The RNA recognition motif (RRM) occurs widely in RNA-binding proteins, but does not always by itself support full binding. For example, it is known that binding of SL1 RNA to the protein U1-70K in the U1 spliceosomal particle is reduced when a region flanking the RRM is truncated. How the RRM flanking regions that together with the RRM make up an ‘extended RRM’ (eRRM) contribute to complex stability and structural organization is unknown. We study the U1-70K eRRM bound to SL1 RNA by thermal dissociation and laser temperature jump kinetics; long-time molecular dynamics simulations interpret the experiments with atomistic resolution. Truncation of the helix flanking the RRM on its N-terminal side, ‘N-helix,’ strongly reduces overall binding, which is further weakened under higher salt and temperature conditions. Truncating the disordered region flanking the RRM on the C-terminal side, ‘C-IDR’, affects the local binding site. Surprisingly, all-atom simulations show that protein truncation enhances base stacking interactions in the binding site and leaves the overall number of hydrogen bonds intact. Instead, the flanking regions of the eRRM act in a distributed fashion via collective interactions with the RNA when external stresses such as temperature or high salt mimicking osmotic imbalance are applied.

中文翻译：

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与 U1-70K 结合的剪接体 SL1 RNA：扩展 RRM 的作用

RNA 识别基序 (RRM) 广泛存在于 RNA 结合蛋白中，但其本身并不总是支持完全结合。例如，已知当 RRM 侧翼的区域被截断时，SL1 RNA 与 U1 剪接体颗粒中的蛋白质 U1-70K 的结合会减少。与 RRM 一起构成“扩展 RRM”（eRRM）的 RRM 侧翼区域如何有助于复杂的稳定性和结构组织尚不清楚。我们通过热解和激光温度跳跃动力学研究了与 SL1 RNA 结合的 U1-70K eRRM；长时间的分子动力学模拟以原子分辨率解​​释实验。截断 RRM N 端侧的螺旋侧翼，“N-螺旋”，大大降低了整体结合，在更高的盐和温度条件下进一步减弱。截断 C 端侧 RRM 侧翼的无序区域“C-IDR”会影响局部结合位点。令人惊讶的是，全原子模拟表明蛋白质截断增强了结合位点的碱基堆叠相互作用，并使氢键的总数保持不变。相反，当施加外部压力（例如温度或高盐模拟渗透失衡）时，eRRM 的侧翼区域通过与 RNA 的集体相互作用以分布式方式发挥作用。