Bas R. Leeflang

Structural characterisation of the exopolysaccharide produced by Lactobacillus delbrückii subspecies bulgaricus rr grown in skimmed milk

The exopolysaccharide of Lactobacillus delbrückii subsp. bulgaricus rr, isolated from skimmed milk, is a heteropolymer of D-galactopyranosyl, D-glucopyranosyl, and L-rhamnopyranosyl residues in the molar ratio 5:1:1. The structure was established by linkage analysis and 1D and 2D NMR spectroscopy of the native polysaccharide, in combination with characterisation of oligosaccharide fragments, obtained by Smith degradation and partial acid hydrolysis, using methylation analysis, EIMS, and 1D and 2D 1H NMR spectroscopy. The polysaccharide has a branched heptasaccharide repeating unit with the following structure: -->2)-[beta-D-Galp-(1-->3)]-alpha-D-Galp-(1-->3)- beta-D-Glcp-(1-->3)-[beta-D-Galp-(1-->4)]-beta-D-Galp-(1-->4)-[alpha-L- Rhap-(1-->3)]-alpha-D-Galp-(1-->.

A 1H-NMR and MD study of intramolecular hydrogen bonds in methyl β-cellobioside

Abstract The existence of an HO-3⋯O-5′ intramolecular hydrogen bond in methyl β-cellobioside in solution in Me 2 SO- d 6 and H 2 O-CD 3 OD (4:1 w/w) was studied by 500-MHz 1 H-NMR spectroscopy and MD simulations. Temperature coefficients for the chemical shift of the hydroxyl resonances in these solvents were determined and the rates of proton exchange in the latter solvent were obtained from NOE data. With H 2 O-CD 3 OD as the solvent, the HO-3⋯O-5′ hydrogen bond was insignificant, but its presence in Me 2 SO- d 6 was confirmed.

Curcacycline A — a novel cyclic octapeptide isolated from the latex of Jatropha curcas L.

From the latex of Jatropha curcas L. (Euphorbiaceae) a novel cyclic octapeptide was isolated, which we named curcacycline A. The compound was found to contain one threonine, one valine, two glycine, and four leucine residues. By two‐dimensional 1H‐NMR spectroscopy (HOHAHA and ROESY), its sequence was determined to be Gly1‐Leu2‐Leu3‐Gly4‐Thr5‐Val6‐Leu7Leu8‐Gly1. Curcacycline A displays a moderate inhibition of (i) classical pathway activity of human complement and (ii) proliferation of human T‐cells.

Characterisation by 1H-n.m.r. spectroscopy of oligosaccharides, derived from arabinoxylans of white endosperm of wheat, that contain the elements →4)[α-l-Araf-(1-ar3)]-β-d-Xylp-(1→ or →4)[α-l-Araf-(1→2)][α-lAraf-(1→3)]-β-d-Xylp-(1→

Abstract The structure of penta- to hepta-saccharides, generated by digestion of purified wheat-endosperm arabinoxylan with endo-(1→4)-β- d -xylanase and isolated by gel-permeation chromatography on Bio-Gel P-6 followed by high-performance anion-exchange chromatography with pulsed amperometric detection, was established using monosaccharide and methylation analysis, f.a.b.-m.s., and 1 H-n.m.r. spectroscopy. The oligosaccharides had a core of (1→4)-linked β- d -xylopyranosyl residues 3- or 2,3-substituted with single α- l -arabinofuranosyl groups, and gave 1 H-n.m.r. spectra typical for each type.

EUROCarbDB: An open-access platform for glycoinformatics.

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb.

Structure of the exopolysaccharide produced by lactococcus lactis subspecies cremoris H414 grown in a defined medium or skimmed milk

The structure of the exopolysaccharide of Lactococcus lactis subsp. cremoris H414, isolated from a defined medium or skimmed milk, was established by linkage analysis on the native polysaccharide, and by characterisation of oligosaccharide fragments, obtained by Smith degradation and partial acid hydrolysis, using methylation analysis, FABMS, EIMS, and 1H-NMR spectroscopy. The polysaccharide has the branched-pentasaccharide repeating unit: [formula: see text]

