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  • 101. Naidoo, Kevin J.
    et al.
    Gamieldien, M. Riedaa
    Yu-Jen Chen, Jeff
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Maliniak, Arnold
    Glucose orientation and dynamics in α-, β-, and γ-cyclodextrins2008Ingår i: The Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 112, nr 47, s. 15151–15157-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We investigate, using molecular dynamics (MD) computer simulations, the conformational behavior of α-, β-, and γ-cyclodextrins (CDs). Our analysis of a 30 ns trajectory of CD solution dynamics reveals the underlying conformational behaviours of the CDs that explain their relative flexibility. The distributions of the torsion angles related to the glycosidic linkages, P(ϕ,ψ) were calculated for the three CDs. Most noticeable is the limited range in ϕ torsion rotations compared with ψ rotations for all the CDs. This difference between the three CDs is amplified in the motion and dynamics of their glucose monomers when we monitor their orientational and librational positions relative to the macrocyclic mean plane. The relaxation times of the monomers to their equilibrium orientations follow the pattern γ-CD > α-CD > β-CD. The root-mean-square deviations of the motion of the monomer centers of mass from the mean macrocyclic planes exhibit the same trend.

  • 102. Nazarenko, E. L.
    et al.
    Perepelov, A. V.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Shevchenko, L. S.
    Daeva, E. D.
    Ivanova, E. P.
    Shashkov, A. S.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structure of the O-specific polysaccharide from Shewanella japonica KMM 3601 containing 5,7-diacetamido-3,5,7,9-tetradeoxy-ᴅ-glycero-ᴅ-talo-non-2-ulosonic acid2011Ingår i: Biochemistry (Moscow), ISSN 0006-2979, E-ISSN 1608-3040, Vol. 76, nr 7, s. 791-796Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Structure of the O-specific polysaccharide chain of the lipopolysaccharide (LPS) of Shewanella japonica KMM 3601 was elucidated. The initial and O-deacylated LPS as well as a trisaccharide representing the O-deacetylated repeating unit of the O-specific  polysaccharide were studied by sugar analysis along with 1H and 13C NMR spectroscopy. The polysaccharide was found to contain a rare higher sugar, 5,7-diacetamido-3,5,7,9-tetradeoxy-ᴅ-glycero-ᴅ-talo-non-2-ulosonic acid (a derivative of 4-epilegionaminic acid, 4eLeg). The following structure of the trisaccharide repeating unit was established:

    →4)-α-4eLegp5Ac7Ac-(2→4)-β-ᴅ-GlcpA3Ac-(1→3)-β-ᴅ-GalpNAc-(1→.

  • 103. Norris, Scott E.
    et al.
    Landström, Jens
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Bull, Thomas E.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Freedberg, Darón I.
    Transient hydrogen bonding in uniformly 13C,  15N labeled carbohydrates in water2012Ingår i: Biopolymers, ISSN 0006-3525, E-ISSN 1097-0282, Vol. 97, nr 3, s. 145-154Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We report NMR studies of transient hydrogen bonding in a polysaccharide (PS) dissolved in water without cosolvent at ambient temperature. The PS portion of the Escherichia coli O142 lipopolysaccharide is comprised of repeating pentasaccharide units of GalNAc (N-acetyl galactosamine), GlcNAc (N-acetyl glucosamine), and rhamnose in a 3:1:1 ratio, respectively. A 105-ns molecular dynamics (MD) simulation on one pentasaccharide repeat unit predicts transient inter-residue hydrogen bonds from the GalNAc NH groups in the PS. To investigate these predictions experimentally, the PS was uniformly 13C,15N enriched and the NH, carbonyl, C2, C4, and methyl resonances of the GalNAc and GlcNAc residues assigned using through-bond triple-resonance NMR experiments. Temperature dependence of amide NH chemical shifts and one-bond NH J couplings support that NH groups on two of the GalNAc residues are donors in transient hydrogen bonds. The remaining GalNAc and GlcNAc NHs do not appear to be donors from either temperature-dependent chemical shifts or one-bond NH J couplings. These results substantiate the presence of weak or partial hydrogen bonds in carbohydrates, and that MD simulations of repeating units in PSs provide insight into overall PS structure and dynamics.

  • 104. Novoa-Carballal, Ramón
    et al.
    Säwén, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Fernandez-Megia, Eduardo
    Correa, Juan
    Riguera, Ricardo
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    The dynamics of GATG glycodendrimers by NMR diffusion and quantitative 13C relaxation2010Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 12, nr 25, s. 6587-6589Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The dynamics of GATG glycodendrimers have been investigated by NMR translational diffusion and quantitative 13C relaxation studies (Lipari-Szabo model-free), allowing the determination of the correlation times describing the dendrimer segmental orientational mobility.

  • 105.
    Olsson, Johan D M
    et al.
    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.
    Oscarson, Stefan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Synthesis of and molecular dynamics simulations on a tetrasaccharide corresponding to the repeating unit of the capsular polysaccharide from Salmonella enteritidis2009Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 7, nr 8, s. 1612-1618Artikel i tidskrift (Refereegranskat)
  • 106.
    Olsson, Ulrika
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Säwén, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Stenutz, Roland
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conformational flexibility and dynamics of two (1→6)-linked disaccharides related to an oligosaccharide epitope expressed on malignant tumour cells2009Ingår i: Chemistry - A European Journal, ISSN 0947-6539, E-ISSN 1521-3765, Vol. 15, nr 35, s. 8886-8894Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The conformational flexibility and dynamics of two (1→6)-linked disaccharides that are related to the action of the glycosyl transferase GnT-V have been investigated. NMR NOE and T-ROE spectroscopy experiments, conformation-dependent coupling constants and molecular dynamics (MD) simulations were used in the analyses. To facilitate these studies, the compounds were synthesised as α-d-[6-13C]-Manp-OMe derivatives, which reduced the 1H NMR spectral overlap and facilitated the determination of two- and three-bond 1H,1H, 1H,13C and 13C,13C-coupling constants. The population distribution for the glycosidic ω torsion angle in α-d-Manp-(1→6)-α-d-Manp-OMe for gt/gg/tg was equal to 45:50:5, whereas in α-d-Manp-OMe it was determined to be 56:36:8. The dynamic model that was generated for β-d-GlcpNAc-(1→6)-α-d-Manp-OMe by MD simulations employing the PARM22/SU01 CHARMM-based force field was in very good agreement with experimental observations. β-d-GlcpNAc-(1→6)-α-d-Manp-OMe is described by an equilibrium of populated states in which the ϕ torsion angle has the exo-anomeric conformation, the ψ torsion angle an extended antiperiplanar conformation and the ω torsion angle a distribution of populations predominantly between the gauchetrans and the gauchegauche conformational states (i.e., gt/gg/tg) is equal to 60:35:5, respectively. The use of site-specific 13C labelling in these disaccharides leads to increased spectral dispersion, thereby making NMR spectroscopy based conformational analysis possible that otherwise might be difficult to attain.

