基于分子模拟技术的不同聚合度多酚与氧化三甲胺脱甲基酶的相互作用机制研究

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

内源性甲醛是影响海产品品质和安全的常见因素,而氧化三甲胺脱甲基酶(trimethylamineN-oxide demethylase,TMAOase)被证明在内源性甲醛的生成过程中具有重要作用,因此抑制TMAOase的活性可以有效控制海产品内源性甲醛的产生。以往研究表明,植物多酚可以显著抑制TMAOase的活性,但关于二者的相互作用研究主要通过抑制动力学和光谱学分析证明它们之间的非共价相互作用,鲜有团队尝试利用分子模拟技术阐明两者间的关键结合位点和构效关系。因此,该研究采用分子对接及分子动力学模拟研究不同聚合度多酚与TMAOase之间的相互作用,并分析复合物的结合稳定性及对TMAOase结构的影响。分子对接结果表明4种不同聚合度的多酚均能与TMAOase形成复合物,其主要通过疏水相互作用和氢键结合,其中原花青素B2与酶的结合能力最强,其可通过疏水性氨基酸His-89、Phe-169、Gly-195、Gly-198、Gly-243和Phe-244以及氢键作用位点Thr-199和Asn-438与TMAOase结合。分子动力学模拟显示4种多酚均能增加TMAOase的表面疏水性并降低其分子内氢键数量,但并未使二级结构发生明显变化。原花青素B2对TMAOase的抑制作用为非竞争性抑制,与酶形成的复合物稳定性最好,且范德华力作为主要相互作用力也参与了复合物的形成和稳定。该研究在分子水平上解析了不同聚合度多酚与TMAOase之间的相互作用机制,为未来TMAOase抑制剂的筛选提供了新思路。

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.