Computer-assisted structural analysis of the branched O-specific polysaccharide of Salmonella arizonae O63 (Arizona O8) on the basis of 13C-n.m.r. data.
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Antigens, Bacterial↗
Biomedical subjects
G M Lipkind
Publications and source records attributed to G M Lipkind.
[Conformation analysis of the N-glycosylation site Asn-X-Thr/Ser in glycoproteins].
Theoretical conformational analysis of oligopeptides CH3CO-Asn-X-Thr-NHCH3 (X = Gly, Ala, Pro), modelling N-glycosylation site, and their glycosylated derivatives CH3CO-(GlcNAc beta 1-4GlcNAc beta 1) Asn-X-Thr-NHCH3 has been carried out. Active conformations of the site are found, corresponding to structural prerequisities of N-glycosylation: Asn residue's position in beta-turn and hydrogen bond formation between side chains of Asn and Thr/Ser residues. In this case the L conformation of the central residue X is most probable. Since Pro residue does not possess this conformation, sequences with X = Pro are not glycosylated. It is shown that glycosylation of the above-mentioned sites is accompanied by reorientation of the Asn residue's side chains.
Amino Acid Sequence↗
[Conformation analysis of carbohydrate chains of glycoconjugates].
A problem of conformations of carbohydrate chains of glycoconjugates-glycoproteins and glycolipids--is reviewed. Experimental data (NMR, X-Ray) and theoretical conformational analysis data are discussed. Spatial structures of O-linked oligosaccharides from blood-group glycoproteins, N-linked oligosaccharides of different types (oligomannosidic, complex, hybrid, bisect) and carbohydrate chains of glycosphingolipids are considered.
Carbohydrate Conformation↗
Nuclear Overhauser effects and conformations of branched trisaccharide methyl beta-glycosides that contain a 3,4-disubstituted galactose residue.
N.O.e. data after pre-irradiation of the anomeric protons and the 3JC,H values associated with the glycosidic linkages for a series of methyl beta-glycosides of trisaccharides that contain 3,4-disubstituted galactose residues have been measured. On the basis of the experimental results and theoretical calculations, it was shown that one preferred conformer (less than 90%) was present for each trisaccharide derivative.
Carbohydrate Conformation↗
Nuclear Overhauser effects and conformations of branched trisaccharide methyl beta-glycosides that contain a 2,3-disubstituted galactose residue.
On the basis of the n.O.e. data and theoretical calculations, it was found that less than 90% of one conformer was present in aqueous solution for each of a series of trisaccharide methyl beta-glycosides with a 2,3-disubstituted galactose residue.
Carbohydrate Conformation↗
[Computer analysis of the structure of branched O-specific polysaccharide of Salmonella arizonae O63 (Arizona 08) from 13C-NMR data].
A computerised approach to the structural analysis of branched regular polysaccharides on the basis of the 13C NMR spectra is described. Deviations from additivity of the glycosidation effects for the monosaccharides arranged in branch points are taken into account. The approach has been verified by using data on bacterial polysaccharide of S. arizonae 063.
Antigens, Bacterial↗
[Principles of spatial organization of group-specific glycoproteins].
Theoretical conformational analysis of O-glycosylated polypeptide chain has been carried out. It is shown that formation of a regular structure is possible, in which the peptide backbone is covered by a layer of well-packed carbohydrate side chains. A beta-barrel is proposed as the spatial model of blood group-specific glycoproteins; it consists of glycosylated beta-hairpins, which interact if they are sterically close. In this beta-barrel the peptide backbone forms an inner "tunnel" which is isolated by the compact carbohydrate coat.
ABO Blood-Group System↗
A computer-assisted structural analysis of regular polysaccharides on the basis of 13C-n.m.r. data.
A computerised approach to the structural analysis of unbranched regular polysaccharides is described, which is based on an evaluation of the 13C-n.m.r. spectra for all possible primary structures within the additive scheme starting from the chemical shifts of the 13C resonances of the constituent monosaccharides and the average values of the glycosylation effects. The analysis reveals a structure (or structures), the evaluated spectrum of which resembles most closely that observed. The approach has been verified by using a series of bacterial polysaccharides of known structure and, in combination with methylation analysis data, for the determination of the presently unknown structures of the O-specific polysaccharides from Salmonella arizonae O59 and O63, and Proteus hauseri O19.
Carbohydrate Conformation↗
[Antigenic polysaccharides of bacteria. 31. The structure of the O-specific polysaccharide chain of Pseudomonas aurantiaca IMB 31 lipopolysaccharide].
The O-specific polysaccharide chain of the Pseudomonas aurantiaca IMV 31 lipopolysaccharide contains N-acetyl-L-fucosamine (FucNAc) and di-N-acetyl-D-bacillosamine (2,4-diacetamido-2,4,6-trideoxyglucose, Bac(NAc)2) in the ratio 2:1. On the basis of methylation, solvolysis with anhydrous hydrogen fluoride, and computer-assisted analysis of 13C-NMR spectrum, it was concluded that the trisaccharide repeating unit of the polysaccharide possesses the following structure: structure: ----3)-beta-D-Bac(NAc)2-(1----3)-alpha-L-FucNAc-(1----3)-alpha-L- FucNAc-(1----.
Antigens, Bacterial↗
[The nuclear Overhauser effect and structural factors determining the conformation of disaccharides].
Conformational analysis of 1.2-, 1.3- and 1.4-linked disaccharides built up of aldohexapyranose residues was performed on the basis of interresidue nuclear Overhauser effects in 1H-NMR spectra and theoretical calculation using atom-atom potential functions. It was shown that the preferred conformation of the disaccharides is determined by the following factors: absolute configurations of monosaccharide residues, configuration and position of the glycosidic linkage, orientation of protons at the aglycon carbon atom involved in the glycosidic linkage and at the adjacent carbons atoms.
