Frank Aaron T, Law Sean M, Brooks Charles L
Department of Chemistry and Biophysics, University of Michigan , 930 North University Avenue, Ann Arbor, Michigan 48109-1055, United States.
J Phys Chem B. 2014 Oct 23;118(42):12168-75. doi: 10.1021/jp508342x. Epub 2014 Oct 15.
We introduce a simple and fast approach for predicting RNA chemical shifts from interatomic distances that performs with an accuracy similar to existing predictors and enables the first chemical shift-restrained simulations of RNA to be carried out. Our analysis demonstrates that the applied restraints can effectively guide conformational sampling toward regions of space that are more consistent with chemical shifts than the initial coordinates used for the simulations. As such, our approach should be widely applicable in mapping the conformational landscape of RNAs via chemical shift-guided molecular dynamics simulations. The simplicity and demonstrated sensitivity to three-dimensional structure should also allow our method to be used in chemical shift-based RNA structure prediction, validation, and refinement.
我们介绍了一种简单快速的方法，可根据原子间距离预测RNA化学位移，其预测准确性与现有预测方法相似，并能首次进行化学位移约束的RNA模拟。我们的分析表明，所应用的约束能够有效地引导构象采样，使其朝着比模拟初始坐标更符合化学位移的空间区域进行。因此，我们的方法应广泛适用于通过化学位移引导的分子动力学模拟来绘制RNA的构象景观。这种简单性以及对三维结构已证明的敏感性，也应使我们的方法能够用于基于化学位移的RNA结构预测、验证和优化。
