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Stereochemical assignment of diastereomeric imidazolidinone ring containing bicyclic sugar-peptide addects: NMR Spectroscopy and molecular calculations
Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
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2004 Ingår i: European Journal of Organic Chemistry, ISSN 1434-193X, nr 22, s. 4641-4647Artikel i tidskrift (Refereegranskat) Published
Ort, förlag, år, upplaga, sidor
2004. nr 22, s. 4641-4647
Identifikatorer
URN: urn:nbn:se:su:diva-23897OAI: oai:DiVA.org:su-23897DiVA, id: diva2:195196
Anmärkning
Part of urn:nbn:se:su:diva-538Tillgänglig från: 2005-05-13 Skapad: 2005-05-13Bibliografiskt granskad
Ingår i avhandling
1. Computational Analysis of Carbohydrates: Dynamical Properties and Interactions
Öppna denna publikation i ny flik eller fönster >>Computational Analysis of Carbohydrates: Dynamical Properties and Interactions
2005 (Engelska)Doktorsavhandling, sammanläggning (Övrigt vetenskapligt)
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.

Ort, förlag, år, upplaga, sidor
Stockholm: Institutionen för organisk kemi, 2005. s. 208
Nyckelord
Carbohydrate, DFT, ab initio, docking calculations, Molecular dynamics, Langevin Dynaimcs, structure analysis, carbohydrate-protein interaction, Chemical shift calculations, Spin spin coupling constants.
Nationell ämneskategori
Organisk kemi
Identifikatorer
urn:nbn:se:su:diva-538 (URN)91-7155-080-1 (ISBN)
Disputation
2005-06-03, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 12 A, Stockholm, 10:00 (Engelska)
Opponent
Handledare
Tillgänglig från: 2005-05-13 Skapad: 2005-05-13 Senast uppdaterad: 2010-02-03Bibliografiskt granskad

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