Protein O-glycosylation analysis

Zauner, Gerhild; Kozak, Radoslaw P.; Gardner, Richard A.; Fernandes, Daryl L.; Deelder, André M.; Wuhrer, Manfred

doi:10.1515/hsz-2012-0144

Cited by 91 publications

(83 citation statements)

References 154 publications

(180 reference statements)

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“…Examples range from interaction between multiple instances of the same PTM at different sites (e.g., prior or priming phosphorylation of site A is necessary for subsequent phosphorylation of site B [14-17]), through hierarchical responses to multiple PTM of the same site [5,37,46], or differential responses to multiple different PTM at different sites [78], and ultimately to crosstalk among different PTM at different sites [79]. A protein with 10 instances of a single PTM could give rise to 1024 (2 n ) different molecular species, but if there are two types of PTM there is the potential to generate 59049 (3 n ) species [46].…”

Section: Discussionmentioning

confidence: 99%

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Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation

Rao

Thelen

et al. 2013

BMC Bioinformatics

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BackgroundReversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are typically studied individually, herein we describe the potential for cross-talk and hierarchical regulation.ResultsThe proximity of Met to Ser/Thr/Tyr within the proteome has not previously been addressed. In order to consider the possibility of a generalized interaction, we performed a trans-kingdom sequence analysis of known phosphorylation sites in proteins from bacteria, fungi, plants, and animals. The proportion of phosphorylation sites that include a Met within a 13-residue window centered upon Ser/Thr/Tyr is significantly less than the occurrence of Met in proximity to all Ser/Thr/Tyr residues. Met residues are present at all positions (-6 to +6, inclusive) within the 13-residue window that we have considered. Detailed analysis of sequences from eight disparate plant taxa revealed that many conserved phosphorylation sites have a Met residue in the proximity. Results from GO enrichment analysis indicated that the potential for phosphorylation and Met oxidation crosstalk is most prevalent in kinases and proteins involved in signalling.ConclusionThe large proportion of known phosphorylation sites with Met in the proximity fulfils the necessary condition for cross-talk. Kinases/signalling proteins are enriched for Met around phosphorylation sites. These proteins/sites are likely candidates for cross-talk between oxidative signalling and reversible phosphorylation.

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Section: Discussionmentioning

confidence: 99%

“…In addition to Ser/Thr/Tyr phosphorylation and Met oxidation, other common reversible PTMs include Ser/Thr O-glycosylation [37], Lys/Arg methylation [38], and Lys acetylation [39]. There are examples of each directly regulating protein activities as well as playing roles in cellular signalling [40-43].…”

Section: Introductionmentioning

confidence: 99%

Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation

Rao

Thelen

et al. 2013

BMC Bioinformatics

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“…The enzyme used for N-glycan release from mammalian proteins is peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase (PNGase) F. In contrast, no enzyme is available for an efficient release of O-glycans. As a consequence, laborious chemical methods with harsh conditions, such as β-elimination or hydrazinolysis, are applied, resulting in consecutive monosaccharide loss ("peeling") [14].…”

Section: Current Methods In Glycosylation Analysis Of Biopharmaceuticalsmentioning

confidence: 99%

Mass spectrometry for glycosylation analysis of biopharmaceuticals

Dotz

Haselberg

Shubhakar

et al. 2015

TrAC Trends in Analytical Chemistry

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“…1C) (6). The cartoons annotating the profile suggest structure only within the confines of peptide:N-glycosidase F and ion compositions obtained by mass profiling (7). Peak overlaps, shoulders, glycomers, and even isobars (at higher resolution) can be identified by cutting fractions (Fig.…”

Section: Chromophoric Labeling N-glycansmentioning

confidence: 98%

Toward a Platform for Comprehensive Glycan Sequencing

Reinhold

Zhang

Hanneman

et al. 2013

Molecular & Cellular Proteomics

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From a series of recently published reports, an analytical platform has been proposed for a quantitative and qualitative measure of N-and O-glycosylation, complete with peptide-glycan connectivity and detailed structural understanding. As distant as this may appear, a best methods approach will appear that must move us beyond the cartoon stage of structural understanding. Thus, with this unifying goal in mind, we summarize a series of individually promising first phase protocols of sample preparation (release, purification, and quantification) that remain congruent with a concluding phase (methylation and MS n ) for documented structural detail. Sequential enzymatic Nglycan and chemical O-glycan release from glycopeptides with intervening solid phase extraction and derivatization will provide for a comparative quantification measure of glycosylation. The O-glycan release will be nonreductive and coupled with Michael addition to a pyrazolone analog (1-phenyl-3-methyl-5-pyrazolone) with both the peptide and glycan labeled. The product glycans are stable to methylation and appropriate for sequential disassembly (MS n ). An application using human serum and cancer samples has been detailed characterizing sLe x and comparable valence epitopes. This integrated platform will provide opportunities at variable points to contrast, share, and advance alternative protocols in a collaborative effort that is greatly needed. This integrated platform provides end point opportunities to confirm structural details compiled from synthetic standards and well characterized biologics by MS n . Molecular & Cellular Proteomics 12: 10.1074/mcp.R112.026823, 866 -873, 2013. A UNIFIED GLYCOMICS PLATFORMThe NHLBI, National Institutes of Health, established a Program of Excellence in Glycosciences that supports a study of glycans ubiquitously found on the surfaces of all mammalian cells. Such structures influence a wide variety of cellular and disease-related processes that are governed by the composition and configuration of the interacting partners and the details of structure and conformation within that supramolecular environment. An example of these cohorts are the selectins (E-, L-, and P-) that bind to sialofucosylated ligands displayed on their respective glycans (1, 2). Following an earlier focus by the NIGMS and the NCI of the National Institutes of Health, the NHLBI introduced this Program of Excellence in Glycosciences to bring a more comprehensive glycomics endeavor to support the growing importance of glycan structures in heart, lung, and blood disease research. The Program of Excellence has established three fundamental goals as follows: (i) to develop and expand core facilities across the country; (ii) to facilitate collaborations and distribute research findings, and (iii) to train future generations of scientists to be cognizant in both glycan biology and chemistry. These are laudable goals by any measure, but what blurs the effort and forward momentum must be the considerations of the last goal. With the expanding list of ...

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Protein O-glycosylation analysis

Cited by 91 publications

References 154 publications

Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation

Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation

Mass spectrometry for glycosylation analysis of biopharmaceuticals

Toward a Platform for Comprehensive Glycan Sequencing

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