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Conformational dynamics of the pentasaccharide LNF-1 from NMR spectroscopy and molecular dynamics simulations
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Manuscript (Other academic)
Identifiers
URN: urn:nbn:se:su:diva-22658OAI: oai:DiVA.org:su-22658DiVA: diva2:189227
Note
Part of urn:nbn:se:su:diva-1023Available from: 2006-05-11 Created: 2006-05-11 Last updated: 2010-01-13Bibliographically approved
In thesis
1. Conformational Dynamics of Carbohydrates Studied by NMR Spectroscopy and Molecular Simulations
Open this publication in new window or tab >>Conformational Dynamics of Carbohydrates Studied by NMR Spectroscopy and Molecular Simulations
2006 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Carbohydrates play important roles in biological processes. Their function is closely related to their conformation. In this thesis, conformational studies of carbohydrates by NMR spectroscopy and molecular dynamics computer simulations are described.

The first two papers discuss the anomalous solubility of β-cyclodextrin compared to other cyclodextrins. Time correlation functions revealed flexibility in all cyclodextrins. Molecular dynamics computer simulations showed that the glycosidic linkages were rather rigid and the flexibility was suggested to be macrocyclic. From spatial distribution functions β-cyclodextrin was found to have greater ability to order the surrounding water than the other cyclodextrins. Paper III deals with some of the difficulties of conformational studies. In Paper IV, a new method, Additative Potential Maximum Entropy, APME, is applied to a disaccharide. Conformational distribution functions are derived from NOEs, J-couplings and residual dipolar couplings and calculated from computer simulations. All distribution functions were found to be in good agreement. In papers V and VI oligosaccharides from human milk are studied. Residual dipolar coupling, J-couplings and cross relaxation rates were measured by NMR spectroscopy and molecular dynamics computer simulations were carried out. Both oligosaccharides showed high flexibility for the β-D-GlcpNAc-(1→3)-β-D-Galp linkage.

Place, publisher, year, edition, pages
Stockholm: Institutionen för organisk kemi, 2006. 156 p.
Keyword
Carbohydrates, NMR, Molecular Dynamics, Conformation, Dynamics, Residual Dipolar Couplings, Cyclodextrins, Oligosaccharides
National Category
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-1023 (URN)01-7155-262-6 (ISBN)
Public defence
2006-06-02, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2006-05-11 Created: 2006-05-11 Last updated: 2010-02-01Bibliographically approved

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