Application of Paramagnetic NMR-Validated Molecular Dynamics Simulation to the Analysis of a Conformational Ensemble of a Branched Oligosaccharide
Application of Paramagnetic NMR-Validated Molecular Dynamics Simulation to the Analysis of a Conformational Ensemble of a Branched Oligosaccharide
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DOI：
10.3390/molecules17066658
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发表时间：
2012-06-01
期刊：
影响因子：
4.6
通讯作者：
Kato, Koichi
中科院分区：
文献类型：
--
作者：
Zhang, Ying;Yamamoto, Sayoko;Kato, Koichi
具有重要生物学意义的低聚糖通常表现出分支共价结构和动态构象多样性。在这里，我们报告了一种我们开发的方法的应用，该方法结合了分子动力学(MD)模拟和稀土元素辅助的顺磁核磁共振光谱，来评估支链低聚糖的动态构象系综。在神经节苷脂GM2的支链四糖的还原末端贴上一个稀土元素螯合标签，以观察假接触位移作为长距离信息源，以验证从MD模拟得到的构象系综。通过对结果的检验，比较了GM2四糖及其非支化衍生物GM3三糖的构象空间。
Oligosaccharides of biological importance often exhibit branched covalent structures and dynamic conformational multiplicities. Here we report the application of a method that we developed, which combined molecular dynamics (MD) simulations and lanthanide-assisted paramagnetic NMR spectroscopy, to evaluate the dynamic conformational ensemble of a branched oligosaccharide. A lanthanide-chelating tag was attached to the reducing end of the branched tetrasaccharide of GM2 ganglioside to observe pseudocontact shifts as the source of long distance information for validating the conformational ensemble derived from MD simulations. By inspecting the results, the conformational space of the GM2 tetrasaccharide was compared with that of its nonbranched derivative, the GM3 trisaccharide.