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  • 1.
    Ali, Tara
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural determination of the O-antigenic polysaccharide from Escherichia coli O1662007Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 342, nr 2, s. 274-278Artikkel i tidsskrift (Fagfellevurdert)
  • 2.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Intramolecular aglycon delivery2008Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 343, nr 10-11, s. 1553-1573Artikkel, forskningsoversikt (Annet vitenskapelig)
  • 3.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Short synthesis of a benzyl ether protected building block for the synthesis of carbocyclic galactopyranose mimics2010Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, nr 8, s. 1056-1060Artikkel i tidsskrift (Fagfellevurdert)
  • 4.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Synthesis of carbasugar-containing non-glycosidically linked pseudodisaccharides and higher pseudooligosaccharides2009Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 17, s. 2285-2310Artikkel, forskningsoversikt (Fagfellevurdert)
  • 5.
    Cumpstey, Ian
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Alonzi, Dominic S.
    Butters, Terry D.
    Carbasugar-thioether pseudodisaccharides related to N-glycan biosynthesis2009Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 4, s. 454-459Artikkel i tidsskrift (Fagfellevurdert)
  • 6.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Li, Shengyu
    Yang, Zhennai
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the exopolysaccharide from Lactobacillus plantarum C88 using NMR spectroscopy and the program CASPER2015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 402, s. 87-94Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Some lactic acid bacteria, such as those of the Lactobacillus genus, have the ability to produce exopolysaccharides (EPSs) that confer favorable physicochemical properties to food and/or beneficial physiological effects on human health. In particular, the EPS of Lactobacillus plantarum C88 has recently demonstrated in vitro antioxidant activity and, herein, its structure has been investigated using NMR spectroscopy and the computer program CASPER (Computer Assisted Spectrum Evaluation of Regular polysaccharides). The pentasaccharide repeating unit of the O-deacetylated EPS consists of a trisaccharide backbone, -> 4)-alpha-DGalp-(1 -> 2)-alpha-D-Glcp-(1 -> 3)-beta-D-Glcp-(1 ->, with terminal D-Glc and D-Gal residues (1.0 and 0.8 equiv per repeating unit, respectively) extending from O3 and O6, respectively, of the -> 4)-alpha-D-Galp-(1 -> residue. In the native EPS an O-acetyl group is present, 0.85 equiv per repeating unit, at O2 of the alpha-linked galactose residue; thus the repeating unit of the EPS has the following structure: -> 4)[beta-D-Glcp-(1 -> 3)][beta-D-Galp-(1 -> 6)]alpha-D-Galp2Ac-(1 -> 2)-alpha-D-Glcp-(1 -> 3)-beta-D-Glcp-(1 ->. These structural features, and the chain length (similar to 10(3) repeating units on average, determined in a previous study), are expected to play an important role in defining the physicochemical properties of the polymer.

  • 7.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lundborg, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies and biosynthetic aspects of the o antigen polysaccharide from Escherichia coli o1742012Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 354, s. 102-105Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the repeating unit of the O-antigenic polysaccharide (PS) from Escherichia coli O174 has been determined. Component analysis together with H-1 and C-13 NMR spectroscopy experiments were employed to elucidate the structure. Inter-residue correlations were determined by H-1, C-13-heteronuclear multiple-bond correlation and H-1, H-1-NOESY experiments. The PS is composed of tetrasaccharide repeating units with the following structure: -> 4)-beta-D-GlcpA-(1 -> 3)-beta-D-Galp-(1 -> 3)-beta-D-GalpNAc-(1 -> vertical bar beta-D-GlcpNAc-(1 -> 2) Cross-peaks of low intensity were present in the NMR spectra consistent with a beta-D-GlcpNAc-(1 -> 2)-beta-D-GlcpA(1 -> structural element at the terminal part of the polysaccharide, which on average is composed of similar to 15 repeating units. Consequently the biological repeating unit has a 3-substituted N-acetyl-D-galactosamine residue at its reducing end.

  • 8.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies and biosynthetic aspects of the O-antigen polysaccharide from Escherichia coli O422015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 403, s. 174-181Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O42 has been investigated by NMR spectroscopy as the main method, which was complemented with sugar analysis, mass spectrometry, and analysis of biosynthetic information. The O-specific chain of the O-deacylated lipopolysaccharide (LPS-OH) consists of branched tetrasaccharide-glycerol repeating units joined by phosphodiester linkages. The lipid-free polysaccharide contains 0.8 equiv of O-acetyl groups per repeating unit and has the following teichoic acid-like structure: Based on biosynthetic aspects, this should also be the biological repeating unit. This O-antigen structure is remarkably similar to that of E. coli O28ac, differing only in the presence or absence, respectively, of a glucose residue at the branching point. The structural similarity explains the serological cross-reactivity observed between strains of these two serogroups, and also their almost identical O-antigen gene cluster sequences. -> 2)-(R)-Gro-(1-P-4)-beta-D-GlcpNAc-(1 -> 3)-beta-D-Galf2Ac-(1 -> 3)-alpha-D-GlcpNAc-(1 -> vertical bar a-D-Glcp-(1 -> 3)

