Taxonomic group: bacteria / Firmicutes
(Phylum: Firmicutes)
Associated disease: diarrhea [ICD11:
ME05.1 
, ICD11:
SA55 ]
NCBI PubMed ID: 37734222Publication DOI: 10.1016/j.carres.2023.108937Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: G. Widmalm <goran.widmalm
su.se>
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
Carbohydrate structures containing alkyl groups as aglycones are useful for investigating enzyme activity and glycan-protein interactions. Moreover, linker-containing oligosaccharides with a spacer group are commonly used to print glycan microarrays or to prepare protein-conjugates as vaccine candidates. The structural accuracy of these synthesized glycans are essential for interpretation of results from biological experiments in which the compounds have been used and NMR spectroscopy can unravel and confirm their structures. An approach for efficient 1H and 13C NMR chemical shift assignments employed a parallel NOAH-10 measurement followed by NMR spin-simulation to refine the 1H NMR chemical shifts, as exemplified for a disaccharide with an azidoethyl group as an aglycone, the NMR chemical shifts of which have been used to enhance the quality of CASPER (http://www.casper.organ.su.se/casper/). The CASPER program has been further developed to aid characterization of linker-containing oligo- and polysaccharides, either by chemical shift prediction for comparison to experimental NMR data or as structural investigation of synthesized glycans based on acquired unassigned NMR data. The ability of CASPER to elucidate structures of linker-containing oligosaccharides is demonstrated and comparisons to assigned or unassigned NMR data show the utility of CASPER in supporting a proposed oligosaccharide structure. Prediction of NMR chemical shifts of an oligosaccharide, corresponding to the repeating unit of an O-antigen polysaccharide, having a linker as an aglycone and a non-natural substituent derivative thereof are presented to exemplify the diversity of structures handled. Furthermore, NMR chemical shift predictions of synthesized polysaccharides, corresponding to bacterial polysaccharides, containing a linker are described showing that in addition to oligosaccharide structures also polysaccharide structures having an aglycone spacer group can be analyzed by CASPER.
NMR, glycan, absolute configuration, aglycone, cosmic truth, p-NOAH
Structure type: oligomer
Location inside paper: Scheme 1, compound 11
Aglycon: (->1)(CH2)5NH2 (5-aminopentyl)
Compound class: CPS
Contained glycoepitopes: IEDB_130701,IEDB_1394181,IEDB_144983,IEDB_152206,IEDB_983930,SB_44,SB_67,SB_72
Methods: NMR-2D, NMR, computer analysis with CASPER
Synthetic data: chemical
Related record ID(s): 22371, 22372
NCBI Taxonomy refs (TaxIDs): 208479
Show glycosyltransferases
There is only one chemically distinct structure:
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(later renamed to: Enterocloster bolteae 16351)