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

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 () and Bing Yang ()
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Dan-Dan Liu: Zhejiang University
Wenlong Ding: Zhejiang University
Jin-Tao Cheng: Zhejiang University
Qiushi Wei: Beihang University
Yinuo Lin: Chinese Academy of Sciences
Tian-Yi Zhu: 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
Bing Yang: Zhejiang University

Nature Communications, 2024, vol. 15, issue 1, 1-13

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-49517-1

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