Biomedical subjects

G Widmalm

Publications and source records attributed to G Widmalm.

At least 55 records · Page 3Linked to original sources

PubMed1998

Structural determination of the O-antigenic polysaccharide from the enterotoxigenic Escherichia coli O147.

The structure of the O-antigenic polysaccharide from enterotoxigenic Escherichia coli O147 has been determined by NMR spectroscopy, and component and methylation analyses. The sequence of the sugar residues could be determined by NOESY and heteronuclear-multiple-bond-connectivity NMR experiments. It is concluded that the polysaccharide is composed of tetrasaccharide repeating units with the following structure: -->4)-beta-D-GalpA-(1-->3)-beta-D-GalpNAc-(1-->2)-alpha-L-Rhap+ ++-(1-->2)-alpha-L-Rhap-(1-->, where Rha represents 6-deoxymannose. The O-antigen of E. coli O147 is identical to the repeating unit of Shigella flexneri serotype 6 lipopolysaccharide, except that the latter contains an O-acetyl group at C3 of the rhamnosyl residue substituted by the N-acetylgalactosamine residue. Immunochemical analyses using a monoclonal antibody specific for the S. flexneri serotype 6 O-antigen showed an identical reactivity with both lipopolysaccharides.

Carbohydrate Sequence↗

PubMed1998

Computer-assisted structural analysis of oligo- and polysaccharides: an extension of CASPER to multibranched structures.

The CASPER program which is used for determination of the structure of oligo- and polysaccharides has been extended. It can now handle a reduced number of experimental signals from an NMR spectrum in the comparison to the simulated spectra of structures that it generates, an improvement which is of practical importance since all signals in NMR spectra cannot always be identified. Furthermore, the program has been enhanced to simulate NMR spectra of multibranched oligo- and polysaccharides. The new developments were tested on four saccharides of known structure but of different complexity and were shown to predict the correct structures.

Aeromonas↗

PubMed1998

MMC and LD simulations of alpha-D-Manp-(1-->2)-beta-D-Glcp-OMe: comparison to long-range heteronuclear NMR coupling constants and to the crystal structure.

The conformational flexibility and the dynamics of alpha-D-Manp(1-->2)-beta-D-Glcp-OMe have been investigated by Metropolis Monte Carlo (MMC) and Langevin dynamics (LD) simulations. The two simulation techniques employ different force fields, namely the HSEA force field and a CHARMm-based force field. The former shows less conformational flexibility than the latter, in which a multiple energy minima conformational space is sampled. Long-range heteronuclear nuclear magnetic resonance (NMR) coupling constants have been measured by selective excitations of the carbons at the glycosidic linkage. Calculated 3J(C,H) values from MMC and LD simulations show excellent agreement to those from NMR experiments. The X-ray crystal structure has a conformation within a region of the conformational space populated in both force fields.

Carbohydrate Conformation↗

PubMed1998

MMC and LD simulations of alpha-D-Glcp-(1-->2)-alpha-D-Glcp-(1-->3)-alpha-D-Glcp-OMe. A model for the terminal trisaccharide in glycoprotein precursors.

The conformational flexibility and the dynamics of alpha-D-Glcp-(1-->2)-alpha-D-Glcp(1-->3)-alpha-D-Glcp-OMe (I) has been investigated by Metropolis-Monte Carlo with the HSEA (Hard Sphere Exo-Anomeric) force field and Langevin dynamics simulations employing two different CHARMm (Chemistry at HARvard Molecular Mechanics) force fields, CHEAT95 and PARM22. The conformational space spanned by the molecule is similar for the two former force fields but differ significantly for the latter. Hydrogen bonding between O2" and O4 of the title compound is analysed in comparison to NMR and preliminary results from X-ray powder diffraction studies.

Carbohydrate Conformation↗

PubMed1997

Structural elucidation of the capsular polysaccharide from Streptococcus pneumoniae type 18B.

The structure of the capsular polysaccharide from Streptococcus pneumoniae type 18B has been determined using NMR spectroscopy and methylation analysis as the principal methods. It is concluded that the polysaccharide is composed of pentasaccharide repeating units with a glycerol phosphate substituting the 3-position of the branch point residue. The carbohydrate backbone in type 18B is identical to that in S. pneumoniae type 18F but without the O-acetyl groups present in that type. [formula: see text] In this structure, the absolute configuration of the glycerol phosphate moiety has not been determined but should be D, in analogy with that determined for the capsular polysaccharide from S. pneumoniae type 18A [T. Rundlöf, G. Widmalm, Anal. Biochem., 243 (1996) 228-233].

