Change search
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Molecular conformations of a disaccharide investigated using NMR spectroscopy
Stockholm University, Faculty of Science, Department of Organic Chemistry.
Stockholm University, Faculty of Science, Department of Physical, Inorganic and Structural Chemistry.
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 Physical, Inorganic and Structural Chemistry.
Show others and affiliations
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. Vol. 35, 89-101 p.
Keyword [en]
carbohydrates, conformation, NMR spectroscopy, residual dipolar couplings, oligosaccharides
National Category
Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-19530DOI: 10.1007/s10858-006-9006-0OAI: oai:DiVA.org:su-19530DiVA: diva2:186054
Available from: 2008-01-15 Created: 2008-01-15 Last updated: 2017-12-13Bibliographically 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
2. Computational Analysis of Carbohydrates: Dynamical Properties and Interactions
Open this publication in new window or tab >>Computational Analysis of Carbohydrates: Dynamical Properties and Interactions
2005 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The approach used in the population analysis included a least-square fit technique to match T1 elaxation parameters. The results showed good agreement with experimental T-ROE build-up curves, and three states were concluded to be involved. In Paper IV, carbohydrate moieties were used in the development of prodrug candidates, to “hide” peptide opioid receptor agonists. Langevin dynamics and quantum chemical methods were employed to elucidate the structural preference of the compound. The results showed a chemical shift difference between hydrogens across the ring for the two isomers as well as a difference in the coupling constant, when taking the dynamics into account. In Paper V, the interaction of the Salmonella enteritidis bacteriophage P22 with its host bacterium, involves an initial hydrolysis of the O-antigenic polysaccharide (O-PS). Docking calculations were used to examine the binding between the Phage P22 tail-spike protein and the O-PS repeating unit. Results indicated a possible active site in conjunction with NMR measurements.

Place, publisher, year, edition, pages
Stockholm: Institutionen för organisk kemi, 2005. 208 p.
Keyword
Carbohydrate, DFT, ab initio, docking calculations, Molecular dynamics, Langevin Dynaimcs, structure analysis, carbohydrate-protein interaction, Chemical shift calculations, Spin spin coupling constants.
National Category
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-538 (URN)91-7155-080-1 (ISBN)
Public defence
2005-06-03, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2005-05-13 Created: 2005-05-13 Last updated: 2010-02-03Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full text

Search in DiVA

By author/editor
Stevensson, BaltzarWidmalm, GöranMaliniak, Arnold
By organisation
Department of Organic ChemistryDepartment of Physical, Inorganic and Structural Chemistry
In the same journal
Journal of Biomolecular NMR
Physical Chemistry

Search outside of DiVA

GoogleGoogle Scholar

doi
urn-nbn

Altmetric score

doi
urn-nbn
Total: 77 hits
CiteExportLink to record
Permanent link

Direct link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf