| 1. |
- Dorst, Kevin, 1992-, et al.
(författare)
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Conformational Preferences at the Glycosidic Linkage of Saccharides in Solution as Deduced from NMR Experiments and MD Simulations : Comparison to Crystal Structures
- 2024
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Ingår i: Chemistry - A European Journal. - 0947-6539 .- 1521-3765. ; 30:15
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Tidskriftsartikel (refereegranskat)abstract
- Glycans are central to information content and regulation in biological systems. These carbohydrate molecules are active either as oligo- or polysaccharides, often in the form of glycoconjugates. The monosaccharide entities are joined by glycosidic linkages and stereochemical arrangements are of utmost importance in determining conformation and flexibility of saccharides. The conformational preferences and population distributions at the glycosidic torsion angles phi and psi have been investigated for O-methyl glycosides of three disaccharides where the substitution takes place at a secondary alcohol, viz., in alpha-l-Fucp-(1 -> 3)-beta-d-Glcp-OMe, alpha-l-Fucp-(1 -> 3)-alpha-d-Galp-OMe and alpha-d-Glcp-(1 -> 4)-alpha-d-Galp-OMe, corresponding to disaccharide structural elements present in bacterial polysaccharides. Stereochemical differences at or adjacent to the glycosidic linkage were explored by solution state NMR spectroscopy using one-dimensional 1H,1H-NOESY NMR experiments to obtain transglycosidic proton-proton distances and one- and two-dimensional heteronuclear NMR experiments to obtain 3JCH transglycosidic coupling constants related to torsion angles phi and psi. Computed effective proton-proton distances from molecular dynamics (MD) simulations showed excellent agreement to experimentally derived distances for the alpha-(1 -> 3)-linked disaccharides and revealed that for the bimodal distribution at the psi torsion angle for the alpha-(1 -> 4)-linked disaccharide experiment and simulation were at variance with each other, calling for further force field developments. The MD simulations disclosed a highly intricate inter-residue hydrogen bonding pattern for the alpha-(1 -> 4)-linked disaccharide, including a nonconventional hydrogen bond between H5 ' in the glucosyl residue and O3 in the galactosyl residue, supported by a large downfield 1H NMR chemical shift displacement compared to alpha-d-Glcp-OMe. Comparison of population distributions of the glycosidic torsion angles phi and psi in the disaccharide entities to those of corresponding crystal structures highlighted the potential importance of solvation on the preferred conformation. The importance of solvation on the preferred conformation of saccharides in solution and in crystals is unraveled by solution-state NMR and computational MD studies of solvated disaccharides. Crystal structures containing solvated glycan structures have glycosidic linkage conformations similar to those of the carbohydrate molecules in solution.
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| 2. |
- Dorst, Kevin, 1992-, et al.
(författare)
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NMR chemical shift prediction and structural elucidation of linker-containing oligo- and polysaccharides using the computer program CASPER
- 2023
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Ingår i: Carbohydrate Research. - 0008-6215 .- 1873-426X. ; 533
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Tidskriftsartikel (refereegranskat)abstract
- Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can unravel and confirm their structures. An approach for efficient 1H and 13C NMR chemical shift assignments employed a parallel NOAH-10 measurement followed by NMR spin-simulation to refine the 1H NMR chemical shifts, as exemplified for a disaccharide with an azidoethyl group as an aglycone, the NMR chemical shifts of which have been used to enhance the quality of CASPER (http://www.casper.organ.su.se/casper/). The CASPER program has been further developed to aid characterization of linker-containing oligo- and polysaccharides, either by chemical shift prediction for comparison to experimental NMR data or as structural investigation of synthesized glycans based on acquired unassigned NMR data. The ability of CASPER to elucidate structures of linker-containing oligosaccharides is demonstrated and comparisons to assigned or unassigned NMR data show the utility of CASPER in supporting a proposed oligosaccharide structure. Prediction of NMR chemical shifts of an oligosaccharide, corresponding to the repeating unit of an O-antigen polysaccharide, having a linker as an aglycone and a non-natural substituent derivative thereof are presented to exemplify the diversity of structures handled. Furthermore, NMR chemical shift predictions of synthesized polysaccharides, corresponding to bacterial polysaccharides, containing a linker are described showing that in addition to oligosaccharide structures also polysaccharide structures having an aglycone spacer group can be analyzed by CASPER.
