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从计算建模中了解甘氨酸N-甲基转移酶的催化起源
Katarzyna Świderek1,2, Iñaki Tuñón3, Ian H Williams2
1Departament de Química Física i Analítica ; Universitat Jaume I , 12071 Castellón , Spain.
Journal of the American Chemical Society
|February 21, 2018
概括
酶催化剂的起源仍有争议. 这项研究表明甘氨酸N-甲基转移酶
科学领域:
- 生物化学
- 计算化学
- 酵素学
背景情况:
- 酶催化作用的确切机制仍在争论中.
- 甘氨酸N-甲基转移酶 (GNMT) 在甲基代谢中起着至关重要的作用.
- 了解酶活性位点的动态是阐明催化效率的关键.
研究的目的:
- 研究活点压缩与静电学在GNMT催化中的作用.
- 理论上研究GNMT及其突变的SN2甲基转移反应.
- 将计算结果与动态同位素效应的实验观测相协调.
主要方法:
- 量子力学/分子力学理论研究.
- 用于QM地区的半实验 (AM1) 和DFT (M06-2X).
- 在蛋白质和溶剂环境中使用OPLS-AA和TIP3P力场.
主要成果:
- 计算的激活自由能量和动态同位素效应 (KIEs) 与实验数据一致.
- 突变没有显著改变甲基捐赠者-接受者距离 (DAD),反驳了压缩假设.
- 活性部位的静电特性与观察到的催化活性和KIE变化有很强的相关性.
结论:
- 酶压缩不是GNMT观察到的KIE变化的主要驱动因素.
- 活性部位内的静电相互作用对于调节GNMT的催化活性至关重要.
- 酶可塑性有效缓冲突变的影响,导致反应性和KIE的微妙变化.
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