德国马克斯-普朗克生物化学研究所Matthias Mann团队近期取得重要工作进展，他们研究绘制了酵母蛋白相互作用组的社会架构图谱。相关研究成果2023年11月15日在线发表于《自然》杂志上。

据介绍，细胞功能是由蛋白质-蛋白质相互作用介导的，绘制相互作用组提供了对生物系统的基本见解。亲和纯化与质谱联用是进行此类图谱绘制的理想工具，但很难识别低拷贝数复合物、膜复合物和被蛋白质标记破坏的复合物。因此，目前人们对相互作用组的了解还远远不够完整，评估报告的相互作用的可靠性是具有挑战的。

研究人员开发了一种灵敏的高通量方法，使用高度可重复的亲和富集与质谱联用，结合定量二维分析策略，来全面绘制酿酒酵母的相互作用组。96孔形式的千倍体积减少使得能够对覆盖整个表达的酵母蛋白质组的内源性GFP标记文库进行重复分析。4159个下拉产生了一个由3927个蛋白质组成的高度结构化网络，这些蛋白质通过31004个相互作用连接，与现有的相互作用图谱相比，蛋白质数量增加了一倍，可靠相互作用的数量增加了三倍。这包括通过丰度相关性推断的非常低丰度的表观遗传复合物、器官膜复合物和不可标记的复合物。

这个几乎饱和的相互作用组揭示了绝大多数酵母蛋白是高度连接的，平均有16个相互作用因子。与人类之间的社交网络类似，蛋白质之间的平均最短距离为4.2次相互作用。AlphaFold Multimer为以前未表征的蛋白质在复合物中的功能作用提供了新的见解。研究人员开发的门户网站（www.yeast-interactome.org）允许对相互作用组数据集进行广泛的探索。

附：英文原文

Title: The social and structural architecture of the yeast protein interactome

Author: Michaelis, Andr C., Brunner, Andreas-David, Zwiebel, Maximilian, Meier, Florian, Strauss, Maximilian T., Bludau, Isabell, Mann, Matthias

Issue&Volume: 2023-11-15

Abstract: Cellular functions are mediated by protein–protein interactions, and mapping the interactome provides fundamental insights into biological systems. Affinity purification coupled to mass spectrometry is an ideal tool for such mapping, but it has been difficult to identify low copy number complexes, membrane complexes and complexes that are disrupted by protein tagging. As a result, our current knowledge of the interactome is far from complete, and assessing the reliability of reported interactions is challenging. Here we develop a sensitive high-throughput method using highly reproducible affinity enrichment coupled to mass spectrometry combined with a quantitative two-dimensional analysis strategy to comprehensively map the interactome of Saccharomyces cerevisiae. Thousand-fold reduced volumes in 96-well format enabled replicate analysis of the endogenous GFP-tagged library covering the entire expressed yeast proteome1. The 4,159 pull-downs generated a highly structured network of 3,927 proteins connected by 31,004 interactions, doubling the number of proteins and tripling the number of reliable interactions compared with existing interactome maps2. This includes very-low-abundance epigenetic complexes, organellar membrane complexes and non-taggable complexes inferred by abundance correlation. This nearly saturated interactome reveals that the vast majority of yeast proteins are highly connected, with an average of 16 interactors. Similar to social networks between humans, the average shortest distance between proteins is 4.2 interactions. AlphaFold-Multimer provided novel insights into the functional roles of previously uncharacterized proteins in complexes. Our web portal (www.yeast-interactome.org) enables extensive exploration of the interactome dataset.

DOI: 10.1038/s41586-023-06739-5