Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• total deposited models into the PDB for all structural determination methods. Lines show glycosylation in the PDB over time, split into N-glycans, O-glycans, S-glycans, and C-glycans. Data contained within each glycan entry. Data contained within each sugar entry. Data contained within each linkage

Introduction of a human- and keyboard-friendly N-glycan nomenclature

• Friedrich Altmann,
• Johannes Helm,
• Martin Pabst and
• Johannes Stadlmann

Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53

• ). Attempt at an application to O-glycans The short, but varied core-region of O-glycans do not lend themselves to the proglycan logic as much as N-glycans. However, its application is possible as demonstrated in an article on chondrocyte glycans [56]. The branches to the core structures can be dealt with in

• much the same way as N-glycan antennae. It appears, however, that the particular core type has to be specified as shown in Figure 12. The very simple and frequently occurring O-glycans T-, Tn- and Sialyl-Tn-antigen may be exempted from such attempts. Likewise, will the rarer core types be left out for

• . Proglycan annotation of oligomannosidic and some hybrid-type N-glycans. Plant and insect N‐glycans. Since the xylose strongly indicates plant N‐glycans, a simplified annotation, possible with the macro‐term “La” for the Lewis A determinant, may be used (grey font). Provisional outline of how O-glycans with

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• , these substructures occurred in many different contexts, such as blood group H, LacdiNAc, or the Sda motif, and particularly in sequences resembling O-glycans, milk oligosaccharides, and glycosphingolipids. At first glance, these two binding specificities may seem unconnected, indicating a rather

• in which its preferred binding motifs occur (O-glycans, milk glycans, GAGs) are absent from most plants, including melons. We thus hypothesize that the role of this lectin might be to recognize non-self epitopes, such as for protection against pathogens, which is a common function in plant lectins [3

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• the addition of GlcNAc to processed N-linked glycan structures. These include all the MGAT enzymes. 7) GalNAc-type O-glycans: O-linked glycans are attached to serine (Ser) or threonine (Thr) on peptides, where GalNAc is the root carbohydrate. This is mediated by a family of about 20 Golgi-resident

• -glycans, O-glycans and glycolipids. 18) ABO blood group synthesis: these are enzymes involved in the biosynthesis of ABO antigens. 19) LacDiNAc: glycogenes involved in the synthesis of LacDiNac structures. 20) Sulfated glycan epitopes: this includes the enzymes attaching sulfate to different types of

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• -glycans are attached to Ser or Thr. Glycan compositions can range from monosaccharides (e.g., Tn antigen for O-glycans [1]) to large polysaccharides (e.g., N-glycans of recombinant human erythropoietin [2]). The most common building blocks of human protein glycans are hexoses (glucose, galactose, and

• glycan composition. The low intensity of these glycopeptide signals resulted in a decreased likelihood for MS/MS selection. Of note, the IgA2 HYT glycopeptide covers a sequence stretch homologous to the hinge region of IgA1, carrying O-glycans. In a previous study the IgA1 peptide has been referred to as

• quantification. Keywords: bioinformatics; cysteine oxidation; glycoproteomics; immunoglobulins; mass spectrometry; Introduction Protein glycosylation mainly occurs in the form of N- and O-glycosylation. N-Glycans are attached to Asn within an amino acid consensus sequence (Asn-Xxx-Ser/Thr, Xxx ≠ Pro) and O

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• epithelial cells, the mixture of O-glycans that glycosylate mucins are extended core 2 structures, while in breast cancer cells, O-glycan mass decreases (hypoglycosylation), and there is an increase in abundance of sialylated core 1 [15]. The upregulation of Tn (αGalNAc) and STn (αNeuAc-2,6-αGalNAc) antigens

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• manually using the mouse or by importing text input files. The interface provides a list of templates: N- O- glycans, glycosphingolipids, glycosaminoglycans(GAGs). Rows of CFG notations for monosaccharides assist with glycan structure drawing on canvas. The application also supports the glycan symbol

• structure can further be used as a query for the search in glycan databases; using match percentage (Similarity) or by the number of components matched (Matched) criteria. Four predefined score matrices are available, named: N-glycans, O-glycans, Sphingolipids and Link_similarity. The “Link_similarity

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• ). Together, and consistent with our N-glycoproteome analyses, this suggests that HCC is associated with an overall decrease in sialylation of N- and O-glycans across the plasma glycoproteome. Conclusion GlypNirO is an automated software pipeline that integrates glyco/peptide identification from Byonic and

