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1. Compound ID: 2381
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P-4)-+
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a-Kdop-(2-4)-a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
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Structure type: oligomer
Trivial name: core-lipid A carbohydrate backbone, epitope I
Compound class: core oligosaccharide, LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150901,IEDB_150908,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 814
Holst O, Bock K, Brade L, Brade H "The structures of oligosaccharide bisphosphates isolated from the lipopolysaccharide of a recombinant Escherichia coli strain expressing the gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] of Chlamydia psittaci 6BC" -
European Journal of Biochemistry 229 (1995) 194-200
The lipopolysaccharide from the recombinant strain Escherichia coli F515-140 containing the cloned gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] from Chlamydia psittaci 6BC was isolated and sequentially de-O-acylated and de-N-acylated. The products were separated by high-performance anion-exchange chromatography into three fractions, two of which contained a single compound. Their structures were elucidated by high-field NMR spectroscopy as α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 1) (tetrasaccharide bisphosphate) [Holst, O., Broer, W., Thomas-Oates, J. E., Mamat, U. & Brade, H. (1993) Eur. J. Biochem. 214, 703-710] and α-Kdo-(2→4)-[α-Kdo-(2→8)-]-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 4) (hexasaccharide bisphosphate). The third fraction comprised two pentasaccharide bisphosphates, which could be separated by affinity chromatography using an immobilized monoclonal antibody specific for the trisaccharide α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo. The bound fraction was identified as α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 2) [Holst, O., Broer, W., Thomas-Oates, J. E., Mamat, U. & Brade, H. (1993) Eur. J. Biochem. 214, 703-710], whereas the unbound fraction was identified as α-Kdo-(2→4)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 3). This novel Kdo tetrasaccharide extends our knowledge on multifunctional Kdo transferases.
Lipopolysaccharide, LPS, oligosaccharide, structure, core, gene, strain, Escherichia, Escherichia coli, acid, Kdo, transferase, phosphate, Chlamydia, recombinant, bisphosphate, Chlamydia psittaci, gseA, HPLC
NCBI PubMed ID: 7744029Publication DOI: 10.1111/j.1432-1033.1995.0194l.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Division of Biochemical Microbiology, Forschungsinstitut Borstel, Germany, Division of Biochemical Microbiology, Institut fur Experimentelle Biologie und Medizin, Forschungsinstitut Borstel, Germany, Department of Chemistry, Carisberg Laboratory, Copenhagen, Denmark
Methods: 13C NMR, 1H NMR, GLC-MS, 31P NMR, HPAEC, affinity chromatography
- Article ID: 1157
Rund S, Lindner B, Brade H, Holst O "Structural analysis of the lipopolysaccharide from Chlamydophila psittaci strain 6BC" -
European Journal of Biochemistry 267(18) (2000) 5717-5726
The lipopolysaccaride of Chlamydophila psittaci 6BC was isolated from tissue culture-grown elementary bodies using a modified phenol/water procedure followed by extraction with phenol/chloroform/light petroleum. Compositional analyses indicated the presence of 3-deoxy-Dmanno-oct-2-ulosonic acid, GlcN, organic bound phosphate and fatty acids in a molar ratio of approximately 3. 3 : 2 : 1.8 : 4.6. Deacylated lipopolysaccharide was obtained after successive microscale treatment with hydrazine and potassium hydroxide, and was then separated by high performance anion-exchange chromatography into two major fractions, the structures of which were determined by 600 MHz NMR spectroscopy as α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN 1,4'-bisphosphate and α-Kdo-(2→4)-[α-Kdo-(2→8)]-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN 1,4'-bisphosphate. The distribution of fatty acids in lipid A was determined by compositional analyses andmatrix-assisted laser desorption/ionization time-of-flight mass spectrometry experiments on lipid A and de-O-acylated lipid A. It was shown that the carbohydrate backbone of lipid A is replaced by a complex mixture of fatty acids, including long-chain and branched (R)-configured 3-hydroxy fatty acids, the latter being exclusively present in an amide linkage
Lipopolysaccharide, strain, structural, serotype, analysis, structural analysis, Chlamydophila psittaci, NMR spectroscopy, mass spectrometry
NCBI PubMed ID: 10971582Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Divisions of Medical and Biochemical Microbiology and Biophysics, Research Center Borstel, Center for Medicine and Biosciences, Germany
Methods: 13C NMR, 1H NMR, NMR-2D, MALDI-TOF MS
- Article ID: 1386
Brabetz W, Lindner B, Brade H "Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12" -
European Journal of Biochemistry 267(17) (2000) 5458-5465
The waaA gene encoding the essential, lipopolysaccharide (LPS)-specific 3-deoxy-Dmanno-oct-2-ulosonic acid (Kdo) transferase was inactivated in the chromosome of a heptosyltransferase I and II deficient Escherichia coli K-12 strain by insertion of gene expression cassettes encoding the waaA genes of Chlamydia trachomatis, Chlamydophila pneumoniae or Chlamydophila psittaci. The three chlamydial Kdo transferases were able to complement the knockout mutation without changing the growth or multiplication behaviour. The LPS of the mutants were serologically and structurally characterized in comparison to the LPS of the parent strain using compositional analyses, high performance anion exchange chromatography, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and specific monoclonal antibodies. The data show that chlamydial Kdo transferases can replace in E. coli K-12 the host's Kdo transferase and retain the product specificities described in their natural background. In addition, we unequivocally proved that WaaA from C. psittaci transfers predominantly four Kdo residues to lipid A, forming a branched tetrasaccharide with the structure α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo.
