通过丁β-乳酸酶去活化抗生素:来自QM/MM和DFT研究的机制性见解
Dingguo Xu1, Hua Guo, Qiang Cui
1Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA.
Journal of the American Chemical Society
|August 19, 2007
概括
这项研究使用了QM/MM和DFT来研究moxalactam通过dizinc L1β-lactamase的水解. 结果显示,添加氧化物到乳环中启动了催化,计算的能量屏障与实验数据一致.
科学领域:
- 生物化学 生物化学
- 计算化学计算化学
- 酶学 是一种酶学.
背景情况:
- 莫克萨拉克坦的水解由二L1β-乳酸酶催化.
- 酶活性部位有两个离子,它们对催化非常重要.
- 了解最初的环开放步骤是阐明催化机制的关键.
研究的目的:
- 为了研究由dizinc L1β-lactamase催化的moxalactam水解中的初始环开放步骤.
- 阐明离子和活性部位残留物在催化中的作用.
- 将计算结果与实验动力学数据进行比较.
主要方法:
- 混合量子力学/分子力学 (QM/MM) 方法.
- 密度函数理论 (DFT) 的计算.
- SCC-DFTB/MM模拟用于潜在的平均力计算.
主要成果:
- 氧核添加到基质乳酸环是主要的初始步骤.
- 一种转基因稳定的中间体通过核友性添加障碍物形成.
- 计算的反应自由能量障碍 (23.5 kcal/mol) 与实验值 (18.5 kcal/mol) 非常一致.
- Asp120调整核友,离子稳定中间体和过渡状态.
结论:
- 离子在moxalactam水解催化过程中发挥着密切的作用.
- Zn(1) 可能起到"氧化离子孔"的作用,而 Zn(2) 则起到电友催化剂的作用.
- 涉及核友添加和金属离子参与的拟议机制得到了计算发现的支持.
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