Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, and Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark.
J Chem Theory Comput. 2007 Jul;3(4):1629-43. doi: 10.1021/ct700034q.
This is the second in a set of two articles where we describe our newly developed scheme to predict conformations of complex oligosaccharides in solution. We apply our fast sugar conformation prediction tool to the case of two complex human milk oligosaccharides LNF-1 and LND-1. As described in detail in the first paper, our protocol initially delivers a set of "unique structures" corresponding to important minima on the potential-energy landscape of a complex sugar using an implicit solvent model. The nuclear Overhauser effect ranking of individual conformations provides a suitable way for comparison with available experiments. The structures obtained agree well with earlier computational predictions but are obtained at a significantly lower computational cost. Sugar conformations corresponding to stable energy minima not found by earlier molecular dynamics studies were also detected using our methodology. In order to evaluate the effects of explicit solvation and thermal fluctuations on several different predicted conformers, we also performed short-time molecular dynamics simulations in an explicit solvent.
这是两篇文章中的第二篇，我们在其中描述了我们新开发的用于预测溶液中复杂寡糖构象的方案。我们将我们的快速糖构象预测工具应用于两种复杂的人乳寡糖 LNF-1 和 LND-1 的情况。如第一篇论文中详细描述的，我们的方案最初使用隐溶剂模型为复杂糖的势能面上的重要极小值提供一组“独特结构”。各个构象的核 Overhauser 效应排序为与可用实验进行比较提供了一种合适的方法。所得到的结构与早期的计算预测吻合良好，但计算成本却大大降低。使用我们的方法还检测到了先前分子动力学研究未发现的对应于稳定能极小值的糖构象。为了评估显式溶剂化和热涨落对几个不同预测构象的影响，我们还在显式溶剂中进行了短时间分子动力学模拟。
