Found 66 structures.
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1. Compound ID: 825
Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_885813
The structure is contained in the following publication(s):
- Article ID: 226
Winn AM, Wilkinson SG "Structure of the O16 antigen of Stenotrophomonas maltophilia" -
Carbohydrate Research 330(2) (2001) 279-283
A polysaccharide containing D-ribose, N-acetyl-D-glucosamine, and N-acetyl-D-mannosamine was isolated from the phenol-soluble lipopolysaccharide extracted from defatted cell walls of the reference strain (560) for serogroup O16 of Stenotrophomonas maltophilia. The results of methylation analysis, chemical degradations, and NMR spectroscopy showed that the polysaccharide is based on a branched trisaccharide repeating-unit of the structure shown below. Although ribose was absent from about half of the units in the isolated polymer, the regularity and spacing of the ladder observed on SDS-PAGE of the parent lipopolysaccharide indicate that this was an artefact of the mild acid hydrolysis used to release the polymer. On the other hand, the effects of mild alkaline hydrolysis on the polymer indicated partial O-acetylation.
Lipopolysaccharide, Stenotrophomonas maltophilia, O-specific polymer
NCBI PubMed ID: 11217982Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: s.g.wilkinson@chem.hull.ac.uk
Institutions: Department of Chemistry, Faculty of Science and the Environment, University of Hull, Hull HU6 7RX, UK
Methods: methylation, NMR, chemical degradation
- Article ID: 4329
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_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
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2. Compound ID: 1756
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a-D-Ribf-(1-4)-+
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-4)-a-D-Rhap-(1-3)-b-D-Manp-(1-4)-b-D-Manp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_137485,IEDB_1394181,IEDB_144983,IEDB_149136,IEDB_152206,IEDB_983930,SB_44,SB_72
The structure is contained in the following publication(s):
- Article ID: 544
Kocharova NA, Mieszala M, Zatonsky GV, Staniszewska M, Shashkov AS, Gamian A, Knirel YA "Structure of the O-polysaccharide of Citrobacter youngae O1 containing an a-D-ribofuranosyl group" -
Carbohydrate Research 339(2) (2004) 321-325
The lipopolysaccharide of Citrobacter youngae O1, strain PCM 1492 was degraded with acid or alkali under mild conditions, and the resultant polysaccharide was isolated by GPC and studied by sugar and methylation analyses and 1H and 13C NMR spectroscopies, including 2D COSY, TOCSY, NOESY and 1H, 13C HSQC experiments. The following structure of the branched tetrasaccharide repeating unit of the O-polysaccharide was established: [structure: see text] where substitution with the α-D-Ribf group is nonstoichiometric. This group occurs rarely in bacterial polysaccharides and is easily cleaved under mild acidic conditions. Studies with polyclonal rabbit antisera against whole cells of C. youngae PCM 1492 and PCM 1506 showed the serological identity of the lipopolysaccharides of C. youngae PCM 1492, PCM 1493 and PCM 1506, which are classified in serogroup O1.
Lipopolysaccharide, O-antigen, serological classification, enterobacteria, bacterial polysaccharide structure, Citrobacter youngae, a-D-Ribofuranose
NCBI PubMed ID: 14698890Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: gamian@immuno.iitd.pan.wroc.pl
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of Immunology of Infectious Diseases, L. Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wiegla 12, 53-114 Wroclaw, Poland
Methods: methylation, NMR-2D, NMR, sugar analysis
- Article ID: 1468
Knirel YA, Kocharova NA, Bystrova OV, Katzenellenbogen E, Gamian A "Structures and serology of the O-specific polysaccharides of bacteria of the genus Citrobacter" -
Archivum Immunologiae et Therapiae Experimentalis 50(6) (2002) 379-391
The review presents the structures of the O-specific polysaccharides (O-antigens) of the lipopolysaccharides isolated from over 25 Citrobacter strains, which represent different species and serogroups. The correlation between O-antigen structure and immunospecificity as well as numerous cross-reactions between Citrobacter and other enterobacterial species are discussed.
