如何Huperzine A进入和离开乙胆酶的结合沟? 引导分子动力学模拟的模拟
Yechun Xu1, Jianhua Shen, Xiaomin Luo
1Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Meteria Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Zhangjiang Hi-Tech Park, Shanghai 201203, P. R. China.
Journal of the American Chemical Society
|October 14, 2005
概括
胡氨酸A (HupA) 更容易与乙胆酶 (AChE) 结合,而不是解离,这可以通过原子级相互作用来解释. 水作为滑剂,在瓶处的硬质障碍对HupA来说是关键.
科学领域:
- 生物化学 生物化学
- 分子生物学分子生物学
- 计算化学的计算化学
背景情况:
- 胡素A (HupA) 是已知的乙胆酶 (AChE) 抑制剂.
- 之前的实验表明,与HupA的结合相比,HupA从ACHE的解结较慢.
- 控制HupA-AChE相互作用的原子层机制仍然不清楚.
研究的目的:
- 研究Huperzine A (HupA) 与Torpedo californica acetylcholinesterase (TcAChE) 在原子水平上的结合和解结合途径.
- 阐明关键的分子相互作用和控制HupA与AChE活性部位的结合和解离的力量.
- 为实验观察到的HupA-AChE结合的动力学提供原子层面的见解.
主要方法:
- 使用定向分子动力学 (SMD) 模拟来建模Hup.A.的进入和退出过程.
- 分析沿着结合和解结合路径的力概况.
- 直接键,水桥和疏水相互作用的识别和分析.
- 传统的分子动力学 (MD) 模拟被用来观察键动力学.
主要成果:
- 在能量方面,HupA与AChE活性部位结合比解离更容易.
- 瓶处的硬质障碍是HupA解离的主要因素,而水分子则充当滑剂.
- 残留物Asp72在进入和退出过程中在紧HupA中起着至关重要的作用,而Gly117-Gly118键翻转是ACHE的内在属性.
结论:
- 这项研究为HupA和ACHE的差异性结合和解结合动力学提供了第一个原子层次的解释.
- 分子动力学模拟揭示了固态阻碍,水滑和特定残留物相互作用 (Asp72) 在HupA-AChE复杂动力学中的关键作用.
- 观察到的键翻转表明ACHE的内在灵活性可能会影响连接体相互作用.
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