Kuttel Michelle M
Department of Computer Science, University of Cape Town, Cape Town, South Africa.
Carbohydr Res. 2008 May 5;343(6):1091-8. doi: 10.1016/j.carres.2008.01.038. Epub 2008 Feb 5.
Four Ramachandran maps of the conformational potential of mean force (PMF) for the galactose disaccharide globobiose (alpha-D-Galp-(1-->4)-beta-D-Galp) were calculated in vacuum, explicit water, with a simple high dielectric constant and a distance-dependent dielectric coefficient, respectively. This simple model of the galactan alpha-(1-->4)-linkage is shown to be conformationally restricted, with only a small range of syn-phi/syn-psi conformations predominating at standard temperature and pressure. This has implications for the preferred conformation and chain dynamics of alpha-galactosides. In addition, comparison of the relevant PMF surfaces reveals the substitution of a high dielectric constant for explicit water solution to be a valid approximation for reproducing the minimum energy conformation of this glycosidic linkage.
分别在真空、显式水、具有简单高介电常数和距离依赖性介电系数的条件下，计算了半乳糖二糖球乳糖（α-D-半乳糖-（1→4）-β-D-半乳糖）的四个平均力构象势（PMF）的拉马钱德兰图。结果表明，这种简单的半乳聚糖α-（1→4）-连接模型在构象上受到限制，在标准温度和压力下，只有一小范围的顺式-φ/顺式-ψ构象占主导。这对α-半乳糖苷的优选构象和链动力学有影响。此外，相关PMF表面的比较表明，用高介电常数代替显式水溶液是再现这种糖苷键最低能量构象的有效近似方法。