  • 107.
    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 O1762008Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 343, nr 4, s. 805-809Artikel i tidskrift (Refereegranskat)
    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).

  • 108. Patel, Dhilon S.
    et al.
    Park, Soohyung
    Wu, Emilia L.
    Yeom, Min Sun
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Klauda, Jeffery B.
    Im, Wonpil
    Influence of Ganglioside GM1 Concentration on Lipid Clustering and Membrane Properties and Curvature2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, nr 9, s. 1987-1999Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Gangliosides are a class of glycosphingolipids (GSLs) with amphiphilic character that are found at the outer leaflet of the cell membranes, where their ability to organize into special domains makes them vital cell membrane components. However, a molecular understanding of GSL-rich membranes in terms of their clustered organization, stability, and dynamics is still elusive. To gain molecular insight into the organization and dynamics of GSL-rich membranes, we performed all-atom molecular-dynamics simulations of bicomponent ganglioside GM1 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers with varying concentrations of GM1 (10%, 20%, and 30%). Overall, the simulations show very good agreement with available experimental data, including x-ray electron density profiles along the membrane normal, NMR carbohydrate proton-proton distances, and x-ray crystal structures. This validates the quality of our model systems for investigating GM1 clustering through an ordered-lipid-cluster analysis. The increase in GM1 concentration induces tighter lipid packing, driven mainly by inter-GM1 carbohydrate-carbohydrate interactions, leading to a greater preference for the positive curvature of GM1-containing membranes and larger cluster sizes of ordered-lipid clusters (with a composite of GM1 and POPC). These clusters tend to segregate and forma large percolated cluster at a 30% GM1 concentration at 293 K. At a higher temperature of 330 K, however, the segregation is not maintained.

  • 109. Patel, Dhilon S.
    et al.
    Pendrill, Robert
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mallajosyula, Sairam S.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    MacKerell, Alexander D., Jr.
    Conformational Properties of alpha- or beta-(1 -> 6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments2014Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 118, nr 11, s. 2851-2871Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Conformational sampling for a set of 10 alpha- or beta-(1 -> 6)-linked oligosaccharides has been studied using explicit solvent Hamiltonian replica exchange (HREX) simulations and NMR spectroscopy techniques. Validation of the force field and simulation methodology is done by comparing calculated transglycosidic J coupling constants and proton-proton distances with the corresponding NMR data. Initial calculations showed poor agreement, for example, with >3 Hz deviation of the calculated (3)J(H5,H6R) values from the experimental data, prompting optimization of the omega torsion angle parameters associated with (1 -> 6)-linkages. The resulting force field is in overall good agreement (i.e., within similar to 0.5 Hz deviation) from experimental (3)J(H5,H6R) values, although some small limitations are evident. Detailed hydrogen bonding analysis indicates that most of the compounds lack direct intramolecular H-bonds between the two monosaccharides; however, minor sampling of the O6 center dot center dot center dot HO2' hydrogen bond is present in three compounds. The results verify the role of the gauche effect between O5 and O6 atoms in gluco- and manno-configured pyranosides causing the omega torsion angle to sample an equilibrium between the gt and gg rotamers. Conversely, galacto-configured pyranosides sample a population distribution in equilibrium between gt and tg rotamers, while the gg rotamer populations are minor. Water radial distribution functions suggest decreased accessibility to the O6 atom in the (1 -> 6)-linkage as compared to the O6' atom in the nonreducing sugar. The role of bridging water molecules between two sugar moieties on the distributions of omega torsion angles in oligosaccharides is also explored.

  • 110. Patel, Dhilon S.
    et al.
    Re, Suyong
    Wu, Emilia L.
    Qi, Yifei
    Klebba, Phillip E.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Yeom, Min Sun
    Sugita, Yuji
    Im, Wonpil
    Dynamics and Interactions of OmpF and LPS: Influence on Pore Accessibility and Ion Permeability2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 4, s. 930-938Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The asymmetric outer membrane of Gram-negative bacteria is formed of the inner leaflet with phospholipids and the outer leaflet with lipopolysaccharides (LPS). Outer membrane protein F (OmpF) is a trimeric porin responsible for the passive transport of small molecules across the outer membrane of Escherichia coli. Here, we report the impact of different levels of heterogeneity in LPS environments on the structure and dynamics of OmpF using all-atom molecular dynamics simulations. The simulations provide insight into the flexibility and dynamics of LPS components that are highly dependent on local environments, with lipid A being the most rigid and O-antigen being the most flexible. Increased flexibility of O-antigen polysaccharides is observed in heterogeneous LPS systems, where the adjacent O-antigen repeating units are weakly interacting and thus more dynamic, compared to homogeneous LPS systems in which LPS interacts strongly with each other with limited overall flexibility due to dense packing. The model systems were validated by comparing molecular-level details of interactions between OmpF surface residues and LPS core sugars with experimental data, establishing the importance of LPS core oligosaccharides in shielding OmpF surface epitopes recognized by monoclonal antibodies. There are LPS environmental influences on the movement of bulk ions (K+ and Cl-), but the ion selectivity of OmpF is mainly affected by bulk ion concentration.

  • 111.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Volpato, Andrea
    Zerbetto, Mirco
    Polimeno, Antonino
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and 13C NMR spin relaxation: conformational preferences of alpha-L-Rhap-alpha-(1 -> 2)-alpha-L-Rhap-OMe in water and dimethyl sulfoxide solutions2016Ingår i: Physical Chemistry, Chemical Physics - PCCP, ISSN 1463-9076, E-ISSN 1463-9084, Vol. 18, nr 4, s. 3086-3096Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide alpha-L-Rhap-alpha-(1 -> 2)-alpha-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-C-13]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)J(CH) and (3)J(CC) coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the psi torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The C-13 NMR spin relaxation parameters T-1, T-2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d(6) at two magnetic field strengths, with standard deviations <= 1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed C-13 relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of C-13 relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.

