Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8349 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8404 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8405 (all data & tools)

Show legend Show as text

Structure type: oligomer
Aglycon: CH2CH2CH3
Contained glycoepitopes: IEDB_127513,IEDB_131174,IEDB_131175,IEDB_131177,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_143254,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 387
  Stuike-Prill R, Pinto BM "Conformational analysis of oligosaccharides corresponding to the cell-wall polysaccharide of the Streptococcus group A by Metropolis Monte Carlo simulations" - Carbohydrate Research 279 (1995) 59-73
  

  Metropolis Monte Carlo simulations have been performed on four substructures from the call-wall polysaccharide antigen of Streptococcus group A to explore the conformational begaviour of these compounds. The compounds examined are the trisaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 1, the tetrasaccharide, propyl 3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 2, the hexasacchride, propyl 3-O-(2-O-(3-O-(3-O-(2-acetamido-2-deoxy-bDglucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 3, and the hexasaccharide, propyl 3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(3-O-(3-O-(2-acetamido-2-deoxy-b-D-glucopyranosyl)-2-O-(a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranosyl)-a-L-rhamnopyranoside, 4. In general, the conformational flexibility of simular glycosidic linkages in different compounds is comparable. However, in a few cases, small differences in the conformations available to these linkages in different structural environments could be detected. Interestingly, a secon conformation found for the b-D-GlcNAc-(1→3)-a-L-Rha linkage in three of the compounds was not populated in the hexasaccharide 4. Futhermore, a conformational locale of the a-L-Rha-(1→3)-a-L-Rha linkage found to by populated in the trisaccaharide 1, tetrasaccahride 2, and hexasaccharide 4 is negligibly populated in the hexasaccharide 3. Ensemble averaged proton-proton disances compare favourably with experimental average distances obtained fro mNMR spectroscopy. The trisaccharide branch point in the hexasaccharides is shown to by a hoghly defined conformational feature. The same unit has been found to by one of the crucial elements recognized by anti-Group A Streptococcus antibodies, a result that has implications for the design of improved immunodiagnostics and vaccines.

  Oligosaccharides, Metropolis Monte Carlo simulations, Cell-wall polysaccharide, Streptococcus group A

  NCBI PubMed ID: 8593633
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Copenhagen, Denmark, Department of Chemistry, Simon Fraser University, Burnaby, B.C. V5A 1S6, Canada
  Methods: NMR, conformation analysis
  
   
  
  Streptococcus sp. A
  CSDB ID 8406 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 419
  Weimar T, Harris SL, Pitner JB, Bock K, Pinto BM "Transferred nuclear Overhauser enhancement experiments show that the monoclonal antibody strep 9 selects a local minimum conformation of a Streptococcus group A trisaccharide-hapten" - Biochemistry 34(41) (1995) 13672-13681
  

  Transferred nuclear Overhauser enhancement (TRNOE) experiments have been performed to investigate the bound conformation of the trisaccharide repeating unit of the Streptococcus Group A cell-wall polysaccharide. Thus, the conformations of propyl 3-O-(2-acetamido-2-deoxy-β-D-glucopyranosyl)-2-O-(α-L-rhamnopyran osyl)-α-L-rhamnopyranoside [C(A')B] (1) as a free ligand and when complexed to the monoclonal antibody Strep 9 were examined. Improved insights about the conformational preferences of the glycosidic linkages of the trisaccharide ligand showed that the free ligand populates various conformations in aqueous solution, thus displaying relatively flexible behavior. The NOE HNAc-H2A', which was not detected in previous work, accounts for a conformation at the β-(1→3) linkage with a phi angle of approximately 180 degrees. Observed TRNOEs for the complex are weak, and their analysis was further complicated by spin diffusion. With the use of transferred rotating-frame Overhauser enhancement (TRROE) experiments, the amount of spin diffusion was assessed experimentally, proving that all of the observed long-range TRNOEs arose through spin diffusion. Four interglycosidic distances, derived from the remaining TRNOEs and TRROEs, together with repulsive constraints, derived from the absence of TRROE effects, were used as input parameters in simulated annealing and molecular mechanics calculations to determine the bound conformation of the trisaccharide. Complexation by the antibody results in the selection of one defined conformation of the carbohydrate hapten. This bound conformation, which is a local energy minimum on the energy maps calculated for the trisaccharide ligand, shows only a change from a +gauche to a -gauche orientation at the psi angle of the α-(1→2) linkage when compared to the global minimum conformation. The results infer that the bound conformation of the Streptococcus Group A cell-wall polysaccharide is different from its previously proposed solution structure (Kreis et al., 1995)

