瑞士苏黎世联邦理工学院Paola Picotti研究组使用蛋白质相互作用标记的实验库，对蛋白质复合物动态进行全局分析。这一研究成果于2024年10月16日在线发表在国际学术期刊《自然—生物技术》上。

研究人员引入了串联超滤结合有限蛋白水解质谱（FLiP-MS），这是一种结构蛋白质组学工作流程。其通过探测复合物结合形式和单体形式蛋白质在蛋白酶敏感性方面的差异，生成特异于蛋白质相互作用（PPI）变化的肽标记库。该库包括映射到蛋白质结合界面的标记和报告伴随PPI变化的结构变化的标记。

将标记库与LiP-MS数据集成，允许从未分级的裂解物中进行蛋白质-蛋白质相互作用（PPI）的全局分析。研究人员将FLiP-MS应用于酿酒酵母，探测DNA复制压力后蛋白质复合物动态的变化，并确定了Spt-Ada-Gcn5乙酰转移酶活性与多个复合物组装状态之间的关联。

FLiP-MS能够在任何扰动下对蛋白质复合物动态进行高通量、蛋白质组范围内的肽级别结构分辨率分析，并提供结合界面的占用信息，从而为研究系统提供全局和分子视角。

研究人员表示，系统地监测蛋白质复合物动态的方法是必要的。

附：英文原文

Title: Global profiling of protein complex dynamics with an experimental library of protein interaction markers

Author: Drig, Christian, Marulli, Cathy, Peskett, Thomas, Volkmar, Norbert, Pantolini, Lorenzo, Studer, Gabriel, Paleari, Camilla, Frommelt, Fabian, Schwede, Torsten, de Souza, Natalie, Barral, Yves, Picotti, Paola

Issue&Volume: 2024-10-16

Abstract: Methods to systematically monitor protein complex dynamics are needed. We introduce serial ultrafiltration combined with limited proteolysis-coupled mass spectrometry (FLiP–MS), a structural proteomics workflow that generates a library of peptide markers specific to changes in PPIs by probing differences in protease susceptibility between complex-bound and monomeric forms of proteins. The library includes markers mapping to protein-binding interfaces and markers reporting on structural changes that accompany PPI changes. Integrating the marker library with LiP–MS data allows for global profiling of protein–protein interactions (PPIs) from unfractionated lysates. We apply FLiP–MS to Saccharomyces cerevisiae and probe changes in protein complex dynamics after DNA replication stress, identifying links between Spt-Ada-Gcn5 acetyltransferase activity and the assembly state of several complexes. FLiP–MS enables protein complex dynamics to be probed on any perturbation, proteome-wide, at high throughput, with peptide-level structural resolution and informing on occupancy of

DOI: 10.1038/s41587-024-02432-8

Source: https://www.nature.com/articles/s41587-024-02432-8