  • 9.
    Fontana, Carolina
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zaccheus, Mona V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Ansaruzzaman, Mohammad
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of a polysaccharide from Vibrio parahaemolyticus strain AN-160002016Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 432, s. 41-49Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of a polysaccharide from Vibrio parahaemolyticus strain AN-16000 has been investigated. The sugar and absolute configuration analysis revealed D-Glc, D-GalN, D-QuiN and L-FucN as major components. The PS was subjected to dephosphorylation with aqueous 40% HF to obtain an oligosaccharide that was analyzed by H-1 and C-13 NMR spectroscopy. The HR-MS spectrum of the oligosaccharide revealed a pentasaccharide composed of two Glc residues, one QuiNAc and one GalNAc, one FucNAc, as well as a glycerol moiety. The structure of the PS was determined using H-1, C-13, N-15 and P-31 NMR spectroscopy; inter-residue correlations were identified by H-1, C-13-heteronuclear multiple-bond correlation, H-1, H-1-NOESY and H-1, P-31-hetero-TOCSY experiments. The PS backbone has the following teichoic acid-like structure: -> 3)-D-Gro-(1-P-6)-beta-D-Glcp-(1 -> 4)-alpha-L-FucpNAc-(1 -> 3)-beta-D-QuipNAc-(1 -> with a side-chain consisting of alpha-D-Glcp-(1 -> 6)-alpha-D-GalpNAc-(1 -> linked to the O3 position of the FucNAc residue.

  • 10. Foster, R. A.
    et al.
    Carlin, N. I. A.
    Majcher, M.
    Tabor, H.
    Ng, L.-K.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural elucidation of the O-antigen of the Shigella flexneri provisionalserotype 88-893: structural and serological similarities with S. flexneri provisional serotype Y394 (1c)2011Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 6, s. 872-876Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the repeating unit of the O-antigen polysaccharide from Shigella flexneri provisional serotype 88-893 has been determined. 1H and 13C NMR spectroscopy as well as 2D NMR experiments were employed to elucidate the structure. The carbohydrate part of the hexasaccharide repeating unit is identical to the previously elucidated structure of the O-polysaccharide from S. flexneri prov. serotype Y394. The O-antigen of S. flexneri prov. serotype 88-893 carries 0.7 mol O-acetyl group per repeating unit located at O-2 of the 3-substituted rhamnosyl residue, as identified by H2BC and BS-CT-HMBC NMR experiments. The O-antigen polysaccharide is composed of hexasaccharide repeating units with the following structure: →2)-α-l-Rhap-(1→2)-α-l-Rhap-(1→3)-α-l-Rhap2Ac-(1→3)[α-d-Glcp-(1→2)-α-d-Glcp-(1→4)]-β-d-GlcpNAc-(1→. Serological studies showed that type antigens for the two provisional serotypes are identical; in addition 88-893 expresses S. flexneri group factor 6 antigen. We propose that provisional serotypes Y394 and 88-893 be designated as two new serotypes 7a and 7b, respectively, in the S. flexneri typing scheme.

  • 11.
    Frigell, Jens
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK), Avdelningen för oorganisk kemi och strukturkemi.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Carbasugar analogues of galactofuranosides: beta-O-linked derivatives and towards beta-S-linked derivatives2011Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 11, s. 1277-1290Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A selectively protected carbasugar analogue of beta-galactofuranose was synthesised from glucose using ring-closing metathesis as the key step. The carbasugar was converted into an alpha-galacto configured 1,2-epoxide, which was an effective electrophile in Lewis acid catalysed coupling reactions with alcohols. The epoxide was opened with regioselective attack at C-1 to give beta-galacto configured C-1 ethers. Using carbohydrates as nucleophiles, we synthesised a number of pseudodisaccharides. The epoxide was also regioselectively opened at C-1 with a sulfur nucleophile under basic conditions to give a beta-galacto configured C-1 thioether.

  • 12.
    Gemma, Emiliano
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lahmann, Martina
    Oscarson, Stefan
    Synthesis of the tetrasaccharide α-D-Glcp-(1→3)-α-D-Manp-(1→2)-α-D-Manp-(1→2)-α-D-Manp recognised by Calreticulin/Calnexin2005Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 340, nr 16, s. 2558-2562Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The title compound as its methyl glycoside was efficiently synthesized using a block synthesis approach. Halide-assisted glycosidations between 6-O-acetyl-2,3,4-tri-O-benzyl-α-d-glucopyranosyl iodide and ethyl 2-O-acetyl-4,6-di-O-benzyl-1-thio-α-d-mannopyranoside using triphenylphosphine oxide as promoter yielded, with complete α-selectivity, a disaccharide building block in high yield. The perbenzylated derivative of this proved to be an excellent donor affording 88% of the protected target tetrasaccharide in an NIS/AgOTf-promoted coupling to a known methyl dimannoside acceptor. Deprotection through catalytic hydrogenolysis then gave the target compound in 47% overall yield.

