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At least 19 recordsLinked to original sources
PubMed2004

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

UNLABELLED: Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. AVAILABILITY: The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html CONTACT: kikuchi@hydra.mki.co.jp.

Carbohydrate Sequence↗
PubMed1986

Carbohydrate sequences detected by murine monoclonal antibodies.

The carbohydrate sequences of cell surface glycolipids change during differentiation and oncogenic transformation. To detect these structural changes, murine monoclonal antibodies have been produced in many different laboratories. Some of these antibodies are used to distinguish various cell types such as normal and transformed cells, while others are used to analyze developmentally regulated antigens. Recently, the structures of many of these carbohydrate antigens have been determined. The availability of these well-defined monoclonal antibodies will be useful for the study of the regulation and function of glycoconjugates.

Animals↗
PubMed1993

Electron ionization-tandem mass spectrometry of glycosphingolipids. Part II. The identification of a carbohydrate sequence corresponding to a novel repetitive blood group A heptaglycosylceramide.

In a previous paper, the presence in human kidney vein tissue of a novel blood group A heptaglycosylceramide based on the type-3 carbohydrate chain GalNAc alpha 1-3(Fuc alpha 1-2)Gal beta 1-3GalNAc alpha 1-3(Fuc alpha 1-2)Gal beta 1-4Glc beta 1-1 Ceramide, was suggested based on thin-layer immunostaining and electron ionization mass spectrometry. Ions corresponding to a structure containing two deoxyhexoses, two hexosamines and three hexoses were identified, but no information was obtained from mass spectrometry concerning the carbohydrate sequence. In the present paper, we report the identification of carbohydrate sequence ions corresponding to a type-3 chain A heptaglycosylceramide by electron ionization-tandem mass spectrometry of a permethylated-reduced glycosphingolipid mixture isolated from human kidney vein tissue. The use of a microchannel-plate-array detector increased the sensitivity for collision-induced dissociation spectra by a factor of at least ten over a conventional electron multiplier.

Blood Group Antigens↗
PubMed2006

The identification and characterization of xenoantigenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney.

The immunogenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney were identified and characterized using MALDI-TOF MS and ESI-QTOF-MS. The MALDI profile, investigated by incubation with exoglycosidases, showed a series of about 40 carbohydrates that were identified as high mannose glycans (Man(3-9)GlcNAc2) and complex bi-, tri-, and tetra-antennary glycans with and without core fucose. The antennae of many of the complex glycans were terminated with alpha-galactose residues, with the numbers of these residues ranging from one up to the number of antennae. Negative ion ESI-MS/MS spectra confirmed the location of the alpha-galactose residues on the ends of the antennae. This total glycan profile of the membrane proteins from porcine kidney will thus provide important information for the study of molecular interactions between antigenic carbohydrates and proteins in xenotransplantation.

Animals↗
PubMed2005

Congruent strategies for carbohydrate sequencing. 1. Mining structural details by MSn.

This report is the first in a series of three focused on establishing congruent strategies for carbohydrate sequencing. The reports are divided into (i) analytical considerations that account for all aspects of small oligomer structure by MSn disassembly, (ii) database support using an ion fragment library and associated tools for high-throughput analysis, and (iii) a concluding algorithm for defining oligosaccharide topology from MSn disassembly pathways. The analytical contribution of this first report explores the limits of structural detail exposed by ion trap mass spectrometry with samples prepared as methyl derivatives and analyzed as metal ion adducts. This data mining effort focuses on correlating the fragments of small oligomers to stereospecific glycan structures, an outcome attributed to a combination of metal ion adduction and analyte conformation. Facile glycosidic cleavage introduces a point of lability (pyranosyl-1-ene) that upon collisional activation initiates subsequent ring fragmentation. Product masses and ion intensities vary with interresidue linkage, branching position, and monomer stereochemistry. Excessive fragmentation is the property of small oligomers where collisional energy within a smaller number of oscillators dissipates through extensive fragmentation. The procedures discussed in this report are unified into a singular strategy using an ion trap mass spectrometer with the sensitivity expected for electron multiplier detection. Although a small set of structures have been discussed, the basic principles considered are fully congruent, with ample opportunities for expansion.

