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NMR Chemical Shift Predictions and Structural Elucidation of Oligo- and Polysaccharides by the Computer Program CASPER
Stockholm University, Faculty of Science, Department of Organic Chemistry.ORCID iD: 0000-0001-5657-8635
Stockholm University, Faculty of Science, Department of Organic Chemistry.ORCID iD: 0000-0001-8303-4481
2017 (English)In: NMR in Glycoscience and Glycotechnology / [ed] Koichi Kato, Thomas Peters, Royal Society of Chemistry, 2017, 335-352 p.Chapter in book (Refereed)
Abstract [en]

Glycans are often linked to proteins or lipids in the form of glycoconjugates but these highly complex molecules also have biological functions as oligosaccharides per se. The limited dispersion in NMR spectra of carbohydrates makes their analysis and interpretation very cumbersome. The computer program CASPER, which is a web-based tool, facilitates prediction 1H and 13C NMR chemical shifts of oligo- or polysaccharide structures defined by the user, makes it possible to carry out an NMR-based sugar analysis including determination of absolute configuration and to perform structure elucidation of unknown glycans using unassigned NMR spectra as input to the program. The output from the program contains, inter alia, tentatively assigned NMR resonances, proposed sugar components, structural suggestions ranked according to the similarity between their predicted chemical shifts and the experimental data as well as 3D structures in pdb-format generated seamlessly by the CarbBuilder program as a part of the CASPER-GUI.

Place, publisher, year, edition, pages
Royal Society of Chemistry, 2017. 335-352 p.
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-146862ISBN: 978-1-78262-310-6 (print)ISBN: 978-1-78801-128-0 (electronic)OAI: oai:DiVA.org:su-146862DiVA: diva2:1141094
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2017-09-14Bibliographically approved
In thesis
1. Structure Elucidations of Bacterial Polysaccharides using NMR Spectroscopy and Bioinformatics
Open this publication in new window or tab >>Structure Elucidations of Bacterial Polysaccharides using NMR Spectroscopy and Bioinformatics
2017 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates are ubiquitous components in nature involved in a range of tasks. They cover every cell and contribute both structural stability as well as identity. Lipopolysaccharides are the outermost exposed part of the bacterial cell wall and the primary target for host-pathogen recognition. Understanding the structure and biosynthesis of these polysaccharides is crucial to combat disease and develop new medicine. Structural determinations can be carried out using NMR spectroscopy, a powerful tool giving information on an atomistic scale. This thesis is focused on method development to study polysaccharide structures as well as application on bacterial lipopolysaccharides. The focus has been to incorporate a bioinformatics approach prior to analysis by NMR spectroscopy, and then computer assisted methods to aid in the subsequent analysis of the spectra.

The third chapter deals with the recent developments of ECODAB, a tool that can help predict structural fragments in Escherichia coli O-antigens. It was migrated to a relational database and the aforementioned predictions can now be made automatically by ECODAB. The fourth chapter gives insight into the program CASPER, a computer program that helps with structure determination of oligo- and polysaccharides. An approach to determine substituent positions in polysaccharides was investigated. The underlying database was also expanded and the improved capabilities were demonstrated by determining O-antigenic structures that could not previously be solved. The fifth chapter is an application to O‑antigen structures of E. coli strains. This is done by a combination of NMR spectroscopy and bioinformatics to predict components as well as linkages prior to spectra analysis. In the first case, a full structure elucidation was performed on E. coli serogroup O63, and in the second case a demonstration of the bioinformatics approach is done to E. coli serogroup O93. In the sixth chapter, a new version of the CarbBuilder software is presented. This includes a more robust building algorithm that helps build sterically crowded polysaccharide structures, as well as a general expansion of possible components. 

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University, 2017. 65 p.
Keyword
Carbohydrates, Bioinformatics, NMR Spectroscopy, Lipopolysaccharide, Glycosyltransferase, Computer-Assisted Structure Elucidation, O-antigen, Biosynthesis
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-146867 (URN)978-91-7649-952-8 (ISBN)978-91-7649-953-5 (ISBN)
Public defence
2017-10-27, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 5: Manuscript.

Available from: 2017-10-04 Created: 2017-09-13 Last updated: 2017-10-04Bibliographically approved

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