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The specific substance from Pneumococcus type 34 the configuration of the glycosidic linkages.

ABSTRACT: 1. The specific compound from Pneumococcus type 34 was isolated from capsular material by ion-exchange chromatography. This separated it from a substance with chemical and serological properties corresponding to those reported for C-substance. 2. The configuration of the two galactofuranosyl linkages in the repeating unit of S.34 was determined and the configurations previously assigned to the other glycosidic linkages were confirmed. 3. The dephosphorylated deacetylated repeating unit is thus O-beta-d-galactofuranosyl-(1-->3)-O-alpha-d-glucopyranosyl-(1-->2)-O-beta-d-galactofuranosyl-(1-->3)-O-alpha-d-galactopyranosyl- (1-->2)-ribitol.

SUBMITTER: Dixon JR

PROVIDER: S-EPMC1265164 | biostudies-other | 1966 Aug

REPOSITORIES: biostudies-other

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Project description:We present an extension of the CHARMM hexopyranose monosaccharide additive all-atom force field to enable modeling of glycosidic-linked hexopyranose polysaccharides. The new force field parameters encompass 1→1, 1→2, 1→3, 1→4, and 1→6 hexopyranose glycosidic linkages, as well as O-methylation at the C(1) anomeric carbon, and are developed to be consistent with the CHARMM all-atom biomolecular force fields for proteins, nucleic acids, and lipids. The parameters are developed in a hierarchical fashion using model compounds containing the key atoms in the full carbohydrates, in particular O-methyl-tetrahydropyran and glycosidic-linked dimers consisting of two molecules of tetrahyropyran or one of tetrahydropyran and one of cyclohexane. Target data for parameter optimization include full two-dimensional energy surfaces defined by the Φ/Ψ glycosidic dihedral angles in the disaccharide analogs as determined by quantum mechanical MP2/cc-pVTZ single point energies on MP2/6-31G(d) optimized structures (MP2/cc-pVTZ//MP2/6-31G(d)). In order to achieve balanced, transferable dihedral parameters for the Φ/Ψ glycosidic dihedral angles, surfaces for all possible chiralities at the ring carbon atoms involved in the glycosidic linkages are considered, resulting in over 5000 MP2/cc-pVTZ//MP2/6-31G(d) conformational energies. Also included as target data are vibrational frequencies, pair interaction energies and distances with water molecules, and intramolecular geometries including distortion of the glycosidic valence angle as a function of the glycosidic dihedral angles. The model-compound optimized force field parameters are validated on full disaccharides through comparison of molecular dynamics results to available experimental data. Good agreement is achieved with experiment for a variety of properties including crystal cell parameters and intramolecular geometries, aqueous densities, and aqueous NMR coupling constants associated with the glycosidic linkage. The newly-developed parameters allow for the modeling of linear, branched, and cyclic hexopyranose glycosides both alone and in heterogenous systems including proteins, nucleic acids and/or lipids when combined with existing CHARMM biomolecular force fields.

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The specific substance from Pneumococcus type 34 the configuration of the glycosidic linkages.

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