Lipopolysaccharide, LPS, gene, Escherichia, Escherichia coli, 3-deoxy-D-manno-oct-2-ulosonic acid, acid, Kdo, transferase, transferases, Chlamydiaceae, genetic complementation, multifunctional 3-deoxy-D-manno-oct-2, product specificity, ulosonic acid transferases
NCBI PubMed ID: 10951204Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: wbrabetz@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Divizion of Medical and Biochemical Microbiology, Research Centre Borstel, Centre for Medicine and Biosciences,Borstel,Germany
- Article ID: 3825
Brooks CL, Müller-Loennies S, Borisova SN, Brade L, Kosma P, Hirama T, MacKenzie CR, Brade H, Evans SV "Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition" -
Biochemistry 49(3) (2010) 570-581
The structures of antigen-binding fragments from two related monoclonal antibodies have been determined to high resolution in the presence of several carbohydrate antigens raised against chlamydial lipopolysaccharide. With the exception of CDR H3, antibodies S54-10 and S73-2 are both derived from the same set of germline gene segments as the previously reported structures S25-2 and S45-18. Despite this similarity, the antibodies differ in specificity and the mechanism by which they recognize their cognate antigen. S54-10 uses an unrelated CDR H3 to recognize its antigen in a fashion analogous to S45-18; however, S73-2 recognizes the same antigen as S45-18 and S54-10 in a wholly unrelated manner. Together, these antibody-antigen structures provide snapshots into how the immune system uses the same set of inherited germline gene segments to generate multiple possible specificities that allow for differential recognition of epitopes and how unrelated CDR H3 sequences can result in convergent binding of clinically relevant bacterial antigens.
antibodies, epitope, recognition, antigens, Chlamydia, binding
NCBI PubMed ID: 20000757Journal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: hebra@fz-borstel.de; svevans@uvic.ca
Institutions: University of Victoria, Department of Biochemistry and Microbiology, PO Box 3055 STN CSC, Victoria, BC, Canada V8P 3P6
Methods: ELISA, serological methods, genetic methods, crystallization, surface plasmon resonance (SPR)
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2. Compound ID: 2382
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a-Kdop-(2-8)-+ P-4)-+
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a-Kdop-(2-4)-a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
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Structure type: oligomer
Trivial name: core-lipid A backbone, epitope J
Compound class: core oligosaccharide, LPS
Contained glycoepitopes: IEDB_130650,IEDB_130657,IEDB_130658,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150755,IEDB_150756,IEDB_150760,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_151769
The structure is contained in the following publication(s):
- Article ID: 814
Holst O, Bock K, Brade L, Brade H "The structures of oligosaccharide bisphosphates isolated from the lipopolysaccharide of a recombinant Escherichia coli strain expressing the gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] of Chlamydia psittaci 6BC" -
European Journal of Biochemistry 229 (1995) 194-200
The lipopolysaccharide from the recombinant strain Escherichia coli F515-140 containing the cloned gene gseA [3-deoxy-D-manno-octulopyranosonic acid (Kdo) transferase] from Chlamydia psittaci 6BC was isolated and sequentially de-O-acylated and de-N-acylated. The products were separated by high-performance anion-exchange chromatography into three fractions, two of which contained a single compound. Their structures were elucidated by high-field NMR spectroscopy as α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 1) (tetrasaccharide bisphosphate) [Holst, O., Broer, W., Thomas-Oates, J. E., Mamat, U. & Brade, H. (1993) Eur. J. Biochem. 214, 703-710] and α-Kdo-(2→4)-[α-Kdo-(2→8)-]-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 4) (hexasaccharide bisphosphate). The third fraction comprised two pentasaccharide bisphosphates, which could be separated by affinity chromatography using an immobilized monoclonal antibody specific for the trisaccharide α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo. The bound fraction was identified as α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 2) [Holst, O., Broer, W., Thomas-Oates, J. E., Mamat, U. & Brade, H. (1993) Eur. J. Biochem. 214, 703-710], whereas the unbound fraction was identified as α-Kdo-(2→4)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcN-(1→6)-α-D-GlcN 1,4'-P2 (compound 3). This novel Kdo tetrasaccharide extends our knowledge on multifunctional Kdo transferases.
