Conformational folding of xyloglucan side chains in aqueous solution from molecular dynamics simulation

• Published in: Carbohydrate research 2005-11, Vol.340 (16), p.2520-2532
• Main Authors: Umemura, Myco, Yuguchi, Yoshiaki
• Format: Article
• Language: English
• Subjects: Aqueous solution; Carbohydrate Conformation; Computer Simulation; Conformational folding; Dihedral angle; Glucans - chemistry; Hydrogen Bonding; Molecular dynamics simulation; Molecular Structure; Solutions - chemistry; Water - chemistry; Xylans - chemistry; Xyloglucan
• ISSN: 0008-6215; 1873-426X
• DOI: 10.1016/j.carres.2005.08.017

Molecular dynamics simulation was carried out on xyloglucan with explicit water molecules to investigate the folding mechanism of side chains onto a main chain in aqueous solution. The model xyloglucan was composed of 12 β- d-glucopyranoses as a main chain substituted with six galactoses and three xyloses as side chains. Two conditions were set for the ribbon-like main chain; one is restricted to be ‘flat’ and the other is without restriction. The free main chain of xyloglucan has a ‘twisted’ conformation as the major one. Conformational folding of side chains onto the main chain was analyzed with dihedral angles at each glycosidic linkage. In a 5-ns calculation, the xyloglucan has a tendency to contract in both the restricted and the free systems, but the mode of contraction is different. Side chains tend to stick onto the flat surface of the main chain in the restricted system, while they do not tightly do so in the free one; instead the main chain takes a twisted and sometimes embowed conformation. This result indicates that the main chain has greater attractive forces to bind side chains when it is flat, while it loses the ability as it is twisted.