  • 13.
    Jonsson, K. Hanna M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural determination of the O-antigenic polysaccharide from Escherichia coli O742009Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 12, s. 1592-1595Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O74 has been determined. Component analysis, together with 1H and 13C NMR spectroscopy as well as 1H,15N-HSQC experiments were employed to elucidate the structure. Inter-residue correlations were determined by 1H,1H-NOESY and 1H,13C-heteronuclear multiple-bond correlation experiments. The PS is composed of tetrasaccharide repeating units with the following structure:

    Full-size image (5K)

    Cross-peaks of low intensity from an α-linked N-acetylglucosamine residue were present in the NMR spectra, and spectral analysis indicates that they originate from the penultimate residue in the polysaccharide. Consequently, the biological repeating unit has a 3-substituted N-acetyl-d-glucosamine residue at its reducing end. The 1H, 13C and 15N NMR chemical shifts of the α- and β-anomeric forms of d-Fucp3NAc are also reported. The repeating unit of the E. coli O74 O-antigen is identical to that of the capsular polysaccharide from E. coli K45.

  • 14.
    Jonsson, K. Hanna M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the O-antigenic polysaccharide from Shigella dysenteriae type 3 and Escherichia coli O124, a reinvestigation2006Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 341, s. 2986-2989Artikkel i tidsskrift (Fagfellevurdert)
  • 15.
    Landström, Jens
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect2010Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, nr 2, s. 330-333Artikkel i tidsskrift (Fagfellevurdert)
  • 16.
    Lundborg, Magnus
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ali, Eunus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    An in silico virtual screening study for the design of norovirus inhibitors: fragment-based molecular docking and binding free energy calculations2013Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 378, s. 133-138Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Gastrointestinal infections caused by noroviruses may be prevented by the inhibition of their binding to histo-blood group carbohydrate antigens. A fragment-based virtual screening approach was used, employing docking followed by molecular dynamics simulations in order to enable binding free energy calculations using the linear interaction energy method. The resulting structures, composed of high-affinity fragments, can be a good starting point for lead optimizations and four molecules that pass both REOS and SYLVIA filters, which can remove known toxic features and assess the synthetic accessibility, respectively, are proposed as inhibitors.

  • 17.
    Mannerstedt, Karin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ekelöf, Kerstin
    Oscarson, Stefan
    Evaluation of Thioglycosides of Kdo as Glycosyl Donor2007Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 342, nr 3-4, s. 631-637Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The use of Kdo thioglycosides as glycosyl donors using DMTST, IBr/AgOTf and NIS/AgOTf as promoters has been evaluated. Activation at low temperature allowed to escape the formation of 2,3-glycal byproducts to give glycosides in high yield and with good β-anomeric selectivity. The use of diethyl ether as solvent and (especially) isopropylidene acetals as protecting groups improved the α-anomeric selectivity. NIS/AgOTf as promoter surprisingly yielded the 3-iodo-product via the glycal intermediate.

  • 18.
    Olsson, Johan D.M.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Oscarson, Stefan
    Synthesis of phosphorylated 3,4-branched trisaccharides corresponding to LPS inner core structures of Neisseria meningitidis and Haemophilus influenzae2010Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, nr 10, s. 1331-1338Artikkel i tidsskrift (Fagfellevurdert)
  • 19.
    Olsson, Ulrika
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural determination of the O-antigenic polysaccharide from the verocytotoxin-producing Escherichia coli O1762008Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 343, nr 4, s. 805-809Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O176 has been determined. Component analysis together with H-1 and C-13 NMR spectroscopy was employed to elucidate the structure. Inter-residue correlations were determined by H-1,H-1 NOESY and H-1, C-13 heteronuclear multiple-bond correlation experiments. The PS is composed of tetrasaccharide repeating units with the following structure: -> 4)-alpha-D-Manp-(1 -> 2)-alpha-D-Manp-(1 -> 2)-beta-D-Manp-(1 -> 3)-alpha-D-GalpNAc-(-> Cross-peaks of low intensity from alpha-linked mannopyranosyl residues were present in the H-1, H-1 TOCSY NMR spectra and further analysis of these showed that they originate from the terminal part of the polysaccharide. Consequently, the biological repeating unit has a 3-substituted N-acetyl-D-galactosamine residue at its reducing end. The repeating unit of the E coli O176 O-antigen is similar to those from E coli 017 and 077, thereby explaining the reported cross-reactivities between the strains, and identical to that of Salmonella cerro (O:6, 14, 18).

