Calculation of the Ramachandran potential of mean force for a disaccharide in aqueous solution
Calculation of the Ramachandran potential of mean force for a disaccharide in aqueous solution
复制标题
DOI：
10.1021/ja9821596
复制
发表时间：
1999-03-17
影响因子：
15
通讯作者：
Brady, JW
中科院分区：
文献类型：
--
作者：
Naidoo, KJ;Brady, JW
采用自适应伞形采样的分子动力学模拟方法计算了α(1—b> 4)-连接的d -木吡喃糖二聚体（4- o - α - d -木吡喃糖- α - d -木吡喃糖）在水（TIP3P）溶液中的平均力的Ramachandran构象势，这是一种戊糖类似物，是研究溶剂结构对生物聚合物水化影响的有用的通用模型。该分子的真空绝热能图与麦芽糖的真空绝热能图非常相似，但溶液pmf却大不相同，其中一个主要的真空最小构象几乎完全消失在溶液中，而全局最小能量构象是一个新的最小构象，在真空表面上根本不存在。这种构象显然是由水分子稳定的，水分子的氢键与每个环上的羟基相连，在两个环之间架起桥梁。新的构象也使两个疏水亚甲基几乎处于范德华接触，减少了它们的暴露表面积。不幸的是，结果重申了水合作用对每个分子化学结构的具体细节的依赖，使得简单的水合作用一般模型的应用更加困难。
Molecular dynamics simulations employing adaptive umbrella sampling have been used to calculate the Ramachandran conformational potential of mean force in aqueous (TIP3P) solution for the alpha(1-->4)-linked dimer of D-xylopyranose (4-O-alpha-D-xylopyranosyl-alpha-D-xylopyranose), a pentose analogue of malto se and a useful general model for the effects of solvent structuring upon biopolymer hydration. The vacuum adiabatic energy map for this molecule closely resembles that for maltose, but the solution pmf is quite different, with one of the principal vacuum minima almost completely disappearing in solution and with the global minimum-energy conformation being a new minimum which does not occur at all on the vacuum surface. This conformation is apparently stabilized by a water molecule which hydrogen bonds to a hydroxyl group on each ring, bridging between the two rings. The new conformation also places the two hydrophobic methylene groups almost in van der Waals contact, reducing their exposed surface area. Unfortunately, the results reaffirm the dependence of hydration effects upon the specific details of each molecule's chemical structure, making the application of simple general models for hydration more difficult.