scholarly journals Development of Serum Glycoproteomic Profiling Technique; Simultaneous Identification of Glycosylation Sites and Site-Specific Quantification of Glycan Structure Changes

2010 ◽  
Vol 9 (9) ◽  
pp. 1819-1828 ◽  
Author(s):  
Koji Ueda ◽  
Sachiko Takami ◽  
Naomi Saichi ◽  
Yataro Daigo ◽  
Nobuhisa Ishikawa ◽  
...  
Keyword(s):  
Glycan Structure ◽  
Site Specific ◽  
Structure Changes ◽  
Glycosylation Sites ◽  
Simultaneous Identification

scholarly journals Defining HIV-1 Envelope N-Glycan Microdomains through Site-Specific Heterogeneity Profiles

2018 ◽  
Vol 93 (1) ◽  
Author(s):  
Audra A. Hargett ◽  
Qing Wei ◽  
Barbora Knoppova ◽  
Stacy Hall ◽  
Zhi-Qiang Huang ◽  
...  
Keyword(s):  
Immune System ◽  
Immune Evasion ◽  
Immune Escape ◽  
High Resolution Mass Spectrometry ◽  
National Laboratory ◽  
Site Specific ◽  
Los Alamos National Laboratory ◽  
Glycosylation Sites ◽  
Env Protein ◽  
Hiv 1

ABSTRACT The HIV-1 envelope (Env) glycans shield the surface of Env from the immune system and form integral interactions important for a functional Env. To understand how individual N-glycosylation sites (NGS) coordinate to form a dynamic shield and evade the immune system through mutations, we tracked 20 NGS in Env from HIV-transmitted/founder (T/F) and immune escape variants and their mutants involving the N262 glycan. NGS were profiled in a site-specific manner using a high-resolution mass spectrometry (MS)-based workflow. Using this site-specific quantitative heterogeneity profiling, we empirically characterized the interdependent NGS of a microdomain in the high-mannose patch (HMP). The changes (shifts) in NGS heterogeneity between the T/F and immune escape variants defined a range of NGS that we further probed for exclusive combinations of sequons in the HMP microdomain using the Los Alamos National Laboratory HIV sequence database. The resultant sequon combinations, including the highly conserved NGS N262, N448, and N301, created an immune escape map of the conserved and variable sequons in the HMP microdomain. This report provides details on how some clustered NGS form microdomains that can be identified and tracked across Env variants. These microdomains have a limited number of N-glycan-sequon combinations that may allow the anticipation of immune escape variants. IMPORTANCE The Env protein of HIV is highly glycosylated, and the sites of glycosylation can change as the virus mutates during immune evasion. Due to these changes, the glycan location and heterogeneity of surrounding N-glycosylation sites can be altered, resulting in exposure of different glycan or proteoglycan surfaces while still producing a viable HIV variant. These changes present a need for vaccine developers to identify Env variants with epitopes most likely to induce durable protective responses. Here we describe a means of anticipating HIV-1 immune evasion by dividing Env into N-glycan microdomains that have a limited number of N-glycan sequon combinations.

scholarly journals Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics

2020 ◽  
Vol 21 (18) ◽  
pp. 6727 ◽  
Author(s):  
Xing Li ◽  
Zhijue Xu ◽  
Xiaokun Hong ◽  
Yan Zhang ◽  
Xia Zou
Keyword(s):  
Protein Interactions ◽  
Glycan Structure ◽  
Biological Processes ◽  
Protein Scaffolds ◽  
New Disease ◽  
The Public ◽  
Disease Biomarkers ◽  
Bioinformatic Tools ◽  
The Past ◽  
Glycosylation Sites

Glycosylation plays critical roles in various biological processes and is closely related to diseases. Deciphering the glycocode in diverse cells and tissues offers opportunities to develop new disease biomarkers and more effective recombinant therapeutics. In the past few decades, with the development of glycobiology, glycomics, and glycoproteomics technologies, a large amount of glycoscience data has been generated. Subsequently, a number of glycobiology databases covering glycan structure, the glycosylation sites, the protein scaffolds, and related glycogenes have been developed to store, analyze, and integrate these data. However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins. In this study, the representative databases of glycan structure, glycoprotein, glycan–protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics are reviewed. We hope this overview could assist readers in searching for information on glycoproteins of interest, and promote further clinical application of glycobiology.

