2024年11月5日，北京大学陈鹏小组在《自然—化学》杂志发表论文，他们提出了通过凝聚增强光交联的时空蛋白质相互作用组分析新方法。

研究人员表示，解决生物分子凝聚物中的蛋白-蛋白相互作用（PPIs）对于阐明其功能和调控机制至关重要。然而，由于凝聚物的瞬态性质和客户的多重定位，使得确定特定隔间的PPI具有挑战性。

研究小组开发了一种凝聚增强、空间定向、代谢结合辅助的光交联策略——称为DenseMAP——用于凝聚物中直接蛋白质相互作用组的时空分辨解剖。DenseMAP利用其凝聚增强光交联剂和空间定向生物素标记，实现了N6-甲基腺苷读取器YTHDF1和YTHDF2的胁迫颗粒特异性相互作用组定位，并揭示了SARS-CoV-2核衣壳蛋白磷酸化在调节病毒复制中的功能作用。

进一步应用DenseMAP对亚区室支架蛋白NPM1进行直接互作组定位，研究者破译了核仁颗粒组分蛋白质组，揭示了SUMOylation在控制核仁蛋白质组稳态中的关键作用。DenseMAP提供了一个平台技术，用于分析不同生理和/或病理环境下，亚细胞和室状凝聚物中的功能性蛋白-蛋白相互作用网络。

附：英文原文

Title: Spatiotemporal protein interactome profiling through condensation-enhanced photocrosslinking

Author: Li, Kexin, Xie, Xiao, Gao, Rui, Chen, Zhaoming, Yang, Mingdong, Wen, Zhihui, Weng, Yicheng, Fan, Xinyuan, Zhang, Gong, Liu, Lu, Zeng, Xiangmei, Han, Yu, Cao, Mengrui, Wang, Xin, Li, Jiaofeng, Yang, Zhenlin, Li, Tingting, Chen, Peng R.

Issue&Volume: 2024-11-05

Abstract: Resolving protein–protein interactions (PPIs) inside biomolecular condensates is crucial for elucidating their functions and regulation mechanisms. The transient nature of condensates and the multiple localizations of clients, however, have rendered it challenging to determine compartment-specific PPIs. Here we developed a condensation-enhanced, spatially directed, metabolic incorporation-assisted photocrosslinking strategy—termed DenseMAP—for spatiotemporally resolved dissection of the direct protein interactome within condensates. By leveraging our condensation-enhanced photocrosslinker and the spatially directed biotin tagging, DenseMAP enabled stress-granule-specific interactome mapping of the N6-methyladenosine readers YTHDF1 and YTHDF2, and uncovered the functional role of phosphorylation on the SARS-CoV-2 nucleocapsid protein in regulating virus replication. Further applying DenseMAP for direct interactome mapping of the subcompartmental scaffold protein NPM1 deciphered nucleolar granular component proteome, and unveiled the critical role of SUMOylation in controlling nucleolar proteome homeostasis. DenseMAP provides a platform technology for analysing functional PPI networks within subcellular and subcompartmental condensates under diverse physiological and/or pathological settings.

DOI: 10.1038/s41557-024-01663-1

Source: https://www.nature.com/articles/s41557-024-01663-1