Carbohydrate Sequence↗
PubMed2005

Congruent strategies for carbohydrate sequencing. 3. OSCAR: an algorithm for assigning oligosaccharide topology from MSn data.

This is the third in a sequence of reports devoted to the development of congruent strategies for carbohydrate sequencing. Two previous reports outlined the strategies for observing structural detail from MSn data and introduced tools that compile, search, and compare fragment spectra in a bottom-up approach to oligosaccharide sequencing. In this third report, we introduce the operational details of an algorithm that we define as the Oligosaccharide Subtree Constraint Algorithm (OSCAR). This algorithm assimilates analyst-selected MSn ion fragmentation pathways into oligosaccharide topology (branching and linkage) using what may be considered a top-down sequencing strategy. Guided by a series of logical constraints, this de novo algorithm provides molecular topology without presumed biosynthetic constraints or external comparisons. In this introductory study, OSCAR is applied to a series of permethylated oligomers and isomeric glycans, and topologies are assigned in a few hundredths of a second.

Algorithms↗
PubMed1984

Novel oligosaccharide chains on polysialoglycoproteins isolated from rainbow trout eggs. A unique carbohydrate sequence with a sialidase-resistant sialyl group, DGa1NAc beta 1 leads to 4(NeuGc2 leads to 3)DGa1NAc.

A series of novel carbohydrate chains all possessing a hitherto unknown trisaccharide unit, Ga1NAc beta 1 leads to 4-(NeuGc2 leads to 3)Ga1NAc beta 1 leads to, have been isolated from trout egg polysialoglycoproteins, a new class of glycoproteins, on alkali-borohydride treatment. On the basis of chemical (methylation, Smith degradation, and hydrazinolysis-nitrous deamination) and direct-probe mass spectrometric methods. deamination) and direct-probe mass spectrometric methods, the structures of a series of the first major type of oligosaccharide alditols having a sialidase-resistant N-glycolyneuraminic acid residue in each molecule were determined. The structures thus determined are novel and all possess a unique carbohydrate sequence (sialidase-resistant unsubstituted sialyl group italicized): Ga1NAc beta 1 leads to 4(NeuGc2 leads to 3)Ga1NAc beta 1 leads to 3Gal beta 1 leads to-4Gal beta 1 leads to 3[(leads to 8NeuGc alpha 2)n leads to 6]Ga1NAcol (n = 0 through 3).

Animals↗
PubMed1980

Expression of blood group I and i active carbohydrate sequences on cultured human and animal cell lines assessed by radioimmunoassays with monoclonal cold agglutinins.

Human monoclonal anti-I and anti-i antibodies, reactive with known carbohydrate sequences, have been used as reagents to quantitate (by radioimmunoassay) and visualize (by immunofluorescence) the expression of the various blood group I and i antigenic determinants in a variety of cultured cell lines commonly used in laboratory investigations. It has been shown that the antigens they recognize are widely distributed on the surface of human and animal cell lines, expressed in varying amounts in different cell lines and on individual cells within a given cell line. In two cell lines, a transformation-associated increase in the expression of I antigen was observed. Because of their precise specificity for defined carbohydrate chain domains, these autoantibodies have become valuable reagents in biological chemistry.

Agglutinins↗
PubMed1997

Structural analysis of oligosaccharide-alditols released by reductive beta-elimination from oviducal mucins of Bufo bufo: characterization of the carbohydrate sequence Gal(alpha1-3)GalNAc(alpha1-3)[Fuc(alpha1-2)]Gal.

