Structure Of Hexasaccharide Research Articles

A fluorogenic probe for core-fucosylated glycan-preferred ENGase

A fluorescence-quenching-based assay system to determine the hydrolytic activity of endo-β-N-acetylglucosaminidases (ENGases), which act on the innermost N-acetylglucosamine (GlcNAc) residue of the chitobiose segment of core-fucosylated N-glycans, was constructed using a dual-labeled fluorescent probe with a hexasaccharide structure. The fluorogenic probe was evaluated using a variety of ENGases, including Endo-M W251N mutant, Endo-F3, and Endo-S, which recognize core fucosylated N-glycans. The occurrence of a hydrolysis reaction was detected by observing an increased fluorescence intensity, ultimately allowing the ENGase activities to be easily and quantitatively evaluated, with the exception of Endo-S. The obtained results clearly indicated the substrate specificities of the examined ENGases.

Status Report on the High-Throughput Characterization of Complex Intact O-Glycopeptide Mixtures.

A very complex mixture of intact, human N- and O-glycopeptides, enriched from the tryptic digest of urinary proteins of three healthy donors using a two-step lectin affinity enrichment, was analyzed by LC-MS/MS, leading to approximately 45,000 glycopeptide EThcD spectra. Two search engines, Byonic and Protein Prospector, were used for the interpretation of the data, and N- and O-linked glycopeptides were assigned from separate searches. The identification rate was very low in all searches, even when results were combined. Thus, we investigated the reasons why was it so, to help to improve the identification success rate. Focusing on O-linked glycopeptides, we noticed that in EThcD, larger glycan oxonium ions better survive the activation than those in HCD. These fragments, combined with reducing terminal Y ions, provide important information about the glycan(s) present, so we investigated whether filtering the peaklists for glycan oxonium ions indicating the presence of a tetra- or hexasaccharide structure would help to reveal all molecules containing such glycans. Our study showed that intact glycans frequently do not survive even mild supplemental activation, meaning one cannot rely on these oxonium ions exclusively. We found that ETD efficiency is still a limiting factor, and for highly glycosylated peptides, the only information revealed in EThcD was related to the glycan structures. The limited overlap of results delivered by the two search engines draws attention to the fact that automated data interpretation of O-linked glycopeptides is not even close to being solved. Graphical abstract ᅟ.

Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS

Purification and liquid chromatography-tandem mass spectrometry (LC-MS/MS) characterization of glycopeptides, originating from protease digests of glycoproteins, enables site-specific analysis of protein N- and O-glycosylations. We have described a protocol to enrich, hydrolyze by chondroitinase ABC, and characterize chondroitin sulfate-containing glycopeptides (CS-glycopeptides) using positive mode LC-MS/MS. The CS-glycopeptides, originating from the Bikunin proteoglycan of human urine samples, had ΔHexAGalNAcGlcAGalGalXyl-O-Ser hexasaccharide structure and were further substituted with 0-3 sulfate and 0-1 phosphate groups. However, it was not possible to exactly pinpoint sulfate attachment residues, for protonated precursors, due to extensive fragmentation of sulfate groups using high-energy collision induced dissociation (HCD). To circumvent the well-recognized sulfate instability, we now introduced Na+ ions to form sodiated precursors, which protected sulfate groups from decomposition and facilitated the assignment of sulfate modifications. Sulfate groups were pinpointed to both Gal residues and to the GalNAc of the hexasaccharide structure. The intensities of protonated and sodiated saccharide oxonium ions were very prominent in the HCD-MS2 spectra, which provided complementary structural analysis of sulfate substituents of CS-glycopeptides. We have demonstrated a considerable heterogeneity of the bikunin CS linkage region. The realization of these structural variants should be beneficial in studies aimed at investigating the importance of the CS linkage region with regards to the biosynthesis of CS and potential interactions to CS binding proteins. Also, the combined use of protonated and sodiated precursors for positive mode HCD fragmentation analysis will likely become useful for additional classes of sulfated glycopeptides.Graphical ᅟ