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| 3. |
- Dorst, Kevin, 1992-, et al.
(författare)
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On the influence of solvent on the stereoselectivity of glycosylation reactions
- 2024
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Ingår i: Carbohydrate Research. - 0008-6215 .- 1873-426X. ; 535
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Tidskriftsartikel (refereegranskat)abstract
- Methodology development in carbohydrate chemistry entails the stereoselective formation of C-O bonds as a key step in the synthesis of oligo- and polysaccharides. The anomeric selectivity of a glycosylation reaction is affected by a multitude of parameters, such as the nature of the donor and acceptor, activator/promotor system, temperature and solvent. The influence of different solvents on the stereoselective outcome of glycosylation reactions employing thioglucopyranosides as glycosyl donors with a non-participating protecting group at position 2 has been studied. A large change in selectivity as a function of solvent was observed and a correlation between selectivity and the Kamlet-Taft solvent parameter pi* was found. Furthermore, molecular modeling using density functional theory methodology was conducted to decipher the role of the solvent and possible reaction pathways were investigated.
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| 4. |
- Eriksson, Lars, 1960-, et al.
(författare)
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Crystal Structure of Methyl 3-O-α-D-Glucopyranosyl 2-Acetamido-2-Deoxy-α-D-Galactopyranoside Hydrate
- 2023
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Ingår i: Journal of Chemical Crystallography. - : Springer Science and Business Media LLC. - 1074-1542 .- 1572-8854. ; 53:3, s. 400-406
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Tidskriftsartikel (refereegranskat)abstract
- Methyl 3-O-α-D-glucopyranosyl 2-acetamido-2-deoxy-α-D-galactopyranoside as a monohydrate, C15H27NO11·H2O, crystallizes in space group P212121, with four molecules in the unit cell. It constitutes the methyl glycoside of the carbohydrate part of the teichoic acid type polysaccharide from Micrococcus sp. A1, in which the disaccharides are joined through phosphodiester linkages. The conformation of the disaccharide is described by the glycosidic torsion angles ϕ = − 31° and ψ = + 1°, and the hydroxymethyl groups of the constituent monosaccharides are present in the gg and gt conformations for the sugar residues having the gluco- and galacto-configuration, respectively. For the N-acetyl group at C2 of the galactosamine residue the torsion angle τH = 147°, i.e., the amide proton has an antiperiplanar relationship to H2 of the sugar ring. The structure shows extensive hydrogen bonding along the a-direction, including the water molecule, and forms sheets with hydrophilic interactions within the sheets as a result of hydrogen bonding between disaccharides as well as hydrophobic interactions between the sheets, in particular, amongst methyl groups of the N-acetyl group of the α-D-GalpNAc residue in the disaccharides.
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| 5. |
- Furevi, Axel, 1992-, et al.
