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ProteomicsDesign and evaluation of a cyclobutane diazirine alkyne tag for photoaffinity labeling in cells
Alkyl diazirines are frequently used in photoaffinity labeling to trap and identify small molecule–protein interactions. How-ever, the alkyl diazirine can preferentially label acidic amino acids and acidic protein surfaces in a pH-dependent manner, presumably via a long-lived alkyl diazo intermediat...
ORGANISM(S): Homo sapiens (Human) 
2024-01-04 | PXD035954 | Pride
Cereblon Diazirine Thalidomide Photoaffinity labeling Binding site mapping 
ProteomicsLabeling preferences of diazirines with protein biomolecules
Diazirines are widely used in photoaffinity labeling (PAL) to trap non-covalent interactions with biomolecules. However, design and interpretation of PAL experiments is challenging without a molecular understanding of the reactivity of diazirines with protein biomolecules. Here, we report a system...
ORGANISM(S): Homo sapiens (Human) 
2022-07-20 | PXD025140 | Pride
Sknsh cells Diazirine Photoaffinity labeling Proteomics Binding sites 
ProteomicsIntracellular targets of the opioids
Opioids are powerful analgesics but carry many contingencies that can lead to opioid-use disorder. Significant energy has been invested in understanding the molecular actions of the opioid alkaloids, particularly their relationship with the opioid receptors at the cell surface. However, there is gro...
ORGANISM(S): Homo sapiens (Human) 
2024-05-07 | PXD045676 | Pride
Heroin Morphine Opioids Lc-ms/ms 
ProteomicsA cleavable chelation-assisted biotin probe enables the discovery of a celecoxib binding site on prostaglandin E synthase
The coxibs are a subset of non-steroidal anti-inflammatory drugs (NSAIDs) that selectively target cyclooxygenase-2 (COX-2) to inhibit prostaglandin signaling and reduce inflammation. However, only celecoxib remains in use, necessitating exploration of broader mechanisms of the coxibs. Here, we rep...
ORGANISM(S): Homo sapiens (Human) 
2024-01-04 | PXD014299 | Pride
Human 
ProteomicsDesign and development of IKZF2 and CK1α dual degraders
Lenalidomide achieves its therapeutic efficacy by recruiting and removing proteins of therapeutic interest through the E3 ligase substrate adapter cereblon. Here, we report the rational design and characterization of 81 cereblon ligands for their ability to degrade the transcription factor Helios (I...
ORGANISM(S): Homo sapiens (Human) 
2024-01-04 | PXD045327 | Pride
Protein degradation Molecular glue 
ProteomicsGenesis and regulation of C-terminal cyclic imides from protein damage
C-Terminal cyclic imides are post-translational modifications (PTMs) that can arise from spontaneous intramolecular cleavage of asparagine or glutamine residues resulting in a form of irreversible protein damage. These protein damage events are recognized and removed by the E3 ligase substrate adapt...
ORGANISM(S): Homo sapiens (Human) 
2024-08-08 | PXD054016 | Pride
Protein cleavage Cyclic imide Cereblon Protein damage Post-translational modifications Deamidation 
Proteomicsselective protein O-glcNAcylation in cells by a proximity-directed O-GlcNAc transferase
O-Linked N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Yet, the study of post-translational modifications like O-GlcNAc has been limited by the lack of strategies to induce O-GlcNA...
ORGANISM(S): Homo sapiens (Human) 
2021-09-08 | PXD016041 | Pride
Ogt Glycoproteomics Nanobody O-glcnac 
ProteomicsThe E3 ubiquitin ligase adaptor cereblon targets the C-terminal cyclic imide degron
The E3 ligase factor cereblon (CRBN) is a target of thalidomide and lenalidomide, which are therapeutic agents used in the treatment of hematopoietic malignancies and as ligands for targeted protein degradation. These agents are proposed to mimic a naturally occurring degron; however, the structural...
ORGANISM(S): Homo sapiens (Human) 
2022-07-28 | PXD034248 | Pride
Degron Cyclic imide Cereblon Protac 
ProteomicsA binding site hotspot map of the FKBP12–rapamycin–FRB ternary complex by photo-affinity labeling and mass spectrometry-based proteomics
Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photo-affinity labeling (PAL) coupled with chemical enrichment and unbiased analysis by mass spectrometry (MS). MS-based binding site hotspot maps provide structural resolution of in...
ORGANISM(S): Homo sapiens (Human) 
2019-07-17 | PXD014319 | Pride
Photo-affinity labeling Structural protemics 
ProteomicsAspartate residues far from the active site drive O-GlcNAc transferase substrate selection
Here we use protein microarray technology and proteome-wide glycosylation profiling to show that conserved aspartate residues in the tetratricopeptide repeat (TPR) lumen of OGT drive substrate selection. Changing these residues to alanines alters substrate selectivity and unexpectedly increases rate...
ORGANISM(S): Homo sapiens (Human) 
2019-07-26 | PXD014731 | Pride
Glycoproteomics O-glcnac 
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