Non-lysosomal Degradation of Singly Phosphorylated Oligosaccharides Initiated by the Action of a Cytosolic Endo-β-N-acetylglucosaminidase

Phosphorylated oligosaccharides (POSs) are produced by the degradation of dolichol-linked oligosaccharides (DLOs) by an unclarified mechanism in mammalian cells. Although POSs are exclusively found in the cytosol, their intracellular fates remain unclear. Our findings indicate that POSs are catabolized via a non-lysosomal glycan degradation pathway that involves a cytosolic endo-β-N-acetylglucosaminidase (ENGase). Quantitative and structural analyses of POSs revealed that ablation of the ENGase results in the significant accumulation of POSs with a hexasaccharide structure composed of Manα1,2Manα1,3(Manα1,6)Manβ1,4GlcNAcβ1,4GlcNAc.In vitroENGase assays revealed that the presence of an α1,2-linked mannose residue facilitates the hydrolysis of POSs by the ENGase. Liquid chromatography-mass spectrometric analyses and fluorescent labeling experiments show that such POSs contain one phosphate group at the reducing end. These results indicate that ENGase efficiently hydrolyzes POSs that are larger than Man4GlcNAc2-P, generating GlcNAc-1-P and neutral Gn1-type free oligosaccharides. These results provide insight into important aspects of the generation and degradation of POSs.

Two Structures of Alliinase from Alliium sativum L.: Apo Form and Ternary Complex with Aminoacrylate Reaction Intermediate Covalently Bound to the PLP Cofactor

Alliinase (alliin lyase EC 4.4.1.4), a PLP-dependent α, β-eliminating lyase, constitutes one of the major protein components of garlic ( Alliium sativum L.) bulbs. The enzyme is a homodimeric glycoprotein and catalyzes the conversion of a specific non-protein sulfur-containing amino acid alliin ((+S)-allyl- L-cysteine sulfoxide) to allicin (diallyl thiosulfinate, the well known biologically active component of freshly crushed garlic), pyruvate and ammonia. The enzyme was crystallized in the presence of (+S)-allyl- L-cysteine, forming dendrite-like monoclinic crystals. In addition, intentionally produced apo-enzyme was crystallized in tetragonal form. These structures of alliinase with associated glycans were resolved to 1.4 Å and 1.61 Å by molecular replacement. Branched hexasaccharide chains N-linked to Asn146 and trisaccharide chains N-linked to Asn328 are seen. The structure of hexasaccharide was found similar to “short chain complex vacuole type” oligosaccharide most commonly seen in plant glycoproteins. An unexpected state of the enzyme active site has been observed in the present structure. The electron density in the region of the cofactor made it possible to identify the cofactor moiety as aminoacrylate intermediate covalently bound to the PLP cofactor. It was found in the present structure to be stabilized by large number of interactions with surrounding protein residues. Moreover, the existence of the expected internal aldimine bond between the ε-amino group of Lys251 and the aldehyde of the PLP is ruled out on the basis of a distinct separation of electron density of Lys251. The structure of the active site cavity in the apo-form is nearly identical to that seen in the holo-form, with two sulfate ions, an acetate and several water molecules from crystallization conditions that replace and mimic the PLP cofactor.

Synthesis and Biological Evaluation of a Heparin‐Like Hexasaccharide with the Structural Motifs for Binding to FGF and FGFR

AbstractA heparin‐like hexasaccharide structure (2) containing the two trisaccharide sequences that interact with acidic fibroblast growth factor (FGF‐1) and with its receptor (FGFR) has been designed on the basis of crystallographic data. This hexasaccharide has been effectively synthesized by a completely stereoselective modular approach and biologically evaluated by determination of its capacity to stimulate FGF‐1‐induced mitogenic activity. It was found that this molecule did not show an appreciable FGF‐1 activating effect. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)

The structure of the glycopeptides from the fish pathogen Flavobacterium columnare

