Massively parallel measurement of protein–protein interactions by sequencing using MP3-seq

巨量平行 条形码 大规模并行测序 可扩展性 计算生物学 蛋白质-蛋白质相互作用 计算机科学 DNA测序 度量(数据仓库) 生物系统 DNA 生物 数据挖掘 遗传学 并行计算 操作系统 数据库
作者
Alexandr Baryshev,Alyssa La Fleur,Benjamin Groves,Cirstyn Michel,David Baker,Ajasja Ljubetič,Georg Seelig
出处
期刊:Nature Chemical Biology [Nature Portfolio]
被引量:3
标识
DOI:10.1038/s41589-024-01718-x
摘要

Protein–protein interactions (PPIs) regulate many cellular processes and engineered PPIs have cell and gene therapy applications. Here, we introduce massively parallel PPI measurement by sequencing (MP3-seq), an easy-to-use and highly scalable yeast two-hybrid approach for measuring PPIs. In MP3-seq, DNA barcodes are associated with specific protein pairs and barcode enrichment can be read by sequencing to provide a direct measure of interaction strength. We show that MP3-seq is highly quantitative and scales to over 100,000 interactions. We apply MP3-seq to characterize interactions between families of rationally designed heterodimers and to investigate elements conferring specificity to coiled-coil interactions. Lastly, we predict coiled heterodimer structures using AlphaFold-Multimer (AF-M) and train linear models on physics-based energy terms to predict MP3-seq values. We find that AF-M-based models could be valuable for prescreening interactions but experimentally measuring interactions remains necessary to rank their strengths quantitatively. A method called massively parallel PPI measurement by sequencing (MP3-seq) is developed for measuring protein–protein interactions at scale. MP3-seq uses DNA barcodes that are associated with specific protein pairs and provides a quantitative measure of interaction strength. Interactions between rationally designed heterodimers and elements conferring interaction specificity were investigated using MP3-seq.
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