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首页> 外文期刊>The journal of physical chemistry, B. Condensed matter, materials, surfaces, interfaces & biophysical >How the Ribosomal A-Site Finger Can Lead to tRNA Species Dependent Dynamics
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How the Ribosomal A-Site Finger Can Lead to tRNA Species Dependent Dynamics

机译：如何导致核糖体A-Site的手指如何导致TRNA物种依赖性动态

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摘要

Proteins are synthesized by the joint action of the ribosome and tRNA molecules, where the rate of synthesis can be affected by numerous factors, such as the concentration of tRNA, the binding affinity of tRNA for the ribosome, or post-transcriptional modifications. Here, we expand this range of contributors by demonstrating how differences in tRNA structure can give rise to tRNA species-specific dynamics in the ribosome. To show this, we perform simulations of A/P hybrid-state formation for two tRNA species (tRNA(Phe) and tRNA(Leu)), which differ in the size of their variable loops (VLs). These calculations reveal that steric interactions between the VL and the ribosomal A-site finger (ASF, i.e., H38 of 23S rRNA) can directly modulate the free-energy landscape for each tRNA species. We also find that tRNA and ASF motions are highly correlated, where fluctuations of the ASF are predictive of tRNA transition events. Finally, by introducing perturbations to the model, we demonstrate that ASF flexibility is a determinant of the rate of A/P hybrid-state formation.
机译：通过核糖体和TRNA分子的关节作用合成蛋白质，其中合成速率可能受到多种因素的影响，例如TRNA浓度，TRNA对核糖体的结合亲和力，或转录后修饰。在这里，我们通过证明TRNA结构的差异可以引起核糖体中的TRNA物种特异性动态的差异来扩展这一系列贡献者。为了表明，我们对两个TRNA物种（TRNA）和TRNA（LEU））进行A / P杂化状态形成的模拟，其在其可变环（VLS）的尺寸中不同。这些计算揭示了VL和核糖体A-位点的空间相互作用（ASF，即23s rRNA的H38）可以直接调节每个TRNA物种的自由能景观。我们还发现TRNA和ASF运动是高度相关的，其中ASF的波动是预测TRNA过渡事件的预测性。最后，通过向模型引入扰动，我们证明ASF灵活性是A / P混合状态形成率的决定因素。

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