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Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids

Author

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  • Dan-Dan Liu

    (Zhejiang University
    Zhejiang University)

  • Wenlong Ding

    (Zhejiang University
    Zhejiang University)

  • Jin-Tao Cheng

    (Zhejiang University
    Zhejiang University)

  • Qiushi Wei

    (Beihang University)

  • Yinuo Lin

    (Chinese Academy of Sciences)

  • Tian-Yi Zhu

    (Zhejiang University
    Zhejiang University)

  • Jing Tian

    (Chinese Academy of Sciences)

  • Ke Sun

    (Westlake University)

  • Long Zhang

    (Zhejiang University)

  • Peilong Lu

    (Westlake University)

  • Fan Yang

    (Zhejiang University School of Medicine)

  • Chao Liu

    (Beihang University)

  • Shibing Tang

    (Chinese Academy of Sciences
    China-New Zealand Joint Laboratory on Biomedicine and Health)

  • Bing Yang

    (Zhejiang University
    Zhejiang University)

Abstract

Latent bioreactive unnatural amino acids (Uaas) have been widely used in the development of covalent drugs and identification of protein interactors, such as proteins, DNA, RNA and carbohydrates. However, it is challenging to perform high-throughput identification of Uaa cross-linking products due to the complexities of protein samples and the data analysis processes. Enrichable Uaas can effectively reduce the complexities of protein samples and simplify data analysis, but few cross-linked peptides were identified from mammalian cell samples with these Uaas. Here we develop an enrichable and multiple amino acids reactive Uaa, eFSY, and demonstrate that eFSY is MS cleavable when eFSY-Lys and eFSY-His are the cross-linking products. An identification software, AixUaa is developed to decipher eFSY mass cleavable data. We systematically identify direct interactomes of Thioredoxin 1 (Trx1) and Selenoprotein M (SELM) with eFSY and AixUaa.

Suggested Citation

  • Dan-Dan Liu & Wenlong Ding & Jin-Tao Cheng & Qiushi Wei & Yinuo Lin & Tian-Yi Zhu & Jing Tian & Ke Sun & Long Zhang & Peilong Lu & Fan Yang & Chao Liu & Shibing Tang & Bing Yang, 2024. "Characterize direct protein interactions with enrichable, cleavable and latent bioreactive unnatural amino acids," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49517-1
    DOI: 10.1038/s41467-024-49517-1
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    References listed on IDEAS

    as
    1. Zhen-Lin Chen & Jia-Ming Meng & Yong Cao & Ji-Li Yin & Run-Qian Fang & Sheng-Bo Fan & Chao Liu & Wen-Feng Zeng & Yue-He Ding & Dan Tan & Long Wu & Wen-Jing Zhou & Hao Chi & Rui-Xiang Sun & Meng-Qiu Do, 2019. "A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    2. Hongxia Zhao & Wenlong Ding & Jia Zang & Yang Yang & Chao Liu & Linzhen Hu & Yulin Chen & Guanglong Liu & Yu Fang & Ying Yuan & Shixian Lin, 2021. "Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    3. Wenlong Ding & Hongxia Zhao & Yulin Chen & Bin Zhang & Yang Yang & Jia Zang & Jing Wu & Shixian Lin, 2020. "Chimeric design of pyrrolysyl-tRNA synthetase/tRNA pairs and canonical synthetase/tRNA pairs for genetic code expansion," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    4. Yi Yang & Haiping Song & Dan He & Shuai Zhang & Shizhong Dai & Shixian Lin & Rong Meng & Chu Wang & Peng R. Chen, 2016. "Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label," Nature Communications, Nature, vol. 7(1), pages 1-10, November.
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