Lipopolysaccharide, structure, O-antigen, O-specific polysaccharide, serology, Citrobacter, immunospecificity
NCBI PubMed ID: 12546064Journal NLM ID: 0114365Publisher: Basel, Boston: Birkhaüser
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4329
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_3Publisher: Springer
Correspondence: knirel@ioc.ac.ru
Editors: Knirel YA, Valvano MA
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 4405
Tichaczek-Goska D, Witkowska D, Cisowska A, Jankowski S, Hendrich AB "The bactericidal activity of normal human serum against Enterobacteriaceae rods with lipopolysaccharides possessing O-antigens composed of mannan" -
Advances in Clinical and Experimental Medicine 21(3) (2012) 289-299
BACKGROUND: The susceptibility of bacteria to the bactericidal activity of serum depends on the structure and organization of the bacterial outer membrane. It is known that the structure of the O-specific polysaccharide chain of lipopolysaccharide (LPS) plays an important role in the resistance of bacteria to host immune defenses. OBJECTIVES: The susceptibility of rods belonging to Enterobacteriaceae family to the bactericidal activity of the normal human serum (NHS) was examined. The mechanisms of complement activation were also investigated. MATERIAL AND METHODS: The study was carried out on 15 strains containing LPSs with O-specific polysaccharides composed of mannan, belonging to the following species: Citrobacter freundii, C. werkmanii, C. braakii, C. youngae, Hafnia alvei, Escherichia coli and Klebsiella pneumoniae. The levels of C3 and C4 complement components, IgG and IgM immunoglobulin in NHS were examined using specific antibodies. The bactericidal activity of NHS and its preparations (HS50/20, HSMgEGTA) was determined. LPSs from E. coli 08 strains were analyzed by polyacrylamide gel electrophoresis (PAGE) in the presence of sodium dodecyl sulphate (SDS). RESULTS: Eleven strains were sensitive to NHS bactericidal activity, and four were resistant. Only one group of strains was fully susceptible to NHS action. In three other groups, both sensitive and resistant strains were found. The majority of the strains remained susceptible to NHS activity irrespective of which pathway of serum activity was blocked. All E. coli 08 strains contained smooth-type LPSs. CONCLUSIONS: Strains belonging to the same serotype showed variable susceptibility to the bactericidal action of normal human serum. Two mechanisms of the bactericidal activity of NHS have been identified.
O-antigen, mannan, human serum, bactericidal effect, complement system
NCBI PubMed ID: 23214191Journal NLM ID: 101138582Publisher: Wroclaw: The University
Correspondence: dorota.tichaczek-goska@am.wroc.pl
Institutions: Department of Biology and Medical Parasitology, Wroclaw Medical University, Wroclaw, Poland
Methods: serological methods
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3. Compound ID: 1860
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a-D-Ribf-(1-4)-+
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-3)-b-D-ManpNAc-(1-4)-b-D-GlcpNAc-(1-3)-b-D-ManpNAc-(1-4)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_885813
The structure is contained in the following publication(s):
- Article ID: 598
Altman E, Schäffer C, Brisson J, Messner P "Isolation and characterization of an amino sugar-rich glycopeptide from the surface layer glycoprotein of Thermoanaerobacterium thermosaccharolyticum E207-71" -
Carbohydrate Research 295 (1996) 245-253
No abstract
structure, characterization, surface, glycopeptide, Clostridium, glycoprotein, amino sugar, S layer, Thermoanaerobacterium
NCBI PubMed ID: 9002194Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: altman@biologysx.lan.nrc.ca
Institutions: Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ont., Canada K1A OR6, Zentrum fur Ultrastrukturforschung und Ludwig Boltzmann-lnstitut fur Molekulare Nanotechnologie, Universitat fur Bodenkultur, A-1180 Vienna, Austria
Methods: methylation, periodate oxidation, NMR-2D, TLC, Smith degradation, HPAEC-PAD, colorimetry
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4. Compound ID: 2353
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R-Lac-(2-3)-b-D-GlcpA-(1-6)-+ a-D-Ribf-(1-3)-+
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-4)-b-D-Glcp-(1-4)-a-D-Galp-(1-4)-b-D-Glcp-(1-4)-b-D-Xylp-(1- |
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Structure type: polymer chemical repeating unit
Compound class: EPS
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_151528,IEDB_167188,IEDB_174332,IEDB_190606,IEDB_423153,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 809
Helm RF, Huang Z, Edwards D, Leeson H, Peery W, Potts M "Structural characterization of the released polysaccharide of desiccation-tolerant Nostoc commune DRH-1" -
Journal of Bacteriology 182(4) (2000) 974-982
The structure of the viscous extracellular polysaccharide (glycan) of desiccation-tolerant Nostoc commune DRH-1 was determined through chromatographic and spectroscopic methods. The polysaccharide is novel in that it possesses a 1-4-linked xylogalactoglucan backbone with D-ribofuranose and 3-O-[(R)-1-carboxyethyl]-D-glucuronic acid (nosturonic acid) pendant groups. The presence of D-ribose and nosturonic acid as peripheral groups is unusual, and their potential roles in modulating the rheological properties of the glycan are discussed. Nosturonic acid was present in the glycans of N. commune from diverse geographic locations, suggesting that this uronic acid is an integral component of this cosmopolitan anhydrophile.
