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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Semiautomated model building for RNA crystallography using a directed rotameric approach
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Semiautomated model building for RNA crystallography using a directed rotameric approach

机译：使用定向旋转异构体方法进行RNA结晶学的半自动模型构建

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摘要

Structured RNA molecules play essential roles in a variety of cellular processes; however, crystallographic studies of such RNA molecules present a large number of challenges. One notable complication arises from the low resolutions typical of RNA crystallography, which results in electron density maps that are imprecise and difficult to interpret. This problem is exacerbated by the lack of computational tools for RNA modeling, as many of the techniques commonly used in protein crystallography have no equivalents for RNA structure. This leads to difficulty and errors in the model building process, particularly in modeling of the RNA backbone, which is highly error prone due to the large number of variable torsion angles per nucleotide. To address this, we have developed a method for accurately building the RNA backbone into maps of intermediate or low resolution. This method is semiautomated, as it requires a crystallographer to first locate phosphates and bases in the electron density map. After this initial trace of the molecule, however, an accurate backbone structure can be built without further user intervention. To accomplish this, backbone conf ormers are first predicted using RNA pseudotorsions and the base-phosphate perpendicular distance. Detailed backbone coordinates are then calculated to conform both to the predicted conformer and to the previously located phosphates and bases. This technique is shown to produce accurate backbone structure even when starting from imprecise phosphate and base coordinates. A program implementing this methodology is currently available, and a plugin for the Coot model building program is under development.
机译：结构化的RNA分子在多种细胞过程中起着至关重要的作用。然而，这种RNA分子的晶体学研究提出了许多挑战。 RNA晶体学的典型低分辨率引起了一个显着的复杂性，这导致了电子密度图的不精确和难以解释。缺乏用于RNA建模的计算工具使这个问题更加严重，因为蛋白质晶体学中常用的许多技术都没有等同于RNA结构的技术。这导致模型建立过程中的困难和错误，特别是在RNA主链的建模中，由于每个核苷酸的扭转角数量众多，因此很容易出错。为了解决这个问题，我们开发了一种将RNA主链准确构建到中分辨率或低分辨率图谱中的方法。此方法是半自动化的，因为它需要晶体学家首先在电子密度图中定位磷酸盐和碱。然而，在此分子的最初痕迹之后，无需进一步的用户干预即可构建准确的骨架结构。为此，首先使用RNA假扭转和碱式磷酸酯垂直距离预测骨架配体。然后计算详细的骨架坐标，以符合预测的构象异构体和先前定位的磷酸酯和碱。该技术显示出即使从不精确的磷酸根和碱基坐标开始也能产生准确的骨架结构。目前可以使用实现此方法的程序，并且正在开发Coot模型构建程序的插件。

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