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Glycosyltransferase functions of E. coli O-antigens
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.
2010 (English)In: Glycobiology, ISSN 0959-6658, E-ISSN 1460-2423, Vol. 20, no 3, 366-368 p.Article in journal (Refereed) Published
Abstract [en]

ECODAB (the E. coli O-antigen database) has been expanded to include information about glycosyltransferases (GTs) involved in the assembly of the O-antigen polysaccharide. Similarity searches have been performed to be able to determine GT functions that have not been reported prior to this work. In addition to suggesting the function of 179 GTs, the approach leads to the prediction of part of the O-antigen structures of a number of serogroups. The procedure suggests a novel way of combining genetic information with experimental techniques in structural analysis of oligo- and polysaccharides.

Place, publisher, year, edition, pages
2010. Vol. 20, no 3, 366-368 p.
Keyword [en]
database, Escherichia coli, glycosyltransferases, O-antigen, polysaccharides
National Category
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-37218DOI: 10.1093/glycob/cwp185ISI: 000274341300010OAI: oai:DiVA.org:su-37218DiVA: diva2:295412
Available from: 2010-02-17 Created: 2010-02-17 Last updated: 2017-12-12Bibliographically 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

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