Molecular dynamics simulation of oligosaccharides containing N-acetyl neuraminic acid.
Molecular dynamics simulation of oligosaccharides containing N-acetyl neuraminic acid.
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含N-乙酰神经氨酸寡糖的分子动力学模拟。
DOI：
10.1002/bip.360340103
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发表时间：
1994
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
αD‐N‐乙酰神经氨酸（Neu5Ac，唾液酸）是一种常见于各种细胞表面糖脂和糖蛋白的碳水化合物残基。该残基通过α（2→3）或α（2→6）键在末端或内部与Gal残基相连。在细胞表面受体sialyl‐LewisX中，存在一个末端α（2→3）连锁。我们实验室之前的研究表明，在溶液中，lewisx采用了相对刚性的结构。为了模拟Neu5Ac残基，将该单糖的真空分子动力学与明确包含溶剂水的模拟进行了比较。两种模拟得到的单糖构象的动力学平均值是相似的。对Neu5Ac α(2→3)Gal β‐O‐甲基二糖的真空计算表明，该二糖可以获得许多低能最小值。从低能最小值开始的分子动力学模拟显示，几个最小值之间的构象转变时间尺度为10-50 ps，而其他最小值之间的大屏障阻止了所研究的时间尺度上的转变。这种双糖在溶剂存在下的模拟显示出较少的构象转变，说明了在其他一些研究中观察到的溶剂的阻尼效应。我们的结果与Neu5Ac α(2→3)Gal β键的多种构象之间的平衡是最一致的。©1994 John Wiley & Sons, Inc
αD‐N‐acetyl neuraminic acid (Neu5Ac, sialic acid) is a commonly occurring carbohydrate residue in various cell surface glycolipids and glycoproteins. This residue is linked terminally or internally to Gal residues via an α(2 → 3) or α(2 → 6) linkage. In the cell surface receptor, sialyl‐LewisX, a terminal α(2 → 3) linkage is present. Previous studies from our laboratory have shown that in solution LewisXadopts a relatively rigid structure. In order to model the Neu5Ac residue, vacuum molecular dynamics of this monosaccharide were compared with simulations that explicitly include solvent water. The dynamical average of the monosaccharide conformation obtained from the two simulations was similar. Vacuum calculations for the disaccharide Neu5Ac α(2 → 3) Gal β‐O‐methyl show that a number of low energy minima are accessible to this disaccharide. Molecular dynamics simulations starting from the low energy minima show conformational transitions with a time scale of 10–50 ps among several of the minima while large barriers between other minima prevent transitions on the time scale studied. Simulations of this disaccharide in the presence of solvent show fewer conformational transitions, illustrating a dampening effect of the solvent that has been observed in some other studies. Our results are most consistent with an equilibrium among multiple conformations for the Neu5Ac α(2 → 3) Gal β linkage. © 1994 John Wiley & Sons, Inc.