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Complete 1H and 13C NMR chemical shift assignments of mono- to tetrasaccharides as basis for NMR chemical shift predictions of oligo- and polysaccharides using the computer program CASPER
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Stockholm University, Faculty of Science, Department of Organic Chemistry.ORCID iD: 0000-0001-5657-8635
Show others and affiliations
(English)Manuscript (preprint) (Other academic)
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-146864OAI: oai:DiVA.org:su-146864DiVA, id: diva2:1141097
Available from: 2017-09-13 Created: 2017-09-13 Last updated: 2018-03-27Bibliographically 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. p. 65
Keywords
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
2. Synthesis and analysis of carbohydrates related to bacterial polysaccharides
Open this publication in new window or tab >>Synthesis and analysis of carbohydrates related to bacterial polysaccharides
2018 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The outer surface of bacteria is composed of around 75% carbohydrates, which are vital for the bacteria to survive and communicate with the host biological system. The thesis discusses different properties of carbohydrates that are essential for understanding the bacterial behavior in biological systems. The first three chapters give an overview of carbohydrates.

The fourth chapter discusses the synthesis of four amide-substituted 3,6-dideoxy-α-D-galactopyranosides, namely, methyl α-3,6-dideoxy-3-formamido-, acetamido-, (R)-3-hydroxybutyramido-, and (4-hydroxybutyramido)-D-galactopyranoside. These sugars were found as components of some bacterial O-antigens; the study is a step toward the synthesis of oligosaccharides that contain them. The fifth chapter describes the exchange kinetics of the formyl and acetyl derivatives that were synthesized. Both of them have two conformational states for the amide side-chain. 13C-NMR saturation transfer experiments are utilized for these measurements to reveal more about their properties in solution.

In chaptr six, NMR and conformational analysis of oligosaccharides related to the O-antigen of Yersinia enterocolitica O:3 bacteria were carried out to obtain more information regarding their 3D structure.

Chapter seven is focusing on the development of CASPER, a program for rapid assignment of 1H- and 13C-NMR chemical shifts of bacterial lipopolysaccharides, by adding more sugars into its database and testing it for naturally occurring LPS as well as extending the scope for synthetic carbohydrates, which is planned to be developed further in the future.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University, 2018. p. 53
Keywords
carbohydrates, synthesis, conformation, NMR, O-antigen, computer-assisted structure elucidation
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-154449 (URN)978-91-7797-216-7 (ISBN)978-91-7797-217-4 (ISBN)
Public defence
2018-05-15, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.

Available from: 2018-04-20 Created: 2018-03-27 Last updated: 2018-04-23Bibliographically approved

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Angles d'Ortoli, ThibaultMobarak, HaniStåhle, JonasWidmalm, Göran
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