  NMR, conformation, Streptococcus, antibodies, monoclonal antibodies, NOE, antigen-antibody interaction

  NCBI PubMed ID: 7577958
  Journal NLM ID: 0370623
  Publisher: American Chemical Society
  Institutions: Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
  Methods: NMR, trNOESY
  
   
  
  Streptococcus sp. A
  CSDB ID 8640 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144825,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 555
  Barone G, Bedini E, Unverzagt C, Parilli M "Synthesis of the pentasaccharide repeating unit of the major O-antigen component from Pseudomonas syringae pv. ribicola NVPPB 1010" - Carbohydrate Research 339(2) (2004) 393-400
  

  The synthesis of the repeating unit of the major O-antigen component from Pseudomonas syringae pv. ribicola NVPPB 1010 is reported. The strategy used was based on the successive coupling of a trisaccharide rhamnosyl trichloroacetimidate with a rhamnosyl acceptor with a free hydroxyl group on C-2. The pentasaccharide was then obtained by coupling with a N-Troc-tri-O-acetyl-glucosamine trichloroacetimidate. The synthesis allowed the oligomerisation of the repeating unit.

  repeating unit, Oligosaccharides, O-chain, glycosylation, Pseudomonas ribicola

  NCBI PubMed ID: 14698898
  Publication DOI: 10.1016/j.carres.2003.10.002
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: parrilli@unina.it
  Institutions: Dipartimento di Chimica Organica e Biochimica, Universita di Napoli ''Federico II'', Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy, Bioorganische Chemie, Gebaude NWI, Universitat Bayreuth,95440 Bayreuth, Germany
  
   
  
  Pseudomonas syringae pv. ribicola NVPPB1010
  CSDB ID 9290 (all data & tools)
• Article ID: 1075
  Ovod V, Zdorovenko EL, Shashkov AS, Kocharova NA, Knirel YA "Structure of the O polysaccharide and serological classification of Pseudomonas syringae pv. ribicola NCPPB 1010" - European Journal of Biochemistry 267(8) (2000) 2372-2379
  

  The O polysaccharide (OPS) moiety of the lipopolysaccharide (LPS) of a phytopathogenic bacterium Pseudomonas syringae pv. ribicola NCPPB 1010 was studied by sugar and methylation analyses, Smith degradation, and 1H- and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY and H-detected 1H,13C HMQC experiments. The OPS structure was elucidated, and shown to be composed of branched pentasaccharide repeating units (O repeats) of two types, major (1) and minor (2), differing in the position of substitution of one of the rhamnose residues. Both O repeats form structurally homogeneous blocks within the same polysaccharide molecule. Although P. syringae pv. ribicola NCPPB 1010 demonstrates genetic relatedness and similarity in the OPS chemical structure to some other P. syringae pathovars, it did not cross-react with any OPS-specific mAbs produced against heterologous P. syringae strains. Therefore, we propose to classify P. syringae pv. ribicola NCPPB 1010 in a new serogroup, O8.

  structure, structural, polysaccharide, Pseudomonas, O-polysaccharide, O polysaccharide, serological, Pseudomonas syringae, classification, linear, heterogeneity

  NCBI PubMed ID: 10759863
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Medical Technology, University of Tampere, Finland
  Methods: NMR-2D, methylation, NMR, sugar analysis, Smith degradation
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB1010
  CSDB ID 4004 (all data & tools)
• Article ID: 1452
  Corsaro MM, De Castro C, Molinaro A, Parrilli M "Structure of lipopolysaccharides from phytopathogenic Gram-negative bacteria" - Book: Recent Research Developments in Phytochemistry (2001) Vol. 5, 119-138
  

  This review collects the structural data of lipopolysaccharide components arising from all phytopathogenic bacteria so far investigated. The structural approaches and the main biological role of these macromolecules are also reported.