Lipopolysaccharide, LPS, oligosaccharide, structure, core, gene, strain, Escherichia, Escherichia coli, acid, Kdo, transferase, phosphate, Chlamydia, recombinant, bisphosphate, Chlamydia psittaci, gseA, HPLC
NCBI PubMed ID: 7744029Publication DOI: 10.1111/j.1432-1033.1995.0194l.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Division of Biochemical Microbiology, Forschungsinstitut Borstel, Germany, Division of Biochemical Microbiology, Institut fur Experimentelle Biologie und Medizin, Forschungsinstitut Borstel, Germany, Department of Chemistry, Carisberg Laboratory, Copenhagen, Denmark
Methods: 13C NMR, 1H NMR, GLC-MS, 31P NMR, HPAEC, affinity chromatography
- Article ID: 1157
Rund S, Lindner B, Brade H, Holst O "Structural analysis of the lipopolysaccharide from Chlamydophila psittaci strain 6BC" -
European Journal of Biochemistry 267(18) (2000) 5717-5726
The lipopolysaccaride of Chlamydophila psittaci 6BC was isolated from tissue culture-grown elementary bodies using a modified phenol/water procedure followed by extraction with phenol/chloroform/light petroleum. Compositional analyses indicated the presence of 3-deoxy-Dmanno-oct-2-ulosonic acid, GlcN, organic bound phosphate and fatty acids in a molar ratio of approximately 3. 3 : 2 : 1.8 : 4.6. Deacylated lipopolysaccharide was obtained after successive microscale treatment with hydrazine and potassium hydroxide, and was then separated by high performance anion-exchange chromatography into two major fractions, the structures of which were determined by 600 MHz NMR spectroscopy as α-Kdo-(2→8)-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN 1,4'-bisphosphate and α-Kdo-(2→4)-[α-Kdo-(2→8)]-α-Kdo-(2→4)-α-Kdo-(2→6)-β-D-GlcpN-(1→6)-α-D-GlcpN 1,4'-bisphosphate. The distribution of fatty acids in lipid A was determined by compositional analyses andmatrix-assisted laser desorption/ionization time-of-flight mass spectrometry experiments on lipid A and de-O-acylated lipid A. It was shown that the carbohydrate backbone of lipid A is replaced by a complex mixture of fatty acids, including long-chain and branched (R)-configured 3-hydroxy fatty acids, the latter being exclusively present in an amide linkage
Lipopolysaccharide, strain, structural, serotype, analysis, structural analysis, Chlamydophila psittaci, NMR spectroscopy, mass spectrometry
NCBI PubMed ID: 10971582Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: oholst@fz-borstel.de
Institutions: Divisions of Medical and Biochemical Microbiology and Biophysics, Research Center Borstel, Center for Medicine and Biosciences, Germany
Methods: 13C NMR, 1H NMR, NMR-2D, MALDI-TOF MS
- Article ID: 1386
Brabetz W, Lindner B, Brade H "Comparative analyses of secondary gene products of 3-deoxy-D-manno-oct-2-ulosonic acid transferases from Chlamydiaceae in Escherichia coli K-12" -
European Journal of Biochemistry 267(17) (2000) 5458-5465
The waaA gene encoding the essential, lipopolysaccharide (LPS)-specific 3-deoxy-Dmanno-oct-2-ulosonic acid (Kdo) transferase was inactivated in the chromosome of a heptosyltransferase I and II deficient Escherichia coli K-12 strain by insertion of gene expression cassettes encoding the waaA genes of Chlamydia trachomatis, Chlamydophila pneumoniae or Chlamydophila psittaci. The three chlamydial Kdo transferases were able to complement the knockout mutation without changing the growth or multiplication behaviour. The LPS of the mutants were serologically and structurally characterized in comparison to the LPS of the parent strain using compositional analyses, high performance anion exchange chromatography, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and specific monoclonal antibodies. The data show that chlamydial Kdo transferases can replace in E. coli K-12 the host's Kdo transferase and retain the product specificities described in their natural background. In addition, we unequivocally proved that WaaA from C. psittaci transfers predominantly four Kdo residues to lipid A, forming a branched tetrasaccharide with the structure α-Kdo-(2→8)-[α-Kdo-(2→4)]-α-Kdo-(2→4)-α-Kdo.