Bacterial Capsules↗

PubMed1997

Structural analysis of the O-antigenic polysaccharide from Vibrio cholerae O10.

The structure of the O-antigenic polysaccharide part of the lipopolysaccharide isolated from Vibrio cholerae O10 has been determined. The main method used has been 1H- and 13C-NMR spectroscopy. Sugar and methylation analyses were also applied to the polysaccharide. The tetrasaccharide repeating unit of the polysaccharide was found to have the following structure: -->3)-alpha-D-ManpNAc-(1-->4)-beta-D-GlcpA-(1-->3)-beta-D-Ga lp-(1-->3)-beta-D-GlcpNAc-(1-->.

Carbohydrate Conformation↗

PubMed1997

Structural studies of the O-antigen polysaccharide from Escherichia coli O138.

The structure of the O-antigen polysaccharide from Escherichia coli O138 has been determined. NMR spectroscopy, together with component and methylation analyses, of native and reduced polysaccharide were the principal methods used. The sequence of the sugar residues could be determined by NOESY and heteronuclear multiple bond connectivity (HMBC) NMR experiments. It is concluded that the polysaccharide is composed of tetrasaccharide repeating units with the following structure: [structure: see text].

Carbohydrate Conformation↗

PubMed1997

The structure of the capsular polysaccharide from Klebsiella type 52, using the computerised approach CASPER and NMR spectroscopy.

The structure of the capsular polysaccharide from Klebsiella type 52 has been elucidated using an improved and extended version of the computerised approach CASPER and NMR spectroscopy as principal methods. A previous suggestion to the structure but without the anomeric prefixes, could be shown correct [H. Björndal et al., Carbohydr. Res., 31 (1973) 93-100]. The polysaccharide has a hexasaccharide repeat with the following structure: [formula: see text]

Bacterial Capsules↗

PubMed1997

Structural studies on the short-chain lipopolysaccharide of Vibrio cholerae O139 Bengal.

A Vibrio cholerae O139 strain, MO10-T4, lacking capsular polysaccharide, produces a short-chain lipopolysaccharide (LPS), similar to enterobacterial SR strains. It was studied by acidic and alkaline degradation, dephosphorylation, sugar and methylation analysis, high-performance anion-exchange chromatography, one- and two-dimensional 1H-, 13C-, and 31P-NMR spectroscopy, and electrospray ionization mass spectrometry. The following structure was proposed for the core region of the LPS: [structure: see text] where PEtn stands for 2-aminoethyl phosphate, Fru for fructose, Hep for L-glycero-D-manno-heptose, and Kdo for 3-deoxy-D-manno-octulosonic acid; unless otherwise stated, the monosaccharide residues are D and present in the pyranose form. An O-acetyl group is present on a secondary position, tentatively O4 of the alpha-linked glucosyl group. Some LPS species contain an additional putative fructose residue whose location remains unknown. An O139-negative mutant strain, Bengal-2R, derived from V. cholerae O139, has also been investigated and shown to produce an O-antigen-lacking LPS similar to those from enterobacterial R strains, some of the LPS species containing the same core region as the strain MO10-T4 LPS and the other lacking the lateral heptose residue. The carbohydrate backbone core structure is the same for the V. cholerae O139 and V. cholerae O1 LPS, thus confirming the close relation between these bacteria; however, the 2-aminoethyl phosphate, the O-acetyl group, and the second fructose residue have not been reported for the O1 LPS. In the V. cholerae O139 strain MO10-T4 LPS, a short O-side chain is attached at position 3 of the 7-substituted heptose residue and has the same structure as one repeating unit of the V. cholerae O139 capsular polysaccharide. Some details of the structure proposed are at variance with those recently published for another V. cholerae O139 strain [Cox, A. D., Brisson, J.-R., Varma, V. & Perry, M. B. (1996) Carbohydr. Res. 290, 43-58; Cox, A. D. & Perry, M. B. (1996) Carbohydr. Res. 290, 59-65.]

Lipopolysaccharides↗

PubMed1997

Structural studies of the O-antigenic polysaccharide from Escherichia coli O167.

The structure of the O-antigenic polysaccharide from Escherichia coli O167:H5 has been investigated. Sugar and methylation analyses, fast-atom-bombardment mass spectrometry and 1H- and 13C-NMR spectroscopy were the main methods used. The structure of the repeating unit of the polysaccharide was found to be: [formula in text]. Oligosaccharide derivatives of the polysaccharide were obtained by HF solvolysis and by a Smith degradation. Furthermore, base treatment of the polysaccharide led to a degraded polymeric material. For the methylated polysaccharide the amide linkage between alanine and the galacturonic acid residue was reductively cleaved with LiBD4 in ethanol, to give, among other things, a 3-O-methyl galactose derivative.

