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Title: Evaluation of selected binding domains for the analysis of ubiquitinated proteomes

Ubiquitination is an abundant post-translational modification that consists of covalent attachment of a 76 amino acid residue polypeptide, ubiquitin, to lysine residues or the N-terminus of proteins. Mono and polyubiquitination have been shown to be involved in many critical eukaryotic cellular functions. Affinity enrichment of ubiquitinated proteins has enabled the global analysis of this key modification. In this context, the use of ubiquitin-binding domains (UBDs) is a promising, but poorly explored alternative to more broadly used immune-affinity or tagged affinity enrichment methods. Herein we evaluate the application of eight selected UBDs with differing and contrasting affinities for ubiquitination states. We performed a micro-scale proteomic comparison, leading to the identification of ~200 ubiquitinated protein candidates per UBD to facilitate comparisons. Western blot analysis using anti-ubiquitin or monoclonal antibodies against polyubiquitination at lysine 48 and 63 suggests that UBDs from Dsk2 and ubiquilin-1 have the broadest specificity capturing most types of ubiquitination, whereas the one from NBR1 seems to be more selective to polyubiquitination. Our data demonstrate that with optimized purification conditions UBDs can be a useful tool for proteomic applications.
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Publication Date:
OSTI Identifier:
Report Number(s):
42294; 40072; 42696; 400412000
DOE Contract Number:
Resource Type:
Journal Article
Resource Relation:
Journal Name: Journal of the American Society for Mass Spectrometry, 24(8):1214-1223
Research Org:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org:
Country of Publication:
United States
Ubiquitination; post-translation modification; affinity purification; proteomics; mass spectrometry.; Environmental Molecular Sciences Laboratory