Systematic analysis of the impact of phosphorylation and O-GlcNAcylation on protein subcellular localization

Sitetack: A Deep Learning Model that Improves PTM Prediction by Using Known PTMs

“…Having shown that encoding known PTM locations of a given type as a separate amino acid can improve prediction accuracy for that PTM, we wondered if including information about a different PTM can improve prediction accuracy. To explore this crosstalk, we chose O-glycosylation with GlcNAc and phosphorylation at serine and threonine, which generally occur in the same subcellular compartments and at the same amino acid residues (serine and threonine) 18,19,34 . Moreover, both had large datasets, which we suspected was important to detect an impact on prediction accuracy 24 .…”

O-GlcNAcylation and immune cell signaling: A review of known and a preview of unknown

“…A recent technique combining metabolic labeling, hydrophilic interaction liquid chromatography, and mass spectrometry has shown success in identifying O-GlcNAcylation and phosphorylation in RNA-binding proteins ( 96 ), offering a technique that may be improvised for other proteins as well. Another recent study took an additional step and systematically analyzed O-GlcNAcylated and phosphorylated proteins in the cytoplasm and nucleus and showed that both modifications are enriched in the nuclear fraction ( 97 ), possibly due to the contribution of PTMs to the nuclear transport of proteins. Thus, comprehensive biochemical studies seem to be the right approach to apply to learn discrete mechanistic roles of protein O-GlcNAcylation in controlling various immune cell functions.…”

“…A quick look into the literature garners attention to the crosstalk between O-GlcNAcylation and phosphorylation that suggests three modes of coexistence of these PTMs based on their proximity ( 4 , 9 , 96 , 97 , 98 ). First, both PTMs target serine and threonine residues, resulting in the competitive occupancy of the same site, in which one modification blocks the other.…”

Standards-Free Absolute Quantitation of Oxidizable Glycopeptides by Coulometric Mass Spectrometry

“…PTMs increase the functional diversity of the proteome and influence many aspects of cell biology . Glycosylation is considered as one of the most complex PTMs and is critical for the functions and characteristics of proteins, such as their conformation, stability, distribution, pharmacokinetic and pharmacodynamic properties, , and protease resistance . Over the past decade, research has revealed that glycosylation is important for cell signaling, − vaccine development, , cellular control of diabetes, − and cancers. − For instance, aberrant glycosylation of immunoglobulin is linked to disease activity and pathogenesis .…”