Umemura Myco, Yuguchi Yoshiaki
Graduate School of Biostudies, Kyoto University, Division of Integrated Life Science, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.
Carbohydr Res. 2005 Nov 21;340(16):2520-32. doi: 10.1016/j.carres.2005.08.017. Epub 2005 Oct 5.
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 beta-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.
对含有明确水分子的木葡聚糖进行了分子动力学模拟，以研究水溶液中侧链在主链上的折叠机制。模型木葡聚糖由12个β-D-吡喃葡萄糖作为主链，被6个半乳糖和3个木糖作为侧链取代。对带状主链设置了两种条件；一种限制为“扁平”，另一种无限制。木葡聚糖的自由主链主要具有“扭曲”构象。通过每个糖苷键处的二面角分析侧链在主链上的构象折叠。在5纳秒的计算中，木葡聚糖在受限和自由系统中都有收缩的趋势，但收缩模式不同。在受限系统中，侧链倾向于附着在主链的平坦表面上，而在自由系统中则不会紧密附着；相反，主链会呈现扭曲且有时弯曲的构象。该结果表明，主链平坦时对结合侧链具有更大的吸引力，而扭曲时则失去这种能力。