Lipopolysaccharide, LPS, gene, Escherichia, Escherichia coli, 3-deoxy-D-manno-oct-2-ulosonic acid, acid, Kdo, transferase, transferases, Chlamydiaceae, genetic complementation, multifunctional 3-deoxy-D-manno-oct-2, product specificity, ulosonic acid transferases
NCBI PubMed ID: 10951204Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: wbrabetz@fz-borstel.de
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, Borstel, Germany, Divizion of Medical and Biochemical Microbiology, Research Centre Borstel, Centre for Medicine and Biosciences,Borstel,Germany
- Article ID: 3825
Brooks CL, Müller-Loennies S, Borisova SN, Brade L, Kosma P, Hirama T, MacKenzie CR, Brade H, Evans SV "Antibodies raised against chlamydial lipopolysaccharide antigens reveal convergence in germline gene usage and differential epitope recognition" -
Biochemistry 49(3) (2010) 570-581
The structures of antigen-binding fragments from two related monoclonal antibodies have been determined to high resolution in the presence of several carbohydrate antigens raised against chlamydial lipopolysaccharide. With the exception of CDR H3, antibodies S54-10 and S73-2 are both derived from the same set of germline gene segments as the previously reported structures S25-2 and S45-18. Despite this similarity, the antibodies differ in specificity and the mechanism by which they recognize their cognate antigen. S54-10 uses an unrelated CDR H3 to recognize its antigen in a fashion analogous to S45-18; however, S73-2 recognizes the same antigen as S45-18 and S54-10 in a wholly unrelated manner. Together, these antibody-antigen structures provide snapshots into how the immune system uses the same set of inherited germline gene segments to generate multiple possible specificities that allow for differential recognition of epitopes and how unrelated CDR H3 sequences can result in convergent binding of clinically relevant bacterial antigens.
antibodies, epitope, recognition, antigens, Chlamydia, binding
NCBI PubMed ID: 20000757Journal NLM ID: 0370623Publisher: American Chemical Society
Correspondence: hebra@fz-borstel.de; svevans@uvic.ca
Institutions: University of Victoria, Department of Biochemistry and Microbiology, PO Box 3055 STN CSC, Victoria, BC, Canada V8P 3P6
Methods: ELISA, serological methods, genetic methods, crystallization, surface plasmon resonance (SPR)
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3. Compound ID: 3415
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?%a-Kdop-(2-4)-a-Kdo-(2-4)-+
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?%b-D-GalpA-(1-6)-b-D-Glcp-(1-4)-+ |
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L-gro-a-D-manHepp-(1-7)-+ | | P-4)-+
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?%D-gro-a-D-manHepp-(1-2)-D-gro-a-D-manHepp-(1-2)-D-gro-a-D-manHepp-(1-2)-D-gro-a-D-manHepp-(1-6)-a-D-GlcpN-(1-4)-a-D-GalpA-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P |
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Structure type: oligomer
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_135394,IEDB_137340,IEDB_140087,IEDB_140088,IEDB_140090,IEDB_140092,IEDB_141807,IEDB_142488,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_2189046,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 1275
Susskind M, Brade L, Brade H, Holst O "Identification of a novel heptoglycan of a a1->2-linked D-glycero-D-manno-heptopyranose. Chemical and antigenic structure of lipopolysaccharides from Klebsiella pneumoniae ssp. pneumoniae rough strain R20 (O1-:K20-)" -
Journal of Biological Chemistry 273(12) (1998) 7006-7017
In a preliminary investigation (Susskind, M., Müller-Loennies, S., Nimmich, W., Brade, H., and Holst, O. (1995) Carbohydr. Res. 269, C1-C7), we identified after deacylation of lipopolysaccharides (LPS) from Klebsiella pneumoniae ssp. pneumoniae rough strain R20 (O1(-):K20(-)) as a major fraction the oligosaccharide,-structure, see text- where Kdo was 3-deoxy-D-manno-oct-2-ulopyranosonic acid and Hepp was manno-heptopyranose. The presence of the threo-hex-4-enuronopyranosyl residue indicated a substituent at O-4 of the second GalA residue linked to O-3 of the second L,D-Hep residue, which had been eliminated by treatment with hot alkali. We now report the complete structure of lipopolysaccharide, which was elucidated by additional characterization of isolated core oligosaccharides and analysis of the lipid A. The substituent at O-4 of the second GalpA is D-GlcpN, which in a fraction of the LPS is substituted at O-6 by three or four residues of D-glycero-D-manno-heptopyranose (D,D-Hepp). The complete carbohydrate backbone of the LPS is as follows, -structure, see text- (L-glycero-D-manno-heptopyranose, L,D-Hepp), where all hexoses possess the D-configuration. Sugars marked with an asterisk are present in nonstoichiometric amounts. The structure is unique with regard to the presence of an α1→2-linked D-glycero-D-manno-heptoglycan (oligosaccharide), which has not been described to date, and does not contain phosphate substituents in the core region. Fatty acid analysis of lipid A identified (R)-3-hydroxytetradecanoic acid as sole amide-linked fatty acid and (R)-3-hydroxytetradecanoic acid, tetradecanoic acid, small amounts of 2-hydroxytetradecanoic acid, hexadecanoic acid, and traces of dodecanoic acid as ester-linked fatty acids, substituting the carbohydrate backbone D-GlcpN4P β1→6 D-GlcpNα1P. The nonreducing GlcN carries four fatty acids, present as two 3-O-tetradecanoyltetradecanoic acid residues, one of which is amide-linked and the other ester-linked to O-3'. The reducing GlcN is substituted in a nature fraction of lipid A by two residues of (R)-3-hydroxytetradecanoic acid, one in amide and the other in ester linkage at O-3. Two minor fractions of lipid A were identified, in one, the amide-linked (R)-3-hydroxytetradecanoic acid at the reducing GlcN is esterified with hexadecanoic acid, resulting in 3-O-hexadecanoyltetradecanoic acid, and in the second, one of the 3-O-tetradecanoyltetradecanoic acid residues at the nonreducing GlcN is replaced by 3-O-dodecanoyltetradecanoic acid. Thus, the complete structure of LPS is as shown in Fig. 1. After immunization of BALB/c mice, two monoclonal antibodies were obtained that were shown to be specific for the core of LPS from K. pneumoniae ssp. pneumoniae, since they did not react with LPS or whole-cell lysates of a variety of other Gram-negative species. Both monoclonal antibodies could be inhibited by LPS but not by isolated oligosaccharides and are thus considered to recognize a conformational epitope in the core region.
