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

• complement the growing glycan content of the PDB. Keywords: carbohydrates; database; N-glycans; N-glycosylation; polysaccharides; validation; website; Introduction Carbohydrate modelling is an important but often cumbersome stage in the macromolecular X-ray structure solution workflow. The accurate

• overall conformation of N-glycans comes to that of validated deposited structures [16]. The PDB-REDO [21] database is a separate resource, albeit linked to the PDB in that the entries that compound PDB-REDO are those original PDB crystallographic entries that included experimental data (i.e., reflection

• 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

• -glycans, at least, no simple words. Next to chemical formulas, the IUPAC code can be regarded as the best, most reliable and yet immediately comprehensible annotation of oligosaccharide structures of any type from any source. When it comes to N-glycans, the venerable IUPAC code has, however, been widely

• supplanted by highly simplified terms for N-glycans that count the number of antennae or certain components such as galactoses, sialic acids and fucoses and give only limited room for exact structure description. The highly illustrative – and fortunately now standardized – cartoon depictions gained much

• alphanumeric descriptions of the hundreds and thousands of N-glycan structures. Here, we present a system that describes N-glycans by defining their terminal elements. To minimize redundancy and length of terms, the common elements of N-glycans are taken as granted. The preset reading order facilitates

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

• A and B together) and basal breast cancer. Here, glycans potentially affected by the enriched TFs are shown in SNFG format [18][19]. The analysis suggests that TF transformations accompanying cancer progression may impact all four major classes of glycans: O- and N-glycans found on glycoproteins

• reticulum. The enzymes involved is such synthesis include the ALG (asparagine-linked N-glycosylation) enzymes and additional proteins (part of OSTA and OSTB) involved in the transfer of the glycan to the nascent protein. 5) Complex N-glycans: This pathway includes glycogenes responsible for processing the N

• β3GlcNAc to this fucose. 15) Type 1 and 2 LacNAc: These enzymes help construct either Galβ1-3GlcNAc (type 1) or Galβ1-4GlcNAc (type 2) lactosamine chains on antennae of N-linked glycan, O-linked glycans, and glycolipids. Also included are GCNT1–3 that can facilitate formation of I-branches on N-glycans. 16

Simulating the enzymes of ganglioside biosynthesis with Glycologue

• Andrew G. McDonald and
• Gavin P. Davey

Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64

• acting as a wildcard character. Double branches are used to form symmetric core structures, such as the trimannosyl core of N-glycans, or O-linked glycan cores based on GalNAc (Equation 3): Capping of branches and linearly extended chains is achieved through termination, of which sialylation is a typical

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

• 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

• -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

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

• 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

• agalactosylated N-glycans on IgG were increased in abundance in HCC (Figure 1a), and the relative abundance of the HexNAc(5)Hex(6)NeuAc(3) composition at multiple sites on alpha-1-antichymotrypsin was decreased in HCC (Figure 1b). N-Glycoproteome analysis To extend our analysis, we next investigated the full

• different glycan structures at specific sites in diverse glycoproteins. Examining the data in more detail identified several sites with multiple glycoforms with statistically significant changes in abundance. Specifically, HCC patients had decreased abundance of disialylated N-glycans at alpha-1-antitrypsin

• N271 and haptoglobin N184 (Figure 3a and 3b), with increased abundance of non-sialylated N-glycans at fibrinogen N78 (Figure 3c), and decreased abundance of trisialylated N-glycans at alpha-2-HS-glycoprotein N176 (Figure 3d). Together, this suggests an overall decrease in sialylation of N-glycans

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• critical process parameters that control the glycosylation critical quality attributes. The advances made in protocols for capillary electrophoresis-laser-induced fluorescence (CE-LIF) measurements of antibody N-glycans have increased the potential for generating large datasets of N-glycosylation values

• conditions (Supporting Information File 1, Table S1). Five of the replicates failed due to sampling errors, leaving a total of 391 electropherograms to identify and quantitate glycans. The N-glycans were enzymatically removed, fluorescently labelled with aminopyrene trisulfonate (APTS), and analyzed by

