Gutierrez Yulia M, Rocklin Gabriel J
Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL.
Center for Synthetic Biology, Northwestern University, Evanston, IL.
bioRxiv. 2024 Dec 21:2024.12.18.629072. doi: 10.1101/2024.12.18.629072.
Amino acid insertions and deletions (indels) are among the most common protein mutations and necessitate changes to a protein's backbone geometry. Examining how indels affect protein folding stability (and especially how indels can increase stability) can help reveal the role of backbone energetics on stability and introduce new protein engineering strategies. Tsuboyama et al. measured folding stability for 57,698 single amino acid insertion or deletion mutants in 405 small domains, and this analysis identified 103 stabilizing mutants (ΔΔG > 1 kcal/mol). Here, we use computational modeling to analyze structural and energetic changes for these stabilizing indel mutants. We find that stabilizing indel mutations tend to have local structural effects and that stabilizing deletions (but less so insertions) are often found in regions of high backbone strain. We also find that stabilizing indels are typically correctly classified as stabilizing by the Rosetta energy function (which explicitly models backbone energetics), but not by an inverse folding (ESM-IF)-based analysis (Cagiada et al. 2024) which predicts absolute stability (ΔG).
氨基酸插入和缺失（indels）是最常见的蛋白质突变类型之一，会导致蛋白质主链几何结构发生变化。研究indels如何影响蛋白质折叠稳定性（特别是indels如何提高稳定性），有助于揭示主链能量学在稳定性方面的作用，并引入新的蛋白质工程策略。津山等人测量了405个小结构域中57,698个单氨基酸插入或缺失突变体的折叠稳定性，该分析确定了103个稳定突变体（ΔΔG > 1千卡/摩尔）。在此，我们使用计算模型来分析这些稳定indel突变体的结构和能量变化。我们发现，稳定的indel突变往往具有局部结构效应，并且稳定缺失（但插入情况较少）通常出现在主链应变较高的区域。我们还发现，稳定的indels通常能被Rosetta能量函数（明确模拟主链能量学）正确分类为稳定，但基于反向折叠（ESM-IF）的分析（卡贾达等人，2024年）却不能，该分析预测的是绝对稳定性（ΔG）。
