An RNA Base Discrete State Model toward Tertiary Structure Prediction
An RNA Base Discrete State Model toward Tertiary Structure Prediction
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DOI：
10.1088/0256-307x/27/11/118702
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发表时间：
2010-11
影响因子：
3.5
通讯作者：
Jian Zhang;Yu-Jie Zhang;Wei Wang
中科院分区：
文献类型：
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作者：
Jian Zhang;Yu-Jie Zhang;Wei Wang
我们报告了一个新的核糖核酸（RNA）的基础离散状态模型，这是第一次在我们的实验室开发，旨在提供一个有效和准确的方式来表示RNA的三维结构预测的RNA结构。由于RNA的自由能在很大程度上取决于碱基对和碱基堆积，而不是骨干轨迹，我们直接建模的RNA碱基配置相对于它的前一个沿着序列。这是在与所有以前的作品中的骨干跟踪表示形成鲜明对比。为了测试离散模型如何忠实地在连续空间中再现链迹，我们从23S核糖体RNA的天然结构中随机选择部分链并重新生长它们。对于优化的16态离散模型，再生长结构与原生结构的均方根距离为1.7 μ m，对于长度为50的长链，该距离逐渐增加到1.3 μ m。效率也很好，例如，对于长度为50的长循环，程序将在几十秒内完成。结合适当的自由能计算方法，我们的模型可能有助于在不久的将来预测RNA的三维结构。
We report a new ribonucleic acid (RNA) base discrete state model, which was first developed in our lab and designed to provide an efficient and accurate way of representing RNA structures toward RNA three-dimensional structure predictions. Since RNA free energy is largely determined by base pairs and base stackings instead of backbone trajectories, we directly model the RNA base configurations with respect to its previous one along the sequence. This is in sharp contrast with all previous works where the backbone trace was represented. To test how faithfully the discrete model can reproduce the chain trace in continuous space, we randomly select partial chains from the native structure of 23S ribosome RNA and re-grow them. The rms distance of the re-grown structures from the native ones is ∼ 1.7 Å for an optimized 16-state discrete model and gradually increases to ∼ 3.3 Å for long chains of length 50. The efficiency is also good, e.g. the program will finish within several tens of second for long loops of length 50. Our model may facilitate the RNA three-dimensional structure predictions in the near future when combined with appropriate free energy evaluation methods.