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Glycan flexibility: Insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Stockholm University, Faculty of Science, Department of Organic Chemistry.
(English)Manuscript (preprint) (Other academic)
Identifiers
URN: urn:nbn:se:su:diva-30114OAI: oai:DiVA.org:su-30114DiVA: diva2:241526
Available from: 2009-10-04 Created: 2009-10-04 Last updated: 2010-01-25Bibliographically approved
In thesis
1. Structure, dynamics and interactions of biomolecules: Investigations by NMR spectroscopy and computational methods
Open this publication in new window or tab >>Structure, dynamics and interactions of biomolecules: Investigations by NMR spectroscopy and computational methods
2009 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis, the structure, dynamics and interactions of proteins and carbohydrates are investigated using mainly NMR spectroscopy and computer simulations.

Oligosaccharides representing a Salmonella O-antigen have been synthesized and their dynamic behavior and interaction with the bacteriophage P22 tail-spike protein have been studied by NMR spectroscopy, MD and docking simulations. A binding mechanism between the protein and the O-antigen has been proposed.

Transient hydrogen bonds have been defined and examined in an E. coli polysaccharide and in a pentasaccharide representing the repeating unit, using MD simulation and NMR spectroscopy.

Conformational dynamics of a trisaccharide representing the repeating unit of an A. salmonicida O-antigen have been investigated by MD simulations. The simulation together with relaxation matrix calculations reveals a conformational exchange on a ns timescale and explains an unusual NOE.

A fragment-based screening for inhibitors of the glycosyltransferase GTB acceptor site has been performed using NMR spectroscopy and SPR. IC50 values of the binding fragments are reported. Complex structures of the fragments and GTB have been proposed using docking simulations.

A fragment-based screening for inhibitors of the WaaG glycosyltransferase donor site has been performed using NMR spectroscopy and three compounds were selected. Structures of the WaaG-fragment complexes have been suggested from docking simulations. Binding of natural substrates and activity has also been investigated by NMR spectroscopy. MD simulations have been carried out on WaaG with and without bound donor substrate. The simulation revealed a conformational change upon substrate binding.

Interactions between HEWL and carbohydrate ligands have been investigated, using a combination of weak affinity chromatography, NMR spectroscopy and computer simulations. KDs of the ligands have been presented as well as the solution structures of two HEWL-disaccharide complexes.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University, 2009. 82 p.
Keyword
NMR spectroscopy, MD simulation, carbohydrate synthesis, protein-ligand interaction, glycosyltransferase
National Category
Chemical Sciences
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-30120 (URN)978-91-7155-953-1 (ISBN)
Public defence
2009-11-13, 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 3: Submitted. Paper 4: Submitted. Paper 5: In progress. Paper 6: In progress. Paper 7: Manuscript.Available from: 2009-10-22 Created: 2009-10-04 Last updated: 2011-11-23Bibliographically approved

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