  Lipopolysaccharide, lipopolysaccharides, structure, core, lipid A, O-polysaccharide, gram negative bacteria

  WWW link: https://books.google.ru/books/about/Recent_Research_Developments_in_Phytoche.html?id=5CJacgAACAAJ&redir_esc=y
  Publisher: Research Signpost, Trivandrum, India
  Editors: Pandalai SG
  Institutions: Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte S.Angelo Via Cintia, 4, 80126 Napoli, Italy
  
   
  
  Pseudomonas syringae pv. ribicola VIII NVPPB 1010
  CSDB ID 31737 (all data & tools)
• Article ID: 3968
  Zdorovenko GM, Zdorovenko EL "Pseudomonas syringae lipopolysaccharides: Immunochemical characteristics and structure as a basis for strain classification" - Mikrobiologiia = Microbiology [Russian] 79(1) (2010) 47-57
  

  Lipopolysaccharide (LPS) preparations of 34 Pseudomonas syringae strains of 19 pathovars were prepared by saline extraction from wet cells and purified by repeated ultracentrifugation. The preparations reacted with homologous O-antisera, obtained by rabbit immunization with heat-killed bacterial cells. Through inhibition of homologous reactions between LPS preparations of heterologous strains (enzyme immunoassay, EIA), it was established for the first time that high serological affinity between strains is observed only if their LPS contains O-specific polysaccharide chains (OPS) comprised of completely identical rather than partially similar units. The central linear part of the OPS was found to be serologically inert when shielded with side groups. Data on immunochemical characteristics of the LPS and OPS structure are analyzed in relation to the design of P. syringae classification scheme.

  Lipopolysaccharide, structure, O-specific polysaccharide, Pseudomonas syringae, classification, immunochemistry

  NCBI PubMed ID: 20411661
  Publication DOI: 10.1134/S0026261710010078
  Journal NLM ID: 0376652
  Publisher: Moskva: Izdatelstvo Nauka
  Correspondence: evelina@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Zabolotnyi Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, ul. Zabolotnogo 154, Kyiv, 03143 Ukraine
  Methods: partial acid hydrolysis, EIA, serological methods, de-N-acetylation/deamination
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB 1010
  CSDB ID 25904 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas syringae pv. ribicola
  CSDB ID 1388 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: repeating unit of the O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_144825,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 555
  Barone G, Bedini E, Unverzagt C, Parilli M "Synthesis of the pentasaccharide repeating unit of the major O-antigen component from Pseudomonas syringae pv. ribicola NVPPB 1010" - Carbohydrate Research 339(2) (2004) 393-400
  

  The synthesis of the repeating unit of the major O-antigen component from Pseudomonas syringae pv. ribicola NVPPB 1010 is reported. The strategy used was based on the successive coupling of a trisaccharide rhamnosyl trichloroacetimidate with a rhamnosyl acceptor with a free hydroxyl group on C-2. The pentasaccharide was then obtained by coupling with a N-Troc-tri-O-acetyl-glucosamine trichloroacetimidate. The synthesis allowed the oligomerisation of the repeating unit.

  repeating unit, Oligosaccharides, O-chain, glycosylation, Pseudomonas ribicola

  NCBI PubMed ID: 14698898
  Publication DOI: 10.1016/j.carres.2003.10.002
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: parrilli@unina.it
  Institutions: Dipartimento di Chimica Organica e Biochimica, Universita di Napoli ''Federico II'', Complesso Universitario Monte Santangelo, Via Cintia 4, 80126 Napoli, Italy, Bioorganische Chemie, Gebaude NWI, Universitat Bayreuth,95440 Bayreuth, Germany
  