  • 20. Perepelov, Andrei V.
    et al.
    Shashkov, Alexander S.
    Guo, Xi
    Filatov, Andrei V.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Knirel, Yuriy A.
    Structure and genetics of the O-antigen of Escherichia coli O169 related to the O-antigen of Shigella boydii type 62015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 414, s. 46-50Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The O-polysaccharide (O-antigen) of Escherichia coli O169 was studied by sugar analysis along with 1D and 2D H-1 and C-13 NMR spectroscopy. The following structure of the branched hexasaccharide repeating unit was established: [GRAPHICS] The O-polysaccharide of E. coli O169 differs from that of Shigella boydii type 6 only in the presence of a side-chain glucose residue. A comparison of the O-antigen biosynthesis gene clusters between the galF to gnd genes in the genomes of the two bacteria revealed their close relationship. The glycosyltransferase gene responsible for the formation of the beta-D-Glcp-(1 -> 6)-alpha-D-Galp linkage in the O-antigen was identified in the gene cluster.

  • 21. Perepelov, Andrei V.
    et al.
    Wang, Quan
    Filatov, Andrei V.
    Xia, Xianghong
    Shashkov, Alexander S.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wang, Lei
    Knirel, Yuriy A.
    Structures and gene clusters of the closely related O-antigens of Escherichia coli O46 and O134, both containing D-glucuronoyl-D-allothreonine2015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 409, s. 20-24Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The O-polysaccharides (O-antigens) were isolated by mild acid degradation of the lipopolysaccharide (LPS) of Escherichia coli O46 and O134. The structures of their linear tetrasaccharide repeating units were established by sugar analysis along with 1D and 2D H-1 and C-13 NMR spectroscopy: [GRAPHICS] where D-aThr indicates D-allothreonine and R indicates O-acetyl substitution (similar to 70% on aThr and similar to 15% on GalNAc) in E. coli O46 whereas the O-acetylation is absent in E. coli O134. Functions of genes in the essentially identical O-antigen gene clusters of E. coli O46 and O134 were tentatively assigned by a comparison with sequences in available databases and found to be in agreement with the O-polysaccharide structures established.

  • 22.
    Roslund, Mattias U.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Säwén, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Landström, Jens
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Rönnols, Jerk
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Jonsson, K. Hanna M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Lundborg, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Svensson, Mona V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Complete 1H and 13C NMR chemical shift assignments of mono-, di-, and trisaccharides as basis for NMR chemical shift predictions of polysaccharides using the computer program CASPER2011Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 11, s. 1311-1319Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The computer program casper uses 1H and 13C NMR chemical shift data of mono- to trisaccharides for the prediction of chemical shifts of oligo- and polysaccharides. In order to improve the quality of these predictions the 1H and 13C, as well as 31P when applicable, NMR chemical shifts of 30 mono-, di-, and trisaccharides were assigned. The reducing sugars gave two distinct sets of NMR resonances due to the α- and β-anomeric forms. In total 35 1H and 13C NMR chemical shift data sets were obtained from the oligosaccharides. One- and two-dimensional NMR experiments were used for the chemical shift assignments and special techniques were employed in some cases such as 2D 1H,13C-HSQC Hadamard Transform methodology which was acquired approximately 45 times faster than a regular t1 incremented 1H,13C-HSQC experiment and a 1D 1H,1H-CSSF-TOCSY experiment which was able to distinguish spin-systems in which the target protons were only 3.3 Hz apart. The 1H NMR chemical shifts were subsequently refined using total line-shape analysis with the PERCH NMR software. The acquired NMR data were then utilized in the casper program (http://www.casper.organ.su.se/casper/) for NMR chemical shift predictions of the O-antigen polysaccharides from Klebsiella O5, Shigella flexneri serotype X, and Salmonella arizonae O62. The data were compared to experimental data of the polysaccharides from the two former strains and the lipopolysaccharide of the latter strain showing excellent agreement between predicted and experimental 1H and 13C NMR chemical shifts.

  • 23.
    Rönnols, Jerk
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Fontana, Carolina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hamark, Christoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Angles d'Ortoli, Thibault
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ståhle, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zaccheus, Mona V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Säwén, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hahn, Liljan E.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Iqbal, Shahzad
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Complete H-1 and C-13 NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligosaccharides using the computer program CASPER2013Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 380, s. 156-166Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    H-1 and C-13 NMR chemical shift data are used by the computer program CASPER to predict chemical shifts of oligo- and polysaccharides. Three types of data are used, namely, those from monosaccharides, disaccharides, and trisaccharides. To improve the accuracy of these predictions we have assigned the H-1 and C-13 NMR chemical shifts of eleven monosaccharides, eleven disaccharides, twenty trisaccharides, and one tetrasaccharide; in total 43 compounds. Five of the oligosaccharides gave two distinct sets of NMR resonances due to the alpha- and beta-anomeric forms resulting in 48 H-1 and C-13 NMR chemical shift data sets. In addition, the pyranose ring forms of Neu5Ac were assigned at two temperatures, due to chemical shift displacements as a function of temperature. The H-1 NMR chemical shifts were refined using total line-shape analysis with the PERCH NMR software. H-1 and C-13 NMR chemical shift predictions were subsequently carried out by the CASPER program (http://www.casper.organ.su.se/casper/) for three branched oligosaccharides having different functional groups at their reducing ends, namely, a mannose-containing pentasaccharide, and two fucose-containing heptasaccharides having N-acetyllactosamine residues in the backbone of their structures. Good to excellent agreement was observed between predicted and experimental H-1 and C-13 NMR chemical shifts showing the utility of the method for structural determination or confirmation of synthesized oligosaccharides.

