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Conformational Dynamics of Carbohydrates Studied by NMR Spectroscopy and Molecular Simulations
Stockholm University, Faculty of Science, Department of Organic Chemistry.
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 [en]
Carbohydrates, NMR, Molecular Dynamics, Conformation, Dynamics, Residual Dipolar Couplings, Cyclodextrins, Oligosaccharides
National Category
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-1023ISBN: 01-7155-262-6 OAI: oai:DiVA.org:su-1023DiVA: diva2:189228
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
List of papers
1. Molecular properties related to the anomalous solubility of β-cyclodextrin
Open this publication in new window or tab >>Molecular properties related to the anomalous solubility of β-cyclodextrin
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2004 In: Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 108, no 14, 4236-4238 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-22653 (URN)
Note
Part of urn:nbn:se:su:diva-1023Available from: 2006-05-11 Created: 2006-05-11Bibliographically approved
2. Molecular structure and dynamics of α, β and γ-cyclodextrins
Open this publication in new window or tab >>Molecular structure and dynamics of α, β and γ-cyclodextrins
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Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-22654 (URN)
Note
Part of urn:nbn:se:su:diva-1023Available from: 2006-05-11 Created: 2006-05-11 Last updated: 2010-01-13Bibliographically approved
3. Conformational Dynamics of Oligosaccharides: NMR Techniques and Computer Simulations
Open this publication in new window or tab >>Conformational Dynamics of Oligosaccharides: NMR Techniques and Computer Simulations
2006 (English)In: NMR Spectroscopy and Computer Modeling of Carbohydrates: Recent Advances / [ed] Johannes F. G Vliegenthar & Robert J. Woods, American Chemical Society (ACS), 2006, 20-39 p.Chapter in book (Refereed)
Abstract [en]

NMR spectroscopy techniques in conjunction with molecular dynamics simulations facilitate description of conformation and dynamics of oligosaccharides in solution. Herein we describe approaches based on hetero-nuclear carbon-proton spin-spin coupling constants useful for assessing conformational preferences at the glycosidic linkage, exemplified for á-cyclodextrin. Furthermore, we utilize hetero-nuclear carbon-proton residual dipolar couplings together with molecular dynamics simulations in the analysis of the conformational dynamics of the milk oligosaccharide Lacto-N-neotetraose.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2006
Series
ACS Symposium Series, 930
National Category
Chemical Sciences
Identifiers
urn:nbn:se:su:diva-22655 (URN)10.1021/bk-2006-0930.ch002 (DOI)9780841239531 (ISBN)
Available from: 2006-05-11 Created: 2006-05-11 Last updated: 2013-07-08Bibliographically approved
4. Molecular conformations of a disaccharide investigated using NMR spectroscopy
Open this publication in new window or tab >>Molecular conformations of a disaccharide investigated using NMR spectroscopy
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2006 (English)In: Journal of Biomolecular NMR, ISSN 0925-2738, E-ISSN 1573-5001, Vol. 35, 89-101 p.Article in journal (Refereed) Published
Abstract [en]

The molecular structure of -l-Rhap-(1→ 2)--l-Rhap-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3 J CH couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, , related to the two glycosidic linkage torsion angles and was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order. Electronic Supplementary Material  Supplementary material is available for this article at http://www.dx.doi.org/10.1007/s10858-006-9006-0 and is accessible for authorized users.

Place, publisher, year, edition, pages
Springer Netherlands, 2006
Keyword
carbohydrates, conformation, NMR spectroscopy, residual dipolar couplings, oligosaccharides
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-19530 (URN)10.1007/s10858-006-9006-0 (DOI)
Available from: 2008-01-15 Created: 2008-01-15 Last updated: 2017-12-13Bibliographically approved
5. Conformational analysis of the tetrasaccharide Lacto-N-neotetraose based on solution state NMR spectroscopy and molecular dynamics simulations
Open this publication in new window or tab >>Conformational analysis of the tetrasaccharide Lacto-N-neotetraose based on solution state NMR spectroscopy and molecular dynamics simulations
2005 In: Journal of Physical Chemistry B, ISSN 1089-5647, Vol. 109, no 36, 17320-17326 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-22657 (URN)
Note
Part of urn:nbn:se:su:diva-1023Available from: 2006-05-11 Created: 2006-05-11Bibliographically approved
6. Conformational dynamics of the pentasaccharide LNF-1 from NMR spectroscopy and molecular dynamics simulations
Open this publication in new window or tab >>Conformational dynamics of the pentasaccharide LNF-1 from NMR spectroscopy and molecular dynamics simulations
Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-22658 (URN)
Note
Part of urn:nbn:se:su:diva-1023Available from: 2006-05-11 Created: 2006-05-11 Last updated: 2010-01-13Bibliographically approved

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