structural, characterization, polysaccharide
NCBI PubMed ID: 10648523Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: helmrf@vt.edu
Institutions: Fralin Biotechnology Center and Department of Biochemistry, Virginia Tech, Blacksburg, Virginia 24061-0346
Methods: periodate oxidation, NMR-2D, partial acid hydrolysis, NMR, MALDI-TOF MS, methanolysis, Li/ethylenediamine degradation
- Article ID: 6324
Uhliariková I, Matulová M, Košťálová Z, Lukavský J, Capek P "Lactylated acidic exopolysaccharide produced by the cyanobacterium Nostoc cf. linckia" -
Carbohydrate Polymers 276 (2022) 118801
Cyanobacteria produce a wide range of metabolites of interest for industrial or medical use. The cultivation of freshwater Nostoc cf. linckia yielded 5.4 g/L of a crude exopolysaccharide (cEPS) with a molecular weight of 1.31 × 105 g/mol. Ion-exchange chromatography of cEPS yielded two dominant fractions, EPS-1 and EPS-2, differing in molecular weight. The lower molecular weight fraction (EPS-1) was subjected to structural studies. Results of chemical and spectroscopic analyses showed that three of the four dominant sugars, glucose, galactose and xylose are 1,4-linked in the backbone in the following order: [→4)-β-D-Xylp-(1→4)-β-D-Glcp-(1→4)-α-D-Galp-(1→4)-β-D-Glcp-(1→]n. Terminal mannose residues were identified as side chains linked at C3 of every third backbone xylose and every second glucose is branched at C6 by 3-O-lactyl-β-D-glucuronic acid (nosturonic acid). Antioxidant properties of EPS were tested using two in vitro methods. Both assays showed that the cEPS was more active than purified EPS-1 and EPS-2 fractions and deproteinized EPS.
structure, acidic exopolysaccharide, Antioxidant activity, nosturonic acid, 3-O-lactyl-β-D-glucuronic acid, Nostoc cf.linckia
NCBI PubMed ID: 34823807Publication DOI: 10.1016/j.carbpol.2021.118801Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: P. Capek
Institutions: Institute of Chemistry, Center for Glycomics, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia, Institute of Botany, National Centre of Competence, Academy of Sciences of the Czech Republic, Dukelská 135, CZ-37982 Třeboň, Czech Republic
Methods: 13C NMR, 1H NMR, methylation, NMR-2D, GC-MS, carboxyl reduction, statistical analysis, HR-ESI-MS, SEC-HPLC, antioxidant activity assay, cultivation, FRAP assay
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5. Compound ID: 4990
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a-D-Ribf-(1-4)-a-D-Glcp-(1-4)-b-D-Glcp-(1-6)-b-D-Glcp-(1-6)-b-D-Glcp-(1-4)-b-D-Glcp-(1-4)-b-D-Glcp-(1-3)-b-D-Galp |
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Structure type: oligomer
Compound class: EPS
Contained glycoepitopes: IEDB_135614,IEDB_136044,IEDB_137472,IEDB_140629,IEDB_141794,IEDB_141806,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_149136,IEDB_190606,IEDB_241101,IEDB_423115,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 1935
Morris VJ, Brownsey GJ, Gunning AP, Harris JE "Gelation of the extracellular polysaccharide produced by Agrobacterium rhizogenes" -
Carbohydrate Polymers 13 (1990) 221-225
It has been shown that the extracellular polysaccharide (EPS) produced by Agrobacterium rhizogenes will form thermoreversible gels. This EPS belongs to a family of polysaccharide structures all of which have the same backbone structure substituted with different side chains. The EPS produced by Rhizobium meliloti IFO 13336 also belongs to this family of structures and T. Harada (Biochem. Soc. Symp., 48 (1983) 97) has reported gelation of this polysaccharide. Thus it is possible that gelation is a common feature of this family of structures. Possible biological and ecological consequences of gelation are discussed.
structure, Rhizobium, Rhizobium leguminosarum, Agrobacterium, extracellular polysaccharides, ecological, gelation
Publication DOI: 10.1016/0144-8617(90)90085-7Journal NLM ID: 8307156Publisher: Elsevier
Institutions: AFRC Institute of Food Research, Norwich Laboratory, Norwich, UK
Methods: gelation, rheological study
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6. Compound ID: 6376
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a-D-Ribf-(1-23)-Subst1
Subst1 = 3-formyl-rifamycin SV = SMILES C[C@@]([C@@](O)([H])[C@@]({23}[C@](O)([H])[C@@]([C@@](OC(C)=O)([H])[C@]([C@](OC)([H])/C=C/O[C@@]1(C(C2=C(O1)C(C)=C(O)C3=C(O)C4=C(C=O)C(O)=C32)=O)C)([H])C)([H])C)([H])C)([H])/C=C/C=C(\C(O)=N\4)C |
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Structure type: monomer
Contained glycoepitopes: IEDB_149136
The structure is contained in the following publication(s):
- Article ID: 2875
Dabbs ER, Yazawa K, Mikami Y, Miyaji M, Morisaki N, Iwasaki S, Furihata K "Ribosylation by mycobacterial strains as a new mechanism of rifampin inactivation" -
Antimicrobial Agents and Chemotherapy 39 (1995) 1007-1009
Several fast-growing Mycobacterium strains were found to inactivate rifampin. Two inactivated compounds (RIP-Ma and RIP-Mb) produced by these organisms were different from previously reported derivatives, i.e., phosphorylated or glucosylated derivatives, of the antibiotic. The structures of RIP-Ma and RIP-Mb were determined to be those of 3-formyl-23-[O-(α-D-ribofuranosyl)]rifamycin SV and 23-[O-(α-D-ribofuranosyl)]rifampin, respectively. To our knowledge, this is the first known example of ribosylation as a mechanism of antibiotic inactivation.
