对核糖核酶H进化的选择压力通过严格的基于自由能量的设计来探索
Ryan L Hayes1,2, Charlotte F Nixon3, Susan Marqusee3,4,5
1Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697.
概括
像多站点λ动力学 (MSλD) 这样的高通量计算方法可以准确预测蛋白质稳定性和进化选择压力. 这可以通过识别具有较少突变的稳定变异来实现更有效的蛋白质设计.
科学领域:
- 计算生物学是一种计算生物学.
- 蛋白质工程是一种蛋白质工程.
- 进化生物学是进化的生物学.
背景情况:
- 高通量方法对于探索自然蛋白质进化和新型蛋白质设计中的蛋白质序列空间至关重要.
- 了解序列稳定性关系是量化进化选择压力和指导蛋白质设计的关键.
研究的目的:
- 应用多站点 λ 动力学 (MSλD) 和化学变性实验来量化进化选择压力.
- 探索序列稳定性关系,以设计具有增强稳定的新型蛋白质.
主要方法:
- 利用多站点λ动力学 (MSλD),一种严格的自由能量模拟方法,计算E. coli* RNase H (ecRNH) 和稳定的共识序列 (AncCcons) 之间的32,768个模拟体的稳定性.
- 采用化学变质实验来验证计算预测.
- 使用基于稳定性和博尔茨曼因子的进化模型量化选择压力.
主要成果:
- 与12个序列的实验数据相比,MSλD准确地预测了蛋白质稳定性,达到0.86的皮尔森相关性和1.18kcal/mol的RMSE.
- 一个设计的金像体表现出类似于AncCcons的稳定性增加,但只有一半的突变.
- 估计的选择温度在110到168K之间,这表明进化选择压力很高.
结论:
- 精确的高通量计算方法,如MSλD,对于有效的蛋白质设计至关重要.
- 高选择压对进化动态和设计准确性有重大影响.
- MSλD能够准确预测蛋白质的稳定性,并识别优化的序列.
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