Molecular dynamics simulation of Lewis blood groups and related oligosaccharides.
Molecular dynamics simulation of Lewis blood groups and related oligosaccharides.
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Lewis血型及相关寡糖的分子动力学模拟。
DOI：
10.1002/bip.360311408
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发表时间：
1991
期刊：
影响因子：
2.9
通讯作者：
Bush,CA
中科院分区：
文献类型：
--
作者：
Mukhopadhyay,C;Bush,CA
没有明确列入溶剂分子的分子动力学模拟已经进行了研究LewisaandLewisbblood组寡糖，和两个血型A四糖具有I型和II型核心链的运动。血型H三糖也进行了研究，并与血型A II型核心链进行了比较。由Rasmussen及其同事开发的势能面与分子力学代码CHARMM一起使用。从构象能量图中获得了组成二糖片段的最低能量极小值。这些二糖片段的最低能量最小值用于构建在实际加热/平衡和动力学模拟之前进一步最小化的三糖和四糖。二糖片段的轨迹，例如，Fuc α-（1 → 4）GlcNAc、Gal β-（1 → 4）GlcNAc等，示出了各种最小值之间的过渡。然而，低聚糖被发现是动态稳定的，没有过渡到其他最低能量构象中观察到的糖苷二面角的时间序列，即使在长达300 ps的轨迹。寡糖中糖苷键的稳定构象不一定与相应的分离二糖的最小能量构象相同。寡糖中糖苷角的平均波动在±15°范围内。这些轨迹计算的结果与从1H-nmr数据中推导出的这些寡糖的相对刚性的单一构象模型一致。
Molecular dynamics simulations without explicit inclusion of solvent molecules have been performed to study the motions of Lewisaand Lewisbblood group oligosaccharides, and two blood group A tetrasaccharides having type I and type II core chains. The blood group H trisaccharide has also been studied and compared with the blood group A type II core chain. The potential energy surface developed by Rasmussen and co‐workers was used with the molecular mechanics code CHARMM. The lowest energy minima of the component disaccharide fragments were obtained from conformational energy mapping. The lowest energy minima of these disaccharide fragments were used to build the tri‐ and tetrasaccharides that were further minimized before the actual heating/equilibration and dynamics simulations. The trajectories of the disaccharide fragments, e.g., Fuc α‐(1 → 4) GlcNAc, Gal β‐(1 → 4) GlcNAc, etc., show transitions among various minima. However, the oligosaccharides were found to be dynamically stable and no transitions to other minimum energy conformations were observed in the time series of the glycosidic dihedral angles even during trajectories as long as 300 ps. The stable conformations of the glycosidic linkages in the oligosaccharides are not necessarily the same as the minimum energy conformation of the corresponding isolated disaccharides. The average fluctuations of the glycosidic angles in the oligosaccharides were well within the range of ±15°. The results of these trajectory calculations were consistent with the relatively rigid single‐conformation models derived for these oligosaccharides from1H‐nmr data.