Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, U.K.
J Am Chem Soc. 2014 Feb 12;136(6):2204-7. doi: 10.1021/ja4105396. Epub 2014 Feb 4.
Recent improvements in the accuracy of structure-based methods for the prediction of nuclear magnetic resonance chemical shifts have inspired numerous approaches for determining the secondary and tertiary structures of proteins. Such advances also suggest the possibility of using chemical shifts to characterize the conformational fluctuations of these molecules. Here we describe a method of using methyl chemical shifts as restraints in replica-averaged molecular dynamics (MD) simulations, which enables us to determine the conformational ensemble of the HU dimer and characterize the range of motions accessible to its flexible β-arms. Our analysis suggests that the bending action of HU on DNA is mediated by a mechanical clamping mechanism, in which metastable structural intermediates sampled during the hinge motions of the β-arms in the free state are presculpted to bind DNA. These results illustrate that using side-chain chemical shift data in conjunction with MD simulations can provide quantitative information about the free energy landscapes of proteins and yield detailed insights into their functional mechanisms.
近年来，基于结构的方法在预测核磁共振化学位移方面的准确性不断提高，这激发了许多用于确定蛋白质二级和三级结构的方法。这些进展还表明，有可能利用化学位移来表征这些分子的构象波动。在这里，我们描述了一种使用甲基化学位移作为复制平均分子动力学 (MD) 模拟中的约束条件的方法，这使我们能够确定 HU 二聚体的构象集合，并描述其柔性 β-臂可达到的运动范围。我们的分析表明，HU 对 DNA 的弯曲作用是由机械夹紧机制介导的，在自由状态下 β-臂铰链运动中采样的亚稳态结构中间体被预先塑造以与 DNA 结合。这些结果表明，将侧链化学位移数据与 MD 模拟结合使用，可以提供有关蛋白质自由能景观的定量信息，并深入了解其功能机制。
