原子 Brownian 动力学模拟酸酸化的化模拟
T Shen1, C F Wong, J A McCammon
1Department of Physics, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093-0365, USA. tshen@ucsd.edu
Journal of the American Chemical Society
|September 13, 2001
概括
我们开发了一种新的模拟方法,用于动力学. 酸化显著改变的结构,影响其功能和我们如何解释NMR数据.
科学领域:
- 计算化学的计算化学
- 分子动力学分子动力学
- 生物物理学的生物物理.
背景情况:
- 了解的结构动态对于药物发现和蛋白质功能至关重要.
- 模拟的行为需要高效和稳定的计算方法.
- 该LINCS算法是分子动力学模拟的关键组成部分.
研究的目的:
- 使用LINCS算法实现一个全原子布朗动力学模拟模型用于.
- 研究酸化对Gly-Ser-Ser-Ser的结构偏好的影响.
- 通过将计算的NMR合常数与实验数据进行比较来验证模拟模型.
主要方法:
- 使用了一个全原子布朗动力学模拟模型,与LINCS (LINear Constraint Solver) 算法集成.
- 在UHBD (休斯顿大学布朗动力学) 软件中使用自适应时间步骤来提高计算效率和稳定性.
- 计算核磁共振 (NMR) (3)J合常数,使用来自布朗轨迹的卡普勒斯方程.
主要成果:
- 在Gly-Ser-Ser-Ser中,中部血清残留物的酸化诱导了从C(7eq) 到alpha(R) 结构的显著形状变化.
- 计算的 (3) J 合常数与单个酸化的实验数据有很好的一致性.
- 计算和实验 (3) J 合常数之间的一致性对于双电荷酸化来说不那么精确.
结论:
- 实现的基于LINCS的布朗动力学模型为研究形变化提供了有价值的工具.
- 酸化是一种关键的翻译后修饰,可以大大改变的结构和动态.
- 模拟模型显示了预测和解释NMR数据的潜力,有助于结构生物学研究.
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