Molecular dynamics simulations and the conformational mobility of blood group oligosaccharides.
Molecular dynamics simulations and the conformational mobility of blood group oligosaccharides.
复制标题
血型寡糖的分子动力学模拟和构象迁移率。
DOI：
10.1002/bip.360290414
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发表时间：
1990
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：
Yan,ZY;Bush,CA
在没有明确考虑溶剂的情况下进行分子动力学模拟，以探索 A 型和 H 型寡糖的构象迁移率。 Rasmussen 及其同事的势能力场与 CHARMM 程序一起用于许多由岩藻糖、半乳糖、葡萄糖、N-乙酰氨基葡萄糖和 N-乙酰半乳糖胺组成的二糖和三糖模型，这些模型被选择代表血型寡糖的各种片段。与早期研究的结果一致，每种吡喃糖苷都发现了稳定的椅式构象，在长达 800 ps 的模拟中没有检测到任何转变。外环二面角，包括 C5-C6 的外环二面角，通常在大约 5-30 ps 的时间尺度上显示出许多转变。血型寡糖的一些但不是全部糖苷键的二面角在 30-50 ps 的时间尺度上显示转变，这意味着血型寡糖的内部运动程度强烈依赖于键立体化学。对于在这些模拟中显示出有限内部运动的某些血型 A 和 H 寡糖，我们认为计算结果与我们之前对 1H 核 Overhauser 增强 (NOE) 数据的分析一致，该数据意味着在广泛的温度和溶剂条件下具有单一构象。虽然轨迹与被解释为指示刚性构象的 13 CT1 值一致，但提出了作为磁场强度的函数的 13 C-NOE 和T 1 测量作为内部运动的实验检测的改进方法，该方法建议用于这些模拟中的某些寡糖。这些模拟的结果与相似分子量的肽的结果有很大不同，因为寡糖显示出少得多的内部运动。
Molecular dynamics simulations were carried out without explicit consideration of solvent to explore the conformational mobility of blood group A and H oligosaccharides. The potential energy force field of Rasmussen and co‐workers was used with the CHARMM program on a number of disaccharide and trisaccharide models composed of fucose, galactose, glucose, N‐acetyl glucosamine, and N‐acetyl galactosamine chosen to represent various fragments of blood group oligosaccharides. In agreement with results of earlier studies, stable chair conformations were found for each pyranoside from which no transitions were detected in simulations as long as 800 ps. Exocyclic dihedral angles, including that of C5—C6, generally show numerous transitions on a time scale of approximately 5–30 ps. The dihedral angles of some but not all glycosidic linkages of blood group oligosaccharides show transitions on the time scale of 30–50 ps, implying that the extent of internal motion in blood group oligosaccharides depends strongly on linkage stereochemistry. For certain blood group A and H oligosaccharides that show limited internal motion in these simulations, we argue that the calculations are consistent with our previous analysis of1H nuclear Overhauser enhancement (NOE) data that imply single conformations over a wide range of temperature and solvent conditions. While the trajectories are consistent with13CT1values that have been interpreted as indicating rigid conformations, measurements of13C‐NOE andT1as a function of magnetic field strength are proposed as an improved method for experimental detection of the internal motion that is suggested for certain oligosaccharides in these simulations. The results of these simulations differ substantially from those of peptides of a similar molecular weight in that the oligosaccharides show much less internal motion.