Carbohydrate Conformation↗
[Antigenic bacterial polysaccharides. 23. The structure of the O-specific polysaccharide chain of Salmonella arizonae 059 lipopolysaccharide].
The O-specific polysaccharide of Salmonella arizonae O59 (Arizona 19) is composed of D-galactose, N-acetyl-D-glucosamine, and N-acetyl-L-fucosamine (FucNAc, 2-acetamido-2,6-dideoxy-L-galactose) in the ratio 1:1:1. The computerized calculation of the 13C NMR spectrum of the polysaccharide, based on the monosaccharide composition, spectra of the free monosaccharides and glycosydation effects, together with the chemical analysis (methylation and Smith degradation) showed that the polysaccharide is built up of trisaccharide repeating units of the following structure: ----3)-alpha-L-FucNAcp(1----3)-beta-D-GlcNAcp-(1----2)-beta- D-Galp-1(----. The molecular basis of serological interrelations between S. arizonae O59 and Pseudomonas aeruginosa O7 (Lányi) is discussed.
Antigens, Bacterial↗
[Antigenic bacterial polysaccharides. 24. The structure of the O-specific polysaccharide chain of Salmonella arizonae 063 (Arizona 08) lipopolysaccharide].
The O-specific polysaccharide chain of the Salmonella arizonae O63 lipopolysaccharide is composed of D-glucose, D-galactose, N-acetyl-D-galactosamine, and 3-acetamido-3,6-dideoxy-D-galactose (Fuc3NAc) residues in the ratio 1:1:2:1. On the basis of methylation analysis and calculations of 13C-NMR-spectra of the polysaccharide and of the product of its selective cleavage with anhydrous hydrogen fluoride, the linear polymer lacking 3-acetamido-3,6-dideoxygalactose, it was concluded that the polysaccharide has the following structure: (Formula: see text).
Antigens, Bacterial↗
[Computer analysis of polysaccharides with linear repetitive link from 13C-NMR data].
The possibility of computerised analysis of primary structures of polysaccharides on the basis of 13C NMR data and average values of alpha- and beta-effects of glycosidation was evaluated. Theoretical 13C NMR spectra for all possible structures of some linear polysaccharides were calculated by using additive scheme of glycosidation effects. In each case it was found that the structure characterised by the least sum of squared deviations of chemical shifts for the signals in the calculated and experimental spectra corresponds to the sequence and modes of linkages between monosaccharide residues in polysaccharides determined by an independent way.
Carbohydrate Sequence↗
[Experimental and theoretical conformation analysis of the O-antigenic polysaccharide from Pseudomonas cepacia strain 3181. I. Disaccharide links].
Nuclear Overhauser effects, with preirradiation of glycoside bond anomeric protons, coupling constants 3J C3, H1' and 3J C1', H4 and linkage optical rotations A were measured for L-Rha beta 1-3-L-Rha alpha 1-OMe and L-Rha alpha 1-3-L-Rha alpha 1-OMe which are the models of the disaccharide units of the Pseudomonas cepacia polysaccharide. Theoretical conformational analysis was carried out in terms of a mechanical molecular model approximation. The spatial structures of these disaccharides as well as of D-Rha alpha 1-2-D-Rha beta 1-OMe in aqueous solutions were discussed basing on the obtained results.
Antigens, Bacterial↗
[Experimental and theoretical conformation analysis of the O-antigenic polysaccharide from Pseudomonas cepacia strain 3181. II. The polysaccharide].
The spatial structure of Pseudomonas cepacia 3181 polysaccharide in aqueous solution is discussed basing on the data of nuclear Overhauser effect, observed with preirradiation of anomeric protons of all 3 D-rhamnose residues in the repeat unit, and theoretical conformational analysis. It is shown that conformational states of the free disaccharides and corresponding disaccharide units of the polysaccharide are similar. All conformations of the polysaccharide may be described by one shape representing an extended structure with characteristic turns in the D-Rha alpha 1-2-D-Rha beta 1-3-D-Rha units.
Antigens, Bacterial↗
[Theoretical conformation analysis of tetrasaccharide-repeated links of the Shigella flexneri O-antigenic polysaccharide].
Theoretical conformational analysis of four tetrasaccharide repeating units of the Shigella flexneri serogroup Y polysaccharide has been carried out. Interdependency of conformational states of neighbouring disaccharide units in the oligosaccharides has been investigated and conformational distribution of tetrasaccharides in solution calculated. Taking into account the entropy of oligosaccharide chains is shown to lead to significant correction of the results.
Antigens, Bacterial↗
[Conformation analysis of oligosaccharide determinants of group substances with Le specificity].
Theoretical conformational analysis of the tri- and tetrasaccharides determining group specificity Lea, Leb, and H has been carried out. It is shown that these oligosaccharides are structurally rigid systems and in aqueous solution are present predominantly (statistical weight greater than 95%) in the only conformation.
Epitopes↗
[Theoretical conformation analysis of specific O-antigenic polysaccharides. Polysaccharide of Shigella dysenteriae of serotype 2].
Theoretical conformational analysis of Shigella dysenteriae serotype 2 polysaccharide containing repeating unit: -4Gal beta 1-3GalNAc alpha 1-3(GlcNAc alpha 1-4)GalNAc alpha 1-4Glc alpha 1- has been carried out. It is shown that spatial forms of the polymer are determined by conformational states of Glc alpha 1-4Gal links which form the internal bends of the chain. The structures of low energy are shown to be left three-fold helices with an axially projected repeat of approximately 12 A. N-Acetamide groups of side residues alpha-D-GlcNAc are the most accessible for intermolecular interactions and may determine immunological specificity of the polysaccharide.
Antigens, Bacterial↗