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Automatic structure determination of regular polysaccharides based solely on NMR spectroscopy
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.
2011 (English)In: Biomacromolecules, ISSN 1525-7797, E-ISSN 1526-4602, Vol. 12, no 11, 3851-3855 p.Article in journal (Refereed) Published
Abstract [en]

The structural analysis of polysaccharides requires that the sugar components and their absolute configurations are determined. We here show that this can be performed based on NMR spectroscopy by utilizing butanolysis with (+)- and (-)-2-butanol that gives the corresponding 2-butyl glycosides with characteristic 1H and 13C NMR chemical shifts. The subsequent computer-assisted structural determination by CASPER can then be based solely on NMR data in a fully automatic way as shown and implemented herein. The method is additionally advantageous in that reference data only have to be prepared once and from a user's point of view only the unknown sample has to be derivatized for use in CASPER.

Place, publisher, year, edition, pages
2011. Vol. 12, no 11, 3851-3855 p.
National Category
Organic Chemistry Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:su:diva-70868DOI: 10.1021/bm201169yISI: 000296830600003OAI: oai:DiVA.org:su-70868DiVA: diva2:483486
Funder
Swedish Research CouncilKnut and Alice Wallenberg Foundation
Note

authorCount :3

Available from: 2012-01-25 Created: 2012-01-24 Last updated: 2017-12-08Bibliographically approved
In thesis
1. Computer-Assisted Carbohydrate Structural Studies and Drug Discovery
Open this publication in new window or tab >>Computer-Assisted Carbohydrate Structural Studies and Drug Discovery
2011 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates are abundant in nature and have functions ranging from energy storage to acting as structural components. Analysis of carbohydrate structures is important and can be used for, for instance, clinical diagnosis of diseases as well as in bacterial studies. The complexity of glycans makes it difficult to determine their structures. NMR spectroscopy is an advanced method that can be used to examine carbohydrates at the atomic level, but full assignments of the signals require much work. Reliable automation of this process would be of great help. Herein studies of Escherichia coli O-antigen polysaccharides are presented, both a structure determination by NMR and also research on glycosyltransferases which assemble the polysaccharides. The computer program CASPER has been improved to assist in carbohydrate studies and in the long run make it possible to automatically determine structures based only on NMR data.

Detailed computer studies of glycans can shed light on their interactions with proteins and help find inhibitors to prevent unwanted binding. The WaaG glycosyltransferase is important for the formation of E. coli lipopolysaccharides. Molecular docking analyses of structures confirmed to bind this enzyme have provided information on how inhibitors could be composed. Noroviruses cause gastroenteritis, such as the winter vomiting disease, after binding human histo-blood group antigens. In one of the projects, fragment-based docking, followed by molecular dynamics simulations and binding free energy calculations, was used to find competitive binders to the P domain of the capsid of the norovirus VA387. These novel structures have high affinity and are a very good starting point for developing drugs against noroviruses. The protein targets in these two projects are carbohydrate binding, but the techniques are general and can be applied to other research projects.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University, 2011. 78 p.
Keyword
Carbohydrates, molecular docking, molecular dynamics simulation, fragment-based virtual screening, NMR spectroscopy, computer-aided drug design, computer-aided structure elucidation, glycosyltransferases, Escherichia coli
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-56411 (URN)978-91-7447-245-5 (ISBN)
Public defence
2011-05-25, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 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 4: Submitted. Paper 5: Manuscript. Paper 6. Manuscript.Available from: 2011-05-03 Created: 2011-04-15 Last updated: 2012-07-03Bibliographically approved
2. 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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