Semiautomated model building for RNA crystallography using a directed rotameric approach
Semiautomated model building for RNA crystallography using a directed rotameric approach
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DOI：
10.1073/pnas.0911888107
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发表时间：
2010-05-04
影响因子：
11.1
通讯作者：
Pyle, Anna Marie
中科院分区：
文献类型：
--
作者：
Keating, Kevin S.;Pyle, Anna Marie
结构化RNA分子在各种细胞过程中发挥重要作用；然而，这种RNA分子的晶体学研究提出了大量的挑战。一个值得注意的复杂性来自RNA晶体学的低分辨率，这导致电子密度图不精确且难以解释。由于缺乏用于RNA建模的计算工具，这一问题更加严重，因为蛋白质晶体学中常用的许多技术都没有与RNA结构等效的技术。这导致了模型构建过程中的困难和错误，特别是在RNA主链的建模中，由于每个核苷酸有大量可变的扭转角，这很容易出错。为了解决这个问题，我们开发了一种方法来准确地将RNA主干构建成中低分辨率的地图。这种方法是半自动化的，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基。然而，在分子的初始痕迹之后，无需进一步的用户干预就可以建立准确的主结构。为了实现这一点，首先使用RNA假扭转和碱基-磷酸盐垂直距离来预测主链构象。然后计算详细的主骨架坐标，以符合预测的构象和先前定位的磷酸盐和碱。即使从不精确的磷酸盐和碱坐标开始，这种技术也显示出精确的主链结构。一个实现这种方法的程序目前是可用的，并且一个用于Coot模型构建程序的插件正在开发中。
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 conformers 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.