• analysis of a plasma glycoproteome dataset demonstrated that GlypNirO can be used to detect changes in site-specific glycosylation occupancy and structure of N- and O-glycosylation in complex glycoproteomes. Specifically, we found that HCC was associated with decreased sialylation of both N- and O-glycans

• peptide. For N-linked searches (N-X-S/T) a database of 164 N-glycans was used (Supporting Information File 1, Table S41) and for the O-linked searches (at any S/T) a database of 49 O-glycans (Supporting Information File 1, Table S42) was used. All glycan modifications were set as “Rare 1” allowing each

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• modifications of glycocalyx proteins are N-glycans (asparagine-linked) and O-glycans (serine- or threonine-linked), while glycosphingolipids are the major subclass of glycosylated lipids in the cell membrane of human cells (Figure 2). While many core elements of glycocalyx oligosaccharides are conserved between

• host proteins and cell types, for example the invariant N-acetyl-D-glucosamine or N-acetyl-D-galactosamine residues that attach N- or O-glycans, respectively, to the peptide side chains, the large variety and possible permutations of “capping” residues (for example D-mannopyranosides, D

Expanding the scope of cyclopropene reporters for the detection of metabolically engineered glycoproteins by Diels–Alder reactions

• Anne-Katrin Späte,
• Verena F. Schart,
• Julia Häfner,
• Andrea Niederwieser,
• Thomas U. Mayer and
• Valentin Wittmann

Beilstein J. Org. Chem. 2014, 10, 2235–2242, doi:10.3762/bjoc.10.232

• proteins and mucin-type O-glycans [30]. Here, we show that 1 and 2 can be employed for both labeling of cell-surface glycoconjugates (detected by confocal fluorescence microscopy) and isolated glycoproteins (detected by Western blot). Results and Discussion For the synthesis of the cyclopropene-tagged

Synthesis of mucin-type O-glycan probes as aminopropyl glycosides

• David Benito-Alifonso,
• Rachel A. Jones,
• Anh-Tuan Tran,
• Hannah Woodward,
• Nichola Smith and
• M. Carmen Galan

Beilstein J. Org. Chem. 2013, 9, 1867–1872, doi:10.3762/bjoc.9.218

• . Keywords: glycosylation; mucin-type oligosaccharides; O-glycans; oligosaccharide synthesis; Introduction Mucins are heavily glycosylated glycoproteins that may be membrane-associated or secreted in gel form and play an important biological role in the respiratory and intestinal tracks [1][2][3]. Mucins

De novo synthesis of D- and L-fucosamine containing disaccharides

• Daniele Leonori and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2013, 9, 332–341, doi:10.3762/bjoc.9.38

• bacterium. In 2001, the P. aeruginosa pilin O-linked glycans were found to be linear trisaccharides that are covalently attached to serine (Figure 1). The O-glycans contain a D-fucosamine residue at the protein-binding site. This unusual monosaccharide is not present in eukaryotes, and therefore may be used

Automated synthesis of sialylated oligosaccharides

• Davide Esposito,
• Mattan Hurevich,
• Bastien Castagner,
• Cheng-Chung Wang and
• Peter H. Seeberger

Beilstein J. Org. Chem. 2012, 8, 1601–1609, doi:10.3762/bjoc.8.183

• allow for access to synthetic sialosides, an intense effort has been devoted to identifying sialic acid building blocks with superior sialylation properties [10]. In turn, only limited attention has been given to the design of more efficient nucleophiles for sialylations. In naturally occurring N- and O

• -glycans the terminal sialic acid residue is most often connected to the C3 or C6 hydroxy group of galactose. Therefore, differently protected galactose precursors have been exploited for sialylation reactions. The obtained disaccharides have been used to prepare synthetic sialosides [11][12][13]. A

The use of glycoinformatics in glycochemistry

• Thomas Lütteke

Beilstein J. Org. Chem. 2012, 8, 915–929, doi:10.3762/bjoc.8.104

• structures stored in the databases. An analysis of mammalian carbohydrate structures present in Glycosciences.DB, for example, revealed that this data set contained 3299 oligosaccharides, which are part of N-glycans, O-glycans or glycolipids from 38 mammalian species. Only ten different monosaccharides were