Several tri- to hexasaccharide-alditols of the jelly coat surrounding the eggs of Bufo bufo were studied by methylation analysis, MALDI-TOF mass spectrometry, and 1H-NMR spectroscopy. As observed for six other amphibian species, these carbohydrate chains are highly species-specific. The main characteristics of the species Bufo bufo consists in the presence of the new carbohydrate sequence Gal(alpha1-3)GalNAc(alpha1-3)[Fuc(alpha1-2)]Gal, in which a blood group A determinant is substituted with an external alpha1-3 linked galactose unit. Since the role of carbohydrates appears more and more apparent during the fertilization processes, the species-specificity of these carbohydrate moieties should be relevant to the species-specific gamete recognition which characterizes most amphibians.

Animals↗
PubMed2002

Differences between neonates and adults in carbohydrate sequences and reaction kinetics of plasmin and alpha(2)-antiplasmin.

This study investigates reaction kinetics by slow-binding kinetics methods of both adult and fetal plasmin (Types 1 and 2) with adult and fetal alpha(2)-antiplasmin. In addition, carbohydrate sequences of Fetal and Adult Plasminogen Types 1 and 2, as well as fetal and adult alpha(2)-antiplasmin, were determined by mass spectrometric analysis. All curves of plasmin-alpha(2)-antiplasmin interaction followed the same pattern, indicating reversible slow-binding inhibition with an initial loose complex and a following tight complex. Differences between fetal and adult plasmin reactions with alpha(2)-antiplasmin were predominantly due to the initial loose complex. Values for K(i initial) in the reaction with adult alpha(2)-antiplasmin were 1.5 and 1.6 nM for Fetal Plasmin Types 1 and 2, respectively; compared to 0.3 and 0.7 nM for the corresponding adult types. Increasing concentrations of tranexamic acid resulted in a continuous increase of K(i initial) until a plateau was reached which was similar for all plasmin types. Almost identical values could be obtained when fetal alpha(2)-antiplasmin was used instead of adult alpha(2)-antiplasmin. Mass spectrometric analyses of the glycans present on plasminogen revealed a higher level of truncated N-glycans on the fetal material compared to the adult. The O-glycans of fetal and adult plasminogen were closely similar and only minor differences were observed between N-glycans of fetal and adult alpha(2)-antiplasmin. In conclusion, both fetal plasmin isoforms are less inhibited by alpha(2)-antiplasmin compared to the adult plasmin variants. These findings are important for the understanding of the physiology of the fibrinolytic system in neonates and provide further evidence that differences in glycosylation could be associated with marked effects on protein function.

Adult↗
PubMed2001

Differences between neonates and adults in tissue-type-plasminogen activator (t-PA)-catalyzed plasminogen activation with various effectors and in carbohydrate sequences of fibrinogen chains.

Our study investigates the effect of fetal and adult soluble fibrin (SF), fetal and adult fibrinogen Aalpha- and gamma-chains, as well as adult CNBr-fibrinogen fragments on tissue-type plasminogen activator (t-PA)-catalyzed plasminogen activation of both fetal and adult Glu-plasminogen types 1 and 2. In addition, we determined carbohydrate sequences of fetal and adult Bbeta- and gamma-chains by mass spectrometric analysis. In the absence of an effector, no substantial differences in the rate of plasmin formation could be seen between the fetal and adult plasminogen types. In the presence of an effector, both fetal Glu-plasminogen types revealed lower values for k(cat app) than the respective adult types. No differences could be seen in the values for K(m app). The resulting differences in catalytic efficiencies between the fetal and adult plasminogen types were much less than previously reported. No differences could be seen between fetal and adult effectors in stimulating t-PA-catalyzed plasminogen activation. Detailed analyses of the activation kinetics revealed a longer initial phase of slow plasmin formation of both fetal Glu-plasminogen types compared to their respective adult types, indicating a slower plasmin-induced modification of CNBr-fibrinogen fragments or SF by fetal plasmin. Mass spectrometric analysis of the N-glycans present on adult and fetal Bbeta- and gamma-fibrinogen chains showed the presence of a major monosialylated biantennary structure with lesser amounts of the disialylated form. In contrast to previous data, we conclude that catalytic efficiency of t-PA-catalyzed plasminogen activation in neonates is only slightly lower than in adults.