Lipopolysaccharide, lipopolysaccharides, LPS, structure, core, strain, analysis, antigenic, identification, Kdo, Klebsiella, chemical, rough, D-glycero-D-manno-heptose, galacturonic acid, Klebsiella pneumoniae, heptan
NCBI PubMed ID: 9507008Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Institutions: Division of Medical and Biochemical Microbiology, Research Center Borstel, Center for Medicine and Biosciences, D-23845 Borstel, Germany.
Methods: 13C NMR, 1H NMR, methylation, MALDI-MS, serological methods
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4. Compound ID: 6684
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3HOMyr-(1-2)-+
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P-4)-+ |
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Lau-(1-3)-3HOMyr-(1-2)-+ | |
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a-Kdop-(2-4)-a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
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Myr-(1-3)-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
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Structure type: oligomer
Compound class: LOS, LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_176772,IEDB_534864
The structure is contained in the following publication(s):
- Article ID: 2672
Dziarski R, Gupta D "Heparin, sulfated heparinoids, and lipoteichoic acids bind to the 70-kDa peptidoglycan/lipopolysaccharide receptor protein on lymphocytes" -
Journal of Biological Chemistry 269 (1994) 2100-2110
The same 70-kDa protein, present on the surface of mouse lymphocytes, served as the predominant binding site for heparin, heparinoids, and bacterial lipoteichoic acids, as well as peptidoglycan and lipopolysaccharides. This conclusion was supported by the following results: (a) all of these compounds photoaffinity cross-linked to one major 70-kDa 6.5-7.0 pI protein that co-migrated on two-dimensional polyacrylamide gel electrophoresis; (b) peptide maps of the 70-kDa proteins digested with chymotrypsin, subtilisin, protease V, or papain yielded the same peptides for heparin-, lipoteichoic acid-, peptidoglycan-, and lipopolysaccharide-binding proteins; (c) cross-linking of peptidoglycan, lipopolysaccharide, lipoteichoic acid, and heparin was competitively inhibited by the same compounds with the same order of potency, i.e. carboxyl-reduced sulfated heparin > peptidoglycan > pentosan polysulfate > heparin > chitin > dextran sulfate > trestatin sulfate > polyanetholesulfonate > fucoidan > beta-cyclodextrin tetradecasulfate > heparan sulfate > carrageenan lambda > lipoteichoic acids > Re-lipopolysaccharide > lipopolysaccharide > lipid A > polygalacturonic acid; and (d) cross-linking of each of these ligands was not inhibited by carboxyl-reduced heparin, dextran, beta-cyclodextrin, trestatin, carrageenan kappa, chondroitin 4-sulfate, chondroitin 6-sulfate, beta-D-glucan, carboxy-methylcellulose, levan, alpha-D-mannan, and glycogen. The minimum size of the molecule that bound was 7-9 glycan residues, whereas, di- and trisaccharides did not bind. There was a logarithmic linear relationship between the strength of the binding and the length of the polymer (up to > 1500 glycan residues), which indicates an avidity effect of the cooperative binding of one polymeric molecule to several receptor molecules on the cell surface. The 70-kDa receptor, therefore, has a broad, but limited specificity of binding for non-charged (peptidoglycan and chitin), highly negatively charged (heparin and heparinoids), and weakly negatively charged (lipoteichoic acids, lipopolysaccharides, and lipid A) ligands.
NCBI PubMed ID: 8294463Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Institutions: Northwest Center for Medical Education, Indiana University School of Medicine, Gary 46408
- Article ID: 3838
D'Errico G, Silipo A, Mangiapia G, Vitiello G, Radulescu A, Molinaro A, Lanzetta R, Paduano L "Characterization of liposomes formed by lipopolysaccharides from Burkholderia cenocepacia, Burkholderia multivorans and Agrobacterium tumefaciens: from the molecular structure to the aggregate architecture" -
Physical Chemistry Chemical Physics 12(41) (2010) 13574-13585
The microstructure of liposomes formed by the lipopolysaccharides (LPS) derived from Burkholderia cenocepacia ET-12 type strain LMG 16656, Burkholderia multivorans strain C1576 and Agrobacterium tumefaciens strain TT111 has been investigated by a combined experimental strategy, including dynamic light scattering (DLS), small-angle neutron scattering (SANS) and electron paramagnetic resonance (EPR). The results highlight that the LPS molecular structure determines, through a complex interplay of hydrophobic, steric and electrostatic interactions, the morphology of the aggregates formed in aqueous medium. All the considered LPS form liposomes that in most cases present a multilamellar arrangement. The thickness of the hydrophobic domain of each bilayer and the local ordering of the acyl chains are determined not only by the molecular structure of the LPS glycolipid portion (lipid A), but also, indirectly, by the bulkiness of the saccharidic portion. In the case of a long polysaccharidic chain, such as that of the LPS derived from Burkholderia multivorans, liposomes coexist with elongated micellar aggregates, whose population decreases if a typical phospholipid, such as dioleoyl phosphatidylethanolamine (DOPE) is introduced in the liposome formulation. The effect of temperature has also been considered: for all the considered LPS an extremely smooth transition of the acyl chain self-organization from a gel to a liquid crystalline phase is detected around 30-35 degrees C. In the biological context, our results suggest that the rich biodiversity of LPS molecular structure could be fundamental to finely tune the structure and functional properties of the outer membrane of Gram negative bacteria.
lipopolysaccharides, structure, Burkholderia, lipid A, liposomes, glycolipid, outer membrane, Agrobacterium tumefaciens, phospholipid, phosphatidylethanolamine, bilayer
NCBI PubMed ID: 20852798Publication DOI: 10.1039/C0CP00066CJournal NLM ID: 100888160Publisher: Royal Society of Chemistry
Institutions: Department of Chemistry, University of Naples Federico II, Naples, Italy, Department of Organic Chemistry and Biochemistry, University of Naples “Federico II”, Naples, Italy, Institut für Festkörperforsching Forschungszentrum Jülich and Jülich Centre for Neutron Science, Garching bei M, Germany
Methods: light scattering, EPR, small-angle neutron scattering (SANS)
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5. Compound ID: 6713
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
EtN-(1--P--4)--+ | | | |
| | | | |
a-D-Galp-(1-6)-+ HEP-(1-7)-+ | | | | |
| | | | | | |
a-D-GlcpNAc-(1-2)-a-D-Glcp-(1-2)-a-D-Galp-(1-3)-a-D-Glcp-(1-3)-b-Hepp-(1-3)-b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| | |
P-?)-+ Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Ra-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_130693,IEDB_135394,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140092,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_176772,IEDB_190606,IEDB_534864,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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6. Compound ID: 6714
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
EtN-(1--P--4)--+ | | | |
| | | | |
a-D-Galp-(1-6)-+ HEP-(1-7)-+ | | | | |
| | | | | | |
a-D-Glcp-(1-2)-a-D-Galp-(1-3)-a-D-Glcp-(1-3)-b-Hepp-(1-3)-b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| | |
P-?)-+ Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rb1-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140092,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_176772,IEDB_190606,IEDB_534864,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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7. Compound ID: 6715
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
EtN-(1--P--4)--+ | | | |
| | | | |
a-D-Galp-(1-6)-+ HEP-(1-7)-+ | | | | |
| | | | | | |
a-D-Galp-(1-3)-a-D-Glcp-(1-3)-b-Hepp-(1-3)-b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| | |
P-?)-+ Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rb2-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140092,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_176772,IEDB_190606,IEDB_534864,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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8. Compound ID: 6716
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
EtN-(1--P--4)--+ | | | |
| | | | |
HEP-(1-7)-+ | | | | |
| | | | | |
a-D-Galp-(1-6)-a-D-Glcp-(1-3)-b-Hepp-(1-3)-b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| | |
P-?)-+ Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rb3-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140092,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_176772,IEDB_190606,IEDB_534864,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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9. Compound ID: 6717
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
EtN-(1--P--4)--+ | | | |
| | | | |
HEP-(1-7)-+ | | | | |
| | | | | |
a-D-Glcp-(1-3)-b-Hepp-(1-3)-b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| | |
P-?)-+ Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rc-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_176772,IEDB_534864,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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10. Compound ID: 6718
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
EtN-(1--P--4)--+ | | | |
| | | | |