Carbohydrate Conformation↗

PubMed1997

Structure of the O-specific polysaccharide of Proteus penneri strain 25 containing N-(L-alanyl) and multiple O-acetyl groups in a tetrasaccharide repeating unit.

Based on sugar and methylation analyses, O-deacetylation, Smith degradation, and 1H and 13C NMR spectroscopy, including 2D COSY, 1H-detected 1H, 13C heteronuclear single-quantum coherence (HSQC), and 1H-detected 1H, 13C heteronuclear multiple-bond connectivity (HMBC) experiments, the following structure of the O-specific polysaccharide of Proteus penneri strain 25 was established: [formula: see text] where D-GlcN(L-Ala) is 2-(L-alanylamido)-2-deoxy-D-glucose.

Acetylation↗

PubMed1997

Structural analysis of the O-antigenic polysaccharide from the enteropathogenic Escherichia coli O142.

The polysaccharide part of the lipopolysaccharide obtained from the enteropathogenic Escherichia coli O142 has been isolated, and its structure determined. Together with 1H-NMR and 13C-NMR spectroscopy, sugar and methylation analyses show that the polysaccharide is composed of repeating pentasaccharide units. Sequential information on the O-polysaccharide was obtained by two-dimensional NMR techniques, namely heteronuclear-multiple-bond-connectivity and NOESY experiments. The repeating unit of the O-polysaccharide of E. coli strain O142 has the following structure: [structure: see text].

Carbohydrate Sequence↗

PubMed1997

Structure determination of the O-antigenic polysaccharide from the enterotoxigenic Escherichia coli (ETEC) O101.

The O-antigenic polysaccharide of the lipopolysaccharide from the enterotoxigenic Escherichia coli O101 has been investigated. The composition and sequence of the repeating units was established by sugar and methylation analysis together with 1H and 13C NMR spectroscopy. The sequence was corroborated using the computer program CASPER. The structure of the repeating unit of the polysaccharide from E. coli O101 is as follows: -->6)-alpha-D-GlcpNAc-1-->4-alpha-D-GalpNAc-(1-->.

Carbohydrate Conformation↗

PubMed1997

Conformational analysis and molecular dynamics simulation of alpha-(1-->2) and alpha-(1-->3) linked rhamnose oligosaccharides: reconciliation with optical rotation and NMR experiments.

Molecular mechanics and dynamics calculations were carried out on the disaccharides alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1-->OMe) (1) and alpha-L-Rhap-(1-->3)-alpha-L-Rhap-(1-->OMe) (2), and the trisaccharide alpha-L-Rhap-(1-->2)-alpha-L-Rhap-(1--> 3)-alpha-L-Rhap-(1-->OMe) (3). The semiflexible conformational behavior of these molecules was characterized by the occupation of a combination of different glycosidic linkage and side-chain conformational positions whose relative occupations were sensitive to dielectric screening. Molecular dynamics simulations of the trisaccharide 3 showed little difference between the linkage conformations in the trisaccharide and the component disaccharides 1 and 2 Experimental optical rotation data of 1 and 2 were obtained as a function of temperature in varying solvents. The molecular models were combined with the semiempirical theory of Stevens and Sathyanarayana to yield calculated optical rotations. Interpretation of the data of both 1 and 2 implied that a combination of conformations, both in glycosidic and side-chain positions, could explain the experimental data. Solvents effects were important in influencing the conformational mix and averaged optical rotation. Three-bond heteronuclear coupling constants 3JC H were obtained for the glycosidic linkages of 1 and 2 in D2O and DMSO. Analysis of the coupling constants with a Karplus curve showed that small reductions in the glycosidic torsion angles of the conformations of the models used here of ca. 10 degrees-15 degrees in phi and 5 degrees-10 degrees in psi were required to give better agreement with experiment; a combination of conformations for both 1 and 2 was consistent with the data. There was a negligible influence on the coupling constants of 1 on changing the solvent from D2O to DMSO.

Carbohydrate Conformation↗

PubMed1997

Conformational analysis of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-alpha-D-galactopyranoside by MM and Langevin dynamics simulations.

