PXD031159

PXD031159 is an original dataset announced via ProteomeXchange.

Title	Uncover New Reactivity of Genetically Encoded Alkyl Bromide Unnatural Amino Acids
Description	Genetically encoded unnatural amino acids (Uaas) with electrophilic moieties are excellent tools to investigate protein-protein interactions (PPIs) both in vitro and in vivo. These Uaas, including a series of alkyl bromide-based Uaas, 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 Uaa, 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 interfaces even without cysteine residues, which will greatly expand the power of BprY in studying PPIs.
HostingRepository	PRIDE
AnnounceDate	2024-10-07
AnnouncementXML	Submission_2024-10-07_11:02:24.256.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD031159
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Xin Shu
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2022-01-21 13:05:08	ID requested
⏵ 1	2024-10-07 11:02:25	announced

10.6019/PXD031159;

Shu X, Asghar S, Yang F, Li ST, Wu H, Yang B, Uncover New Reactivity of Genetically Encoded Alkyl Bromide Non-Canonical Amino Acids. Front Chem, 10():815991(2022) [pubmed]

10.3389/fchem.2022.815991;

submitter keyword: chemical cross-linking, and SUMO interactome, unnatural Amino Acid,protein-protein interactions, genetic code expansion

Xin Shu
contact affiliation	Zhejiang University
contact email	sx725@zju.edu.cn
lab head
Xin Shu
contact affiliation	Zhejiang university
contact email	sx725@zju.edu.cn
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD031159
     1. Label: PRIDE project
     2. Name: Uncover New Reactivity of Genetically Encoded Alkyl Bromide Unnatural Amino Acids