  • 112.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Eriksson, Lars
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för material- och miljökemi (MMK).
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Methyl 4-O-benzyl-alpha-l-rhamno-pyrano-side2014Ingår i: Acta Crystallographica Section E: Structure Reports Online, ISSN 1600-5368, E-ISSN 1600-5368, Vol. 70, s. o561-o562Artikel i tidskrift (Refereegranskat)
  • 113.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Jonsson, K. Hanna M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Glycan synthesis, structure, and dynamics: A selection2013Ingår i: Pure and Applied Chemistry, ISSN 0033-4545, E-ISSN 1365-3075, Vol. 85, nr 9, s. 1759-1770Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Glycan structural information is a prerequisite for elucidation of carbohydrate function in biological systems. To this end we employ a tripod approach for investigation of carbo hydrate 3D structure and dynamics based on organic synthesis; different experimental spectroscopy techniques, NMR being of prime importance; and molecular simulations using, in particular, molecular dynamics (MD) simulations. The synthesis of oligosaccharides in the form of glucosyl fluorides is described, and their use as substrates for the Lam16A E115S glucosyl synthase is exemplified as well as a conformational analysis of a cyclic beta-(1 -> 3)-heptaglucan based on molecular simulations. The flexibility of the N-acetyl group of aminosugars is by MD simulations indicated to function as a gatekeeper for transitions of glycosidic torsion angles to other regions of conformational space. A novel approach to visualize glycoprotein (GP) structures is presented in which the protein is shown by, for example, ribbons, but instead of stick or space-filling models for the carbohydrate portion it is visualized by the colored geometrical figures known as CFG representation in a 3D way, which we denote 3D-CFG, thereby effectively highlighting the sugar residues of the glycan part of the GP and the position(s) on the protein.

  • 114.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mutter, Shaun T.
    Mensch, Carl
    Barron, Laurence D.
    Blanch, Ewan W.
    Popelier, Paul L. A.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Johannessen, Christian
    Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity2019Ingår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 20, nr 5, s. 695-705Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

  • 115.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Säwén, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conformation and Dynamics at a Flexible Glycosidic Linkage Revealed by NMR Spectroscopy and Molecular Dynamics Simulations: Analysis of β-ʟ-Fucp-(1→6)-α-ᴅ-Glcp-OMe in Water Solution2013Ingår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 47, s. 14709-14722Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The intrinsic flexibility of carbohydrates facilitates different 3D structures in response to altered environments. At glycosidic (1 -> 46)-linkages, three torsion angles are variable, and herein the conformation and dynamics of beta-1.-Fucp-(1 -> 6)-alpha-D-Glcp-OMe are investigated using a combination of NMR spectroscopy and molecular dynamics (MD) simulations. The disaccharide shows evidence of conformational averaging for the psi and co torsion angles, best explained by a four-state conformational distribution. Notably, there is a significant population of conformations having psi = 85 degrees (clinal) in addition to those having psi = 180 degrees (anfiperiplanar). Moderate differences in C-13 R-1 relaxation rates are found to be best explained by axially symmetric tumbling in combination with minor differences in librational motion for the two residues, whereas the isomerization motions are occurring too slowly to significantly to the observed relaxation rates. The MD simulation was found to give a reasonably good agreement with experiment, especially with respect to diffusive properties, among which the rotational anisotropy, D parallel to/D parallel to, is found to be 2.35. The force field employed showed too narrow omega torsion angles in the gauche trans and gauche gauche states as well as overestimating the population of the gauche trans conformer. This information can subsequently be used in directing parameter developments and emphasizes the need for refinement of force fields for (1 -> 6)-linked carbohydrates.

  • 116.
    Pendrill, Robert
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sørensen, Ole W.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Suppressing one-bond homonuclear 13C,13C scalar couplings in the J-HMBC NMR experiment: application to 13C site-specifically labeled oligosaccharides2014Ingår i: Magnetic Resonance in Chemistry, ISSN 0749-1581, E-ISSN 1097-458X, Vol. 52, nr 3, s. 82-86Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Site-specific C-13 isotope labeling is a useful approach that allows for the measurement of homonuclear C-13,C-13 coupling constants. For three site-specifically labeled oligosaccharides, it is demonstrated that using the J-HMBC experiment for measuring heteronuclear long-range coupling constants is problematical for the carbons adjacent to the spin label. By incorporating either a selective inversion pulse or a constant-time element in the pulse sequence, the interference from one-bond C-13,C-13 scalar couplings is suppressed, allowing the coupling constants of interest to be measured without complications. Experimental spectra are compared with spectra of a nonlabeled compound as well as with simulated spectra. The work extends the use of the J-HMBC experiments to site-specifically labeled molecules, thereby increasing the number of coupling constants that can be obtained from a single preparation of a molecule.

  • 117. 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 62015Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 414, s. 46-50Artikel i tidskrift (Refereegranskat)
    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.

  • 118. 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-allothreonine2015Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 409, s. 20-24Artikel i tidskrift (Refereegranskat)
    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.

  • 119. Perepelov, Andrei V.
    et al.
    Weintraub, Andrej
    Liu, Bin
    Senchenkova, Sof'ya N.
    Shashkov, Alexander S.
    Feng, Lu
    Wang, Lei
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Knirel, Yuriy A.
    The O-polysaccharide of Escherichia coli O112ac has the same structure as that of Shigella dysenteriae type 2 but is devoid of O-acetylation: a revision of the S. dysenteriae type 2 O-polysaccharide structure2008Ingår i: Carbohydrate Research, ISSN 0008-6215, Vol. 343, nr 5, s. 977-981Artikel i tidskrift (Refereegranskat)
  • 120. Pope, Giovanna M.
    et al.
    Hung, Ivan
    Gan, Zhehong
    Mobarak, Hani
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Harper, James K.
    Exploiting C-13/N-14 solid-state NMR distance measurements to assign dihedral angles and locate neighboring molecules2018Ingår i: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, Vol. 54, nr 49, s. 6376-6379Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The RESPDOR NMR method rapidly provides multiple C-13/N-14 distance measurements in natural abundance solids. In this study, C-13/N-14 RESPDOR information is shown, for the first time, to provide accurate molecular conformation and to locate non-bonded neighboring molecules.

  • 121. Rademacher, Christoph
    et al.
    Landström, Jens
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sindhuwinata, Nora
    Palcic, Monica M.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Peters, Thomas
    NMR-based exploration of the acceptor binding site of human blood group B galactosyltransferase with molecular fragments2010Ingår i: Glycoconjugate Journal, ISSN 0282-0080, E-ISSN 1573-4986, Vol. 27, nr 3, s. 349-358Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A substantial body of work has been devoted to the design and synthesis of glycosyltransferase inhibitors. A major obstacle has always been the demanding chemistry. Therefore, only few potent and selective inhibitors are known to date. Glycosyltransferases possess two distinct binding sites, one for the donor substrate, and one for the acceptor substrate. In many cases binding to the donor site is well defined but data for acceptor binding is sparse. In particular, acceptor binding sites are often shallow, and in many cases the dimensions of the binding pocket are not well defined. One approach to glycosyltransferase inhibitors is to chemically link donor site and acceptor site ligands to generate high affinity binders. Here, we describe a novel approach to identify acceptor site ligands from a fragment library. We have chosen human blood group B galactosyltransferase (GTB) as a biologically important model target. The approach utilizes a combination of STD NMR, spin-lock filtered NMR experiments and surface plasmon resonance measurements. Following this route we have identified molecular fragments from a fragment library that bind to the acceptor site of GTB with affinities of the order of a natural acceptor substrate. Unlike natural substrates these fragments allow for straightforward chemical modifications and, therefore will serve as scaffolds for potent GTB inhibitors. In general, the approach described is applicable to any glycosyltransferase and may assist in the development of novel glycosyltransferase inhibitors.