scholarly journals Site-specific N-glycosylation of HeLa cell glycoproteins

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lilla Turiák ◽  
Simon Sugár ◽  
András Ács ◽  
Gábor Tóth ◽  
Ágnes Gömöry ◽  
...  
Keyword(s):  
Hela Cell ◽  
Cell Line ◽  
Bovine Serum ◽  
Culture Media ◽  
Cancer Cell Line ◽  
Hela Cell Line ◽  
Glycosylation Pattern ◽  
Site Specific ◽  
Glycosylation Sites

Abstract We have characterized site-specific N-glycosylation of the HeLa cell line glycoproteins, using a complex workflow based on high and low energy tandem mass spectrometry of glycopeptides. The objective was to obtain highly reliable data on common glycoforms, so rigorous data evaluation was performed. The analysis revealed the presence of a high amount of bovine serum contaminants originating from the cell culture media – nearly 50% of all glycans were of bovine origin. Unaccounted, the presence of bovine serum components causes major bias in the human cellular glycosylation pattern; as is shown when literature results using released glycan analysis are compared. We have reliably identified 43 (human) glycoproteins, 69 N-glycosylation sites, and 178 glycoforms. HeLa glycoproteins were found to be highly (68.7%) fucosylated. A medium degree of sialylation was observed, on average 46.8% of possible sialylation sites were occupied. High-mannose sugars were expressed in large amounts, as expected in the case of a cancer cell line. Glycosylation in HeLa cells is highly variable. It is markedly different not only on various proteins but also at the different glycosylation sites of the same protein. Our method enabled the detailed characterization of site-specific N-glycosylation of several glycoproteins expressed in HeLa cell line.

Glycan profiles of the 27 N-glycosylation sites of the HIV envelope protein CN54gp140

2012 ◽  
Vol 393 (8) ◽  
pp. 719-730 ◽  
Author(s):  
Martin Pabst ◽  
Martina Chang ◽  
Johannes Stadlmann ◽  
Friedrich Altmann
Keyword(s):  
Ion Trap ◽  
Ionization Mass ◽  
Site Specific ◽  
Fragmentation Energy ◽  
Glycosylation Sites ◽  
Immunodeficiency Virus ◽  
Challenging Tasks ◽  
Hiv Envelope ◽  
Standard Software ◽  
Actual Mass

Abstract Hope rests on the envelope proteins of human immunodeficiency virus (HIV) as protective vaccines and thus their antibody binding sites are of prime interest. 2G12 and other human antibodies bind to a cluster of oligomannose N-glycans. Owing to the extreme number and density of N-glycosylation sites gp160 and its recombinant form gp140 represent challenging tasks for site-specific glycosylation analysis. We have conducted a glycosylation analysis of CN54gp140 by liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) using an ion trap as well as a Q-TOF instrument and standard software for glycopeptide identification. First, a deglycosylated sample of the protease digest served to locate the elution positions of peptides covering all of the 27 potential N-glycosylation sites. Then, the assignments of the similarly eluting glycopeptides were verified by collision-induced decay MS/MS experiments with elevated fragmentation energy. The acquisition of site-specific glycan profiles was facilitated by the use of buffered eluent, which rounds up all glycoforms of a peptide into one peak. Calculation of the molecular mass drawn on the weighted averages of the glycans at each site led to the actual mass of gp140 of approximately 120 kDa.

scholarly journals Glycosylation of CD44 is implicated in CD44-mediated cell adhesion to hyaluronan.