NCBI PubMed ID: 7785970Publication DOI: 10.1128/aac.39.4.1007Journal NLM ID: 0315061Institutions: Division of Experimental Chemotherapy, Chiba University, Japan
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7. Compound ID: 6377
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a-D-Ribf-(1-23)-Subst
Subst = rifampin = SMILES CO[C@H]1/C=C/O[C@@]5(C)Oc4c(C)c(O)c3c(O)c(NC(=O)/C(C)=C/C=C/[C@H](C)[C@H](O)[C@@H](C){23}[C@@H](O)[C@@H](C)[C@H](OC(C)=O)[C@@H]1C)c(/C=N\N2CCN(C)CC2)c(O)c3c4C5=O |
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Structure type: monomer
Contained glycoepitopes: IEDB_149136
The structure is contained in the following publication(s):
- Article ID: 2875
Dabbs ER, Yazawa K, Mikami Y, Miyaji M, Morisaki N, Iwasaki S, Furihata K "Ribosylation by mycobacterial strains as a new mechanism of rifampin inactivation" -
Antimicrobial Agents and Chemotherapy 39 (1995) 1007-1009
Several fast-growing Mycobacterium strains were found to inactivate rifampin. Two inactivated compounds (RIP-Ma and RIP-Mb) produced by these organisms were different from previously reported derivatives, i.e., phosphorylated or glucosylated derivatives, of the antibiotic. The structures of RIP-Ma and RIP-Mb were determined to be those of 3-formyl-23-[O-(α-D-ribofuranosyl)]rifamycin SV and 23-[O-(α-D-ribofuranosyl)]rifampin, respectively. To our knowledge, this is the first known example of ribosylation as a mechanism of antibiotic inactivation.
NCBI PubMed ID: 7785970Publication DOI: 10.1128/aac.39.4.1007Journal NLM ID: 0315061Institutions: Division of Experimental Chemotherapy, Chiba University, Japan
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8. Compound ID: 10256
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b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-4)-b-D-GlcpNAc-(1-5)-a-D-Ribf-(1--/(->?) folic acid/ |
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Structure type: oligomer
Aglycon: (->?) folic acid
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_149136,IEDB_151531,IEDB_153212,IEDB_241099,IEDB_423114,SB_74,SB_85
The structure is contained in the following publication(s):
- Article ID: 4246
White RH "Structures of the modified folates in the extremely thermophilic archaebacterium Thermococcus litoralis" -
Journal of Bacteriology 175 (1993) 3661-3663
The chemical structures of the two modified folates present in Thermococcus litoralis were established. These compounds, each containing a core structure of 1-[4-[[1-(2-amino-7-methyl-4-oxo-6-pteridinyl)-ethyl]amino]phenyl]-1-deoxy-[1-α-D-ribofuranosyl]-ribitol, were characterized. The five position of the ribose in this core structure was β-linked to the C-1 of a poly-β(1→4)N-acetylglucosamine having a chain length of four or five N-acetylglucosamine residues. Thus, these compounds are N-acetylglucosamine homologs of the modified folates found in Pyrococcus furiosus.
NCBI PubMed ID: 8501071Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Institutions: Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308
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9. Compound ID: 12698
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EtN-(1--P--6)--+ EtN-(1--P--6)--+ EtN-(1--P--6)--+
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EtN-(1--P--6)--b-ManpNAc-(1-4)-b-ManpNAc-(1-4)-b-ManpNAc-(1-4)-b-ManpNAc-(1-4)-b-ManpN-(1-4)-b-Glcp-(1-?)-Gro
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a-Ribf-(1-3)-+ |
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Structure type: structural motif or average structure
Compound class: cell wall polysaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_241118,IEDB_885813,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5049
Vinogradov E, Aubry A, Logan SM "Structural characterization of wall and lipidated polysaccharides from Clostridium perfringens ATCC 13124" -
Carbohydrate Research 448 (2017) 88-94
Cell surface polysaccharides produced by C. perfringens ATCC 13124 were analyzed using NMR, chemical and immunological methods. Two distinct polymers were identified. The more abundant PS1 had a structure based on a polymer of β-mannosamine with a number of modifications, including varying levels of substitution at O-6 with PEtN, N-acetylation, and different linkages between monosaccharides. The shortest variant of PS1 represented a lipoteichoic acid. It contained only 1-4-linkages between ManNAc residues, minor branching α-Ribf, and glucosyl-glycerol at the reducing end, which was acylated with linear saturated fatty acids C16, C18, and C20 (dominant). Other non-lipidated variants of PS1 contained less PEtN, no α-Ribf, up to 50% 1-3-linkages, and up to 25% ManN with the free amino group. The minor polysaccharide PS2 had a linear regular structure with a -4-α-Rha-3-β-Gal-4-β-GalNAc3PCho- repeating unit, where PCho indicates phosphocholine.