  • 24. Shashkov, Alexander S.
    et al.
    Wang, Tianwei
    Perepelov, Andrei V.
    Weintraub, Andrej
    Liu, Bin
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Knirel, Yuriy A.
    Structure elucidation and biosynthesis gene cluster organization of the O-antigen of Escherichia coli O1702015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 417, s. 11-14Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Enterotoxigenic Escherichia coli are causative agents of diarrhea in humans as well as animals, and E. coli O170 belongs to this virotype. Upon mild acid degradation of the lipopolysaccharide of E. coli O170, the branched O-polysaccharide chain was partially cleaved at beta-D-glactofuranosidic linkages to give multiple products, including a linear tetrasaccharide and oligomers thereof. Studies of the acid degradation products and O-deacylated lipopolysaccharide by 1D and 2D H-1 and C-13 NMR spectroscopy enabled elucidation of the following O-polysaccharide structure: -> 4)-beta-D-GlcpNAc-(1 -> 4)-beta-D-GlcpA-(1 -> 3)-beta-D-Galf-(1 -> 3)-beta-D-GlcNAc-(1 -> [GRAPHICS] beta-D-Galf Functions of genes in the O-antigen biosynthesis gene cluster were tentatively assigned and found to be in agreement with the O-polysaccharide structure.

  • 25. Shashkov, Alexander S.
    et al.
    Zhang, Wenwen
    Perepelov, Andrei V.
    Weintraub, Andrej
    Liu, Bin
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Knirel, Yuriy A.
    Structure of the O-polysaccharide of Escherichia coli O1322016Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 427, s. 44-47Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Mild acid degradation of the lipopolysaccharide of Escherichia coli O132 released its O-polysaccharide. Analysis by 1D and 2D H-1 and C-13 NMR spectroscopy prior and subsequent to O-deacetylation, in conjunction with sugar analysis, revealed a linear pentasaccharide repeating unit of the O-polysaccharide having the following structure: -> 2)-alpha-D-Galf-(1 -> 3)-alpha-L-Rhap2Ac-(1 -> 4)-alpha-D-Glcp-(1 -> 2)-alpha-L-Rhap-(1 -> 3)-beta-D-GlcpNAc-(1 -> Putative functions of genes in the O-antigen gene cluster of E. coli O132 are consistent with the O-polysaccharide structure.

  • 26.
    Svensson, Mona V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural elucidation of the O-antigenic polysaccharide from Escherichia coli O1752011Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 3, s. 449-453Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O175 has been elucidated. Component analysis together with 1H and 13C NMR spectroscopy experiments were used to determine the structure. Inter-residue correlations were determined by 1H,1H-NOESY, and 1H,13C-heteronuclear multiple-bond correlation experiments. The PS is composed of pentasaccharide repeating units with the following structure:

    →2)-α-d-Glcp-(1→4)-α-d-GlcpA-(1→3)-α-d-Manp-(1→2)-α-d-Manp-(1→3)-β-d-GalpNAc-(1→

    Cross-peaks of low intensity from an α-linked glucopyranosyl residue were present in the 1H,1H-TOCSY NMR spectra. The α-d-Glcp residue is suggested to originate from the terminal part of the polysaccharide and consequently the biological repeating unit has a 3-substituted N-acetyl-d-galactosamine residue at its reducing end. The repeating unit of the E. coli O175 O-antigen is similar to those from E. coli O22 and O83, both of which carry an α-d-Glcp-(1→4)-d-GlcpA structural element, thereby explaining the reported cross-reactivities between the strains.