1996 ◽  
Vol 132 (6) ◽  
pp. 1199-1208 ◽  
Author(s):  
A Bartolazzi ◽  
A Nocks ◽  
A Aruffo ◽  
F Spring ◽  
I Stamenkovic
Keyword(s):  
Cell Adhesion ◽  
Regulatory Mechanism ◽  
Cell Attachment ◽  
Glycosylation Site ◽  
Side Chain ◽  
Site Specific ◽  
Coated Substrate ◽  
Glycosylation Sites ◽  
Coated Surfaces

CD44-mediated cell adhesion to hyaluronate is controlled by mechanisms which are poorly understood. In the present work we examine the role of N-linked glycosylation and Ser-Gly motifs in regulating CD44-hyaluronate interaction. Our results show that treatment of a panel of human cell lines which constitutively express CD44 with the inhibitor of N-linked glycosylation tunicamycin results in the loss of attachment of these cells to hyaluronate-coated substrate. In contrast, treatment of the same cells with deoxymannojirimycin, which inhibits the conversion of high mannose oligosaccharides to complex N-linked carbohydrates, results in either no change or an increase in CD44-mediated adhesion to hyaluronate, suggesting that complex N-linked oligosaccharides may not be required for and may even inhibit CD44-HA interaction. Using human melanoma cells stably transfected with CD44 N-linked glycosylation site-specific mutants, we show that integrity of five potential N-linked glycosylation sites within the hyaluronate recognition domain of CD44 is critical for hyaluronate binding. Mutation of any one of these potential N-linked glycosylation sites abrogates CD44-mediated melanoma cell attachment to hyaluronate-coated surfaces, suggesting that all five sites are necessary to maintain the HA-recognition domain in the appropriate conformation. We also demonstrate that mutation of serine residues which constitute the four Ser-Gly motifs in the membrane proximal domain, and provide potential sites for glycosaminoglycan side chain attachment, impairs hyaluronate binding. Taken together, these observations indicate that changes in glycosylation of CD44 can have profound effects on its interaction with hyaluronic acid and suggest that glycosylation may provide an important regulatory mechanism of CD44 function.

scholarly journals Site-specific O-Glycosylation on the MUC2 Mucin Protein Inhibits Cleavage by the Porphyromonas gingivalis Secreted Cysteine Protease (RgpB)

2013 ◽  
Vol 288 (20) ◽  
pp. 14636-14646 ◽  
Author(s):  
Sjoerd van der Post ◽  
Durai B. Subramani ◽  
Malin Bäckström ◽  
Malin E. V. Johansson ◽  
Malene B. Vester-Christensen ◽  
...  
Keyword(s):  
Porphyromonas Gingivalis ◽  
Terminal Region ◽  
Mucus Layer ◽  
Epithelial Surface ◽  
Site Specific ◽  
C Terminus ◽  
Glycosylation Sites ◽  
Major Structural Component ◽  
Recombinant Fragments ◽  
Culture Supernatants

The colonic epithelial surface is protected by an inner mucus layer that the commensal microflora cannot penetrate. We previously demonstrated that Entamoeba histolytica secretes a protease capable of dissolving this layer that is required for parasite penetration. Here, we asked whether there are bacteria that can secrete similar proteases. We screened bacterial culture supernatants for such activity using recombinant fragments of the MUC2 mucin, the major structural component, and the only gel-forming mucin in the colonic mucus. MUC2 has two central heavily O-glycosylated mucin domains that are protease-resistant and has cysteine-rich N and C termini responsible for polymerization. Culture supernatants of Porphyromonas gingivalis, a bacterium that secretes proteases responsible for periodontitis, cleaved the MUC2 C-terminal region, whereas the N-terminal region was unaffected. The active enzyme was isolated and identified as Arg-gingipain B (RgpB). Two cleavage sites were localized to IR↓TT and NR↓QA. IR↓TT cleavage will disrupt the MUC2 polymers. Because this site has two potential O-glycosylation sites, we tested whether recombinant GalNAc-transferases (GalNAc-Ts) could glycosylate a synthetic peptide covering the IRTT sequence. Only GalNAc-T3 was able to glycosylate the second Thr in IRTT, rendering the sequence resistant to cleavage by RgpB. Furthermore, when GalNAc-T3 was expressed in CHO cells expressing the MUC2 C terminus, the second threonine was glycosylated, and the protein became resistant to RgpB cleavage. These findings suggest that bacteria can produce proteases capable of dissolving the inner protective mucus layer by specific cleavages in the MUC2 mucin and that this cleavage can be modulated by site-specific O-glycosylation.

