Quality and Technology, Department of Food Science, University of Copenhagen, Rolighedsvej 30, Copenhagen, Denmark.
Carbohydr Res. 2010 Feb 26;345(4):474-86. doi: 10.1016/j.carres.2009.12.009. Epub 2009 Dec 22.
The conformational and hydration properties of the two disaccharides methyl beta-cellobioside and methyl beta-laminarabioside were investigated by NMR spectroscopy and explicit solvation molecular dynamics simulations using the carbohydrate solution force field (CSFF). Adiabatic maps produced with this force field displayed 4 minima A: (Phi=300 degrees , Psi=280 degrees), B: (Phi=280 degrees , Psi=210 degrees), C: (Phi=260 degrees , Psi=60 degrees), and D: (Phi=60 degrees , Psi=260 degrees) for methyl beta-cellobioside and 3 minima A: (Phi=290 degrees , Psi=130 degrees), B: (Phi=270 degrees , Psi=290 degrees), and C: (Phi=60 degrees , Psi=120 degrees) for methyl beta-laminarabioside. Molecular dynamics simulations were initiated from all minima. For each disaccharide, the simulation started from the A minimum was conducted for 50ns, while the other minima were explored for 10ns. The simulations revealed two stable minima for both compounds. For methyl beta-cellobioside, the simulation minima in aqueous solution were shifted from their adiabatic map counterparts, while the simulation minima for methyl beta-laminarabioside coincided with the corresponding adiabatic map minima. To validate the simulation results, NMR-derived NOEs and coupling constants across the glycoside linkage, (3)J(HC) and (3)J(CH), were compared with values calculated from the MD trajectories. For each disaccharide, the best agreement was obtained for the simulations started at the A minimum. For both compounds, inter-ring water bridges in combination with the direct hydrogen bonds between the same groups were found to be determining factors for the overall solution structure of the disaccharides which differed from solid-state structures. Comparison with helical parameters showed that the preferred glycosidic dihedral configurations in the methyl beta-cellobioside simulation were not highly compatible with the structure of cellulose, but that curdlan helix structures agreed relatively well with the methyl beta-laminarabioside simulation. Polymers generated using glycosidic dihedral angles from the simulations revealed secondary structure motifs that that may help to elucidate polymer associations and small-molecule binding.
通过 NMR 光谱和使用碳水化合物溶液力场 (CSFF) 的显式溶剂化分子动力学模拟研究了两种二糖甲基-β-纤维二糖苷和甲基-β-半乳吡喃糖苷的构象和水合性质。使用该力场生成的绝热图显示了甲基-β-纤维二糖苷的 4 个最小值 A：（Phi=300 度，Psi=280 度）、B：（Phi=280 度，Psi=210 度）、C：（Phi=260 度，Psi=60 度）和 D：（Phi=60 度，Psi=260 度），以及甲基-β-半乳吡喃糖苷的 3 个最小值 A：（Phi=290 度，Psi=130 度）、B：（Phi=270 度，Psi=290 度）和 C：（Phi=60 度，Psi=120 度）。分子动力学模拟从所有最小值开始。对于每种二糖，从 A 最小值开始的模拟进行了 50ns，而其他最小值的探索进行了 10ns。模拟结果表明，两种化合物都有两个稳定的最小值。对于甲基-β-纤维二糖苷，水溶液中的模拟最小值与它们的绝热图对应物不同，而甲基-β-半乳吡喃糖苷的模拟最小值与相应的绝热图最小值一致。为了验证模拟结果，比较了通过 NMR 获得的糖苷键（3）J（HC）和（3）J（CH）的 NOE 和偶合常数与从 MD 轨迹计算的值。对于每种二糖，从 A 最小值开始的模拟得到了最佳的一致性。对于这两种化合物，发现环间水桥与相同基团之间的直接氢键相结合是决定二糖整体溶液结构的因素，这与固态结构不同。与螺旋参数的比较表明，在甲基-β-纤维二糖苷模拟中，糖苷键二面角的首选构象配置与纤维素的结构不太兼容，但卷曲螺旋结构与甲基-β-半乳吡喃糖苷模拟相对吻合。使用模拟中的糖苷键二面角生成的聚合物揭示了可能有助于阐明聚合物缔合和小分子结合的二级结构模体。