  • 27.
    Svensson, Mona V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the O-antigenic polysaccharide from Escherichia coli O1772011Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 14, s. 2300-2303Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from Escherichia coli O177 has been determined. Component analysis together with 1H and 13C NMR spectroscopy experiments was used to determine the structure. Inter-residue correlations were determined by 1H,13C-heteronuclear multiple-bond correlation and 1H,1H-NOESY experiments. PS is composed of tetrasaccharide repeating units with the following structure:

    →2)-α-l-Rhap-(1→3)-α-l-FucpNAc-(1→3)-α-l-FucpNAc-(1→3)-β-d-GlcpNAc-(1→

    An α-l-Rhap residue is suggested to be present at the terminal part of the polysaccharide, which on average is composed of ∼20 repeating units, since the 1H and 13C chemical shifts of an α-linked rhamnopyranosyl group could be assigned by a combination of 2D NMR spectra. Consequently, the biological repeating unit has a 3-substituted N-acetyl-d-glucosamine residue at its reducing end. The repeating unit of the E. coli O177 O-antigen shares the →3)-α-l-FucpNAc-(1→3)-β-d-GlcpNAc-(1→ structural element with the O-antigen from E. coli O15 and this identity may then explain the reported cross-reactivity between the strains.

  • 28.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Roslund, Mattias
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Cumpstey, Ian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Synthesis and conformational analysis of carbasugar bioisosteres of alpha-L-iduronic acid and its methyl glycoside2010Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, nr 8, s. 984-993Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The synthesis of two novel carbasugar analogues of α-l-iduronic acid is described in which the ring-oxygen is replaced by a methylene group. In analogy with the conformational equilibrium described for α-l-IdopA, the conformation of the carbasugars was investigated by 1H and 13C NMR spectroscopy. Hadamard transform NMR experiments were utilised for rapid acquisition of 1H,13C-HSQC spectra and efficient measurements of heteronuclear long-range coupling constants. Analysis of 1H NMR chemical shifts and JH,H coupling constants extracted by a total-lineshape fitting procedure in conjunction with JH,C coupling constants obtained by three different 2D NMR experiments, viz., 1H,13C-HSQC-HECADE, J-HMBC and IPAP-HSQC-TOCSY-HT, as well as effective proton–proton distances from 1D 1H,1H T-ROE and NOE experiments showed that the conformational equilibrium 4C12S5a1C4 is shifted towards 4C1 as the predominant or exclusive conformation. These carbasugar bioisosteres of α-l-iduronic acid do not as monomers show the inherent flexibility that is anticipated to be necessary for biological activity.

  • 29.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Östervall, Jennie
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Landersjö, Clas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Edblad, Malin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Karolinska Univ Hosp, Div Clin Microbiol, Dept Lab Med, Karolinska Inst, Huddinge, Sweden .
    Ansaruzzaman, Mohammad
    Int Ctr Diarrhoeal Dis Res, Dhaka 1000, Bangladesh .
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the O-antigenic polysaccharide from Plesiomonas shigelloides strain AM365652012Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 348, s. 99-103Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the repeating unit of the O-antigenic polysaccharide from Plesiomonas shigelloides strain AM36565 has been determined. Component analysis and H-1 and C-13 NMR spectroscopy experiments were employed to elucidate the structure. Inter-residue correlations were determined by H-1,C-13 heteronuclear multiple-bond correlation, H-1-H-1-NOESY, and H-1,C-13-HSQC-H-1,H-1-NOESY experiments. The O-antigen polysaccharide is composed of repeating units with the following structure: -> 3)-alpha-L-Rhap-(1 -> 2)-alpha-L-Rhap-(1 -> 4)[(beta-D-GalpNAc-(1 -> 3)]-alpha-D-GlcpNAc-(1 ->, in which the monosaccharide side-chain substitutes the backbone in half of the repeating units. A matrix-assisted laser desorption/ionization mass spectrometry experiment suggested that the polysaccharide consists of two regions, one with tetrasaccharide repeating units and one with trisaccharide repeating units.

  • 30.
    Teodorović, Peter
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Slättegård, Rikard
    Oscarson, Stefan
    Improved Synthesis of 1,3,4,6-tetra-O-acetyl-2-Azido-2-deoxy-α-D-mannopyranose2005Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 340, nr 17, s. 2675-2676Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    By improved (anhydrous) work-up conditions of a triflate displacement reaction, the yield in the preparation of the versatile synthetic intermediate 1,3,4,6-tetra-O-acetyl-2-azido-2-deoxy-α-d-mannopyranose has been significantly enhanced. This important precursor is now available in three efficient steps from d-glucose.

  • 31. Thorsheim, Karin
    et al.
    Siegbahn, Anna
    Johnsson, Richard E.
    Stalbrand, Henrik
    Manner, Sophie
    Bartholomeyzik, Teresa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ellervik, Ulf
    Chemistry of xylopyranosides2015Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 418, s. 65-88Artikkel, forskningsoversikt (Fagfellevurdert)
    Abstract [en]

    Xylose is one of the few monosaccharidic building blocks that are used by mammalian cells. In comparison with other monosaccharides, xylose is rather unusual and, so far, only found in two different mammalian structures, i.e. in the Notch receptor and as the linker between protein and glycosaminoglycan (GAG) chains in proteoglycans. Interestingly, simple soluble xylopyranosides can not only initiate the biosynthesis of soluble GAG chains but also function as inhibitors of important enzymes in the biosynthesis of proteoglycans. Furthermore, xylose is a major constituent of hemicellulosic xylans and thus one of the most abundant carbohydrates on Earth. Altogether, this has spurred a strong interest in xylose chemistry. The scope of this review is to describe synthesis of xylopyranosyl donors, as well as protective group chemistry, modifications, and conformational analysis of xylose.

