Uncover new reactivity of genetically encoded alkyl bromide non-canonical amino acids

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Authors
Shu, Xin
Asghar, Sana
Yang, Fan
Li, Shang-Tong
Wu, Haifan
Yang, Bing
Issue Date
2022-02-18
Type
Article
Language
en_US
Keywords
Protein-protein interactions , Genetic code expansion , Non-canonical amino acid , Chemical cross-linking , SUMO interactome
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Abstract

Genetically encoded non-canonical amino acids (ncAAs) with electrophilic moieties are excellent tools to investigate protein-protein interactions (PPIs) both in vitro and in vivo. These ncAAs, including a series of alkyl bromide-based ncAAs, mainly target cysteine residues to form protein-protein cross-links. Although some reactivities towards lysine and tyrosine residues have been reported, a comprehensive understanding of their reactivity towards a broad range of nucleophilic amino acids is lacking. Here we used a recently developed OpenUaa search engine to perform an in-depth analysis of mass spec data generated for Thioredoxin and its direct binding proteins cross-linked with an alkyl bromide-based ncAA, BprY. The analysis showed that, besides cysteine residues, BprY also targeted a broad range of nucleophilic amino acids. We validated this broad reactivity of BprY with Affibody/Z protein complex. We then successfully applied BprY to map a binding interface between SUMO2 and SUMO-interacting motifs (SIMs). BprY was further applied to probe SUMO2 interaction partners. We identified 264 SUMO2 binders, including several validated SUMO2 binders and many new binders. Our data demonstrated that BprY can be effectively used to probe protein-protein interaction interfaces even without cysteine residues, which will greatly expand the power of BprY in studying PPIs.

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This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
Citation
Shu X, Asghar S, Yang F, Li S-T, Wu H and Yang B (2022) Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids. Front. Chem. 10:815991. doi: 10.3389/fchem.2022.815991
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Frontiers Media S.A.
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22962646
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