structure, polysaccharide, NMR spectroscopy, Clostridium perfringens
NCBI PubMed ID: 28628892Publication DOI: 10.1016/j.carres.2017.06.003Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: Evguenii.Vinogradov@nrc-cnrc.gc.ca
Institutions: National Research Council of Canada, Vaccine Program, Human Health Therapeutics, Ottawa Canada, K1A OR6
Methods: 13C NMR, 1H NMR, NMR-2D, de-O-acylation, SDS-PAGE, sugar analysis, Western blotting, GPC, ion-exchange chromatography, HF treatment, N-acetylation, immunization, lysozyme treatment
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10. Compound ID: 12699
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EtN-(1--P--6)--+ EtN-(1--P--6)--+
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EtN-(1--P--6)--b-ManpNAc-(1-4)-b-ManpNAc-(1-4)-b-ManpNAc-(1-4)-b-ManpNAc-(1-4)-b-ManpN-(1-4)-b-Glcp-(1-?)-Gro
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a-Ribf-(1-3)-+ |
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Structure type: structural motif or average structure
Compound class: cell wall polysaccharide
Contained glycoepitopes: IEDB_120354,IEDB_123890,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_885813,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5049
Vinogradov E, Aubry A, Logan SM "Structural characterization of wall and lipidated polysaccharides from Clostridium perfringens ATCC 13124" -
Carbohydrate Research 448 (2017) 88-94
Cell surface polysaccharides produced by C. perfringens ATCC 13124 were analyzed using NMR, chemical and immunological methods. Two distinct polymers were identified. The more abundant PS1 had a structure based on a polymer of β-mannosamine with a number of modifications, including varying levels of substitution at O-6 with PEtN, N-acetylation, and different linkages between monosaccharides. The shortest variant of PS1 represented a lipoteichoic acid. It contained only 1-4-linkages between ManNAc residues, minor branching α-Ribf, and glucosyl-glycerol at the reducing end, which was acylated with linear saturated fatty acids C16, C18, and C20 (dominant). Other non-lipidated variants of PS1 contained less PEtN, no α-Ribf, up to 50% 1-3-linkages, and up to 25% ManN with the free amino group. The minor polysaccharide PS2 had a linear regular structure with a -4-α-Rha-3-β-Gal-4-β-GalNAc3PCho- repeating unit, where PCho indicates phosphocholine.
structure, polysaccharide, NMR spectroscopy, Clostridium perfringens
NCBI PubMed ID: 28628892Publication DOI: 10.1016/j.carres.2017.06.003Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: Evguenii.Vinogradov@nrc-cnrc.gc.ca
Institutions: National Research Council of Canada, Vaccine Program, Human Health Therapeutics, Ottawa Canada, K1A OR6
Methods: 13C NMR, 1H NMR, NMR-2D, de-O-acylation, SDS-PAGE, sugar analysis, Western blotting, GPC, ion-exchange chromatography, HF treatment, N-acetylation, immunization, lysozyme treatment
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11. Compound ID: 13161
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a-D-Ribf-(1-3)-+ a-D-Ribf-(1-3)-+ a-D-Ribf-(1-3)-+
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P-3)-b-D-Rhap-(1-4)-b-D-Rhap-(1-4)-{{{-b-D-Rhap-(1-4)-a-D-Glcp-(1-3)-b-D-Rhap-(1-4)-b-D-Rhap-(1-4)-}}}b-D-Rhap-(1-4)-a-D-Glcp-(1-3)-b-D-Rhap-(1-4)-b-D-Rhap-(1-4)-a-D-Rhap-(1-3)-a-D-Rhap-(1-3)-a-D-Rhap-(1-3)-b-D-Galp-(1-3)-Thr-(?--/tetrapeptide (Thr38, Thr, Gly, Ala)/ |
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Structure type: oligomer
Aglycon: tetrapeptide (Thr38, Thr, Gly, Ala)
Trivial name: S-layer glycan
Compound class: surface polysaccharide
Contained glycoepitopes: IEDB_136044,IEDB_137472,IEDB_1394181,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_145010,IEDB_146664,IEDB_149136,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 5205
Richards E, Bouché L, Panico M, Arbeloa A, Vinogradov E, Morris H, Wren B, Logan SM, Del A, Fairweather NF "The S-layer protein of a Clostridium difficile SLCT-11 strain displays a complex glycan required for normal cell growth and morphology" -
Journal of Biological Chemistry 293(47) (2018) 18123-18137
Clostridium difficile is a bacterial pathogen that causes major health challenges worldwide. It has a well-characterized surface (S)-layer, a para-crystalline proteinaceous layer surrounding the cell wall. In many bacterial and archaeal species, the S-layer is glycosylated, but no such modifications have been demonstrated in C. difficile. Here, we show that a C. difficile strain of S-layer cassette type 11, Ox247, has a complex glycan attached via an O-linkage to Thr-38 of the S-layer low-molecular-weight subunit. Using MS and NMR, we fully characterized this glycan. We present evidence that it is composed of three domains: (i) a core peptide-linked tetrasaccharide with the sequence -4-α-Rha-3-α-Rha-3-α-Rha-3-β-Gal-peptide; (ii) a repeating pentasaccharide with the sequence -4-β-Rha-4-α-Glc-3-β-Rha-4-(α-Rib-3-)β-Rha-; and (iii) a nonreducing end-terminal 2,3 cyclophosphoryl-rhamnose attached to a ribose-branched sub-terminal rhamnose residue. The Ox247 genome contains a 24-kb locus containing genes for synthesis and protein attachment of this glycan. Mutations in genes within this locus altered or completely abrogated formation of this glycan, and their phenotypes suggested that this S-layer modification may affect sporulation, cell length, and biofilm formation of C. difficile In summary, our findings indicate that the S-layer protein of SLCT-11 strains displays a complex glycan and suggest that this glycan is required for C. difficile sporulation and control of cell shape, a discovery with implications for the development of antimicrobials targeting the S-layer.