(författare)
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Elucidation of the O-antigen structure of Escherichia coli O93 and characterization of its biosynthetic genes
- 2023
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Ingår i: Glycobiology. - : Oxford University Press (OUP). - 0959-6658 .- 1460-2423. ; 33:4, s. 289-300
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Tidskriftsartikel (refereegranskat)abstract
- The structure of the O-antigen from the international reference strain Escherichia coli O93:-:H16 has been determined. A nonrandom modal chain-length distribution was observed for the lipopolysaccharide, a pattern which is typical when long O-specific polysaccharides are expressed. By a combination of (i) bioinformatics information on the gene cluster related to O-antigen synthesis including putative function on glycosyl transferases, (ii) the magnitude of NMR coupling constants of anomeric protons, and (iii) unassigned 2D H-1, C-13-HSQC, and H-1,H-1-TOCSY NMR spectra it was possible to efficiently elucidate the structure of the carbohydrate polymer in an automated fashion using the computer program CASPER. The polysaccharide also carries O-acetyl groups and their locations were determined by 2D NMR experiments showing that similar to 1/2 of the population was 2,6-di-O-acetylated, similar to 1/4 was 2-O-acetylated, whereas similar to 1/4 did not carry O-acetyl group(s) in the 3-O-substituted mannosyl residue of the repeating unit. The structure of the tetrasaccharide repeating unit of the O-antigen is given by: -> 2)-beta-D-Manp-(1 -> 3)-beta-D-Manp2Ac6Ac-(1 -> 4)-beta-D-GlcpA-(1 -> 3)-alpha-D-GlcpNAc-(1 ->, which should also be the biological repeating unit and it shares structural elements with capsular polysaccharides from E. coli K84 and K50. The structure of the acidic O-specific polysaccharide from Cellulophaga baltica strain NN015840(T) differs to that of the O-antigen from E. coli O93 by lacking the O-acetyl group at O6 of the O-acetylated mannosyl residue.
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| 6. |
- Widmalm, Göran, 1958-
(författare)
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Glycan Shape, Motions, and Interactions Explored by NMR Spectroscopy
- 2024
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Ingår i: JACS Au. - 2691-3704. ; 4:1, s. 20-39
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Forskningsöversikt (refereegranskat)abstract
- Glycans in the form of oligosaccharides, polysaccharides, and glycoconjugates are ubiquitous in nature, and their structures range from linear assemblies to highly branched and decorated constructs. Solution state NMR spectroscopy facilitates elucidation of preferred conformations and shapes of the saccharides, motions, and dynamic aspects related to processes over time as well as the study of transient interactions with proteins. Identification of intermolecular networks at the atomic level of detail in recognition events by carbohydrate-binding proteins known as lectins, unraveling interactions with antibodies, and revealing substrate scope and action of glycosyl transferases employed for synthesis of oligo- and polysaccharides may efficiently be analyzed by NMR spectroscopy. By utilizing NMR active nuclei present in glycans and derivatives thereof, including isotopically enriched compounds, highly detailed information can be obtained by the experiments. Subsequent analysis may be aided by quantum chemical calculations of NMR parameters, machine learning-based methodologies and artificial intelligence. Interpretation of the results from NMR experiments can be complemented by extensive molecular dynamics simulations to obtain three-dimensional dynamic models, thereby clarifying molecular recognition processes involving the glycans.
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| 7. |
- Wiseman, Benjamin, 1976-, et al.
(författare)
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Alternating L4 loop architecture of the bacterial polysaccharide co-polymerase WzzE
- 2023
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Ingår i: Communications Biology. - 2399-3642. ; 6:1
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Tidskriftsartikel (refereegranskat)abstract
- Lipopolysaccharides such as the enterobacterial common antigen are important components of the enterobacterial cell envelope that act as a protective barrier against the environment and are often polymerized by the inner membrane bound Wzy-dependent pathway. By employing cryo-electron microscopy we show that WzzE, the co-polymerase component of this pathway that is responsible for the length modulation of the enterobacterial common antigen, is octameric with alternating up-down conformations of its L4 loops. The alternating up-down nature of these essential loops, located at the top of the periplasmic bell, are modulated by clashing helical faces between adjacent protomers that flank the L4 loops around the octameric periplasmic bell. This alternating arrangement and a highly negatively charged binding face create a dynamic environment in which the polysaccharide chain is extended, and suggest a ratchet-type mechanism for polysaccharide elongation. Cryo-EM structure of bacterial polysaccharide co-polymerase WzzE provides insight into possible mechanisms of lipopolysaccharide elongation and length regulation.
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