scholarly journals Site-specific glycosylation regulates the form and function of the intermediate filament cytoskeleton

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Heather J Tarbet ◽  
Lee Dolat ◽  
Timothy J Smith ◽  
Brett M Condon ◽  
E Timothy O'Brien ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Transferase Activity ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Form And Function ◽  
Glycosylation Sites ◽  
Wide Range ◽  
Dynamics And Function ◽  
Glcnac Transferase ◽  
And Function

Intermediate filaments (IF) are a major component of the metazoan cytoskeleton and are essential for normal cell morphology, motility, and signal transduction. Dysregulation of IFs causes a wide range of human diseases, including skin disorders, cardiomyopathies, lipodystrophy, and neuropathy. Despite this pathophysiological significance, how cells regulate IF structure, dynamics, and function remains poorly understood. Here, we show that site-specific modification of the prototypical IF protein vimentin with O-linked β-N-acetylglucosamine (O-GlcNAc) mediates its homotypic protein-protein interactions and is required in human cells for IF morphology and cell migration. In addition, we show that the intracellular pathogen Chlamydia trachomatis, which remodels the host IF cytoskeleton during infection, requires specific vimentin glycosylation sites and O-GlcNAc transferase activity to maintain its replicative niche. Our results provide new insight into the biochemical and cell biological functions of vimentin O-GlcNAcylation, and may have broad implications for our understanding of the regulation of IF proteins in general.

scholarly journals Selective elongation of the oligosaccharide attached to the second potential glycosylation site of yeast exoglucanase: effects on the activity and properties of the enzyme

1994 ◽  
Vol 304 (3) ◽  
pp. 917-922 ◽  
Author(s):  
R D Basco ◽  
L M Hernández ◽  
M D Muñox ◽  
I Olivero ◽  
E Andaluz ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Thermal Inactivation ◽  
Glycosylation Site ◽  
Translation Product ◽  
Site Specific ◽  
Potential Glycosylation Site ◽  
Glycosylation Sites ◽  
Conformational Constraints ◽  
Specific Elongation ◽  
Protein Portion

Three exoglucanases (Exgs), ExgIa, ExgIb and Exg325, are secreted by Saccharomyces cerevisiae cells. They share a common protein portion with two potential glycosylation sites (sequons) but differ in the amount of N-linked carbohydrate [Basco, R.D., Muñoz, M.D., Hernández, L.M., Váquez de Aldana, C. and Larriba, G. (1993) Yeast 9, 221-234]. ExgIb contains two short oligosaccharides attached to asparagines (Asn) 165 and 325 of the primary translation product [Hernández, L.M., Olivero, I., Alvarado, E. and Larriba, G. (1992) Biochemistry 31, 9823-9831]. Exg325 carries a single, short oligosaccharide bound to Asn325 whereas ExgIa has at least one large oligosaccharide, since it has not been produced by mutant mnn9. To address the question of the origin of ExgIa, both sequons were individually mutated by substituting Gln for Asn. An ExgIa-like isoenzyme was still secreted by mutant Exg165 but not by mutant Exg325. Additional studies on sequential deglycosylation of ExgIa with endo-beta-N-acetylglucosaminidase H (endo H), the susceptibility of both oligosaccharides to the endoglycosidase, and analysis of the presence of GlcNAc at both asparagine residues after total deglycosylation with endo H, indicated that ExgIa contained two oligosaccharides, a short one bound to Asn165 and a large one bound to Asn325, and, accordingly, originated from ExgIb. The elongation of the second oligosaccharide did not result in a higher stability towards thermal inactivation or unfolding, or in an increased resistance to proteases as compared with ExgIb; however, the affinity of the enzyme towards laminarin decreased by 50%. This site-specific elongation occurred in the oligosaccharide that was less susceptible to endo H, indicating that these properties are determined by different conformational constraints.

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