Structure of the polysaccharide S-84 elaborated by Pseudomonas ATCC 31562: depolymerisation using fuming hydrochloric acid.
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Carbohydrate Conformation↗
Biomedical subjects
G Widmalm
Publications and source records attributed to G Widmalm.
A conformational study of alpha-L-Rhap-(1----2)-alpha-L-Rhap-(1----OMe) by NMR nuclear Overhauser effect spectroscopy (NOESY) and molecular dynamics calculations.
The conformational preference of the disaccharide alpha-L-Rhap-(1----2)-alpha-L-Rhap-(1----OMe) (1) about the glycosidic torsion angles, phi and psi, was studied by NMR NOESY spectroscopy and molecular mechanics calculations. The NOE data were consistent with either of two distinct conformations close to minima on a calculated phi/psi potential energy surface. Starting from the lowest energy conformation, a 1-ns molecular dynamics (MD) trajectory was computed in vacuo, from which the NOE curves were simulated and compared to the experimentally observed NOESY data.
Carbohydrate Conformation↗
Conformational states of a TT mismatch from molecular dynamics simulation of duplex d (CGCGATTCGCG).
The TT mismatch region in duplex d (CGCGATTCGCG) was studied using a 500-ps molecular dynamics (MD) simulation in water, and a series of 1-ps MD simulations and energy minimizations in vacuum. The DNA maintained its duplex structure, although the mismatch region showed significantly higher flexibility than the GC regions. The predominant conformation in the 500-ps MD simulation involved an average -42 degrees propeller twist between T6 and T'6, and a -22 degree buckle between A5 and T'7. One hydrogen bond was formed between T6 and T'6, and another between T6 and the O2 of T'7, with both Watson-Crick hydrogen bonds between A5 and T'7 remaining intact. The minimizations resulted in conformations with the equivalent hydrogen-bonding pattern, as well as ones with "wobble pair" hydrogen bonds between T6 and T'6. However, the wobble pair conformation was found to be unstable in the water simulation.
Base Sequence↗
Computer-assisted structural analysis of oligosaccharides using CASPER.
The computer program CASPER for structural analysis has been tested on some oligosaccharides. The program is shown to predict the correct structure of five linear or branched tri- to hexasaccharides using information on components and linkage positions and NMR chemical shifts. Theoligosaccharides are either reducting or methyl glycosides.
Carbohydrate Conformation↗
Structural studies of the Escherichia coli O1A O-polysaccharide, using the computer program CASPER.
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Carbohydrate Sequence↗
CASPER: a computer program used for structural analysis of carbohydrates.
The computer program CASPER and its algorithms are described. The program is aimed at facilitating the determination of structures of oligosaccharides and regular polysaccharides, requiring as input either the one-dimensional 1H or 13C NMR spectrum or the 2D C,H-correlation NMR spectrum together with information on components and linkages. The databases, the method of simulating spectra, options of the program, and techniques for faster calculations are described as well as an example of a structural determination.
Algorithms↗
Structure of the O-antigen polysaccharide from Escherichia coli O18ac: a revision using computer-assisted structural analysis with the program CASPER.
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Antigens, Bacterial↗
Computer-assisted structural analysis of polysaccharides with an extended version of CASPER using 1H- and 13C-n.m.r. data.
The computer program CASPER, used in the structural analysis of polysaccharides composed of repeating units, has been extended. The extended version uses either unassigned 1H- or 13C-n.m.r. chemical shifts or the complete unassigned C,H-correlation spectrum, and can predict the structure of linear and branched oligo- and poly-saccharides. The number of possible structures, consistent with sugar and methylation analysis, can be decreased by the use of 1JC,H and 3JH,H values. The database, which contains 1H- or 13C-n.m.r. chemical shift data for monosaccharides and 1H- or 13C-glycosylation shifts for all types of glycosidic linkages obtained by combination of the monosaccharides, has been increased and now also contains correction values for sugar residues present in branch-point regions. The program has been tested on four polysaccharides of known structure but with different degrees of complexity. For three polysaccharides, the correct structure was suggested; for the fourth, two structures were consistent with the n.m.r. data, one of them being correct.
Carbohydrate Conformation↗
Structural studies of the capsular polysaccharides from Klebsiella types 8 and 82, a reinvestigation.
The structures of the capsular polysaccharides elaborated by Klebsiella types 8 (K8) and 82 (K82) have been reinvestigated. N.m.r. spectroscopy of the original and chemically modified polysaccharides was the principal method used. It is concluded that the polysaccharides are composed of repeating units having the following structures. (Formula: see text). The presence of L-glutamic acid, linked as an amide to the carboxyl group of a uronic acid, has not been observed hitherto in bacterial polysaccharides.
Carbohydrate Conformation↗
Structural studies of the capsular polysaccharide from Streptococcus pneumoniae type 18A.
The structure of the capsular polysaccharide (S18A) elaborated by Streptococcus pneumoniae type 18A has been investigated by using methylation analysis and n.m.r. spectroscopy. It is concluded that the polysaccharide is composed of pentasaccharide repeating-units having the following structure. (formula; see text) In this structure, the absolute configuration of the glycerol 1-phosphate moiety has not been determined but is assumed to be D from biosynthesis considerations. The structure of S18A is, as expected, closely similar to those determined for S18F and S18C.
Carbohydrate Conformation↗
Structural studies of the Escherichia coli O78 O-antigen polysaccharide.
The structure of the O-antigen polysaccharide from Escherichia coli O78 has been investigated; methylation analysis, partial solvolysis with liquid hydrogen fluoride, and 2D-n.m.r. spectroscopy were the principal methods used. It is concluded that the polysaccharide is composed of tetrasaccharide repeating-units having the following structure.----3)-beta-D-GlcpNAc-(1----4)-beta-D-GlcpNAc- (1----4)-beta-D-Manp-(1----4)-alpha-D-Manp-(1----
Antigens, Bacterial↗
Structural studies of the O-antigen polysaccharides of Klebsiella O5 and Escherichia coli O8.
The O-antigen polysaccharides of Klebsiella serotype O5 and Escherichia coli serotype O8 are serologically very similar or identical. The structures of these two polysaccharides have now been re-investigated. N.m.r. spectroscopy, chromium trioxide oxidation, hydrolysis with a specific phage enzyme, and f.a.b. mass spectrometry were the principal methods used. It is concluded that the O-antigen has the following structure, in which D-Man3Me is 3-O-methyl-D-mannose and n is approximately 10. (Formula: see text) Biosynthetic studies indicate that these antigens are synthesised by addition of D-mannopyranosyl groups to the "non-reducing" end of the mannan chain, and it seems possible that addition of a 3-O-methyl-D-mannopyranosyl group involves termination.
Carbohydrate Conformation↗