  • 32. Urbina, Felipe
    et al.
    Nordmark, Eva-Lisa
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Yang, Zhennai
    Weintraub, Andrej
    Scheutz, Flemming
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural elucidation of the O-antigenic polysaccharide from the enteroaggregative Escherichia coli strain 180/C3 and its immunochemical relationship with Escherichia coli O5 and O652005Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 340, nr 4, s. 645-650Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from the enteroaggregative Escherichia coli strain 180/C3 has been determined. Sugar and methylation analysis together with 1H and 13C NMR spectroscopy were the main methods used. The PS is composed of tetrasaccharide repeating units with the following structure:→2)-β-d-Quip3NAc-(1→3)-β-d-Ribf-(1→4)-β-d-Galp-(1→3)-α-d-GalpNAc-(1→Analysis of NMR data indicates that the presented sequence of sugar residues also represents the biological repeating unit of the O-chain. The structure is closely related to that of O-antigen polysaccharide from E. coli O5 and partially to that of E. coli O65. The difference between the O-antigen from the 180/C3 strain and that of E. coli O5 is the linkage to the d-Quip3NAc residue, which in the latter strain is 4-O-substituted. The E. coli O65 O-antigen contains as part of its linear pentasaccharide repeating unit a similar structural element, namely →4)-β-d-GalpA-(1→3)-α-d-GlcpNAc-(1→2)-β-d-Quip3NAc-(1→, thereby indicating that a common epitope could be present for the two polysaccharides. Monospecific anti-E. coli O5 rabbit serum did not distinguish between the two positional isomeric structures neither in slide agglutination nor in an indirect enzyme immunoassay. The anti-O65 serum did react with both the 180/C3 and O5 LPS showing a partial cross-reactivity.

  • 33.
    Vesely, Jan
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Rydner, Lina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Oscarson, Stefan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Variant synthetic pathway to glucuronic acid-containing di- and trisaccharide thioglycoside building blocks for continued synthesis of Cryptococcus neoformans capsular polysaccharide structures2008Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 343, nr 12, s. 2200-2208Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    An alternative pathway to glucuronic acid-containing di- and trisaccharide thioglycoside building blocks, suitable for the synthesis of Cryptococcus neoformans capsular polysaccharide structures, has been developed. As opposed to our earlier synthesis, this approach features the introduction of the glucuronic acid motif at the di- and trisaccharide level through oxidation of a glucose residue. This approach circumvents problems encountered in glycosylations with glucuronic acid donors and benzylation of glucuronic acid-containing derivatives. Selective protection of primary alcohols was obtained at the di- and trisaccharide stage using TBDMS or trityl protecting groups, respectively. After benzylation of the secondary hydroxyl groups and subsequent removal of the TBDMS or trityl group, oxidation of the free primary alcohols to carboxylic acids was performed in high yield using the TEMPO–BAIB reagent mixture, which does not tend to oxidize thioglycosides. The new approach requires a number of extra steps, but has proven to be more reliable and easily reproducible.

  • 34. Vilchez, Samuel
    et al.
    Lundborg, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Urbina, Felipe
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the O-antigenic polysaccharides from the enteroaggregative Escherichia coli strain 94/D4 and the international type strain Escherichia coli O822009Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 344, nr 18, s. 2528-2532Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The structure of the O-antigen polysaccharides (PS) from the enteroaggregative Escherichia coli strain 94/D4 and the international type strain E. coli O82 have been determined. Component analysis and 1H, 13C, and 31P NMR spectroscopy experiments were employed to elucidate the structure. Inter-residue correlations were determined by 1H, 13C-heteronuclear multiple-bond correlation, and 1H, 1H-NOESY experiments. d-GroA as a substituent is linked via its O-2 in a phosphodiester-linkage to O-6 of the α-d-Glcp residue. The PS is composed of tetrasaccharide repeating units with the following structure:

    →4)-α-d-Glcp6-(P-2-d-GroA)-(1→4)-β-d-Galp-(1→4)-β-d-Glcp-(1→3)-β-d-GlcpNAc-(1→

    Cross-peaks of low intensity from an α-d-Glcp residue were present in the NMR spectra and spectral analysis indicates that they originate from the terminal residue of the polysaccharide. Consequently, the biological repeating unit has a 3-substituted N-acetyl-d-glucosamine residue at its reducing end. Enzyme immunoassay using specific anti-E. coli O82 rabbit sera showed identical reactivity to the LPS of the two strains, in agreement with the structural analysis of their O-antigen polysaccharides.

