertheless, no significant change in the secondary structure of enzyme was observed.The inhibitory effect of procyanidin B2 on TMAOase was non-competitive and the stability of complexes were the highest.In addition, the van der Waals force also played a role in the formation of the complexes.In a word, the interaction mechanism between polyphenols and TMAOase was explored at a molecular level, which might provide a new idea for screening of TMAOase inhibitors in the future.

Key words： trimethylamine N-oxide demethylase (TMAOase); polyphenol; interaction mechanism; molecular docking; molecular dynamics

Cite this article

ZENG Xiangquan , CAO Rui , YU Meihong , ZHAO Jinling , CHENG Jieyi , LI Jian . Interaction mechanism between polyphenols with different degree of polymerization and trimethylamine-N-oxide demethylase based on molecular simulation study[J]. Food and Fermentation Industries, 2024 , 50(11) : 85 -94 . DOI: 10.13995/j.cnki.11-1802/ts.036354

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