使用分子动力学模拟分析蛋白质骨干NH和侧链甲基组的动力学分析
Nooriel E Banayan1, Andrew Hsu2, John F Hunt1
1Department of Biological Sciences, Columbia University, 3000 Broadway, New York, New York 10027, United States.
Journal of chemical theory and computation
|July 3, 2024
概括
分子动力学模拟和NMR实验揭示了蛋白质动力学. 优化的模拟准确地预测了Escherichia coli核糖核酶HI的一般化顺序参数,提高了我们对酶灵活性的理解.
科学领域:
- 生物物理学的生物物理.
- 计算生物学 计算生物学
- 结构生物学 结构生物学
背景情况:
- 蛋白质的结构动态对于生物功能至关重要.
- 核磁共振 (NMR) 光谱和分子动力学 (MD) 模拟为这些动力学提供了互补的观点.
- 一般化顺序参数量化分子运动和灵活性.
研究的目的:
- 为了比较由广泛的微秒MD模拟与实验性NMR数据获得的Escherichia coli核糖核酶HI (RNH) 的概括顺序参数.
- 评估OPLS4和AMBER-FF19SB力场在复制实验RNH动态中的准确性.
- 分析脊柱和侧链运动对整体蛋白质灵活性的贡献.
主要方法:
- 使用OPLS4和AMBER-FF19SB力场对RNH进行了2微秒的MD模拟.
- 从模拟轨迹计算的骨干NH和侧链甲基组的概括顺序参数 (S^2和S_axis^2).
- 将模拟顺序参数与从15N和13CH2D旋转放松测量中获得的实验值进行比较.
- 平均模拟订单参数超过50 ns块,以优化与实验数据的一致性.
主要成果:
- 模拟和实验通用顺序参数之间的最佳一致性是通过平均超过50个ns块来实现的.
- 模拟和实验S^2 (NH) 之间的绝对偏差 (MAD) 的中位数为0.030 (OPLS4) 和0.041 (AMBER-FF19SB).
- 对于S_axis^2 (CH3) 的MAD是0.061 (OPLS4) 和0.078 (AMBER-FF19SB),表明了良好的协议.
- 脊柱和侧链的波动几乎没有相关性;旋转器内部的波动是有限的和均的.
结论:
- MD模拟,特别是当在适当的时间尺度上平均时,可以准确地复制实验性NMR衍生的蛋白质动态的一般化顺序参数.
- OPLS4和AMBER-FF19SB的力场提供了可靠的RNH形状动态的描述.
- 侧链灵活性,以低的S_axis^2值表示,主要是由旋转器之间的过渡驱动的,通常由局部骨干灵活性增强.
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