genetics, microbiology, virulence, cell wall, glycosylation, surface layer, Glycomics, Clostridium difficile, nuclear magnetic resonance (NMR), mass spectrometry (MS), Glycoproteomics, glycoprotein structure
NCBI PubMed ID: 30275012Publication DOI: 10.1074/jbc.RA118.004530Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: a.dell@imperial.ac.uk; n.fairweather@imperial.ac.uk
Institutions: From the Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom, the Vaccine Program, Human Health Therapeutics Research Centre, National Research Council, Ottawa, Ontario K1A 0R6, Canada, Biopharmaspec, Suite 3.1, Lido Medical Centre, St. Saviours Road, JE2 7LA Jersey, United Kingdom, the London School of Hygiene and Tropical Medicine, WC1E 7HT, London, United Kingdom
Methods: 13C NMR, 1H NMR, gel filtration, NMR-2D, GC-MS, SDS-PAGE, sugar analysis, DNA techniques, anion-exchange chromatography, MS/MS, LC-ESI-MS, MALDI-TOF/TOF MS, biofilm assays, bioinformatics analysis, adhesion assays, sporulation assays
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12. Compound ID: 13162
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a-D-Ribf-(1-3)-+ a-D-Ribf-(1-3)-+
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P-3:2)-b-D-Rhap-(1-4)-b-D-Rhap-(1-4)-{{{-b-D-Rhap-(1-4)-a-D-Glcp-(1-3)-b-D-Rhap-(1-4)-b-D-Rhap-(1-4)-}}}/n=8/-a-D-Rhap-(1-3)-a-D-Rhap-(1-3)-a-D-Rhap-(1-3)-b-D-Galp-(1--/tetrapeptide (Thr38, Thr, Gly, Ala)/ |
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Structure type: oligomer
Aglycon: tetrapeptide (Thr38, Thr, Gly, Ala)
Trivial name: S-layer glycan
Compound class: surface polysaccharide
Contained glycoepitopes: IEDB_136044,IEDB_137472,IEDB_1394181,IEDB_141794,IEDB_142488,IEDB_144998,IEDB_145010,IEDB_146664,IEDB_149136,IEDB_190606,IEDB_983931,SB_165,SB_166,SB_187,SB_192,SB_195,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 5205
Richards E, Bouché L, Panico M, Arbeloa A, Vinogradov E, Morris H, Wren B, Logan SM, Del A, Fairweather NF "The S-layer protein of a Clostridium difficile SLCT-11 strain displays a complex glycan required for normal cell growth and morphology" -
Journal of Biological Chemistry 293(47) (2018) 18123-18137
Clostridium difficile is a bacterial pathogen that causes major health challenges worldwide. It has a well-characterized surface (S)-layer, a para-crystalline proteinaceous layer surrounding the cell wall. In many bacterial and archaeal species, the S-layer is glycosylated, but no such modifications have been demonstrated in C. difficile. Here, we show that a C. difficile strain of S-layer cassette type 11, Ox247, has a complex glycan attached via an O-linkage to Thr-38 of the S-layer low-molecular-weight subunit. Using MS and NMR, we fully characterized this glycan. We present evidence that it is composed of three domains: (i) a core peptide-linked tetrasaccharide with the sequence -4-α-Rha-3-α-Rha-3-α-Rha-3-β-Gal-peptide; (ii) a repeating pentasaccharide with the sequence -4-β-Rha-4-α-Glc-3-β-Rha-4-(α-Rib-3-)β-Rha-; and (iii) a nonreducing end-terminal 2,3 cyclophosphoryl-rhamnose attached to a ribose-branched sub-terminal rhamnose residue. The Ox247 genome contains a 24-kb locus containing genes for synthesis and protein attachment of this glycan. Mutations in genes within this locus altered or completely abrogated formation of this glycan, and their phenotypes suggested that this S-layer modification may affect sporulation, cell length, and biofilm formation of C. difficile In summary, our findings indicate that the S-layer protein of SLCT-11 strains displays a complex glycan and suggest that this glycan is required for C. difficile sporulation and control of cell shape, a discovery with implications for the development of antimicrobials targeting the S-layer.
