Shajani Zahra, Drobny Gary, Varani Gabriele
Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA.
Biochemistry. 2007 May 22;46(20):5875-83. doi: 10.1021/bi602658x. Epub 2007 May 1.
Recognition of RNA by proteins and small molecules often involves large changes in RNA structure and dynamics, yet very few studies have so far characterized these motional changes. Here we extend to the protein-bound RNA recent 13C relaxation studies of motions in the RNA recognized by human U1A protein, a well-known model for protein-RNA recognition. Changes in relaxation observed upon complex formation demonstrate that the protein-binding site becomes rigid in the complex, but the upper stem-loop that defines the secondary structure of this RNA experiences unexpected motional freedom. By using a helix elongation strategy, we observe that the upper stem-loop moves independently of the remainder of the structure also in the absence of U1A. Surprisingly, RNA residues making important intermolecular contacts in the structure of the complex exhibit increased flexibility in the presence of the protein. Both of these results support the hypothesis that RNA-binding proteins select a structure that optimizes intermolecular contacts in the manifold of conformations sampled by the free RNA and that protein binding quenches these motions. Together with previous studies of the RNA-bound protein, they also demonstrate that protein-RNA interfaces experience complex motions that modulate the strength of individual interactions.
蛋白质和小分子对RNA的识别通常涉及RNA结构和动力学的巨大变化，但迄今为止，很少有研究对这些运动变化进行表征。在这里，我们将最近对人U1A蛋白识别的RNA中运动的13C弛豫研究扩展到与蛋白结合的RNA上，人U1A蛋白是蛋白质-RNA识别的一个著名模型。复合物形成时观察到的弛豫变化表明，蛋白质结合位点在复合物中变得刚性，但定义该RNA二级结构的上部茎环却经历了意想不到的运动自由度。通过使用螺旋延伸策略，我们观察到，即使在没有U1A的情况下，上部茎环也独立于结构的其余部分移动。令人惊讶的是，在复合物结构中形成重要分子间接触的RNA残基在有蛋白质存在时表现出增加的灵活性。这两个结果都支持这样的假设，即RNA结合蛋白选择一种结构，该结构在自由RNA采样的多种构象中优化分子间接触，并且蛋白质结合会抑制这些运动。与之前对RNA结合蛋白的研究一起，它们还表明蛋白质-RNA界面经历复杂的运动，这些运动调节个体相互作用的强度。
