什么是α-螺旋核的时间尺度?
David De Sancho1, Robert B Best
1Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, UK.
Journal of the American Chemical Society
|April 13, 2011
概括
使用分子动力学模拟来研究螺旋形成动力学. 模拟显示了从缩小螺旋状态和线圈再平衡中快速放松,但螺旋核化时间缓慢.
科学领域:
- 蛋白质动力学 蛋白质动力学
- 生物物理化学 生物物理化学
- 计算生物学是一种计算生物学.
背景情况:
- 螺旋体形成对于蛋白质折叠至关重要,但它的动力学是复杂的,并未完全理解.
- 超快速光谱学表明,Ac-WAAAH(+) -NH(2) 的螺旋核形成速度比以前认为的要快.
研究的目的:
- 通过分子动力学模拟,研究Ac-WAAAH(+) -NH(2) 中螺旋形成的动力学.
- 调和实验观测与螺旋形成的理论模型.
主要方法:
- 用珀 ff03w力场和TIP4P/2005水模型进行复制交换分子动力学模拟.
- 使用马尔科夫过程形式主义计算温度依赖的微观速率系数.
- 模拟的温度跳跃产生光放松曲线.
主要成果:
- 模拟的放松曲线与实验数据密切匹配,显示通过双指数函数近似的多相动力学.
- 主要的放松过程被确定为C端螺旋状态收缩和线圈状态再平衡.
- 估计在300 K处的螺旋核形成时间为20-70 ns,与阿雷尼乌斯运动学相一致.
结论:
- 分子动力学模拟准确地捕捉了螺旋形成动力学,包括快速放松和缓慢核形成.
- 这项研究提供了对螺旋形成的详细机理洞察.
- 观察到的快速放松和缓慢核形成之间的差异是由主要的线圈动力学解释的.
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