蛋白质进化中的波动和可预测性的极限
Saverio Rossi1,2, Leonardo Di Bari3,4, Martin Weigt4
1Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy.
概括
蛋白质进化显示出强烈的突变相关性. 祖先序列属性,特别是表观,影响早期进化和祖先序列重建 (ASR) 算法性能.
科学领域:
- 进化生物学是进化的生物学.
- 统计物理学的统计物理.
- 计算生物学是一种计算生物学.
背景情况:
- 蛋白质进化是通过跨越不同时间尺度的突变来表现的.
- 进化中的动态异质性表明了不同地点和时间的突变之间的相关性.
- 物理学中的无序系统为理解这些进化动态提供了类比.
研究的目的:
- 量化蛋白质进化中的时空相关性.
- 为了解开波动来源:祖先序列与随机突变.
- 研究祖先序列特性对进化轨迹和祖先序列重建 (ASR) 的影响.
主要方法:
- 模拟蛋白质进化使用数据驱动的能量景观作为健身代理.
- 从无序的物理系统中应用时空相关函数.
- 使用了标准的祖先序列重建 (ASR) 算法.
主要成果:
- 从祖先序列的波动在较短的进化时间表中占主导地位.
- 对于祖先序列信息持久性而言,有一个特有的时间尺度.
- 在祖先中较强的表皮性相互作用导致更长的持久性和影响进化轨迹.
- 在较长的时间尺度上,祖先的影响会随着遗址的集体进化而减少.
- ASR算法的性能受到祖先序列属性的直接影响,特别是epistasis.
结论:
- 祖先序列属性,特别是表观约束,显著塑造了早期的进化动态.
- 这些特性影响了标准祖先序列重建 (ASR) 方法的准确性和性能.
- 了解这些相关性是解读进化途径和重建祖先状态的关键.
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