   
  
  Pseudomonas syringae pv. ribicola NVPPB1010
  CSDB ID 9466 (all data & tools)

Show legend Show as text

Structure type: oligomer
Trivial name: part of the cell wall polysaccharide
Contained glycoepitopes: IEDB_127513,IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_143254,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 818
  Hoog C, Rotondo A, Johnston BD, Pinto BM "Synthesis and conformational analysis of a pentasaccharide corresponding to the cell-wall polysaccharide of the group A Streptococcus" - Carbohydrate Research 337(21-23) (2002) 2023-2036
  

  The synthesis and conformational analysis of a pentasaccharide corresponding to a fragment of the cell-wall polysaccharide (CWPS) of the bacteria Streptococcus Group A are described. The polysaccharide consists of alternating α-(1→2)- and α-(1→3)-linked L- rhamnopyranose (Rhap) residues with branching 2-acetamido-2-deoxy-D-glucopyranose (GlcpNAc) residues linked β-(1→3) to alternate rhamnose rings. The pentasaccharide is of interest as a possible terminal unit on the CWPS, for use in a vaccine. The syntheses employed a trichloroacetimidate glycosyl donor. Molecular dynamics (MD) calculations of the pentasaccharide with the force fields CVFF and PARM22, both in gas phase and with explicit water present, gave different predictions for the flexibility and preferred conformational space. Metropolis Monte Carlo (MMC) calculations with the HSEA force field were also performed. Experimental data were obtained from 1D transient NOE measurements. Complete build-up curves were compared to those obtained by full relaxation matrix calculations in order to derive a model of the conformation. Overall, the best fit between experimental and calculated data was obtained with MMC simulations using the HSEA force field. Molecular dynamics and MMC simulations of a tetrasaccharide corresponding to the Group A-variant polysaccharide, which differs in structure from Group A in lacking the GlcpNAc residues, were also performed for purposes of comparison

  conformation, synthesis, structure, tetrasaccharide, chemistry, phase, terminal, polysaccharide, Streptococcus, analysis, group, linked, molecular, water, conformational, dynamics, molecular dynamics, bacteria, cell wall, conformational analysis, calculation, fragment, pentasaccharide, rhamnose, glycosyl, comparison, measurement, vaccine, experimental, simulation, NOE, relaxation, cell wall polysaccharide, model, order, use, ring, flexibility, force field, HSEA, matrix, Monte Carlo, prediction, transient

  NCBI PubMed ID: 11744630
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Department of Chemistry, Simon Fraser University, British Columbia, V5A 1S6, Burnaby, Canada
  Methods: NMR-2D
  
   
  
  Streptococcus pneumoniae sp. A
  CSDB ID 2434 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1075
  Ovod V, Zdorovenko EL, Shashkov AS, Kocharova NA, Knirel YA "Structure of the O polysaccharide and serological classification of Pseudomonas syringae pv. ribicola NCPPB 1010" - European Journal of Biochemistry 267(8) (2000) 2372-2379
  

  The O polysaccharide (OPS) moiety of the lipopolysaccharide (LPS) of a phytopathogenic bacterium Pseudomonas syringae pv. ribicola NCPPB 1010 was studied by sugar and methylation analyses, Smith degradation, and 1H- and 13C NMR spectroscopy, including 2D COSY, TOCSY, NOESY and H-detected 1H,13C HMQC experiments. The OPS structure was elucidated, and shown to be composed of branched pentasaccharide repeating units (O repeats) of two types, major (1) and minor (2), differing in the position of substitution of one of the rhamnose residues. Both O repeats form structurally homogeneous blocks within the same polysaccharide molecule. Although P. syringae pv. ribicola NCPPB 1010 demonstrates genetic relatedness and similarity in the OPS chemical structure to some other P. syringae pathovars, it did not cross-react with any OPS-specific mAbs produced against heterologous P. syringae strains. Therefore, we propose to classify P. syringae pv. ribicola NCPPB 1010 in a new serogroup, O8.