genetics, microbiology, virulence, cell wall, glycosylation, surface layer, Glycomics, Clostridium difficile, nuclear magnetic resonance (NMR), mass spectrometry (MS), Glycoproteomics, glycoprotein structure
NCBI PubMed ID: 30275012Publication DOI: 10.1074/jbc.RA118.004530Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: a.dell@imperial.ac.uk; n.fairweather@imperial.ac.uk
Institutions: From the Department of Life Sciences, Imperial College London, SW7 2AZ London, United Kingdom, the Vaccine Program, Human Health Therapeutics Research Centre, National Research Council, Ottawa, Ontario K1A 0R6, Canada, Biopharmaspec, Suite 3.1, Lido Medical Centre, St. Saviours Road, JE2 7LA Jersey, United Kingdom, the London School of Hygiene and Tropical Medicine, WC1E 7HT, London, United Kingdom
Methods: 13C NMR, 1H NMR, gel filtration, NMR-2D, GC-MS, SDS-PAGE, sugar analysis, DNA techniques, anion-exchange chromatography, MS/MS, LC-ESI-MS, MALDI-TOF/TOF MS, biofilm assays, bioinformatics analysis, adhesion assays, sporulation assays
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13. Compound ID: 13261
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a-Ribf-(1-3)-+
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-4)-b-D-GlcpA2Me-(1-4)-b-Xylp-(1-3)-b-D-Glcp-(1-4)-b-Arap-(1- |
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Structure type: fragment of a bigger structure
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_167188,IEDB_174332,IEDB_423153,IEDB_581506,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5251
Jensen S, Petersen BO, Omarsdottir S, Paulsen BS, Duus JØ, Olafsdottir ES "Structural characterisation of a complex heteroglycan from the cyanobacterium Nostoc commune" -
Carbohydrate Polymers 91(1) (2013) 370-376
An alkali-extractable O-methylated ribofuranose-containing heteroglycan, Nc-5-s, was isolated from wild-growing field colonies of the cyanobacterium Nostoc commune collected in Iceland, using ethanol fractionation and anion-exchange chromatography. The average molecular weight was estimated to be 1500 kDa. Structural characterisation of the heteroglycan was performed by high-field NMR spectroscopy (1D proton, 2D-COSY, 2D-NOESY, 2D-TOCSY, 1H 13C-HSQC, HMBC, H2BC and HSQC-NOESY) as well as monosaccharide analysis after methanolysis by GC and supported by linkage analysis by GC-MS. According to the data obtained, the structure of Nc-5-s is composed of repeating units of 1, 1a, 1b and 2 and 2a in approximate molar ratio of (10:25:50:5:10). [structures]
structure elucidation, polysaccharides, cyanobacteria, Nostoc commune, high-field NMR
NCBI PubMed ID: 23044145Publication DOI: 10.1016/j.carbpol.2012.08.063Journal NLM ID: 8307156Publisher: Elsevier
Correspondence: Olafsdottir ES
Institutions: Carlsberg Laboratory, Copenhagen, Denmark, Faculty of Pharmaceutical Sciences, School of Health Sciences, University of Iceland, Hagi, Reykjavik, Iceland, Department of Pharmacognosy, Institute of Pharmacy, University of Oslo, Oslo, Norway
Methods: 13C NMR, 1H NMR, NMR-2D, partial acid hydrolysis, GC-MS, acid hydrolysis, ion-exchange chromatography, extraction, methylation analysis, NaBH4 reduction, HPGPC
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14. Compound ID: 13269
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/Variants 0/-+
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-4)-b-D-GlcpA2Me-(1-4)-b-Xylp-(1-3)-b-D-Glcp-(1-4)-b-Arap-(1-
/Variants 0/ is:
59%a-Ribf-(1-3)-
OR (exclusively)
29%a-Araf2Me-(1-3)- |
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Structure type: fragment of a bigger structure
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136907,IEDB_140630,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_167188,IEDB_174332,IEDB_423153,IEDB_581506,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 5254
Olafsdottir A, Thorlacius GE, Omarsdottir S, Olafsdottir ES, Vikingsson A, Freysdottir J, Hardardottir I "A heteroglycan from the cyanobacterium Nostoc commune modulates LPS-induced inflammatory cytokine secretion by THP-1 monocytes through phosphorylation of ERK1/2 and Akt" -
Phytomedicine 21(11) (2014) 1451-1457
Cyanobacteria (blue-green algae) have been consumed as food and used in folk medicine since ancient times to alleviate a variety of diseases. Cyanobacteria of the genus Nostoc have been shown to produce complex exopolysaccharides with antioxidant and antiviral activity. Furthermore, Nostoc sp. are common in cyanolichen symbiosis and lichen polysaccharides are known to have immunomodulating effects. Nc-5-s is a heteroglycan isolated from free-living colonies of Nostoc commune and its structure has been characterized in detail. The aim of this study was to determine the effects of Nc-5-s on the inflammatory response of lipopolysaccharide (LPS)-stimulated human THP-1 monocytes and how the effects are mediated. THP-1 monocytes primed with interferon-γ and stimulated with LPS in the presence of Nc-5-s secreted less of the pro-inflammatory cytokine interleukin (IL)-6 and more of the anti-inflammatory cytokine IL-10 than THP-1 monocytes stimulated without Nc-5-s. In contrast, Nc-5-s increased LPS-induced secretion of the pro-inflammatory cytokines tumor necrosis factor (TNF)-α and IL-8. Nc-5-s decreased LPS-induced phosphorylation of the extracellular regulated kinase (ERK)1/2 and Akt kinase, but did not affect phosphorylation of the p38 kinase, activation of the nuclear factor kappa B pathway, nor DNA binding of c-fos. These results show that Nc-5-s has anti-inflammatory effects on IL-6 and IL-10 secretion by THP-1 monocytes, but its effects are pro-inflammatory when it comes to TNF-α and IL-8. Furthermore, they show that the effects of Nc-5-s may be mediated through the ERK1/2 pathway and/or the Akt/phosphoinositide 3-kinase pathway and their downstream effectors. The ability of Nc-5-s to decrease IL-6 secretion, increase IL-10 secretion and moderate ERK1/2 activation indicates a potential for its development as an anti-inflammatory agent.
