Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria

Yuwan Chen, Wen Zhou, Yufei Xia, Weijie Zhang, Qun Zhao, Xinwei Li, Hang Gao, Zhen Liang, Guanghui Ma, Kaiguang Yang (), Lihua Zhang () and Yukui Zhang
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Yuwan Chen: Chinese Academy of Sciences
Wen Zhou: Chinese Academy of Sciences
Yufei Xia: Chinese Academy of Sciences
Weijie Zhang: Chinese Academy of Sciences
Qun Zhao: Chinese Academy of Sciences
Xinwei Li: Chinese Academy of Sciences
Hang Gao: Chinese Academy of Sciences
Zhen Liang: Chinese Academy of Sciences
Guanghui Ma: Chinese Academy of Sciences
Kaiguang Yang: Chinese Academy of Sciences
Lihua Zhang: Chinese Academy of Sciences
Yukui Zhang: Chinese Academy of Sciences

Nature Communications, 2023, vol. 14, issue 1, 1-16

Abstract: Abstract Current methods for intracellular protein analysis mostly require the separation of specific organelles or changes to the intracellular environment. However, the functions of proteins are determined by their native microenvironment as they usually form complexes with ions, nucleic acids, and other proteins. Here, we show a method for in situ cross-linking and analysis of mitochondrial proteins in living cells. By using the poly(lactic-co-glycolic acid) (PLGA) nanoparticles functionalized with dimethyldioctadecylammonium bromide (DDAB) to deliver protein cross-linkers into mitochondria, we subsequently analyze the cross-linked proteins using mass spectrometry. With this method, we identify a total of 74 pairs of protein-protein interactions that do not exist in the STRING database. Interestingly, our data on mitochondrial respiratory chain proteins ( ~ 94%) are also consistent with the experimental or predicted structural analysis of these proteins. Thus, we provide a promising technology platform for in situ defining protein analysis in cellular organelles under their native microenvironment.

Date: 2023
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DOI: 10.1038/s41467-023-39485-3

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