  structure, structural, polysaccharide, Pseudomonas, O-polysaccharide, O polysaccharide, serological, Pseudomonas syringae, classification, linear, heterogeneity

  NCBI PubMed ID: 10759863
  Journal NLM ID: 0107600
  Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
  Correspondence: knirel@ioc.ac.ru
  Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Medical Technology, University of Tampere, Finland
  Methods: NMR-2D, methylation, NMR, sugar analysis, Smith degradation
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB1010
  CSDB ID 4106 (all data & tools)
• Article ID: 1452
  Corsaro MM, De Castro C, Molinaro A, Parrilli M "Structure of lipopolysaccharides from phytopathogenic Gram-negative bacteria" - Book: Recent Research Developments in Phytochemistry (2001) Vol. 5, 119-138
  

  This review collects the structural data of lipopolysaccharide components arising from all phytopathogenic bacteria so far investigated. The structural approaches and the main biological role of these macromolecules are also reported.

  Lipopolysaccharide, lipopolysaccharides, structure, core, lipid A, O-polysaccharide, gram negative bacteria

  WWW link: https://books.google.ru/books/about/Recent_Research_Developments_in_Phytoche.html?id=5CJacgAACAAJ&redir_esc=y
  Publisher: Research Signpost, Trivandrum, India
  Editors: Pandalai SG
  Institutions: Dipartimento di Chimica Organica e Biochimica, Complesso Universitario Monte S.Angelo Via Cintia, 4, 80126 Napoli, Italy
  
   
  
  Pseudomonas syringae pv. ribicola VIII NVPPB 1010
  CSDB ID 31738 (all data & tools)
• Article ID: 3968
  Zdorovenko GM, Zdorovenko EL "Pseudomonas syringae lipopolysaccharides: Immunochemical characteristics and structure as a basis for strain classification" - Mikrobiologiia = Microbiology [Russian] 79(1) (2010) 47-57
  

  Lipopolysaccharide (LPS) preparations of 34 Pseudomonas syringae strains of 19 pathovars were prepared by saline extraction from wet cells and purified by repeated ultracentrifugation. The preparations reacted with homologous O-antisera, obtained by rabbit immunization with heat-killed bacterial cells. Through inhibition of homologous reactions between LPS preparations of heterologous strains (enzyme immunoassay, EIA), it was established for the first time that high serological affinity between strains is observed only if their LPS contains O-specific polysaccharide chains (OPS) comprised of completely identical rather than partially similar units. The central linear part of the OPS was found to be serologically inert when shielded with side groups. Data on immunochemical characteristics of the LPS and OPS structure are analyzed in relation to the design of P. syringae classification scheme.

  Lipopolysaccharide, structure, O-specific polysaccharide, Pseudomonas syringae, classification, immunochemistry

  NCBI PubMed ID: 20411661
  Publication DOI: 10.1134/S0026261710010078
  Journal NLM ID: 0376652
  Publisher: Moskva: Izdatelstvo Nauka
  Correspondence: evelina@ioc.ac.ru
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Zabolotnyi Institute of Microbiology and Virology, National Academy of Sciences of Ukraine, ul. Zabolotnogo 154, Kyiv, 03143 Ukraine
  Methods: partial acid hydrolysis, EIA, serological methods, de-N-acetylation/deamination
  
   
  
  Pseudomonas syringae pv. ribicola NCPPB 1010
  CSDB ID 25905 (all data & tools)
• Article ID: 5461
  Knirel YA, Naumenko OI, Senchenkova SN, Perepelov AV "Chemical methods for selective cleavage of glycosidic linkages in structural analysis of bacterial polysaccharides" - Russian Chemical Reviews = Uspekhi Khimii 88(4) (2019) 406-424
  