  • 122. Rojas-Macias, Miguel A.
    et al.
    Ståhle, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Luetteke, Thomas
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Development of the ECODAB into a relational database for Escherichia coli O-antigens and other bacterial polysaccharides2015Ingår i: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 25, nr 3, s. 341-347Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Escherichia coli O-antigen database (ECODAB) is aweb-based application to support the collection of E. coli O-antigen structures, polymerase and flippase amino acid sequences, NMR chemical shift data of O-antigens as well as information on glycosyltransferases (GTs) involved in the assembly of O-antigen polysaccharides. The database content has been compiled from scientific literature. Furthermore, the system has evolved from being a repository to one that can be used for generating novel data on its own. GT specificity is suggested through sequence comparison with GTs whose function is known. The migration of ECODAB to a relational database has allowed the automation of all processes to update, retrieve and present information, thereby, endowing the system with greater flexibility and improved overall performance. ECODAB is freely available at http://www.casper.organ.su.se/ECODAB/. Currently, data on 169 E. coli unique O-antigen entries and 338 GTs is covered. Moreover, the scope of the database has been extended so that polysaccharide structure and related information from other bacteria subsequently can be added, for example, from Streptococcus pneumoniae.

  • 123.
    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 CASPER2011Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 11, s. 1311-1319Artikel i tidskrift (Refereegranskat)
    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.

  • 124. Rosén Klement, Maria L.
    et al.
    Öjemyr, Linda
    Tagscherer, Katrin E.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Wieslander, Åke
    Institutionen för biokemi och biofysik.
    A processive lipid glycosyltransferase in the small human pathogen Mycoplasma pneumoniae: involvement in host immune response2007Ingår i: Molecular Microbiology, ISSN 1365-2958, Vol. 65, nr 6, s. 1444-1457Artikel i tidskrift (Refereegranskat)
  • 125.
    Rönnols, Jerk
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Burkhardt, Anja
    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.
    pK(a)-Determination and Conformational Studies by NMR Spectroscopy of D-Altrose-Containing and other Pseudodisaccharides as Glycosidase Inhibitor Candidates2012Ingår i: European Journal of Organic Chemistry, ISSN 1434-193X, E-ISSN 1099-0690, nr 1, s. 74-84Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The pK(a) values of six amine-linked pseudodisaccharides have been determined by using an NMR-based titration method. The pK(a) varies significantly depending on the linkage position and is inversely correlated with the number of electronegative groups in the beta-position to the amino group. Four of the pseudodisaccharides contain alpha-altroside moieties, the conformations of which were determined in the protonated and neutral states, again by using NMR techniques. In the neutral state, 2-amino-2-deoxyaltrosides and 3-amino-3-deoxyaltrosides were both found to occupy C-4(1) and S-O(2) conformations. On protonation, little change in the population distribution was seen for the 3-amino-3-deoxyaltrosides, but for the 2-amino-2-deoxyaltrosides, a shift in equilibrium position towards the skew conformer (more than 80% populated) takes place, and also a small amount of the other chair conformer (i.e., C-1(4), approximately 10% populated) was observed. 3-Amino-3-deoxyaltrosides have been shown to act as glycosidase inhibitors and insights into conformational equilibria as a function of protonation state should facilitate the design of better glycosidase inhibitors based on flexible monosaccharide amines.

  • 126.
    Rönnols, Jerk
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Engström, Olof
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Schnupf, Udo
    Säwén, Elin
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Brady, John W.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Inter-residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations2019Ingår i: ChemBioChem (Print), ISSN 1439-4227, E-ISSN 1439-7633, Vol. 20, s. 2519-2528Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo- and polysaccharides linked to lipids and proteins. Their three-dimensional structure is defined by two or three torsion angles at each glycosidic linkage. In addition, transglycosidic hydrogen bonding between sugar residues may be important. Herein we investigate the presence of these inter-residue interactions by NMR spectroscopy in D2O/[D-6]DMSO (70:30) or D2O and by molecular dynamics (MD) simulations with explicit water as solvent for disaccharides with structural elements alpha-d-Manp-(1 -> 2)-d-Manp, beta-d-GlcpNAc-(1 -> 2)-d-Manp, and alpha-d-Glcp-(1 -> 4)-beta-d-Glcp, all of which have been suggested to exhibit inter-residue hydrogen bonding. For the disaccharide beta-d-GlcpNAc-(1 -> 2)-beta-d-Manp-OMe, the large extent of O5 '...HO3 hydrogen bonding as seen from the MD simulation is implicitly supported by the H-1 NMR chemical shift and (3)J(HO3,H3) value of the hydroxy proton. In the case of alpha-d-Glcp-(1 -> 4)-beta-d-Glcp-OMe, the existence of a transglycosidic hydrogen bond O2 '...HO3 was proven by the presence of a cross-peak in H-1,C-13 HSQC-TOCSY experiments as a result of direct TOCSY transfer between HO3 of the reducing end residue and H2 ' (detected at C2 ') of the terminal residue. The occurrence of inter-residue hydrogen bonding, albeit transient, is judged important for the stabilization of three-dimensional structures, which may be essential in maintaining a conformational state for carbohydrate-protein interactions of glycans to take place in biologically important environments.