Proteolytic digestion of the phenol–water extraction product of the fish pathogen Flavobacterium columnare afforded a mixture of glycopeptides in which the oligosaccharide moiety was an unusual hexasaccharide composed of 4- O-methyl-2-acetamido-2-deoxy- d-glucuronic acid (GlcNAcA), d-glucuronic acid ( d-GlcA), 2,3-di- O-acetyl- d-xylose ( d-Xyl), 2- O-methyl- d-glucuronic acid ( d-GlcA), d-mannose ( d-Man), and 2- O-methyl- l-rhamnose ( l-Rha). By the application of high-resolution 1D and 2D NMR, mass spectrometry, and chemical analysis, the hexasaccharide structure was determined to be: where all monosaccharides have the d-configuration except for 2- O-methyl- l-rhamnose; and were in the pyranose form. Only one carbohydrate structure was found. The peptide part was represented by tri- to hepta-peptides with a minimal common tripeptide fragment Asp-Ser-Ala, extended with Ala and Val.

Interaction of heparin with Ca2+: A model study with a synthetic heparin‐like hexasaccharide

AbstractThe binding of Ca2+ to synthetic hexasaccharide 1, containing the structural motifs of the regular region of heparin, has been investigated using NMR spectroscopy and molecular modeling. The NMR data of the calcium salt of 1 indicate the existence of specific Ca2+ binding, and molecular modeling results predict three different types of binding sites with different negative potential and preorganized geometry. The presence of Ca2+ does not seem to affect the overall helical structure of hexasaccharide 1, although it seems to have a marked influence on the flexibility of the oligosaccharide backbone.

Structurally defined epitopes of Haemophilus ducreyi lipooligosaccharides recognized by monoclonal antibodies

By use of enzyme-linked immunosorbent assay and immunoblotting techniques, the migration patterns and binding epitopes of lipooligosaccharides (LOS) from 10 Haemophilus ducreyi strains were investigated with two monoclonal antibodies (MAbs), MAHD6 and MAHD7, raised against LOS from H. ducreyi ITM 2665. Closely related LOS, with defined structures, from Haemophilus influenzae, Bordetella pertussis, Aeromonas spp., and synthetic glycoproteins were also included in the analyses. The MAbs bound to conserved epitopes of LOS exposed on the surface of H. ducreyi. The MAb MAHD6 reacted with 8 of the 10 LOS from H. ducreyi but with none of the other Haemophilus or Bordetella spp. with structurally defined LOS. It is suggested that MAb MAHD6 binds to a LOS epitope (-DD-Hepp-1-->6-beta-D-Glcp-). This LOS epitope is not present in the hexasaccharide structure of LOS from H. ducreyi ITM 4747 (E. K. H. Schweda, A. C. Sundström, L. M. Eriksson, J. A. Jonasson, and A. A. Lindberg, J. Biol. Chem. 269:12040-12048, 1994). Because MAb MAHD6 reacts with the epitope mentioned above, it also discriminates between the two LOS structures, the hexasaccharide group and the nonasaccharide group, of H. ducreyi strains. MAb MAHD7 recognizes the common conserved inner core region of the LOS because it reacts with all H. ducreyi strains and with LOS with minor components in the inner core epitope structure. Rabbit polyclonal sera raised against the LOS from strains CCUG 4438 and CCUG 7470 were tested with the 10 LOS from the H. ducreyi strains. The antiserum to CCUG 7470 reacted with all H. ducreyi strains as did MAb MAHD7, whereas the antiserum to CCUG 4438 reacted with only its homologous strain and strain ITM 4747. Also, the LOSs of our reference strains CCUG 4438 and CCUG 7470 were structurally analyzed by use of sugar analyses and electrospray ionization-mass spectrometry. The hexasaccharide and nonasaccharide structures obtained from LOS of strains CCUG 4438 and CCUG 7470 were identical to the described LOS structures from H. ducreyi ITM 4747 and ITM 2665, respectively. In conclusion, the MAb MAHD6 recognizes an epitope present in the nonasaccharide LOS group, whereas the MAb MAHD7 recognizes a conserved epitope on LOS of H. ducreyi, which is present in all strains of H. ducreyi tested. Two major groups of oligosaccharides were distinguished by their LOS structures and the reactivity of monoclonal as well as polyclonal antibodies. The majority of H. ducreyi strains possess a nonasaccharide structure of LOS.

