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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
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
Karolinska Institute.
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
2013 (engelsk)Inngår i: ChemPlusChem, ISSN 2192-6506, Vol. 78, nr 11, s. 1327-1329Artikkel i tidsskrift (Fagfellevurdert) 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.

sted, utgiver, år, opplag, sider
2013. Vol. 78, nr 11, s. 1327-1329
Emneord [en]
analytical methods, antigens, carbohydrates, CASPER, NMR spectroscopy
HSV kategori
Forskningsprogram
organisk kemi
Identifikatorer
URN: urn:nbn:se:su:diva-93838DOI: 10.1002/cplu.201300273ISI: 000326900600005OAI: oai:DiVA.org:su-93838DiVA, id: diva2:649199
Forskningsfinansiär
EU, FP7, Seventh Framework Programme, 215536Swedish Research CouncilKnut and Alice Wallenberg FoundationTilgjengelig fra: 2013-09-17 Laget: 2013-09-17 Sist oppdatert: 2016-10-18bibliografisk kontrollert
Inngår i avhandling
1. NMR spectroscopy in structural and conformational analysis of bacterial polysaccharides
Åpne denne publikasjonen i ny fane eller vindu >>NMR spectroscopy in structural and conformational analysis of bacterial polysaccharides
2013 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
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.

sted, utgiver, år, opplag, sider
Stockholm: Department of Organic Chemistry, Stockholm University, 2013. s. 83
Emneord
Nuclear Magnetic Resonance, carbohydrates, O-antigen polysaccharide
HSV kategori
Forskningsprogram
organisk kemi
Identifikatorer
urn:nbn:se:su:diva-93833 (URN)978-91-7447-758-0 (ISBN)
Disputas
2013-10-18, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (engelsk)
Opponent
Veileder
Forskningsfinansiär
EU, FP7, Seventh Framework Programme, 215536
Merknad

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 6: Manuscript.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

Tilgjengelig fra: 2013-09-26 Laget: 2013-09-17 Sist oppdatert: 2018-03-14bibliografisk kontrollert

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