  • 127.
    Rönnols, Jerk
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Manner, Sophie
    Ellervik, Ulf
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conformational effects due to stereochemistry and C3-substituents in xylopyranoside derivatives as studied by NMR spectroscopy2014Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 12, nr 40, s. 8031-8035Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Glycosaminoglycans contain a beta-D-xylopyranose residue at its reducing end, which links the polysaccharide to the protein in proteoglycans. 2-Naphthyl beta-D-xylopyranosides have shown inhibition of tumor growth and we herein investigate conformation and dynamics of compounds structurally and stereochemically modified at the C3 position as well as the influence of solvent. The 3-deoxygenated compound, the 3-C-methyl-substituted beta-D-xylopyranoside, beta-D-ribopyranoside, the 3-C-methyl-substituted beta-D-ribopyranoside as well as 2-naphthyl beta-D-xylopyranoside were analyzed by NMR spectroscopy. Conformational equilibria were dependent on the solvent of choice, either methanol-d(4) or chloroform-d, with mainly C-4(1) and C-1(4) conformations present but also skew conformations to some extent. Intramolecular hydrogen bonding was concluded to be important for the 3-C-methyl-substituted beta-D-xylopyranosides in the non-polar solvent. Dynamic NMR (DNMR) spectroscopy was carried out for the 3-deoxygenated compound, which at 25 degrees C in methanol-d(4) exists with equally populated states of the C-4(1) and the C-1(4) conformations, but at -100 degrees C only a few percent is present of the latter. Using C-13 NMR detection for DNMR, resonance lines were shown to broaden at -40 degrees C and to sharpen again below -90 degrees C, without the emergence of a second set of NMR resonances, a typical behavior for an unequally populated equilibrium. The enthalpy and entropy activation barriers were calculated and resulted in Delta H-double dagger = 47.3 kJ mol(-1) and Delta S-double dagger = 54 J mol(-1) K-1.

  • 128.
    Rönnols, Jerk
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Manner, Sophie
    Siegbahn, Anna
    Ellervik, Ulf
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Exploration of conformational flexibility and hydrogen bonding of xylosides in different solvents, as a model system for enzyme active site interactions2013Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 11, nr 33, s. 5465-5472Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The predominantly populated conformation of carbohydrates in solution does not necessarily represent the biologically active species; rather, any conformer accessible without too large an energy penalty may be present in a biological pathway. Thus, the conformational preferences of a naphthyl xyloside, which initiates in vivo synthesis of antiproliferative glycosaminoglycans, have been studied by using NMR spectroscopy in a variety of solvents. Equilibria comprising the conformations 4C12SO and 1C4 were found, with a strong dependence on the hydrogen bonding ability of the solvent. Studies of fluorinated analogues revealed a direct hydrogen bond from the hydroxyl group at C2 to the fluorine atom at C4 by a 1hJF4,HO2 coupling. Hydrogen bond directionality was further established via comparisons of fluorinated levoglucosan molecules.

  • 129.
    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 CASPER2013Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 380, s. 156-166Artikel i tidskrift (Refereegranskat)
    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.

  • 130.
    Rönnols, Jerk
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Walvoort, Marthe T. C.
    van der Marel, Gijsbert A.
    Codee, Jeroen D. C.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Chair interconversion and reactivity of mannuronic acid esters2013Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 11, nr 46, s. 8127-8134Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Mannopyranosyluronic acids display a very unusual conformation behavior in that they often prefer to adopt a C-1(4) chair conformation. They are endowed with a strikingly high reactivity when used in a glycosylation reaction as a glycosyl donor. To investigate the unusual conformational behavior a series of mannuronic acid ester derivatives, comprising anomeric triflate species and O-methyl glycosides, was examined by dynamic NMR experiments, through lineshape analysis of H-1 and F-19 NMR spectra at various temperatures from -80 degrees C to 0 degrees C. Exchange rates between C-4(1) and C-1(4) chair conformations were found to depend on the electronic properties and the size of the C2 substituent (F, N-3 or OBn) and the aglycon, with higher exchange rates for the glycosyl triflates and smaller C2 substituents. Low temperature F-19 exchange spectroscopy experiments showed that the covalently bound anomeric triflates did not exchange with free triflate species present in the reaction mixture. To relate the conformational behavior of the intermediate triflates to their reactivity in a glycosylation reaction, their relative reactivity was determined via competition reactions monitored by H-1 NMR spectroscopy at low temperature. The 2-O-benzyl ether compound was found to be most reactive whereas the 2-fluoro compound - the most flexible of the studied compounds - was least reactive. Whereas the ring-flip of the mannuronic acids is important for the enhanced reactivity of the donors, the rate of the ring-flip has little influence on the relative reactivity.

  • 131. Sardzik, Robert
    et al.
    Green, Anthony P.
    Laurent, Nicolas
    Both, Peter
    Fontana, Carolina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Voglmeir, Josef
    Weissenborn, Martin J.
    Haddoub, Rose
    Grassi, Paola
    Haslam, Stuart M.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Flitsch, Sabine L.
    Chemoenzymatic Synthesis of O-Mannosylpeptides in Solution and on Solid Phase2012Ingår i: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 134, nr 10, s. 4521-4524Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    O-Mannosyl glycans are known to play an important role in regulating the function of alpha-dystroglycan (alpha-DG), as defective glycosylation is associated with various phenotypes of congenital muscular dystrophy. Despite the well-established biological significance of these glycans, questions regarding their precise molecular function remain unanswered. Further biological investigation will require synthetic methods for the generation of pure samples of homogeneous glycopeptides with diverse sequences. Here we describe the first total syntheses of glycopeptides containing the tetrasaccharide NeuNAc alpha 2-3Gal beta 1-4GlcNAc beta 1-2Man alpha, which is reported to be the most abundant O-mannosyl glycan on alpha-DG. Our approach is based on biomimetic stepwise assembly from the reducing end and also gives access to the naturally occurring mono-, di-, and trisaccharide substructures. In addition to the total synthesis, we have developed a one-pot enzymatic cascade leading to the rapid synthesis of the target tetrasaccharide. Finally, solid-phase synthesis of the desired glycopeptides directly on a gold microarray platform is described.

  • 132. Sarkar, Anita
    et al.
    Fontana, Carolina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Imberty, Anne
    Perez, Serge
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conformational Preferences of the O-Antigen Polysaccharides of Escherichia coli O5ac and O5ab Using NMR Spectroscopy and Molecular Modeling2013Ingår i: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 14, nr 7, s. 2215-2224Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Escherichia coli serogroup O5 comprises two different subgroups (O5ab and O5ac), which are indiscernible from the point of view of standard immunological serotyping. The structural similarities between the O-antigen polysaccharides (PSs) of these two strains are remarkable, with the only difference being the glycosidic linkage connecting the biological tetrasaccharide repeating units. In the present study, a combination of NMR spectroscopy and molecular modeling methods were used to elucidate the conformational preferences of these two PSs. The NMR study was based on the analysis of intra- and inter-residue proton-proton distances using NOE build-up curves. Molecular models of the repeating units and their extension to polysaccharides were obtained, taking into account the conformational flexibility as assessed by the force field applied and a genetic algorithm. The agreements between experimentally measured and calculated distances could only be obtained by considering an averaging of several low energy conformations observed in the molecular models.

