Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity
Biphasic folding kinetics of RNA pseudoknots and telomerase RNA activity
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DOI：
10.1016/j.jmb.2007.01.006
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发表时间：
2007-03-30
影响因子：
5.6
通讯作者：
Chen, Shi-Jie
中科院分区：
文献类型：
--
作者：
Cao, Song;Chen, Shi-Jie
使用组合主方程和动力学簇方法，我们研究了RNA假结折叠和展开动力学。能量参数是根据最近发展的RNA二级结构和伪结折叠热力学的Vfold模型计算的。折叠动力学理论是基于完整的构象系，包括所有的原生态和非原生态。预测的折叠和展开途径、激活屏障、阿伦尼乌斯图和限速步骤导致了一些发现。首先，对于PK5伪结，错误折叠的5'发夹在折叠过程中作为一个稳定的动力学陷阱出现，而从这种错误折叠状态中解脱出来是整个折叠过程的限速步骤。计算得到的速率常数和激活势垒与实验数据吻合较好。其次，作为该模型的应用，我们研究了人类端粒酶RNA （hTR）假结的动力学折叠途径。预测的折叠和展开途径不仅支持了发夹和假结之间的构象转换在hTR活性中的作用，而且揭示了构象转换的分子机制。此外，对于实验研究的hTR突变，其发夹中间体是不稳定的，该模型预测了一个长寿命的瞬态发夹结构，并且瞬态发夹中间体和天然假结之间的切换可能是观察到的hTR活性的原因。这一发现将有助于解决观测到的hTR活动与缺乏稳定发夹之间的明显矛盾。(c) 2007 Elsevier Ltd.版权所有。
Using a combined master equation and kinetic cluster approach, we investigate RNA pseudoknot folding and unfolding kinetics. The energetic parameters are computed from a recently developed Vfold model for RNA secondary structure and pseudoknot folding thermodynamics. The folding kinetics theory is based on the complete conformational ensemble, including all the native-like and non-native states. The predicted folding and unfolding pathways, activation barriers, Arrhenius plots, and rate-limiting steps lead to several findings. First, for the PK5 pseudoknot, a misfolded 5' hairpin emerges as a stable kinetic trap in the folding process, and the detrapping from this misfolded state is the rate-limiting step for the overall folding process. The calculated rate constant and activation barrier agree well with the experimental data. Second, as an application of the model, we investigate the kinetic folding pathways for human telomerase RNA (hTR) pseudoknot. The predicted folding and unfolding pathways not only support the proposed role of conformational switch between hairpin and pseudoknot in hTR activity, but also reveal molecular mechanism for the conformational switch. Furthermore, for an experimentally studied hTR mutation, whose hairpin intermediate is destabilized, the model predicts a long-lived transient hairpin structure, and the switch between the transient hairpin intermediate and the native pseudoknot may be responsible for the observed hTR activity. Such finding would help resolve the apparent contradiction between the observed hTR activity and the absence of a stable hairpin. (c) 2007 Elsevier Ltd. All rights reserved.