Institute for Molecular Science and Okazaki Institute for Integrative Bioscience, 5-1 Higashiyama, Myodaiji, Okazaki 444-8787, Japan.
Molecules. 2012 May 31;17(6):6658-71. doi: 10.3390/molecules17066658.
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.
具有生物重要性的寡糖通常具有支化的共价结构和动态构象多样性。在这里，我们报告了一种方法的应用，该方法结合了分子动力学 (MD) 模拟和镧系元素辅助顺磁 NMR 光谱学，用于评估支化寡糖的动态构象集合。在 GM2 神经节苷脂的支化四糖的还原端连接了一个镧系螯合标签，以观察伪接触位移作为验证来自 MD 模拟的构象集合的远程信息的来源。通过检查结果，将 GM2 四糖的构象空间与非支化衍生物 GM3 三糖的构象空间进行了比较。
