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海藻糖作为水合壳层中溶剂水分子的“动态还原剂”的分子动力学模拟

Molecular dynamics simulations of trehalose as a 'dynamic reducer' for solvent water molecules in the hydration shell.

作者信息

Choi Youngjin, Cho Kum Won, Jeong Karpjoo, Jung Seunho

机构信息

Bio/Molecular Informatics Center, Konkuk University, Seoul 143-701, Republic of Korea.

出版信息

Carbohydr Res. 2006 Jun 12;341(8):1020-8. doi: 10.1016/j.carres.2006.02.032. Epub 2006 Mar 20.

Abstract

Systematic computational work for a series of 13 disaccharides was performed to provide an atomic-level insight of unique biochemical role of the alpha,alpha-(1-->1)-linked glucopyranoside dimer over the other glycosidically linked sugars. Superior osmotic and cryoprotective abilities of trehalose were explained on the basis of conformational and hydration characteristics of the trehalose molecule. Analyses of the hydration number and radial distribution function of solvent water molecules showed that there was very little hydration adjacent to the glycosidic oxygen of trehalose and that the dynamic conformation of trehalose was less flexible than any of the other sugars due to this anisotropic hydration. The remarkable conformational rigidity that allowed trehalose to act as a sugar template was required for stable interactions with hydrogen-bonded water molecules. Trehalose made an average of 2.8 long-lived hydrogen bonds per each MD step, which was much larger than the average of 2.1 for the other sugars. The stable hydrogen-bond network is derived from the formation of long-lived water bridges at the expense of decreasing the dynamics of the water molecules. Evidence for this dynamic reduction of water by trehalose was also established based on each of the lowest translational diffusion coefficients and the lowest intermolecular coulombic energy of the water molecules around trehalose. Overall results indicate that trehalose functions as a 'dynamic reducer' for solvent water molecules based on its anisotropic hydration and conformational rigidity, suggesting that macroscopic solvent properties could be modulated by changes in the type of glycosidic linkages in sugar molecules.

摘要

对一系列13种二糖进行了系统的计算工作,以从原子层面深入了解α,α-(1→1)-连接的吡喃葡萄糖苷二聚体相对于其他糖苷连接糖所具有的独特生化作用。基于海藻糖分子的构象和水合特性,解释了海藻糖卓越的渗透和冷冻保护能力。对溶剂水分子的水合数和径向分布函数的分析表明,海藻糖糖苷氧附近的水合作用非常少,并且由于这种各向异性水合作用,海藻糖的动态构象比其他任何糖都缺乏灵活性。与氢键结合的水分子进行稳定相互作用需要海藻糖具有显著的构象刚性,以便作为糖模板发挥作用。在每个分子动力学(MD)步骤中,海藻糖平均形成2.8个长寿命氢键,这比其他糖的平均2.1个氢键要多得多。稳定的氢键网络源自长寿命水桥的形成,代价是水分子动力学的降低。基于海藻糖周围水分子的最低平动扩散系数和最低分子间库仑能,也证实了海藻糖对水动力学的这种降低作用。总体结果表明,基于其各向异性水合作用和构象刚性,海藻糖充当溶剂水分子的“动力学减速器”,这表明糖分子中糖苷键类型的变化可以调节宏观溶剂性质。

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