  • 133. Senchenkova, Sof'ya N.
    et al.
    Zhang, Yuanyuan
    Perepelov, Andrei V.
    Guo, Xi
    Shashkov, Alexander S.
    Weintraub, Andrej
    Liu, Bin
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Knirel, Yuriy A.
    Structure and gene cluster of the O-antigen of Escherichia coli O165 containing 5-N-acetyl-7-N-[(R)-3-hydroxybutanoyl]pseudaminic acid2016Ingår i: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 26, nr 4, s. 335-342Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Upon mild acid degradation of the lipopolysaccharide of Escherichia coli O165, the O-polysaccharide chain was cleaved at the glycosidic linkage of 5-N-acetyl-7-N-[(R)-3-hydroxybutanoyl]pseudaminic acid (Pse5Hb7Ac). Analysis of the resulting linear tetrasaccharide and alkali-treated lipopolysaccharide by 1H/13C 1D and 2D nuclear magnetic resonance spectroscopy enabled elucidation of the following structure of the O-polysaccharide: →8)-α-Psep5Hb7Ac-(2 → 6)-β-D-Galp-(1 → 4)-β-D-Glсp-(1 → 3)-α-DGlсpNAc-(1→. The β-D-Galp-(1 → 4)-β-D-Glсp-(1 → 3)-D-GlсpNAc structural element is also present in the O-polysaccharide of E. coli O82. The content of the O-antigen gene cluster of E. coli O165 was found to be consistent with the O-polysaccharide structure established. Functions of proteins encoded in the gene cluster, including enzymes involved in the Pse5Hb7Ac biosynthesis and glycosyltransferases, were putatively assigned by comparison with sequences in available databases.

  • 134. 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 O1702015Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 417, s. 11-14Artikel i tidskrift (Refereegranskat)
    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.

  • 135. 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 O1322016Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 427, s. 44-47Artikel i tidskrift (Refereegranskat)
    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.

  • 136. Shen, Zhengnan
    et al.
    Mobarak, Hani
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Li, Wei
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Yu, Biao
    Synthesis of β-(1 -> 2)-Linked 6-Deoxy-L-altropyranose Oligosaccharides via Gold(I)-Catalyzed Glycosylation of an ortho-Hexynylbenzoate Donor2017Ingår i: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 82, nr 6, s. 3062-3071Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The ss-(1 -> 2)-linked 6-deoxy-L-altropyranose di- to pentasaccharides 2-5, relevant to the O-antigen of the infectious Yersinia enterocolitica 0:3, were synthesized for the first time. The challenging 1,2-cis-altropyranosyl linkage was assembled effectively via glycosylation with 2-O-benzyl-3,4-di-O-benzoyl-6-deoxy-L-altropyranosyl ortho-hexynylbenzoate (7) under the catalysis of PPh3AuNTf2. NMR and molecular modeling studies showed that the pentasaccharide (5) adopted a left-handed helical conformation. [GRAPHICS]

  • 137. Siegbahn, Anna
    et al.
    Aili, Ulrika
    Ochocinska, Agata
    Olofsson, Martin
    Rönnols, Jerk
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Mani, Katrin
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ellervik, Ulf
    Synthesis, conformation and biology of naphthoxylosides2011Ingår i: Bioorganic & Medicinal Chemistry, ISSN 0968-0896, E-ISSN 1464-3391, Vol. 19, nr 13, s. 4114-4126Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Proteoglycans (PG) are polyanionic proteins consisting of a core protein substituted with carbohydrate chains, that is, glycosaminoglycans (GAG). The biosynthesis of GAG can be manipulated by simple xylosides carrying hydrophobic aglycons, which can enter the cell and initiate the biosynthesis. While the importance of the aglycon is well investigated, there is far less information on the effect of modifications in the xylose residue.

    We have developed a new synthetic protocol, based on acetal protection and selective benzylation, for modification of the three hydroxyl groups in xylose. Thus we have synthesized twelve analogs of 2-naphthyl β-d-xylopyranoside (XylNap), where each hydroxyl group has been epimerized or replaced by methoxy, fluoro, or hydrogen.

    To gain more information about the properties of xylose, conformational studies were made on some of the analogs. It was found that the 4C1 conformation is highly predominant, accompanied by a nonnegligible population of the 2S0 conformation. However, deoxygenation at C3 results in a large portion of the 1C4 conformation.

    The GAG priming ability and proliferation activity of the twelve analogs, were investigated using a matched pair of human breast fibroblasts and human breast carcinoma cells. None of the analogs initiated the biosynthesis of GAG, but an inhibitory effect on endogenous PG production was observed for analogs fluorinated or deoxygenated at C4. From our data it seems reasonable that all three hydroxyl groups in XylNap are essential for the priming of GAG chains and for selective toxicity for tumor cells.

  • 138. Siegbahn, Anna
    et al.
    Manner, Sophie
    Persson, Andrea
    Tykesson, Emil
    Holmqvist, Karin
    Ochocinska, Agata
    Rönnols, Jerk
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Sundin, Anders
    Mani, Katrin
    Westergren-Thorsson, Gunilla
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ellervik, Ulf
    Rules for priming and inhibition of glycosaminoglycan biosynthesis; probing the beta 4GalT7 active site2014Ingår i: Chemical Science, ISSN 2041-6520, E-ISSN 2041-6539, Vol. 5, nr 9, s. 3501-3508Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    beta-1,4-Gatactosyltransferase 7 (beta 4GalT7) is an essential enzyme in the biosynthesis of glycosaminoglycan (GAG) chains of proteoglycans (PGs). Mammalian cells produce PGs, which are involved in biological processes such as cell growth and differentiation. The PGs consist of a core protein, with one or several GAG chains attached. Both the structure of the PGs and the GAG chains, and the expression of the enzymes involved in their biosynthesis and degradation, vary between normal cells and tumor cells. The biosynthesis of GAG chains is initiated by xylosylation of a serine residue of the core protein, followed by galactosylation by beta 4GalT7. The biosynthesis can also be initiated by exogenously added beta-D-xylopyranosides with hydrophobic aglycons, which thus can act as acceptor substrates for beta 4GalT7. To determine the structural requirements for beta 4GalT7 activity, we have cloned and expressed the enzyme and designed a focused library of 2-naphthyl beta-D-xylopyranosides with modifications of the xylose moiety. Based on enzymatic studies, that is galactosylation and its inhibition, conformational analysis and molecular modeling using the crystal structure, we propose that the binding pocket of beta 4GalT7 is very narrow, with a precise set of important hydrogen bonds. Xylose appears to be the optimal acceptor substrate for galactosylation by beta 4GalT7. However, we show that modifications of the xylose moiety of the beta-D-xylopyranosides can render inhibitors of galactosylation. Such compounds will be valuable tools for the exploration of GAG and PG biosynthesis and a starting point for development of anti-tumor agents.

