Inverse Kinematics, Sterics & Data - To Fit RNA Backbone

描述(由申请人提供)：该项目建议通过结合数学、分子图形学、结晶学和结构生物信息学的方法和经验，为结晶学家开发一种更容易、更准确的工具来将RNA骨架匹配到密度中。RNA骨架构象的细节对于发现大小RNA分子的许多重要的生物医学新角色是至关重要的：特定的适体结合、剪接的控制、从siRNA到核糖体系统中蛋白质相互作用的特异性，特别是对于从机制上理解核酶催化。然而，以RNA或RNP晶体结构的典型分辨率将RNA主干原子正确地拟合到电子密度图中是非常困难的：即使有一个简化的糖折叠描述，每个残基也有6个可变的二面角，而且只有磷酸和碱基才能真正清楚地看到。如果添加氢原子，那么在目前沉积的结构中，相当大比例的寡核苷酸残基显示出物理上不可能的空间碰撞，这表明精细化是从错误的角度组合开始的。Snoeyink小组将使用反向运动学和相关方法来解决RNA骨架的多维搜索问题，以改进蛋白质设计中对蛋白质骨架替代方案的搜索，修改后的方法将考虑到由相当精确但部分的磷酸盐和碱基位置和取向知识提供的约束的不寻常性质。筛选分子合理性的可能几何解决方案的必要步骤将由Richardson集团的全原子接触分析和质量过滤数据库统计提供，此前在蛋白质晶体结构和RNA结构生物信息学的评估和改进方面取得了成功。实用工具将建立在现有的King和/或MAGE系统上，这些系统已经具有模型和地图显示以及模型操纵和分析的能力。易用性将受益于理查森实验室的结晶学和模型校正经验，以及感兴趣的RNA结晶学家的Beta测试；速度和健壮性将受益于Snoeyink集团在算法和良好编程实践方面的专业知识。

DESCRIPTION (provided by applicant): This project proposes to develop a much easier and more accurate tool for crystallographers to fit RNA backbone into density, by combining methods and experience from mathematics, molecular graphics, crystallography, and structural bioinformatics. The details of RNA backbone conformation are critical to many of the biomedically important new roles being found for both large and small RNA molecules: specific aptamer binding, control of splicing, specificity of protein interactions in systems from SiRNA to ribosomes, and especially to a mechanistic understanding of ribozyme catalysis. However, the correct fitting of RNA backbone atoms into electron density maps at the resolutions typical for RNA or RNP crystal structures is very difficult: even with a simplified sugar pucker description, there are 6 variable dihedral angles per residue, and only the phosphate and the base can be seen really clearly. If the hydrogen atoms are added, then a substantial percentage of oligonucleotide residues in currently deposited structures show physically impossible steric clashes, indicating that refinement started from the wrong combination of angles. The multi-dimensional search problem for RNA backbone will be addressed with inverse kinematics and related methods used by the Snoeyink group to improve the search for protein backbone alternatives in protein design, modified to allow for the unusual nature of the constraints provided by the fairly precise but partial knowledge of phosphate and base positions and orientations. The necessary step of screening the possible geometrical solutions for molecular reasonableness will be provided by the Richardson group's all-atom contact analysis and quality-filtered database statistics, previously shown successful on the assessment and improvement of protein crystal structures and on RNA structural bioinformatics. Practical tools will be built onto the existing KiNG and/or Mage systems that already have capabilities for model and map display and for model manipulation and analysis. Usability will benefit from Richardson lab crystallographic and model correction experience and from beta-testing by interested RNA crystallographers; speed and robustness will benefit from the Snoeyink group's expertise with algorithms and good programming practice.