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首页> 外文期刊>Biochemistry >Structural energetics and base-pair opening dynamics in sarcin-ricin domain RNA
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Structural energetics and base-pair opening dynamics in sarcin-ricin domain RNA

机译：sarcin-ricin结构域RNA中的结构能学和碱基对开放动力学

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摘要

The sarcin- ricin domain is a universal element of the RNA from the large ribosomal subunit. The domain is part of the binding site for elongation factors and is specifically cleaved by the toxins alpha- sarcin and ricin. In this work, we have mapped the energetics and dynamics of individual structural motifs in a 29- mer RNA oligomer containing the sarcin- ricin domain. The stability of individual base pairs in the structure was characterized from measurements of the exchange rates of imino protons using nuclear magnetic resonance spectroscopy at 10 degrees C. The measurements also provided the rates of opening and closing for selected base pairs. The results reveal that the structural stabilization free energies in the sarcin- ricin domain are broadly distributed between 2.9 and 10.6 kcal/ mol. One of the least stable sites in the structure is the noncanonical G- A base pair located next to the phosphodiester bond that is cleaved by alpha-sarcin. The low stability of this base pair supports the proposal that cleavage by R-sarcin occurs by a base flipping mechanism. The opening dynamics of other base pairs is affected by elements of the structure such as the bulged- G motif and its cross- strand stacking. Participation in these motifs increases the lifetimes of the bases in an open, solvent- accessible conformation.
机译：sarcin-ricin结构域是大核糖体亚基中RNA的通用元素。该结构域是延伸因子结合位点的一部分，并被毒素α-sarcin和蓖麻毒蛋白特异性切割。在这项工作中，我们绘制了包含sarcinricin域的29-mer RNA寡聚体中各个结构基序的能量和动力学图。各个碱基对在结构中的稳定性是通过使用核磁共振波谱在10摄氏度下对亚氨基质子交换速率的测量来表征的。这些测量还提供了选定碱基对的打开和闭合速率。结果表明，Sarcinricin域中的结构稳定自由能广泛分布在2.9 kcal / mol与10.6 kcal / mol之间。结构中最不稳定的位点之一是非经典的G- A碱基对，位于被α-sarcin裂解的磷酸二酯键旁边。该碱基对的低稳定性支持了通过碱基翻转机制发生R-sarcin切割的提议。其他碱基对的开放动力学受结构元素的影响，例如凸出的G基序及其交叉链堆叠。参与这些基序可以延长碱基在开放的，溶剂可及的构型中的寿命。

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