Adult↗
PubMed1984

The incorporation of glycolipids with defined carbohydrate sequence into liposomes and the effects on partition in aqueous two-phase systems.

A glycolipid with a defined carbohydrate sequence, derived from the glycoprotein fetuin, has been synthesised and incorporated into liposomes. The effect of the glycolipid on partition of the liposomes in aqueous two-phase systems has been investigated. Incorporation of glycolipid into liposomes changed their partition behaviour in a concentration-dependent manner. The effects on partition of the sequential removal of the terminal carbohydrates were investigated. Partition behaviour appeared to be determined by the net effect of a range of factors including the nature of the terminal carbohydrate, interactions of the lipid region of the glycolipid and possibly carbohydrate chain length. The electrostatic potential difference which can be created between the phases (by the inclusion of certain ions, notably phosphate) appeared to have no detectable effect on partition, even when N-acetylneuraminic acid was present as the terminal carbohydrate of the glycolipid.

Glycolipids↗
PubMed1990

Expression and distribution of carbohydrate sequences in chick germ cells: a comparative study with lectins and the NC-1/HNK-1 monoclonal antibody.

The expression of end-chain sugar residues and of oligosaccharidic sequences has been investigated in chick germ cells at critical stages during the migration, proliferation and sexual differentiation of these cells. Fluorescent lectins and indirect immunofluorescence studies using the NC-1/HNK-1 monoclonal antibody indicate a remarkable control of glycosylation during germ cell embryonal life. Besides a retained expression of glucose/mannose residues, it was found that alpha- and beta-galactose residues, N-acetyllactosamine and N-N' diacetylchitobiose sequences as well as the sulfated trisaccharidic NC-1 epitope were detectable in a stage-specific pattern. Present at a very high density in the cytoplasm and on the surface of the early germ cells at premigrative and migratory stages, the staining for these carbohydrate sequences gradually disappeared when the germ cells settled and proliferated in the developing gonadal primordia. The disaccharide Gal beta 1----3 Gal NAc was exclusively detected in migrating PGCs. In sexualized gonads, acetyllactosamine and/or diacetylchitobiose were similarly reexpressed in both oogonia and spermatogonia. Spermatogonia displayed beta-galactose residues and a high immunoreactivity with the NC1 Mab, indicating modulations in PGC glycosylations related to the acquisition of sexual phenotypes. In addition NC-1 was found to be expressed in the somatic component of the undifferentiated gonad and in the testis interstitial gland.

Animals↗
PubMed1992

cDNA, amino acid and carbohydrate sequence of barley seed-specific peroxidase BP 1.

The major peroxidase of barley seed BP 1 was characterized. Previous studies showed a low carbohydrate content, low specific activity and tissue-specific expression, and suggested that this basic peroxidase could be particularly useful in the elucidation of the structure-function relationship and in the study of the biological roles of plant peroxidases (S.K. Rasmussen, K.G. Welinder and J. Hejgaard (1991) Plant Mol Biol 16: 317-327). A cDNA library was prepared from mRNA isolated from seeds 15 days after flowering. Full-length clones were obtained and showed 3' end length variants, a G+C content of 69% in the translated region, a 90% G or C preference in the wobble position of the codons and a typical signal peptide sequence. N-terminal amino acid sequencing and sequence analysis of tryptic peptides verified 98% of the sequence of the mature BP 1 which contains 309 amino acid residues. BP 1 is the first characterized plant peroxidase which is not blocked by pyroglutamate. BP 1 polymorphism was observed. BP 1 is less than 50% identical to other plant peroxidases which, taken together with its developmentally dependent expression in the endosperm 15-20 days after flowering, suggests a unique biological role of this enzyme. The barley peroxidase is processed at the C-terminus and might be targeted to the vacuole. The single site of glycosylation is located near the C-terminus in the N-glycosylation sequon -Asn-Cys-Ser- in which Cys forms part of a disulphide bridge. The major glycan is a typical plant modified-type structure, Man alpha 1-6(Xyl beta 1-2)Man beta 1-4GlcNAc beta 1-4(Fuc alpha 1-3)GlcNAc. The BP 1 gene was RFLP-mapped on barley chromosome 3, and we propose Prx5 as the name for this new peroxidase locus.