The conformational space of methyl 6-O-[(R)- and (S)-1-carboxyethyl]-alpha-D-galactopyranoside has been investigated. A grid search employing energy minimization at each grid point over the three major degrees of freedom, namely phi, psi and omega, identified low energy regions. The R-isomer shows five low energy conformers within ca. 1 kcal mol(-1) of the global energy minimum. The S-isomer has two conformers within a few tenths of a kcal mol(-1) of the global energy minimum. Langevin dynamics simulations have been have been performed at 300 K for 30 ns of each isomer. The phi dihedral angle has as its major conformer (g-) for the R-isomer whereas it is the (g+) conformer for the S-isomer. For the psi dihedral angle the (t) conformer has the highest population for both isomers. The dihedral angle omega has the (g+) conformer most highly populated, both for the R- and S-isomer. The above five and two conformational states for the R- and S-isomers, respectively, make up 90% in each case of the populated states during the Langevin dynamics (LD) simulations. Rate constants for the omega dihedral angle have been calculated based on a number correlation function. Three bond homo- and heteronuclear, i.e. proton and carbon-13, coupling constants have been calculated from the dynamics trajectories for comparison to experimental values. The heteronuclear coupling constant H2',C6 has been measured for the S-isomer and found to be 3.3 Hz. The J value calculated from the LD simulations, namely 2.6 Hz, is in fair agreement with experiment. A comparison to the X-ray structure of the R-isomer shows that the conformation of the crystalline compound occupies the low energy region most highly populated as a single R-conformer (30%) during the LD simulations.

Carbohydrate Conformation↗

PubMed1997

Nuclear magnetic resonance studies of the C-terminal human growth hormone fragment I179-C182-[SS]-C189-P191 and the related trisulfide peptide I179-C182-[SSS]-C189-P191.

The synthetic C-terminal hGH fragment I179-C182-[SS]-C189-P191 and the related trisulfide peptide I179-C182-[SSS]-C189-P191 have been studied using homonuclear 1H-NMR methods and distance geometry calculations. The 1H-NMR spectra of both the disulfide (diS) and the trisulfide (triS) were completely assigned. Amide proton exchange rates, NOEs and the temperature dependence of the NH chemical shifts indicate a hydrogen bond in triS between Val185 and Ser188 stabilizing a turn in this region. 3JH,H coupling constants and NOEs were measured and used as input for distance geometry calculations. For triS two families of structures with averaged pairwise backbone root mean square deviations for Cys182-Cys189 of 1.3-1.5 A were found, only one of which is compatible with experimental data. For diS only one family of structures was found, but with such a low structural definition (back bone rmsd > 2 A) that no interpretation into a consensus structure is useful. The generated structures were compared to the crystal structure of the terminal loop in hGH, complexed to its binding proteins. The resemblance was low between the solution structures of the tridecapeptides and the terminal hGH loop.

Crystallography, X-Ray↗

PubMed1996

A method for determination of the absolute configuration of chiral glycerol residues in natural products using TEMPO oxidation and characterization of the glyceric acids formed.

A method has been developed for determination of the absolute configuration of glycerol residues in natural products. It is required that the glycerol moiety contain a primary nonsubstituted hydroxymethyl group or that such a group can be obtained by modification without racemization. The method employs TEMPO oxidation of the primary hydroxyl group, hydrolysis, butanolysis with chiral 2-butanol, and acetylation. The acetylated (+)-2-butyl esters of the glyceric acid formed by oxidation are analyzed by gas-liquid chromatography. The esterification can also be performed with other chiral alcohols, e.g., (-)-2-octanol. The method is general and applicable to both primary and secondary substituted glycerols. It has recently been used for determination of the chiral glycerol-1-phosphate residue of the Escherichia coli O28 O-antigen, and now we report the absolute configurations of the glycerol moieties in Streptococcus pneumoniae type 18A and Streptococcus agalactaie type III. All studied glycerol residues were found to have the D-configuration.

Carbohydrate Sequence↗

PubMed1996

The structures of oligosaccharides isolated from the lipopolysaccharide of Moraxella catarrhalis serotype B, strain CCUG 3292.

The oligosaccharides from the lipopolysaccharides of Moraxella catarrhalis serotype B, strain CCUG 3292, were isolated after mild acid hydrolysis and separated by high-performance anion-exchange chromatography. The structures of the oligosaccharides were established by fast atom bombardment mass spectrometry and nuclear magnetic resonance spectroscopy. It is concluded that the oligosaccharides comprise a mixture of mainly a nona- and a deca-saccharide. [formula: see text] Smaller amounts of undeca-saccharides and of truncated forms, namely, hexa-, hepta-, and octa-saccharides, were also detected.

Carbohydrate Conformation↗