  This review is devoted to methods for the selective cleavage of glycosidic bonds. The mechanisms of reactions underlying these methods are considered and examples of their practical application in the structural analysis of bacterial polysaccharides are given. Specific methods for the selective cleavage of polysaccharides, remaining relevant for researchers, include the Smith degradation based on destruction of monosaccharides containing vicinal diol groups, dephosphorylation of phosphate-containing polysaccharides with hydrofluoric acid and the hydrolytic cleavage of glycosyl phosphate bonds in the latter compounds. Non-specific methods, including partial acid hydrolysis, acetolysis and solvolysis with anhydrous organic (CF3SO3H, MeSO3H, CF3CO2H) and inorganic (HF) acids do not make any specific demands on the composition and structure of the polysaccharide and are sensitive to its fine structural features. The review addesses the issue of stability of glycosidic bonds in various monosaccharides to reagents used for non-specific selective cleavage.

  structural analysis, Bacterial polysaccharide, selective cleavage, glycosidic bond

  Publication DOI: 10.1070/RCR4856
  Journal NLM ID: 0404506
  Publisher: London: Chemical Society
  Correspondence: Yu.A. Knirel
  Institutions: N.D. Zelinskii Institute of Organic Chemistry, Russian Academy of Sciences
  Methods: partial acid hydrolysis, HF solvolysis, acid hydrolysis, mild acid hydrolysis, alkaline degradation, b-elimination, Smith degradation, deamination, de-O-acetylation, HF treatment, reduction with NaBD4, triflic acid solvolysis, acetolysis, Li/ethylenediamine degradation, hydrazinolysis, reduction with NaBH4, mild acid degradation, trifluoroacetic acid solvolysis, partial solvolysis with anhydrous trifluoroacetic acid, de-N-acetylation with hydrazine, part acid hydrolysis, HF solvolysis; published polymerization frame was shifted for conformity with other records.
  
   
  
  Pseudomonas syringae pv. ribicola
  CSDB ID 1389 (all data & tools)

Show legend Show as text

Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_137472,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149136,IEDB_151531,IEDB_190606,IEDB_225177,IEDB_885823,IEDB_983931,SB_192

• Article ID: 1106
  Petersson C, Jachymek W, Kenne L, Niedziela T, Lugowski C "Structural studies of the O-specific chain of Hafnia alvei strain PCM1190 lipopolysaccharide" - Carbohydrate Research 298 (1997) 219-227
  

  The structure of the O-specific side-chain of the lipopolysaccharide of Hafnia alvei strain PCM1190 has been investigated. Methylation analysis, partial acid hydrolysis, Smith degradation, NMR spectroscopy, MALDI-TOF, and FAB mass spectrometry in combination with colision-induced-decomposition MS/MS were the principal methods used. It was concluded that the polysaccharide is composed of heptasaccharide repeating units having the following structure: [see formula in text].

  Lipopolysaccharide, O-antigen, Hafnia alvei, MS/MS

  NCBI PubMed ID: 9183004
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Institutions: Department of Chemistry, Swedish University of Agricultural Sciences, P.O. Box 7015, S-750 07 Uppsala, Sweden, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, ul. Czerska 12, PL-53-114 Wroclaw, Poland
  Methods: NMR-2D, methylation, FAB-MS, partial acid hydrolysis, NMR, Smith degradation, MALDI-TOF MS, CID-MS/MS
  
   
  
  Hafnia alvei PCM 1190
  CSDB ID 4049 (all data & tools)
• Article ID: 4328
  Knirel YA "Structure of O-antigens" - Book: Bacterial lipopolysaccharides: Structure, chemical synthesis, biogenesis and interaction with host cells (2011) Chapter 3, 41-115
  

  The lipopolysaccharide (LPS) is the major constituent of the outer leaflet of the outer membrane of Gram-negative bacteria. Its lipid A moiety is embedded in the membrane and serves as an anchor for the rest of the LPS molecule. The outermost repetitive glycan region of the LPS is linked to the lipid A through a core oligosaccharide (OS), and is designated as the O-specific polysaccharide (O-polysaccharide, OPS) or O-antigen. The O-antigen is the most variable portion of the LPS and provides serological specificity, which is used for bacterial serotyping. The OPS also provides protection to the microorganisms from host defenses such as complement mediated killing and phagocytosis, and is involved in interactions of bacteria with plants and bacteriophages. Studies of the OPSs ranging from the elucidation of their chemical structures and conformations to their biological and physico-chemical properties help improving classification schemes of Gram-negative bacteria. Furthermore, these studies contributed to a better understanding of the mechanisms of pathogenesis of infectious diseases, as well as provided information to develop novel vaccines and diagnostic reagents.

