Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.
Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension.
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DOI：
10.1016/j.jmb.2016.06.002
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发表时间：
2016-07-17
影响因子：
5.6
通讯作者：
Thirumalai D
中科院分区：
文献类型：
--
作者：
Hori N;Denesyuk NA;Thirumalai D
由于-1程序性核糖体移码和假结（PK）RNA对力的反应之间存在潜在联系，因此已经对PK进行了许多单分子拉伸实验，以破译程序性核糖体移码的机制。部分出于这些实验的动机，我们使用RNA的粗粒度模型进行了模拟，以描述PK在机械力（fs）和单价盐浓度（Cs）范围内的响应。粗粒度模拟定量再现实验中观察到的多步热熔融，从而验证了我们的模型。在模拟中得到的自由能变化与实验非常吻合。通过改变f和C，我们计算出的相图显示了一系列的结构转变，填充不同的中间状态。当f和C改变时，茎环三级相互作用首先断裂，然后是3′端发夹（I F）的解折叠。最后，5′-末端发夹散开，产生一个延伸状态（E I）。对相界的理论分析表明，E → I（I → F）相变的破裂临界力为（logCm）α，α=1（0.5）。这种关系被用来获得优先离子-RNA相互作用系数，它可以在单分子实验中定量测量，如以前对DNA发夹所做的那样。我们工作的一个副产品是，移码效率可能是由核糖体在翻译过程中首次遇到的5′端发夹的稳定性决定的。
Because of the potential link between −1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single-molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed ribosomal frameshifting. Motivated in part by these experiments, we performed simulations using a coarse-grained model of RNA to describe the response of a PK over a range of mechanical forces (fs) and monovalent salt concentrations (Cs). The coarse-grained simulations quantitatively reproduce the multistep thermal melting observed in experiments, thus validating our model. The free energy changes obtained in simulations are in excellent agreement with experiments. By varying f and C, we calculated the phase diagram that shows a sequence of structural transitions, populating distinct intermediate states. As f and C are changed, the stem–loop tertiary interactions rupture first, followed by unfolding of the 3′-end hairpin (I⇌F). Finally, the 5′-end hairpin unravels, producing an extended state (E⇌I). A theoretical analysis of the phase boundaries shows that the critical force for rupture scales as (logCm)α with α=1 (0.5) for E⇌I (I⇌F) transition. This relation is used to obtain the preferential ion–RNA interaction coefficient, which can be quantitatively measured in single-molecule experiments, as done previously for DNA hairpins. A by-product of our work is the suggestion that the frameshift efficiency is likely determined by the stability of the 5′-end hairpin that the ribosome first encounters during translation.
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DOI：
10.1073/pnas.0905046106
发表时间：
2009-08-04
影响因子：
11.1
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影响因子：
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通讯作者：
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DOI：
10.1073/pnas.1403457111
发表时间：
2014-04-15
影响因子：
11.1
作者：
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通讯作者：
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