Effect of Structural Variability of the Ceramide Part on the Saccharide-Ceramide Linkage in Model Glycolipids Studied by Molecular Mechanics and Molecular Dynamics Methods

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Title:Effect of Structural Variability of the Ceramide Part on the Saccharide-Ceramide Linkage in Model Glycolipids Studied by Molecular Mechanics and Molecular Dynamics Methods
Creators:
Gálová, Zuzana
Kožár, Tibor
Journal or Publication Title:
Collection of Czechoslovak Chemical Communications, 61, 10, pp. 1405-1431
Uncontrolled Keywords:Molecular dynamics, Molecular mechanics, Conformational analysis, β-Glycosidic linkage, Monoglycosyl-ceramide, Glycosphingolipids

Abstract

Conformational analysis was performed for model glycosphingolipid molecules with a view to studying the effect of structural variability of the lipidic part and its flexibility on the saccharide-ceramide linkage. In addition to systematic and random molecular mechanics sampling techniques (the RAMM program), molecular dynamics simulations (Biosym DISCOVER program) were carried out to analyze the conformational energy surface of the model glycolipid molecules. The influence of the structural variability and flexibility of the lipidic part is demonstrated by prediction of the stability of different conformations around the carbohydrate-ceramide linkage. The α<sub>2</sub>, α<sub>1</sub> and Θ<sub>1</sub> torsional angles are the most important structural parameters with respect to the carbohydrate-ceramide connection. Two dominant conformations for the saccharide-ceramide linkage were observed, with the α<sub>2</sub>/α<sub>1</sub>/Θ<sub>1</sub> dihedral angles in the -<i>sc</i>/+<i>ac</i>/<i>ap </i>and -<i>sc</i>/<i>ap</i>/-<i>sc </i>regions. While each of the calculation methods predicts similar flexibility in the α<sub>2</sub>/α<sub>1</sub> space, the flexibility around the Θ<sub>1</sub> angle differs considerably, reflecting the parametrization and set-up of the modelling protocol.

Title:Effect of Structural Variability of the Ceramide Part on the Saccharide-Ceramide Linkage in Model Glycolipids Studied by Molecular Mechanics and Molecular Dynamics Methods
Creators:
Gálová, Zuzana
Kožár, Tibor
Uncontrolled Keywords:Molecular dynamics, Molecular mechanics, Conformational analysis, β-Glycosidic linkage, Monoglycosyl-ceramide, Glycosphingolipids
Divisions:Life and Chemical Sciences > Institute of Organic Chemistry and Biochemistry > Collection of Czechoslovak Chemical Communications
Journal or Publication Title:Collection of Czechoslovak Chemical Communications
Volume:61
Number:10
Page Range:pp. 1405-1431
ISSN:0010-0765
E-ISSN:1212-6950
Publisher:Institute of Organic Chemistry and Biochemistry
Related URLs:
URLURL Type
http://dx.doi.org/10.1135/cccc19961405UNSPECIFIED
ID Code:1046
Item Type:Article
Deposited On:06 Feb 2009 17:06
Last Modified:06 Feb 2009 16:06

Citation

Gálová, Zuzana; Kožár, Tibor (1996) Effect of Structural Variability of the Ceramide Part on the Saccharide-Ceramide Linkage in Model Glycolipids Studied by Molecular Mechanics and Molecular Dynamics Methods. Collection of Czechoslovak Chemical Communications, 61 (10). pp. 1405-1431. ISSN 0010-0765

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