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Computational Analysis of Carbohydrates: Dynamical Properties and Interactions
Stockholm University, Faculty of Science, Department of Organic Chemistry.
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 [en]
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: urn:nbn:se:su:diva-538ISBN: 91-7155-080-1 (print)OAI: oai:DiVA.org:su-538DiVA: diva2:195198
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
List of papers
1. Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates
Open this publication in new window or tab >>Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates
2003 In: Carbohydrate Research, ISSN 0008-6215, Vol. 338, no 5, 393-398 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23894 (URN)
Note
Part of urn:nbn:se:su:diva-538Available from: 2005-05-13 Created: 2005-05-13Bibliographically approved
2. 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
3. A conformational dynamics study of a-L-Rhap-(1-->2)[a-L-Rhap-(1-->3)]-a-L-Rhap-OMe in solution by NMR experiments and molecular simulations
Open this publication in new window or tab >>A conformational dynamics study of a-L-Rhap-(1-->2)[a-L-Rhap-(1-->3)]-a-L-Rhap-OMe in solution by NMR experiments and molecular simulations
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Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-23896 (URN)
Note
Part of urn:nbn:se:su:diva-538Available from: 2005-05-13 Created: 2005-05-13 Last updated: 2010-01-13Bibliographically approved
4. Stereochemical assignment of diastereomeric imidazolidinone ring containing bicyclic sugar-peptide addects: NMR Spectroscopy and molecular calculations
Open this publication in new window or tab >>Stereochemical assignment of diastereomeric imidazolidinone ring containing bicyclic sugar-peptide addects: NMR Spectroscopy and molecular calculations
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2004 In: European Journal of Organic Chemistry, ISSN 1434-193X, no 22, 4641-4647 p.Article in journal (Refereed) Published
Identifiers
urn:nbn:se:su:diva-23897 (URN)
Note
Part of urn:nbn:se:su:diva-538Available from: 2005-05-13 Created: 2005-05-13Bibliographically approved
5. Interaction studies of a Salmonella enteritidis O-antigen octasaccharide to Phage P22 tail spike protein by NMR spectroscopy and molecular modelling
Open this publication in new window or tab >>Interaction studies of a Salmonella enteritidis O-antigen octasaccharide to Phage P22 tail spike protein by NMR spectroscopy and molecular modelling
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Manuscript (Other academic)
Identifiers
urn:nbn:se:su:diva-23898 (URN)
Note
Part of urn:nbn:se:su:diva-538Available from: 2005-05-13 Created: 2005-05-13 Last updated: 2010-01-13Bibliographically approved

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