Structural variations in the glycosaminoglycan-protein linkage region of recombinant decorin expressed in Chinese hamster ovary cells.

Decorin is a small fibroblast proteoglycan consisting of a core protein and a single chondroitin/dermatan sulfate chain. The structure of the carbohydrate-protein linkage region of the recombinant decorin expressed in Chinese hamster ovary cells was investigated. The decorin was secreted in the culture medium and isolated by anion-exchange chromatography. The glycosaminoglycan chain was released from the decorin by beta-elimination using alkaline NaBH4, and then digested with chondroitinase ABC. These treatments resulted in a major and a few minor hexasaccharide alditols derived from the carbohydrate-protein linkage region. Their structures were analyzed by enzymatic digestion in conjunction with high-performance liquid chromatography. Two of these compounds have the conventional hexasaccharide core, deltaHexA alpha1-3GalNAc beta1-4GlcA beta1-3Gal beta1-3Gal beta1-4Xyl-ol. One is nonsulfated, and the other is monosulfated on C4 of the GalNAc residue. They represent 12% and 60% of the total linkage region, respectively. The other compound has the hexasaccharide alditol with an internal iduronic acid residue deltaHexA alpha1-3GalNAc(4-sulfate)beta1-4IdoA alpha1-3Gal beta1-3Gal beta1-4Xyl-ol, which was previously demonstrated in one of the five linkage hexasaccharide alditols isolated from dermatan sulfate proteoglycans of bovine aorta (Sugahara et al., J. Biol. Chem., 270, 7204-7212, 1995). The compound accounts for 11% of the total linkage region. These structural variations in the linkage hexasaccharide region of the decorin strikingly contrast to the uniformity demonstrated in the linkage hexasaccharide structure of human inter-alpha-trypsin inhibitor (Yamada et al., Glycobiology, 5, 335-341, 1995) and urinary trypsin inhibitor (Yamada et al., Eur. J. Biochem., 233, 687-693, 1995), both of which have a single chondroitin sulfate chain with a uniform linkage hexasaccharide structure, deltaHexA alpha1-3GalNAc(4-sulfate)beta1-4GlcA beta1-3Gal(4-sulfate)beta1-3Gal beta1-4Xyl, containing a 4-O-sulfated Gal residue.

The uniform galactose 4-sulfate structure in the carbohydrate-protein linkage region of human urinary trypsin inhibitor.

The carbohydrate-protein linkage region of a chondroitin 4-sulfate chain attached to urinary trypsin inhibitor (UTI) was isolated from human urine and characterized structurally. The chondroitin 4-sulfate chain was released from UTI by beta-elimination using alkaline NaBH4 then digested with chondroitinase ABC. These treatments resulted in only a single hexasaccharide alditol derived from the carbohydrate-protein linkage region. Chemical and enzymic analyses and 600-MHz 1H-NMR spectroscopy revealed that the hexasaccharide alditol had the following structure: delta HexA alpha 1-3GalNAc(4-sulfate) beta 1-4GlcA beta 1- 3Gal(4-sulfate) beta 1-3Gal beta 1-4Xyl-ol, where delta HexA, GlcA and Xyl-ol represent 4-deoxy-alpha-L-threo-hex-4-enepyranosyluronic acid, D-glucuronic acid and D-xylitol, respectively. This structure contained the novel 4-sulfated Gal residue, which was first demonstrated in one of the three linkage hexasaccharide-serines isolated from chondroitin 4-sulfate of rat chondrosarcoma [Sugahara, K., Yamashina, I., de Waard, P., Van Halbeek, H. & Vliegenhart, J. F. G. (1988) J. Biol. Chem. 263, 10168-10174]. This disulfated structure was recently identified as the sole structural component in the linkage hexasaccharide alditol fraction isolated from inter-alpha-trypsin inhibitor (ITI) in human plasma [Yamada, S., Oyama, M., Kinugasa, H., Nakagawa, T., Kawasaki, T., Nagasawa, S., Khoo, K.-H., Morris, H.R., Dell, A. & Sugahara, K. (1995) Glycobiology 5, 335-341]. The structural uniformity in the linkage hexasaccharide structure of ITI and UTI is in marked contrast to the heterogeneity demonstrated in the linkage hexasaccharides isolated from cartilaginous chondroitin sulfate whose linkage regions are sometimes but not always phosphorylated on the Xyl residue or sulfated on the Gal residue(s). The uniform structure containing the novel 4-sulfated Gal residue in the linkage region of UTI and ITI may imply its significance in the biosynthetic mechanism of chondroitin sulfate.

Structure of the Klebsiella type 10 capsular polysaccharide

The capsular polysaccharide from Klebsiella Type 10 was found to contain d-galactose, d-glucose, d-mannose, and d-glucuronic acid in the ratios 3:1:1:1. Acid hydrolysis of the polysaccharide gave one aldobiouronic acid, one aldotriouronic acid, one aldotetraouronic acid, and two neutral disaccharides the structures of which were established. The native and carboxyl-reduced polysaccharide have been subjected as appropriate to methylation analysis and Smith degradation. Degradation of the methylated polysaccharide with base established the identity of the sugar unit preceding the glucosyluronic acid residue. The anomeric configurations of the sugar residues were determined by oxidation of the acetylated native and carboxyl-reduced polysaccharides with chromium trioxide. Based on these studies, the hexasaccharide structure 1 has been assigned to the repeating unit of the K-10 polysaccharide. ▪

The carbohydrate moiety of band 3 glycoprotein of human erythrocyte membranes. Structures of lower molecular weight oligosaccharides.

Band 3 glycoprotein purified from human blood group A erythrocyte membranes was subjected to hydrazinolysis to release carbohydrate moieties. The neutral oligosaccharide fraction, which constituted more than 85% of the total carbohydrates released, was fractionated by gel chromatography on a column of Sephadex G-50 into two fractions, i.e. higher molecular weight and lower molecular weight fractions. From the lower molecular weight fraction, three oligosaccharides were obtained by chromatographies on columns of Bio-Gel P-4, concanavalin A-Sepharose, and lentil lectin-Sepharose. Their structures were investigated by a combination of compositional analyses, glycosidase treatments, methylation and Smith periodate degradation, and proposed to be: Gal beta 1 - 4GlcNAc beta 1 - 2Man alpha 1 - 6(GlcNAc beta 1 -4) (Gal beta 1 - 4GlcNAc beta 1 - 2Man alpha 1 - 3)Man beta 1 - 4GlcNAc beta 1 - 4(Fuc alpha 1 - 6)GlcNAc, Gal beta 1 - 4GlcNAc beta 1 - 2Man alpha 1 - 6(Gal beta 1 - 4GlcNAc beta 1 - 2Man alpha 1 - 3)Man beta 1 - 4GlcNAc beta 1 - 4(Fuc alpha 1 - 6)GlcNAc, and GlcNAc beta 1 - 2Man alpha 1 - 6(GlcNAc beta 1 - 4) (Glc NAc beta 1 - 2Man alpha 1-3) Man beta 1 - 4GlcNAc beta 1 - 4(+/-Fuc alpha 1 - 6)GlcNAc. It was also demonstrated in this study that most of the higher molecular weight oligosaccharides, whose peripheral structure had previously been reported (Tsuji, T., Irimura, T., and Osawa, T. (1980) Biochem. J. 187, 677-686), also contained the same core hexasaccharide structure, Man alpha 1 - 6(Man alpha 1-3)Man beta 1 - 4GlcNAc beta 1 - 4(Fuc alpha 1-6)GlcNAc, as that of the lower molecular weight oligosaccharides.