Curr. Biotech. ›› 2018, Vol. 8 ›› Issue (2): 153-160.DOI: 10.19586/j.2095-2341.2017.0137

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Study on Biodegradation Mechanism of Amide by Molecular Simulation

ZHANG Yu, LIU Zhifeng, CHEN Ming, LIU Shijun, XU Hongbo, TANG Zhishu   

  1. 1.Shaanxi Collaborative Innovation Center of Chinese Medicinal Resource Industrialization, Shaanxi University of Chinese Medicine, Shaanxi Xianyang 712083, China; 2.College of Environment Science and Engineering, Hunan University, Changsha 410082, China
  • Received:2017-10-16 Online:2018-03-25 Published:2017-11-24

酰胺生物降解机制的分子模拟研究

张娱1,刘智峰2,陈明2,刘世军1,许洪波1,唐志书1*   

  1. 1.陕西中医药大学陕西省中药资源产业化协同创新中心, 陕西 咸阳 712083; 2.湖南大学环境科学与工程学院, 长沙 410082
  • 通讯作者: 唐志书，教授，博士，硕士研究生导师，主要从事中药资源开发与综合利用研究。E-mail：tzs6565@163.com
  • 作者简介:张娱，讲师，研究方向为固体废弃物资源化。E-mail：zhangyu19432@163.com。
  • 基金资助:
    国家自然科学基金项目（51679085）;陕西中医药大学科研基金项目（2015PY10）资助。

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Abstract: In order to explore the microscopic degradation mechanism of amide degrading enzymes, we used molecular docking method to investigate the binding modes of amide to amidase. The theoretical models of their structures were obtained. According to the lowest score function principle, the results showed that the best conformation scoring function between RhAmidase and L-methioninamide were -86.741 9, re-rank scores were -76.022 4. And we used LPC/CSU Server to study the interactions between RhAmidase and L-methioninamide. Results showed that hydrophobic interaction was the strongest contacts in the complex. The amino acid residues ARG256 A, LEU353 A, TYR346 A, ARG225 A, THR218 A and PRO222 A were detected to play significant roles in catalytic processes.

Key words: amide, amidase, biodegradation

摘要： 为探索酰胺生物降解酶的微观降解机制，用分子对接的方法模拟了酰胺与酰胺酶的相互作用，得到其复合物结构的理论模型，根据打分函数最低原则筛选出的RhAmidase与L-Methioninamide之间最佳构象打分函数为-86.741 9，二次打分函数为-76.022 4。同时，应用LPC/CSU Server研究了最佳构象的相互作用情况，结果表明，酰胺与酰胺酶之间以疏水作用数量最多，酰胺酶的ARG256 A、LEU353 A、TYR346 A、ARG225 A、THR218 A和PRO222 A在催化过程中起到了重要作用。

关键词: 酰胺, 酰胺酶, 生物降解

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