a-D-Glcp-(1-3)-b-Hepp-(1-3)-b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| |
Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: RcP- -form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_176772,IEDB_534864,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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11. Compound ID: 6719
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
a-Kdop-(2-4)-a-Kdop-(2-4)-+ | | |
| | | |
b-Hepp-(1-3)-+ | | | |
| | | | |
EtN-(1--P--4)--b-Hepp-(1-5)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| |
Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rd1-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_176772,IEDB_534864
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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12. Compound ID: 6720
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
b-Hepp-(1-5)-+ | | |
| | | |
a-Kdop-(2-4)-a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| |
Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rd2-form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_176772,IEDB_534864
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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13. Compound ID: 6721
|
3HOMyr-(1-2)-+
|
P-4)-+ |
| |
Lau-(1-3)-R-3HOMyr-(1-2)-+ | |
| | |
b-Hepp-(1-3)-b-Hepp-(1-5)-+ | | |
| | | |
a-Kdop-(2-4)-a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1-P
| |
Myr-(1-3)-R-3HOMyr-(1-3)-+ 3HOMyr-(1-3)-+ |
Show graphically |
Structure type: oligomer
Trivial name: Rd1P- -form LPS
Compound class: LPS
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_135394,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_176772,IEDB_534864
The structure is contained in the following publication(s):
- Article ID: 3043
Kato N, Arakawa Y, Sugiyama T, Ito H, Naito S, Kido N, Ohta M, Sasaki K "Crystallization and analyses of crystals of various chemotypes of R-form lipopolysaccharides from Salmonella spp." -
Microbiology and Immunology 38 (1994) 629-637
Various chemotypes (Re, Rd2, Rd1P-, Rd1, RcP-, Rc, Rb3, Rb2, Rb1, and Ra) of R-form lipopolysaccharides (LPSs) of Salmonella spp. were crystallized by treatment with 70% ethanol containing 250 mM MgCl2, and crystals of the LPSs were observed electron microscopically and analyzed by electron diffraction and synchrotron X-ray diffraction. All the LPSs tested formed three-dimensional crystals showing very similar shapes; hexagonal plate, solid column, discoid, square or rectangular plate, lozenge plate and truncated hexangular or rectangular pyramid forms. Electron diffraction patterns from the hexagonal plate crystals of all these LPSs obtained by electron irradiation from the direction perpendicular to the basal plane showed that they consist of hexagonal lattices with the lattice constant of 4.62 A. The crystals of all the LPSs thus formed gave ring-like X-ray diffraction patterns because of their small sizes. The long-axis values were calculated from the X-ray diffraction patterns from crystals of all the LPSs in the low-angle region and they corresponded roughly to the length of the proposed primary chemical structures of the R cores of the LPSs. The volume occupied by a single molecule of all the LPSs were calculated from the molecular weights based on the proposed structures and the crystallographic data obtained by electron diffraction, X-ray diffraction, and density determination.
NCBI PubMed ID: 7799836Publication DOI: 10.1111/j.1348-0421.1994.tb01833.xJournal NLM ID: 7703966Publisher: Japanese Society For Bacteriology
Institutions: Department of Bacteriology, Nagoya University School of Medicine, Aichi, Japan
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14. Compound ID: 6723
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Ara4N-(1--P--4)--+
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EtN-(1--P--?)--a-Kdop-(2-?)-a-Kdop-(2-?)-+ |
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L-gro-a-D-manHepp-(1-7)-+ | |
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a-D-Galp-(1-6)-+ | EtN-(1---P---P---4)-+ | | LIP-(1-2)-+
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a-D-Galp-(1-3)-a-D-Glcp-(1-3)-L-gro-a-D-manHepp-(1-3)-L-gro-a-D-manHepp-(1-?)-a-Kdop-(2-6)-b-D-GlcpN-(1-6)-a-D-GlcpN-(1---P---P---1)-EtN-(?--/Ethanolamine/
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P-?)-+ LIP-(1-2)-+ |
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Structure type: oligomer
Aglycon: Ethanolamine
Compound class: LOS
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_130650,IEDB_130657,IEDB_130658,IEDB_130659,IEDB_130670,IEDB_133751,IEDB_135394,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_137777,IEDB_137778,IEDB_140088,IEDB_140092,IEDB_140529,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150760,IEDB_150901,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 3047
Helander IM, Kilpeläinen I, Vaara M "Increased substitution of phosphate groups in lipopolysaccharides and lipid A of the polymyxin-resistant pmrA mutants of Salmonella typhimurium: a 31P-NMR study" -
Molecular Microbiology 11 (1994) 481-487
De-O-acylated lipopolysaccharides (LPS) of three polymyxin-resistant Salmonella typhimurium pmrA mutants and their parent strains were analysed by 31P-NMR (nuclear magnetic resonance) in order to assess, in relation to polymyxin resistance, the types and degree of substitution of phosphates of the LPS and lipid A. In the pmrA mutant LPS phosphate diesters predominated over phosphate monoesters, whereas the latter were more abundant in the parent wild-type LPS. The increase in the proportion of phosphate diesters was traced to both the core oligosaccharide and the lipid A part. In the latter, the ester-linked phosphate at position 4' was to a large extent (79-88%) substituted with 4-amino-4-deoxy-L-arabinose, whereas in the wild-type LPS the 4'-phosphate was mainly present as monoester. In each LPS, regardless of the pmrA mutation, the glycosidically linked phosphate of lipid A was largely unsubstituted.