• capillary electrophoresis. The N-glycans were separated using a 5 minute separation across a 30 cm capillary. N-Glycan peaks in the electropherograms were annotated for all 391 electropherograms separately demonstrating that varying culture conditions resulted in significant differences in the

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• , implicated in protein folding and structural stability, and mediating interactions with receptors and with the environment. All N-glycans share a common core from which linear or branched arms stem from, with functionalization specific to different species and to the cells’ health and disease state. This

• diversity generates a rich collection of structures, all diversely able to trigger molecular cascades and to activate pathways, which also include adverse immunogenic responses. These events are inherently linked to the N-glycans’ 3D architecture and dynamics, which remain for the large part unresolved and

• undetected because of their intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans’ 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• -factor for the proper synthesis of N-glycans [13]. Subsequently, pioneer structures based on ᴅ-fructofuranose [14], ᴅ-tagatofuranose or ᴅ-psicofuranose [15][16] have been prepared, but their inhibitory activity could not have been tested due to their low stability under standard conditions [16]. Further

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

Synthesis of 1,4-imino-L-lyxitols modified at C-5 and their evaluation as inhibitors of GH38 α-mannosidases

• Maroš Bella,
• Sergej Šesták,
• Ján Moncoľ,
• Miroslav Koóš and
• Monika Poláková

Beilstein J. Org. Chem. 2018, 14, 2156–2162, doi:10.3762/bjoc.14.189

• swainsonine, interferes with the glycosylation pathway where it specifically inhibits GH38 glycoside hydrolases [23][24]. Up to date, swainsonine is the most potent Golgi mannosidase II (GMII) inhibitor. It is known that inhibition of the biosynthesis of complex N-glycans in the Golgi apparatus influences

Synthetic and semi-synthetic approaches to unprotected N-glycan oxazolines

• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 416–429, doi:10.3762/bjoc.14.30

• for any further protecting group manipulations, and simplifying synthetic strategies. As an alternative to total synthesis, significant quantities of several structurally complicated N-glycans can be isolated from natural sources, such as egg yolks and soy bean flour. Enzymatic transformations of

• these materials, in concert with DMC-mediated oxazoline formation as a final step, allow access to a selection of N-glycan oxazoline structures both in larger quantities and in a more expedient fashion than is achievable by total synthesis. Keywords: DMC, ENGase; glycosyl oxazolines; N-glycans

• ] (ENGases, EC 3.2.1.96), a class of enzyme which specifically cleave between the innermost two GlcNAc residues of N-glycans attached to N-linked glycoproteins, all operate via a two-step mechanism involving neighbouring group participation of the 2-acetamide group and an oxazoline as a high energy

Glyco-gold nanoparticles: synthesis and applications

• Federica Compostella,
• Olimpia Pitirollo,
• Alessandro Silvestri and
• Laura Polito

Beilstein J. Org. Chem. 2017, 13, 1008–1021, doi:10.3762/bjoc.13.100

• system in response to pathogens mediated by lectins, like DC-SIGN. Mammalian cell surface lectins, expressed on the surface of dendritic cells (DC) and macrophages, recognize in a multivalent way a vast array of glycans on the exterior of pathogens. Natural carbohydrate ligands include high-mannose N

• -glycans, such as those found on the HIV gp120 protein, and Lewis-type glycans. Ligand recognition often initiates events which are able to trigger specific signaling and result in a robust immune activation in humans. For example, galactofuranose (Galf) functionalized AuNPs were found able to elicit a pro

Expression, purification and structural analysis of functional GABA transporter 1 using the baculovirus expression system

• Jing Hu,
• Chris Weise,
• Christoph Böttcher,
• Hua Fan and
• Jian Yin

Beilstein J. Org. Chem. 2017, 13, 874–882, doi:10.3762/bjoc.13.88

• Galanthusnivalis agglutinin (GNA, digoxigenin-conjugated lectin) (Figure 1F), indicating the predominance of the paucimannose structure in insect cells. In contrast, mammalian N-glycans have terminal sialic acid residues with more antennal diversity. The band at approximately 250 kDa corresponds to an oligomeric

