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Facile Structural Elucidation of Glycans Using NMR Spectroscopy Data and the Program CASPER: Application to the O-Antigen Polysaccharide of Escherichia coli O155
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Karolinska Institute.
Stockholm University, Faculty of Science, Department of Organic Chemistry.
2013 (English)In: ChemPlusChem, ISSN 2192-6506, Vol. 78, no 11, 1327-1329 p.Article in journal (Refereed) Published
Abstract [en]

The program CASPER was successfully employed to rapidly elucidate a new O-antigen polysaccharide structure (obtained from a strain of Escherichia coli serogroup O155), using solelyunassigned NMR spectroscopy data as input information. Thus, what is considered the most tedious and time-consuming part of the structural elucidation process has been reduced from several hours (or even days) of manual interpretation to about four minutes of automated analysis.

Place, publisher, year, edition, pages
2013. Vol. 78, no 11, 1327-1329 p.
Keyword [en]
analytical methods, antigens, carbohydrates, CASPER, NMR spectroscopy
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-93838DOI: 10.1002/cplu.201300273ISI: 000326900600005OAI: oai:DiVA.org:su-93838DiVA: diva2:649199
Funder
EU, FP7, Seventh Framework Programme, 215536Swedish Research CouncilKnut and Alice Wallenberg Foundation
Available from: 2013-09-17 Created: 2013-09-17 Last updated: 2016-10-18Bibliographically approved
In thesis
1. NMR spectroscopy in structural and conformational analysis of bacterial polysaccharides
Open this publication in new window or tab >>NMR spectroscopy in structural and conformational analysis of bacterial polysaccharides
2013 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates constitute one of the three major classes of biomolecules found in all living cells and, unlike nucleic acids and proteins, their polymeric structures are not based on a template. The structural diversity of these molecules confers them an enormous capacity to encode information in biological systems, acting as efficient mediators in the interaction of the cell with the environment. In order to understand the roles of glycans in biological processes it is of key importance to have a detailed understanding of their structures and conformational preferences, and NMR spectroscopy is one of most powerful techniques for the study of these molecules in solution.

This thesis is focused on the structural and conformational analysis of lipopolysaccharides from Gram-negative bacteria. In the first two projects (Chapter 2 and 3) the structural analyses of the biological repeating units of the O-antigen polysaccharides from E. coli O174ab and O115 are described; in both cases a combination of NMR spectroscopy and gas chromatography techniques were used. Special emphasis was made in the characterization of the O-acetylation patterns observed in the native O-antigen polysaccharide from E. coli O115. Chapter 4 describes the development of a new methodology for the determination of the absolute configuration of monosaccharide components of glycans. This methodology was used in the structural elucidation of the O-antigen PS of E. coli O155 (Chapter 5) that was carried out in a semi-automated manner using the program CASPER and unassigned NMR data. The conformational preferences of O-antigen PS of E. coli O5ac and O5ab are analyzed in Chapter 6, using a combination of NMR spectroscopy and molecular modeling methods. In Chapter 7 the structural analysis is focused on the core region of the LPS, and the structures of the deacylated lipooligosaccharides of three rough mutants of B. melitesis are reported. In several of the aforementioned chapters, the biosynthetic aspects behind the assembly of the respective PSs were examined on the bases of genetic information available in the NCBI and ECODAB databases.  Finally, in Chapter 8, different NMR pulse sequences available for the study of proteins and nucleic acids were evaluated and optimized for the structural analysis of 13C uniformly-labeled oligo- and polysaccharides.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University, 2013. 83 p.
Keyword
Nuclear Magnetic Resonance, carbohydrates, O-antigen polysaccharide
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-93833 (URN)978-91-7447-758-0 (ISBN)
Public defence
2013-10-18, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Funder
EU, FP7, Seventh Framework Programme, 215536
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 6: Manuscript. Paper 7: Manuscript.

Available from: 2013-09-26 Created: 2013-09-17 Last updated: 2013-10-08Bibliographically approved

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