NCBI PubMed ID: 8152372Journal NLM ID: 8712028Publisher: Blackwell Publishing
Institutions: Department of Molecular Bacteriology, National Public Health Institute, Helsinki, Finland
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15. Compound ID: 6933
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a-Kdop-(2-8)-+ P-4)-+
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a-Kdop-(2-4)-a-Kdop-(2-4)-a-Kdop-(2-6)-b-D-GlcpNAc-(1-6)-a-D-GlcpNAc-(1---P---/BSA/ |
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Structure type: oligomer
Aglycon: BSA
Trivial name: neoglycoconjugate
Contained glycoepitopes: IEDB_130650,IEDB_130657,IEDB_130658,IEDB_130659,IEDB_130662,IEDB_135394,IEDB_135813,IEDB_137340,IEDB_140092,IEDB_141807,IEDB_150077,IEDB_150755,IEDB_150756,IEDB_150760,IEDB_150901,IEDB_150908,IEDB_151531,IEDB_151767,IEDB_151768,IEDB_151769,IEDB_156486,IEDB_156487,IEDB_164045
The structure is contained in the following publication(s):
- Article ID: 3163
Müller-Loennies S, Gronow S, Brade L, Mackenzie R, Kosma P, Brade H "A monoclonal antibody against a carbohydrate epitope in lipopolysaccharide differentiates Chlamydophila psittaci from Chlamydophila pecorum, Chlamydophila pneumoniae, and Chlamydia trachomatis" -
Glycobiology 16(3) (2006) 184-196
Lipopolysaccharide (LPS) of Chlamydophila psittaci but not of Chlamydophila pneumoniae or Chlamydia trachomatis contains a tetrasaccharide of 3-deoxy-α-D-manno-oct-2-ulopyranosonic acid (Kdo) of the sequence Kdo(2→8)[Kdo(2→4)]Kdo(2→4)Kdo. After immunization with the synthetic neoglycoconjugate antigen Kdo(2→8)[Kdo(2→4)]Kdo(2→4) Kdo-BSA, we obtained the mouse monoclonal antibody (mAb) S69-4 which was able to differentiate C. psittaci from Chlamydophila pecorum, C. pneumoniae, and C. trachomatis in double labeling experiments of infected cell monolayers and by enzyme-linked immunosorbent assay (ELISA). The epitope specificity of mAb S69-4 was determined by binding and inhibition assays using bacteria, LPS, and natural or synthetic Kdo oligosaccharides as free ligands or conjugated to BSA. The mAb bound preferentially Kdo(2→8)[Kdo(2→4)]Kdo(2→4)Kdo(2→4) with a K(d) of 10 microM, as determined by surface plasmon resonance (SPR) for the monovalent interaction using mAb or single chain Fv. Cross-reactivity was observed with Kdo(2→4)Kdo(2→4)Kdo but not with Kdo(2→8)Kdo(2→4)Kdo, Kdo disaccharides in 2→4- or 2→8-linkage, or Kdo monosaccharide. MAb S69-4 was able to detect LPS on thin-layer chromatography (TLC) plates in amounts of <10 ng by immunostaining. Due to the high sensitivity achieved in this assay, the antibody also detected in vitro products of cloned Kdo transferases of Chlamydia. The antibody can therefore be used in medical and veterinarian diagnostics, general microbiology, analytical biochemistry, and studies of chlamydial LPS biosynthesis. Further contribution to the general understanding of carbohydrate-binding antibodies was obtained by a comparison of the primary structure of mAb S69-4 to that of mAb S45-18 of which the crystal structure in complex with its ligand has been elucidated recently (Nguyen et al., 2003, Nat. Struct. Biol., 10, 1019-1025).
Kdo, diagnostic, neoglycoconjugate, immunofluorescence
NCBI PubMed ID: 16282606Publication DOI: 10.1093/glycob/cwj055Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: hebra@fz-borstel.de
Institutions: Research Center Borstel, Leibniz Center for Medicine and Biosciences, Borstel, Germany, Institute for Biological Sci-ences, National Research Council Canada, Ottawa, Ontario, Canada K1A 0R6, Department of Chemistry, University of Natural Resources and Applied Life Sciences, A-1190 Vienna, Austri
Methods: serological methods, genetic methods
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