Amino Acid Sequence↗
PubMed1994

The pili of Pseudomonas aeruginosa strains PAK and PAO bind specifically to the carbohydrate sequence beta GalNAc(1-4)beta Gal found in glycosphingolipids asialo-GM1 and asialo-GM2.

Pseudomonas aeruginosa employs pili to mediate adherence to epithelial cell surfaces. The pilus adhesin of P. aeruginosa strains PAK and PAO has been shown to bind to the glycolipid asialo-GM1 (Lee et al., 1994--accompanying article). PAK and PAO pili were examined for their abilities to bind to the synthetic beta GalNAc(1-4)beta Gal (a minimal structural carbohydrate receptor sequence of asialo-GM1 and asialo-GM2 proposed by Krivan et al., 1988a) using solid-phase binding assays. Both pili specifically bound to beta GalNAc(1-4)beta Gal. The binding of beta GalNAc(1-4)beta Gal-Biotin to the immobilized PAK and PAO pili was inhibited by corresponding free pili. The receptor binding domain of the PAK pilus resides in the C-terminal disulphide-looped region (residues 128-144) of the pilin structural subunit (Irvin et al., 1989). Biotinylated synthetic peptides corresponding the C-terminal residues 128-144 of P. aeruginosa PAK and PAO pilin molecules were shown to bind to the beta GalNAc(1-4)beta Gal-(bovine serum albumin (BSA)). The binding of biotinylated peptides to beta GalNAc(1-4)beta GAL-BSA was inhibited by PAK pili, Ac-KCTSDQDEQFIPKGCSK-OH (AcPAK(128-144)ox-OH) and Ac-ACKSTQDPMFTPKGCDN-OH (AcPAO(128-144)ox-OH) peptides. (In these peptides Ac denotes N alpha-acetylation of the N-terminus, -OH means a peptide with a free alpha-carboxyl group at the C-terminus and the 'ox' denotes the oxidation of the sulphhydryl groups of Cys-129 and Cys-142.) Both acetylated peptides were also able to inhibit the binding of beta GalNAc(1-4)beta Gal-biotin to the corresponding BSA-Peptide(128-144)ox-OH conjugates.(ABSTRACT TRUNCATED AT 250 WORDS)

Adhesins, Bacterial↗
PubMed2001

LINUCS: linear notation for unique description of carbohydrate sequences.

The use of proteomics databases has become indispensable for daily work of molecular biologists, but this situation has not yet been achieved for carbohydrate applications. One obvious reason is that existing data collections are only rarely annotated and no cross-linking to other resources exists. The existence of a generally accepted linear, canonical description for carbohydrates which can be readily processed by computers will enable efficient automatic cross-linking of distributed carbohydrate data collections by serving as a unique and unambiguous database access key. Various possibilities to derive a canonical notation are discussed. They can be divided into attempts that require structure description alone and alternatives that profit from the fact that a preferred graph direction (non-reducing to reducing end) exists within the structure. To open a fruitful discussion among glycoscientists a possible solution is presented where the reducing monosaccharide unit is selected as graph root and linkage information is used to define the priority of the various branches. A Web interface (http://www.dkfz.de/spec/linucs/) has been created that directly converts the commonly used extended representation of complex carbohydrates into the preferred canonical description or into its inverted form.

Algorithms↗