Sequence determination of oligosaccharides and regular polysaccharides using NMR spectroscopy and a novel Web-based version of the computer program CASPER.
A WWW-interface to a program for structure elucidation of oligo- and polysaccharides using NMR data, CASPER, is presented. The interface and the underlying program have been extensively tested using published data and it was able to simulate 13C NMR spectra of >200 structures with an average error of about 0.3 ppm/resonance. When applied to the repeating units of Escherichia coli O-antigens the published structures were found among the five highest ranked structures in 75% of the cases. The average deviation between calculated and experimental 13C chemical shifts was 0.45 ppm. Oligosaccharide spectra were calculated with even better accuracy (0.23 ppm/resonance) and the correct structure was ranked 1st or 2nd in all the cases examined. Additional NMR experiments that may be required to distinguish between candidate structures are aided by the assignments provided by the program. This computational approach is also suitable for use in structural confirmation of chemically or enzymatically synthesized oligosaccharides. The program is found at http://www.casper.organ.su.se/casper.
Centre for Medical Innovations, Karolinska Institutet, SE-171 77 Stockholm, Sweden.
Per-Erik
PE
Jansson
Roland
R
Stenutz
Göran
G
Widmalm
D002240:Carbohydrate Sequence; D003198:Computer Simulation; D020407:Internet; D019906:Nuclear Magnetic Resonance, Biomolecular; D009844:Oligosaccharides / Q000737:chemistry*; D011134:Polysaccharides / Q000737:chemistry*; D012984:Software
D009844:Oligosaccharides; D011134:Polysaccharides