协同多个质子转移的动态同位素效应:对二氧化碳二氧化碳酶II活性位模型的直接动态研究
Zorka Smedarchina1, Willem Siebrand, Antonio Fernández-Ramos
1Steacie Institute for Molecular Sciences, National Research Council of Canada, Ottawa, Ontario, Canada K1A 0R6. Zorka.Smedarchina@nrc.ca
Journal of the American Chemical Society
|January 8, 2003
概括
二氧化碳无水酶II 的使用.
科学领域:
- 生物化学 生物化学
- 计算化学的计算化学
- 酶动力学 酶动力学
背景情况:
- 碳酸无水酶II对于从体液中去除二氧化碳至关重要.
- 酶的活性部位结构是已知的,但水分子的排列不清楚.
- 通过水桥的质子转移是速度限制的步骤.
研究的目的:
- 使用活性位点模型计算二氧化碳无水酶II的反应速率常数.
- 研究质子转移的机制,包括道化.
- 将计算结果与实验数据进行比较.
主要方法:
- 使用58个原子,包括离子和甲基利米达的活性位点建模.
- 关于结构和力场计算的近似密度函数理论 (SCC-DFTB).
- 使用近似瞬间方法和变化过渡状态理论进行直动力学计算.
主要成果:
- 一个单一的过渡状态表明协同的三重质子转移.
- 量子计算显示了比实验更高的率和KIE.
- 经典计算产生较低的利率,但显著更高的KIEs.
- 道被证实是质子转移的主要机制.
- 一个两水桥模型,虽然度低,但对质子运输非常有效.
结论:
- 在二氧化碳无水酶II中,质子转移是通过穿过两水桥的道进行的.
- 这种双水桥机制对于酶的高催化效率至关重要.
- 协同转移得到了KIE对度的依赖的支持.
- 这种机制不同于效率较低的异酶,它们可能使用阶段性转移.
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