An interaction is detected between two proteins using chemically reactive or photo-activatable cross-linking reagents that covalently link amino acids in close proximity, followed by mass spectrometry analysis to identify the linked peptides (reviewed in PMID 37406423, 37104977). Experiments may be carried with live cells or cell lysates in which all proteins are expressed at endogenous levels (e.g. PMID 34349018, 35235311) or with recombinant proteins (e.g., PMID 28537071).

Publication

Spatiotemporal protein interactome profiling through condensation-enhanced photocrosslinking.

Li K, Xie X, Gao R, Chen Z, Yang M, Wen Z, Weng Y, Fan X, Zhang G, Liu L, Zeng X, Han Y, Cao M, Wang X, Li J, Yang Z, Li T, Chen PR

Resolving protein-protein interactions (PPIs) inside biomolecular condensates is crucial for elucidating their functions and regulation mechanisms. The transient nature of condensates and the multiple localizations of clients, however, have rendered it challenging to determine compartment-specific PPIs. Here we developed a condensation-enhanced, spatially directed, metabolic incorporation-assisted photocrosslinking strategy-termed DenseMAP-for spatiotemporally resolved dissection of the direct protein interactome within condensates. By leveraging ... [more]

Nat Chem Nov. 05, 2024; (); [Pubmed: 39501047]

Throughput

High Throughput

Additional Notes

DenseMAP (SG BirA-directed proximity labeling, XL-MS) was carried out to identify high confidence protein interactors for SARS-CoV-2 N protein in SGs with Ratio (+/- biotin) greater than on equal to 2, ratio (+/- UV) greater than or equal to 2, P less than or equal to 0.05

Related interactions

Interaction	Experimental Evidence Code	Dataset	Throughput	Score	Curated By	Notes
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Armstrong SD (2024)	High	-	BioGRID	3730645
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Broderick K (2025)	High	-	BioGRID	3800361
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Cai T (2021)	High	-	BioGRID	-
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Chen X (2024)	High	-	BioGRID	3753658
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Chen Z (2021)	High	-	BioGRID	2893648
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Gordon DE (2020)	High	0.6135	BioGRID	2875345
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Gordon DE (2020)	High	0.6135	BioGRID	2652389
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Liu H (2022)	High	-	BioGRID	-
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Nabeel-Shah S (2022)	High	-	BioGRID	3659546
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Ren J (2024)	High	-	BioGRID	-
N DDX21	Affinity Capture-MS Affinity Capture-MS An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner is identified by mass spectrometric methods.	Yang Z (2024)	High	-	BioGRID	-
DDX21 N	Affinity Capture-Western Affinity Capture-Western An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.	Ariumi Y (2022)	Low	-	BioGRID	-
DDX21 N	Affinity Capture-Western Affinity Capture-Western An interaction is inferred when a bait protein is affinity captured from cell extracts by either polyclonal antibody or epitope tag and the associated interaction partner identified by Western blot with a specific polyclonal antibody or second epitope tag. This category is also used if an interacting protein is visualized directly by dye stain or radioactivity. Note that this differs from any co-purification experiment involving affinity capture in that the co-purification experiment involves at least one extra purification step to get rid of potential contaminating proteins.	Chen M (2022)	Low	-	BioGRID	-
DDX21 N	PCA PCA A Protein-Fragment Complementation Assay (PCA) is a protein-protein interaction assay in which a bait protein is expressed as fusion to one of the either N- or C- terminal peptide fragments of a reporter protein and prey protein is expressed as fusion to the complementary N- or C- terminal fragment of the same reporter protein. Interaction of bait and prey proteins bring together complementary fragments, which can then fold into an active reporter, e.g. the split-ubiquitin assay.	Chen M (2022)	Low	-	BioGRID	-

Curated By

BioGRID

Interaction Summary

N

DDX21

Gene Ontology Biological Process

Gene Ontology Molecular Function

ATP-dependent RNA helicase activity [TAS]poly(A) RNA binding [IDA]

Gene Ontology Cellular Component

Cross-Linking-MS (XL-MS)