• but not the terminal trimming of N-glycans is involved in the regulation of the correct membrane glycoprotein folding since the inhibition of N-glycosylation processing by 1-deoxymannojirimycin (dMM) results in a mannose-rich type of N-glycan that does not affect either the protein stability or

• intracellular trafficking [11]. Therefore, the correct folding of GAT1/GFP protein in insect cells should not be affected by the lack of terminal trimming, including the sialylation of N-glycans. The low GABA uptake activity of GAT1/GFP fusion protein in insect cells should result from the terminal mannose

Synthesis and in vitro cytotoxicity of acetylated 3-fluoro, 4-fluoro and 3,4-difluoro analogs of D-glucosamine and D-galactosamine

• Štěpán Horník,
• Lucie Červenková Šťastná,
• Petra Cuřínová,
• Jan Sýkora,
• Kateřina Káňová,
• Roman Hrstka,
• Ivana Císařová,
• Martin Dračínský and
• Jindřich Karban

Beilstein J. Org. Chem. 2016, 12, 750–759, doi:10.3762/bjoc.12.75

• expression of highly branched N-glycans in PC-3 cells, the 6-O-deacetylated analog 3 showed only negligible cytotoxicity [2] implying that the inhibition of proliferation and perturbation of N-glycan biosynthesis occur by different mechanisms. Increased cytotoxicity as a result of 1-O-deacylation was noted

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

Synthetic glycopeptides and glycoproteins with applications in biological research

• Ulrika Westerlind

Beilstein J. Org. Chem. 2012, 8, 804–818, doi:10.3762/bjoc.8.90

• β-subunit of human follicle-stimulating hormone (hFSH) glycoprotein was prepared, containing two complex type N-glycans, modified with core fucose and terminal sialic acid glycan residues [57]. The FSH β-subunit was prepared by sequential native chemical ligation. Initially, a larger C-terminal

• and extent of glycosylation [62][63]. The synthesis of homogeneously glycosylated EPO for improvements in therapy is therefore desirable. Kajihara and co-workers have prepared a number of erythropoietin analogues by expressed protein ligation [64][65]. Complex-type N-glycans were attached through

• at other unnatural positions. The synthetic EPO analogues modified with two or three complex type N-glycans, were evaluated in a cell proliferation assay showing that the analogues induced cell-proliferation in vitro. However, cell-proliferation activity in vivo was very weak for both analogues

Chemo-enzymatic modification of poly-N-acetyllactosamine (LacNAc) oligomers and N,N-diacetyllactosamine (LacDiNAc) based on galactose oxidase treatment

• Christiane E. Kupper,
• Ruben R. Rosencrantz,
• Birgit Henßen,
• Helena Pelantová,
• Stephan Thönes,
• Anna Drozdová,
• Vladimir Křen and
• Lothar Elling

Beilstein J. Org. Chem. 2012, 8, 712–725, doi:10.3762/bjoc.8.80

• structures were synthesised, which are interesting binding ligands for a variety of glycan-binding proteins. These novel chemically branched structures may serve as analogues for branched N-glycans. Experimental Materials Galactose oxidase was purchased from Worthington (Lakewood, NJ) and peroxidase from

Acid- mediated reactions under microfluidic conditions: A new strategy for practical synthesis of biofunctional natural products

• Katsunori Tanaka and
• Koichi Fukase

Beilstein J. Org. Chem. 2009, 5, No. 40, doi:10.3762/bjoc.5.40

• benzylidene acetal groups, and dehydration, which are the keys to the practical synthesis of N-glycans and the immunostimulating natural product, pristane. A distinctly different reactivity from that in conventional batch stirring was found; the vigorous micromixing of the reactants with the concentrated

• industrial synthesis of the bioactive natural products. Review 1. Application of microfluidic systems to the synthesis of asparagine-linked oligosaccharides Among the various types of oligosaccharide structures, asparagine-linked oligosaccharides (N-glycans) are prominent in terms of diversity and complexity

• [34]. It is becoming clear that they are involved in a variety of important physiological events, such as cell-cell recognition, adhesion, signal transduction, quality control, and circulatory residence of proteins [35][36][37][38]. However, isolating large quantities of structurally pure N-glycans