  • 139. Siegbahn, Anna
    et al.
    Thorsheim, Karin
    Ståhle, Jonas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Manner, Sophie
    Hamark, Christoffer
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Persson, Andrea
    Tykesson, Emil
    Mani, Katrin
    Westergren-Thorsson, Gunilla
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Ellervik, Ulf
    Exploration of the active site of beta 4GalT7: modifications of the aglycon of aromatic xylosides2015Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 13, nr 11, s. 3351-3362Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Proteoglycans (PGs) are macromolecules that consist of long linear polysaccharides, glycosaminoglycan (GAG) chains, covalently attached to a core protein by the carbohydrate xylose. The biosynthesis of GAG chains is initiated by xylosylation of the core protein followed by galactosylation by the galactosyltransferase beta 4GalT7. Some beta-D-xylosides, such as 2-naphthyl beta-D-xylopyranoside, can induce GAG synthesis by serving as acceptor substrates for beta 4GalT7 and by that also compete with the GAG synthesis on core proteins. Here we present structure-activity relationships for beta 4GalT7 and xylosides with modifications of the aromatic aglycon, using enzymatic assays, cell studies, and molecular docking simulations. The results show that the aglycons reside on the outside of the active site of the enzyme and that quite bulky aglycons are accepted. By separating the aromatic aglycon from the xylose moiety by linkers, a trend towards increased galactosylation with increased linker length is observed. The galactosylation is influenced by the identity and position of substituents in the aromatic framework, and generally, only xylosides with beta-glycosidic linkages function as good substrates for beta 4GalT7. We also show that the galactosylation ability of a xyloside is increased by replacing the anomeric oxygen with sulfur, but decreased by replacing it with carbon. Finally, we propose that reaction kinetics of galactosylation by beta 4GalT7 is dependent on subtle differences in orientation of the xylose moiety.

  • 140.
    Ståhle, Jonas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Fontana, Carolina
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Weintraub, Andrej
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Elucidation of the O-antigen structure of Escherichia coli O632019Ingår i: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 29, nr 2, s. 179-187Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structure of the O-antigen polysaccharide (PS) from the Shiga-toxin producing Escherichia coli O63 has been elucidated using a combination of bioinformatics, component analyses and NMR spectroscopy. The O-antigen is comprised of tetrasaccharide repeating units with the following structure: 2)--d-Quip3N(d-allo-ThrAc)-(12)--d-Ribf-(14)--d-Galp-(13)--d-GlcpNAc-(1 in which the N-acetylated d-allo-threonine is amide-linked to position 3 of the 3-amino-3-deoxy-d-Quip sugar residue. The presence of a predicted flippase and polymerase encoded in the O63 gene cluster is consistent with the Wzx/Wzy biosynthetic pathway and consequently the biological repeating unit has likely an N-acetyl-d-glucosamine residue at its reducing end. A bioinformatics approach based on predictive glycosyltransferase function present in ECODAB (E. coli O-antigen database) suggested the structural element -d-Galp-(13)-d-GlcpNAc in the O-antigen. Notably, multiple gene sequence alignment of fdtA and qdtA from E. coli to that in E. coli O63 resulted in discrimination between the two, confirmation of the latter in E. coli O63, and consequently, together with qdtB, biosynthesis of dTDP-d-Quip3N. The E. coli O63 O-antigen polysaccharide differs in two aspects from that of E. coli O114 where the latter carries instead an l-serine residue, and the glycosidic linkage positions to and from the Quip3N residue are both changed. The structural characterization of the O63 antigen repeat supports the predicted functional assignment of the O-antigen cluster genes.

  • 141.
    Ståhle, Jonas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    NMR Chemical Shift Predictions and Structural Elucidation of Oligo- and Polysaccharides by the Computer Program CASPER2017Ingår i: NMR in Glycoscience and Glycotechnology / [ed] Koichi Kato, Thomas Peters, Royal Society of Chemistry, 2017, s. 335-352Kapitel i bok, del av antologi (Refereegranskat)
    Abstract [en]

    Glycans are often linked to proteins or lipids in the form of glycoconjugates but these highly complex molecules also have biological functions as oligosaccharides per se. The limited dispersion in NMR spectra of carbohydrates makes their analysis and interpretation very cumbersome. The computer program CASPER, which is a web-based tool, facilitates prediction 1H and 13C NMR chemical shifts of oligo- or polysaccharide structures defined by the user, makes it possible to carry out an NMR-based sugar analysis including determination of absolute configuration and to perform structure elucidation of unknown glycans using unassigned NMR spectra as input to the program. The output from the program contains, inter alia, tentatively assigned NMR resonances, proposed sugar components, structural suggestions ranked according to the similarity between their predicted chemical shifts and the experimental data as well as 3D structures in pdb-format generated seamlessly by the CarbBuilder program as a part of the CASPER-GUI.

  • 142.
    Ståhle, Jonas
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the O-antigen polysaccharide from Escherichia coli O63 and biosynthetic aspects thereofManuskript (preprint) (Övrigt vetenskapligt)
  • 143.
    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 O1752011Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 3, s. 449-453Artikel i tidskrift (Refereegranskat)
    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.

  • 144.
    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 O1772011Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 346, nr 14, s. 2300-2303Artikel i tidskrift (Refereegranskat)
    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.

  • 145.
    Svensson, Mona V.
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Zhang, Xue
    Huttunen, Eine
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural studies of the capsular polysaccharide produced by Leuconostoc mesenteroides ssp. cremoris PIA22011Ingår i: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 12, nr 7, s. 2496-2501Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The structure of the capsular polysaccharide (CPS) produced by Leuconostoc mesenteroides ssp. cremoris PIA2 has been determined using component analysis and NMR spectroscopy. 1H and 13C resonances were assigned using 2D NMR experiments, and sequential information was obtained by 1H,1H-NOESY and 1H,13C-HMBC experiments. The CPS consists of linear pentasaccharide repeating units with the following structure: →3)-β-d-Galf-(1→6)-β-d-Galf-(1→2)-β-d-Galf-(1→6)-β-d-Galf-(1→3)-β-d-Galp-(1→, in which four out of the five sugar residues have the furanoid ring form, a structural entity found in bacteria but not in mammals. The analysis of the magnitude of the homonuclear three-bond coupling constants of the anomeric protons for the five-membered sugar rings indicates that the sugar residues substituted at a primary carbon atom show one kind of conformational preferences, whereas those substituted at a secondary carbon atom show another kind of conformational preferences.