  Lipopolysaccharide, synthesis, lipopolysaccharides, structure, Bacterial, host, O-antigen, O antigen, cell, O antigens, O-antigens, chemical, interaction, cells, PDF, chemical synthesis, biogenesis

  Publication DOI: 10.1007/978-3-7091-0733-1_3
  Publisher: Springer
  Correspondence: knirel@ioc.ac.ru
  Editors: Knirel YA, Valvano MA
  Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
  
   
  
  Hafnia alvei 1190
  CSDB ID 27551 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4153 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4154 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_133754,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4155 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4156 (all data & tools)

Show legend Show as text

Structure type: oligomer
Contained glycoepitopes: IEDB_131174,IEDB_131175,IEDB_133754,IEDB_135610,IEDB_135813,IEDB_136105,IEDB_137340,IEDB_141807,IEDB_151531,IEDB_225177,IEDB_885823

• Article ID: 1109
  Pitner JB, Beyer WF, Venetta TM, Nycz C, Mitchell MJ, Harris SL, Mariño-Albernas JR, Auzanneau FI, Forooghian F, Pinto BM "Bivalency and epitope specificity of a high-affinity IgG3 monoclonal antibody to the Streptococcus Group A carbohydrate antigen. Molecular modeling of a Fv fragment" - Carbohydrate Research 324(1) (2000) 17-29
  

  The binding of Strep 9, a mouse monoclonal antibody (mAb) of the IgG3 subclass directed against the cell-wall polysaccharide of Group A Streptococcus (GAS), has been characterized. The intact antibody and proteolytic fragments of Strep 9 bind differently to GAS: the intact mAb and F(ab)2' have greater affinity for the carbohydrate epitope than the monomeric Fab or F(ab)'. A mode of binding in which Strep 9 binds bivalently to portions of the polysaccharide on adjacent chains on GAS is proposed. A competitive ELISA protocol using a panel of carbohydrate inhibitors shows that the branched trisaccharide, β-D-GlcpNAc-(1→3)-[α-L-Rhap-(1→2)]-α-L-Rhap, and an extended surface are key components of the epitope recognized by Strep 9. Microcalorimetry measurements with the mAb and two synthetic haptens, a tetrasaccharide and a hexasaccharide, show enthalpy-entropy compensation as seen in other oligosaccharide-protein interactions. Molecular modeling of the antibody variable region by homology modeling techniques indicates a groove-shaped combining site that can readily accommodate extended surfaces. Visual docking of an oligosaccharide corresponding to the cell-wall polysaccharide into the site provides a putative model for the complex, in which a heptasaccharide unit occupies the site and the GlcpNAc residues of two adjacent branched trisaccharide units occupy binding pockets within the groove-shaped binding site.

  antigen, Streptococcus, carbohydrate, group, molecular, antibodies, antibody, epitope, monoclonal, monoclonal antibodies, monoclonal antibody, specificity, fragment, modeling, epitope specificity, carbohydrate antigen

  NCBI PubMed ID: 10723608
  Journal NLM ID: 0043535
  Publisher: Elsevier
  Correspondence: bpinto@sfu.ca
  Institutions: Becton Dickinson Research Center, PO Box 12016, Research Triangle Park, NC 27709, USA, Department of Chemistry and Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby,BC, Canada V5A 1S6
  Methods: ELISA
  
   
  
  Streptococcus pneumoniae A
  CSDB ID 4157 (all data & tools)