酶活性部位的介电松:用宏观连续模型解释的分子动力学模拟
1Department of Physics, University of Cyprus, PO 20537, CY 1678 Nicosia, Cyprus. archonti@ucy.ac.cy
Journal of the American Chemical Society
|November 1, 2001
概括
蛋白质中的介电松对于化学过程至关重要. 理论模型显示,蛋白质侧链的重排有助于充电自由能量,需要不同的介电常数来进行静态和放松步骤.
科学领域:
- 生物物理学的生物物理.
- 计算化学计算化学
- 酶的机制 酶的机制
背景情况:
- 介电松对于蛋白质的化学过程至关重要,如连接体结合和电荷转移.
- 介电松的实验性表征具有挑战性,需要理论方法.
- 将分子动力学 (MD) 模拟与连续模型进行比较,可以提供有价值的定性见解.
研究的目的:
- 为了分析充电插入过程,模拟阿斯巴提尔-tRNA合成酶活性部位中的脱质/突变.
- 为了研究涉及连接体和侧链重排的介电松.
- 将MD模拟与介电连续模型进行比较,以深入了解蛋白质活性部位的行为.
主要方法:
- 在MD和介电连续模型中进行电荷插入模拟.
- 在充电插入过程中对电介 relaxation 的分析.
- 用阿斯巴酸基质和阿斯巴拉金类型的建模复合物.
主要成果:
- 介电松涉及到活性部位的显著的连接体和侧链重排.
- 这些重新安排占了总体收费自由能源的很大一部分.
- 连续模型需要不同的介电常数用于静态 (约. 1) 和放松 (3-6) 的步骤.
结论:
- 该研究量化了介电松对在酶活性位点充电自由能量的贡献.
- 在连续模型中,静态和放松相需要不同的介电常数.
- 活性部位的局部蛋白质极化性与非特定区域相比.
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