Department of Biochemistry and Biophysics, University of North Carolina, USA.
Nat Methods. 2012 Apr 15;9(6):603-8. doi: 10.1038/nmeth.1976.
Molecular modeling guided by experimentally derived structural information is an attractive approach for three-dimensional structure determination of complex RNAs that are not amenable to study by high-resolution methods. Hydroxyl radical probing (HRP), which is performed routinely in many laboratories, provides a measure of solvent accessibility at individual nucleotides. HRP measurements have, to date, only been used to evaluate RNA models qualitatively. Here we report the development of a quantitative structure refinement approach using HRP measurements to drive discrete molecular dynamics simulations for RNAs ranging in size from 80 to 230 nucleotides. We first used HRP reactivities to identify RNAs that form extensive helical packing interactions. For these RNAs, we achieved highly significant structure predictions given the inputs of RNA sequence and base pairing. This HRP-directed tertiary structure refinement approach generates robust structural hypotheses that are useful for guiding explorations of structure-function inter-relationships in RNA.
通过实验得出的结构信息进行分子建模是一种很有吸引力的方法，可用于确定那些无法通过高分辨率方法进行研究的复杂 RNA 的三维结构。羟基自由基探测（HRP）在许多实验室中经常进行，可测量单个核苷酸的溶剂可及性。到目前为止，HRP 测量仅用于定性评估 RNA 模型。在这里，我们报告了一种使用 HRP 测量来驱动离散分子动力学模拟的定量结构精修方法的开发，该方法适用于大小在 80 到 230 个核苷酸的 RNA。我们首先使用 HRP 反应性来识别形成广泛螺旋包装相互作用的 RNA。对于这些 RNA，鉴于 RNA 序列和碱基配对的输入，我们实现了非常显著的结构预测。这种 HRP 指导的三级结构精修方法生成了稳健的结构假设，可用于指导 RNA 结构-功能关系的探索。
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