NMR Studies of the Free α Subunit of Human Chorionic Gonadotropin

Human chorionic gonadotropin (hCG) is a heterodimeric glycoprotein hormone that is involved in the maintenance of the corpus luteum in early pregnancy. Glycosylation at Asn52 of its alpha subunit (alpha hCG) is essential for signal transduction, whereas the N-glycan at Asn78 stabilizes the structure of the protein. In this study, an almost complete 1H-NMR and a partial 13C-NMR spectral assignment for the amino acids and the N-glycans of alpha hCG and of an enzymatically deglycosylated form, which had a single GlcNAc residue at each of its two glycosylation sites, has been achieved. The secondary structure of alpha hCG is solution, which was determined based on NOE data, is partially similar to that of the alpha subunit in the crystal structure of hCG, but large structural differences are found for amino acid residues 33-58. In the crystal structure of hCG, residues 33-37 and 54-58 of the alpha subunit are part of an intersubunit seven-stranded beta-barrel and residues 41-47 constitute a 3(10)-helix. In contrast, in free alpha hCG in solution, amino acids 33-58 are part of a large disordered loop, indicating that in intact hCG interactions with the beta subunit of hCG stabilize the conformation of the alpha subunit. The NMR data of alpha hCG and its deglycosylated counterpart are very similar, indicating that removal of carbohydrate residues other than GlcNAc-1 does not notably affect the conformation of the protein part. However, numerous 1H-NOEs between the GlcNAc-1 residue at Asn78 and several amino acid residues show that this GlcNAc residue is tightly packed against the protein, being an integral part of the structure of the alpha subunit. 1H-NOEs across the glycosidic linkages of the glycan, resonance-line widths, and 1H and 13C chemical shifts of the other monosaccharides suggest that the remainder of the glycans at Asn78, and the glycans at Asn52 are largely extended in solution.

Development of a 1H NMR structural-reporter-group concept for the primary structural characterisation of α-D-glucans

An NMR study of proton chemical shift patterns of known linear alpha-D-glucopyranose di- and trisaccharide structures was carried out. Chemical shift patterns for (alpha1-->2)-, (alpha1-->3)-, (alpha1-->4)- and (alpha1-->6)-linked D-glucose residues were analysed and compared to literature data. Using these data, a 1H NMR structural-reporter-group concept was formulated to function as a tool in the structural analysis of alpha-D-glucans.

CROSREL: Full relaxation matrix analysis for NOESY and ROESY NMR spectroscopy

SummaryA method is proposed for quantitative analysis of ROESY peak intensities, to which corrections are applied for their offset dependence and for direct HOHAHA effects. Additionally the effects of anisotropic and internal motion can be assessed. This method has been implemented for full relaxation matrix analysis in the CROSREL program. Although CROSREL is applicable to NOESY data, its use for ROESY peak intensities has been evaluated here, because of its innovative character in this respect. The agreement between calculated and experimental intensities is expressed by a weighted residual Rw factor, similar to X-ray crystallography. The merits of the program have been tested on methyl(d3) β-cellobioside, for which a ROESY buildup series has been acquired, and for which extensive MD simulations have been performed. It is concluded that correction for direct HOHAHA effects is obligatory for the analysis of ROESY data. Extension of the model for methyl β-cellobioside with internal and anisotropic motion, as was derived from MD data, did not improve the results obtained for assumed isotropic tumbling of a rigid model. It has been shown that ROESY peak intensities can be analysed successfully by the CROSREL program.

Conformational analysis of methyl β-cellobioside by ROESY NMR spectroscopy and MD simulations in combination with the CROSREL method

Methyl beta-cellobioside has been studied extensively by molecular dynamics (MD) simulations in water and by ROESY NMR spectroscopy in order to establish its solution structure. The MD simulations were started with four significantly different minimal energy conformations. The MD trajectories were analysed with respect to interproton distances and mobility, in order to find models for application in the analysis of NMR data. The ROESY spectra were analysed by using the CROSREL method, which allows quantitative analysis of ROESY spectra through correction for the offset dependence and incorporation of HOHAHA transfer estimates. These results were compared with data obtained from an initial rate analysis of the ROESY data and with the MD data. It is concluded that methyl beta-cellobioside in aqueous solution is in the same extended conformation that is also found in the solid state.