  • 35.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    A perspective on the primary and three-dimensional structures of carbohydrates2013Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 378, s. 123-132Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Carbohydrates, in more biologically oriented areas referred to as glycans, constitute one of the four groups of biomolecules. The glycans, often present as glycoproteins or glycolipids, form highly complex structures. In mammals ten monosaccharides are utilized in building glycoconjugates in the form of oligo-(up to about a dozen monomers) and polysaccharides. Subsequent modifications and additions create a large number of different compounds. In bacteria, more than a hundred monosaccharides have been reported to be constituents of lipopolysaccharides, capsular polysaccharides, and exopolysaccharides. Thus, the number of polysaccharide structures possible to create is huge. NMR spectroscopy plays an essential part in elucidating the primary structure, that is, monosaccharide identity and ring size, anomeric configuration, linkage position, and sequence, of the sugar residues. The structural studies may also employ computational approaches for NMR chemical shift predictions (CASPER program). Once the components and sequence of sugar residues have been unraveled, the three-dimensional arrangement of the sugar residues relative to each other (conformation), their flexibility (transitions between and populations of conformational states), together with the dynamics (timescales) should be addressed. To shed light on these aspects we have utilized a combination of experimental liquid state NMR techniques together with molecular dynamics simulations. For the latter a molecular mechanics force field such as our CHARMM-based PARM22/SU01 has been used. The experimental NMR parameters acquired are typically H-1, H-1 cross-relaxation rates (related to NOEs), (3)JCH and (3)JCC trans-glycosidic coupling constants and H-1, C-13-and H-1, H-1-residual dipolar couplings. At a glycosidic linkage two torsion angles phi and psi are defined and for 6-substituted residues also the omega torsion angle is required. Major conformers can be identified for which highly populated states are present. Thus, in many cases a well-defined albeit not rigid structure can be identified. However, on longer timescales, oligosaccharides must be considered as highly flexible molecules since also anti-conformations have been shown to exist with H-C-O-C torsion angles of similar to 180 degrees, compared to syn-conformations in which the protons at the carbon atoms forming the glycosidic linkage are in close proximity. The accessible conformational space governs possible interactions with proteins and both minor changes and significant alterations occur for the oligosaccharides in these interaction processes. Transferred NOE NMR experiments give information on the conformation of the glycan ligand when bound to the proteins whereas saturation transfer difference NMR experiments report on the carbohydrate part in contact with the protein. It is anticipated that the subtle differences in conformational preferences for glycan structures facilitate a means to regulate biochemical processes in different environments. Further developments in the analysis of glycan structure and in particular its role in interactions with other molecules, will lead to clarifications of the importance of structure in biochemical regulation processes essential to health and disease.

  • 36.
    Zaccheus, Mona V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Broeker, Nina K.
    Lundborg, Magnus
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Uetrecht, Charlotte
    Barbirz, Stefanie
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the O‐antigen polysaccharide from Escherichia coli TD2158 having O18 serogroup specificity and aspects of its interaction with the tailspike endoglycosidase of the infecting bacteriophage HK6202012Inngår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 357, s. 118-125Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    We have analyzed the O-antigen polysaccharide of the previously uncharacterized Escherichia coli strain TD2158 which is a host of bacteriophage HK620. This bacteriophage recognizes and cleaves the polysaccharide with its tailspike protein (TSP). The polysaccharide preparation as well as oligosaccharides obtained from HK620TSP endoglycosidase digests were analyzed with NMR spectroscopy. Additionally, sugar analysis was performed on the O-antigen polysaccharide and MALDI-TOF MS was used in oligosaccharide analysis. The present study revealed a heterogeneous polysaccharide with a hexasaccharide repeating unit of the following structure: α-D-Glcp-(1→6|) →2)-α-L-Rhap-91→6)-α-D-Glcp-(1→4)-α-D-Ga|lp-(1→3)-α-D-GlcpNAc-(1→ β-D-Glcp/β-D-GlcpNAc-(1→3) A repeating unit with a D-GlcNAc substitution of D-Gal has been described earlier as characteristic for serogroup O18A1. Accordingly, we termed repeating units with D-Glc substitution at D-Gal as O18A2. NMR analyses of the polysaccharide confirmed that O18A1- and O18A2-type repeats were present in a 1:1 ratio. However, HK620TSP preferentially bound the D-GlcNAc-substituted O18A1-type repeating units in its high affinity binding pocket with a dissociation constant of 140 μM and disfavored the O18A2-type having a β-D-Glcp-(1→3)-linked group. As a result, in hexasaccharide preparations, O18A1 and O18A2 repeats were present in a 9:1 ratio stressing the clear preference of O18A1-type repeats to be cleaved by HK620TSP.

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