  • 146.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hinterholzinger, Florian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Landersjö, Clas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conformational flexibility of the pentasaccharide LNF-2 deduced from NMR spectroscopy and molecular dynamics simulations2012Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 10, nr 23, s. 4577-4585Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Human milk oligosaccharides (HMOs) are important as prebiotics since they stimulate the growth of beneficial bacteria in the intestine and act as receptor analogues that can inhibit the binding of pathogens. The conformation and dynamics of the HMO Lacto-N-fucopentaose 2 (LNF-2), alpha-L-Fucp-(1 -> 4)-[beta-D-Galp-(1 -> 3)]-beta-D-GlcpNAc-(1 -> 3)-beta-D-Galp-(1 -> 4)-D-Glcp, having a Lewis A epitope, has been investigated employing NMR spectroscopy and molecular dynamics (MD) computer simulations. 1D H-1, H-1-NOESY experiments were used to obtain proton-proton cross-relaxation rates from which effective distances were deduced and 2D J-HMBC and 1D long-range experiments were utilized to measure trans-glycosidic (3)J(CH) coupling constants. The MD simulations using the PARM22/SU01 force field for carbohydrates were carried out for 600 ns with explicit water as solvent which resulted in excellent sampling for flexible glycosidic torsion angles. In addition, in vacuo MD simulations were performed using an MM3-2000 force field, but the agreement was less satisfactory based on an analysis of heteronuclear trans-glycosidic coupling constants. LNF-2 has a conformationally well-defined region consisting of the terminal branched part of the pentasaccharide, i.e., the Lewis A epitope, and a flexible beta-D-GlcpNAc-(1 -> 3)-beta-D-Galp-linkage towards the lactose unit, which is situated at the reducing end. For this beta-(1 -> 3)-linkage a negative. torsion angle is favored, when experimental NMR data is combined with the MD simulation in the analysis. In addition, flexibility on a similar time scale, i.e., on the order of the global overall molecular reorientation, may also be present for the. torsion angle of the beta-D-Galp-(1 -> 4)-D-Glcp-linkage as suggested by the simulation. It was further observed from a temperature variation study that some H-1 NMR chemical shifts of LNF-2 were highly sensitive and this study indicates that Delta delta/Delta T may be an additional tool for revealing conformational dynamics of oligosaccharides.

  • 147.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Hinterholzinger, Florian
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Landersjö, Clas
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Conformational studies of lacto-N-fucocopentaose 2 by NMR spectroscopy and molecular dynamic simulations2009Ingår i: Abstracts of Papers, 238th ACS National Meeting, Washington, DC, United States, August 16-20, 2009, American Chemical Society , 2009Konferensbidrag (Övrigt vetenskapligt)
  • 148.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Huttunen, Eine
    Zhang, Xue
    Yang, Zhennai
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Structural analysis of the exopolysaccharide produced by Streptococcus thermophilus ST1 solely by NMR spectroscopy2010Ingår i: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 47, nr 2, s. 125-134Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The use of lactic acid bacteria in fermentation of milk results in favorable physical and rheological properties due to in situ exopolysaccharide (EPS) production. The EPS from S. thermophilus ST1 produces highly viscous aqueous solutions and its structure has been investigated by NMR spectroscopy. Notably, all aspects of the elucidation of its primary structure including component analysis and absolute configuration of the constituent monosaccharides were carried out by NMR spectroscopy. An array of techniques was utilized including, inter alia, PANSY and NOESY-HSQC TILT experiments. The EPS is composed of hexasaccharide repeating units with the following structure: → 3)[α-d-Glcp-(1 → 4)]-β-d-Galp-(1 → 4)-β-d-Glcp-(1 → 4)[β-d-Galf-(1 → 6)]-β-d-Glcp-(1 → 6)-β-d-Glcp-(1 →, in which the residues in square brackets are terminal groups substituting backbone sugar residues that consequently are branch-points in the repeating unit of the polymer. Thus, the EPS consists of a backbone of four sugar residues with two terminal sugar residues making up two side-chains of the repeating unit. The molecular mass of the polymer was determined using translational diffusion experiments which resulted in Mw = 62 kDa, corresponding to 64 repeating units in the EPS.

  • 149.
    Säwén, Elin
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Massad, Tariq
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för biokemi och biofysik.
    Landersjö, Clas
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Damberg, Peter
    Widmalm, Göran
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Population distribution of flexible molecules from maximum entropy analysisusing different priors as background information: application to the phi,psi-conformational space of the a-(1→2)-linked mannose disaccharide presentin N- and O-linked glycoproteins2010Ingår i: Organic and biomolecular chemistry, ISSN 1477-0520, E-ISSN 1477-0539, Vol. 8, nr 16, s. 3684-3695Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The conformational space available to the flexible molecule a-D-Manp-(1→2)-a-D-Manp-OMe, amodel for the a-(1→2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determinedusing experimental data and molecular simulation combined with a maximum entropy approach thatleads to a converged population distribution utilizing different input information. A database survey ofthe Protein Data Bank where structures having the constituent disaccharide were retrieved resulted inan ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave thedatabase (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linkedstructures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealeda two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. Thesetwo different conformation ensembles of the disaccharide were compared to measured experimentalspectroscopic data for the molecule in water solution. However, neither of the two populations werecompatible with experimental data from optical rotation, NMR 1H,1H cross-relaxation rates as well ashomo- and heteronuclear 3J couplings. The conformational distributions were subsequently used asbackground information to generate priors that were used in a maximum entropy analysis. Theresulting posteriors, i.e., the population distributions after the application of the maximum entropyanalysis, still showed notable deviations that were not anticipated based on the prior information.Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidictorsion angles f and y were carried out in which the importance of electronegative substituents on thecoupling pathway was deemed essential resulting in four derived equations, two 3JCOCC and two 3JCOCHbeing different for the f and y torsions, respectively. These Karplus relationships are denotedJCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between theMD- and DB-posteriors. The information entropies show that the current reparametrization of theKarplus relationships constitutes a significant improvement. The fH torsion angle of the disaccharide isgoverned by the exo-anomeric effect and for the dominating conformation fH = -40◦ and yH = 33◦.The minor conformational state has a negative yH torsion angle; the relative populations of the majorand the minor states are ~3 : 1. It is anticipated that application of the methodology will be useful toflexible molecules ranging from small organic molecules to large biomolecules.

  • 150.
    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 glycoside2010Ingår i: Carbohydrate Research, ISSN 0008-6215, E-ISSN 1873-426X, Vol. 345, nr 8, s. 984-993Artikel i tidskrift (Refereegranskat)
    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.

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