Deep indel mutagenesis reveals the impact of insertions and deletions on protein stability and function

Amino acid insertions and deletions (indels) are an abundant class of genetic variants. However, compared to substitutions, the effects of indels are not well understood and poorly predicted. Here we address this shortcoming by performing deep indel mutagenesis (DIM) of structurally diverse proteins. Indel tolerance is strikingly different to substitution tolerance and varies extensively both between different proteins and within different regions of the same protein. Although state of the art variant effect predictors perform poorly on indels, we show that both experimentally-measured and computationally-predicted substitution scores can be repurposed as good indel variant effect predictors by incorporating information on protein secondary structures. Quantifying the effects of indels on protein-protein interactions reveals that insertions can be an important class of gain-of-function variants. Our results provide an overview of the impact of indels on proteins and a method to predict their effects genome-wide.氨基酸插入缺失（indels）是一类数量丰富的遗传变异类型。然而相较于氨基酸替换，学界对indels的效应机制尚未完全明晰，其效应预测也存在较大不足。为此，我们针对结构多样的蛋白质开展了深度indel诱变（deep indel mutagenesis, DIM）实验以填补这一研究空白。研究发现，indel耐受性与氨基酸替换耐受性存在显著差异，且在不同蛋白质之间以及同一蛋白质的不同区域内均呈现出广泛的异质性。当前最先进的变异效应预测工具在indel预测任务中表现欠佳，我们的研究表明，通过引入蛋白质二级结构信息，可将实验测得与计算预测得到的氨基酸替换得分重新适配为高效的indel变异效应预测工具。通过量化indels对蛋白质-蛋白质相互作用的影响，我们发现插入变异可作为一类重要的功能获得性变异类型。本研究系统阐明了indels对蛋白质的影响，并提供了一种可在全基因组范围内预测其效应的方法。