Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance
Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance
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DOI：
10.1093/molbev/msab095
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发表时间：
2021-03-29
影响因子：
10.7
通讯作者：
Lindorff-Larsen, Kresten
中科院分区：
文献类型：
--
作者：
Cagiada, Matteo;Johansson, Kristoffer E.;Lindorff-Larsen, Kresten
理解和预测氨基酸取代如何影响蛋白质是我们对蛋白质功能和进化的基本理解的关键。氨基酸的变化可能以多种方式影响蛋白质的功能，包括对活性的直接扰动或对蛋白质折叠和稳定性的间接影响。我们分析了6，749种实验确定的变体效应，这些效应来自两种蛋白质（NUDT 15和PTEN）的丰度和活性的多重测定，以量化这些效应，并发现三分之一的变体导致功能丧失，大约一半的功能丧失变体也具有低细胞丰度。我们分析了功能丧失的结构和机制起源，并使用实验数据来寻找对酶活性重要的残基。我们对蛋白质稳定性和进化保守性进行了计算分析，并展示了我们如何预测变体导致活性或丰度丧失的位置。通过这种方式，我们的研究结果将热力学稳定性和进化保守性与蛋白质适应度景观的不同性质的实验研究联系起来。
Understanding and predicting how amino acid substitutions affect proteins are keys to our basic understanding of protein function and evolution. Amino acid changes may affect protein function in a number of ways including direct perturbations of activity or indirect effects on protein folding and stability. We have analyzed 6,749 experimentally determined variant effects from multiplexed assays on abundance and activity in two proteins (NUDT15 and PTEN) to quantify these effects and find that a third of the variants cause loss of function, and about half of loss-of-function variants also have low cellular abundance. We analyze the structural and mechanistic origins of loss of function and use the experimental data to find residues important for enzymatic activity. We performed computational analyses of protein stability and evolutionary conservation and show how we may predict positions where variants cause loss of activity or abundance. In this way, our results link thermodynamic stability and evolutionary conservation to experimental studies of different properties of protein fitness landscapes.