A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain.-猫眼课题宝

DOI：

10.1016/j.cub.2014.09.072

发表时间：

2014-11-17

期刊：

CURRENT BIOLOGY

影响因子：

9.2

通讯作者：

中科院分区：

生物学1区

文献类型：

作者：

Olson, C. Anders;Wu, Nicholas C.;Sun, Ren

来源链接：

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4254498/?report=classic

来自两个或更多个突变的适应性效应的非加性，称为上位性，可以导致有害突变的补偿或有益突变的否定。最近的证据表明上位性在个体进化途径中的重要性。然而，分子进化中一个尚未解决的问题是，在不同的遗传背景下，适应性效应的变化有多频繁，变化有多显著。为了回答这个问题，我们定量了蛋白G（GB1）IgG结合结构域中所有位置之间的所有单突变和双突变的影响。通过观察所有可能的进化途径的前两个步骤，这种适应性特征使得能够表征整个蛋白质分子中成对上位性的程度和幅度。此外，我们开发了一种新的方法来定量确定单突变对结构稳定性的影响（ΔΔGU）。这使得确定的重要性，稳定性的影响，功能上位。我们的研究结果说明共同的生物物理机制发生的积极和消极上位性。我们的研究结果表明普遍的正上位性内的构象动态网络的残基。稳定性分析表明，显着的负上位性，这是更常见的比正上位性，主要发生在不稳定的突变组合之间。此外，我们表明，虽然显着的正上位性是罕见的，许多有害的突变是有益的，在至少一个替代的突变背景。整个结构域的条件有益突变的分布表明，序列空间的功能部分可以显着扩大上位性。

Non-additivity in fitness effects from two or more mutations, termed epistasis, can result in compensation of deleterious mutations or negation of beneficial mutations. Recent evidence shows the importance of epistasis in individual evolutionary pathways. However, an unresolved question in molecular evolution is how often and how significantly fitness effects change in alternative genetic backgrounds. To answer this question we quantified the effects of all single mutations and double mutations between all positions in the IgG-binding domain of protein G (GB1). By observing the first two steps of all possible evolutionary pathways, this fitness profile enabled the characterization of the extent and magnitude of pairwise epistasis throughout an entire protein molecule. Furthermore, we developed a novel approach to quantitatively determine the effects of single mutations on structural stability (ΔΔGU). This enabled determination of the importance of stability effects in functional epistasis. Our results illustrate common biophysical mechanisms for occurrences of positive and negative epistasis. Our results show pervasive positive epistasis within a conformationally dynamic network of residues. The stability analysis shows that significant negative epistasis, which is more common than positive epistasis, mostly occurs between combinations of destabilizing mutations. Furthermore, we show that although significant positive epistasis is rare, many deleterious mutations are beneficial in at least one alternative mutational background. The distribution of conditionally beneficial mutations throughout the domain demonstrates that the functional portion of sequence space can be significantly expanded by epistasis.