polysaccharides, Nostoc commune, IL-10 ERK1/2, IL-6, THP-1 cells
NCBI PubMed ID: 24877713Publication DOI: 10.1016/j.phymed.2014.04.023Journal NLM ID: 9438794Publisher: Stuttgart: Urban & Fischer Verlag
Correspondence: Hardardottir I
Institutions: Department of Biochemistry and Molecular Biology, Faculty of Medicine, Biomedical Center, University of Iceland, Iceland, Department of Immunology, Faculty of Medicine, Biomedical Center, University of Iceland, Iceland, Center for Rheumatology Research, Landspitali - The National University Hospital of Iceland, Iceland, Department of Immunology, Landspitali - The National University Hospital of Iceland, Iceland, Faculty of Pharmaceutical Sciences, University of Iceland, Iceland
Methods: Western blotting, ion-exchange chromatography, extraction, cytokine assay, HPGPC
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15. Compound ID: 14550
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a-D-Ribf-(1-3)-+
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R-Lac-(2-3)-b-D-GlcpA-(1-6)-b-D-Glcp-(1-4)-a-D-Galp-(1-4)-b-D-Glcp-(1-4)-b-D-Xylp |
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Structure type: oligomer
Compound class: EPS
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_136906,IEDB_137472,IEDB_140630,IEDB_141794,IEDB_142488,IEDB_146664,IEDB_149136,IEDB_151528,IEDB_167188,IEDB_174332,IEDB_190606,IEDB_423153,IEDB_983931,SB_192,SB_7
The structure is contained in the following publication(s):
- Article ID: 5775
Gonzales KN, Troncoso OP, Torres FG, Lopez D "Molecular α-relaxation process of exopolysaccharides extracted from Nostoc commune cyanobacteria" -
International Journal of Biological Macromolecules 161 (2020) 1516-1525
Broadband dielectric spectroscopy was used to investigate the molecular a-relaxation of the exopolysaccharides (EPS) extracted from Nostoc commune cyanobacteria. The EPS were modified in different ways. EPS were carboxymethylated to obtain carboxymethyl-exopolysaccharides (CEPS). EPS and CEPS were doped with ammonium iodide and 1-butyl-3-methylimidazolium chloride. An a relaxation process was observed for all specimens. The temperature dependence of the relaxation times for pure and doped, EPS and CEPS polymers exhibited non-Arrhenius behavior. This relaxation process was associated with the glass transition of the complex heteropolysaccharides produced by the cyanobacteria. The molecular mobility at the glass transition, Tg, was affected by both the carboxymethylation treatment and the doping. The fragility index also decreased for the doped specimens, which may be attributed to an increase in the mobility of the polymer chains due to the plasticizing effect of the doping agents.
exopolysaccharides, engineering, carboxymethylation, Nostoc commune, α-Relaxation, BDS, doping
NCBI PubMed ID: 32755710Publication DOI: 10.1016/j.ijbiomac.2020.07.268Journal NLM ID: 7909578Publisher: Butterworth-Heinemann
Correspondence: Fernando G. Torres
Institutions: Department of Mechanical Engineering, Pontificia Universidad Católica del Perú (Lima 32 Perú). Av. Universitaria 1801, Lima 32, Lima, Peru, Institute of Polymer Science and Technology, Spanish Council for Scientific Research (ICTP-CSIC), Madrid, Spain
Methods: GLC-MS, X-ray, sugar analysis, FTIR, SEM, carboxymethylation, DSC, broadband dielectric spectroscopy (BDS)
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