Inverse Kinematics, Sterics & Data - To Fit RNA Backbone

逆运动学、立体学

• 批准号: 7071107
• 负责人: JANE Shelby RICHARDSON
• 金额: $ 20.52万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-06-01 至 2009-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7071107
• 关键词: RNA; X ray crystallography; bioinformatics; biomechanics; computational biology; computer graphics /printing; conformation; mathematics; molecular biology information system; nucleic acid structure; structural biology

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.

描述（由申请人提供）：本项目旨在通过结合数学、分子图形学、晶体学和结构生物信息学的方法和经验，为晶体学家开发一种更容易和更准确的工具，以将RNA骨架拟合到密度中。RNA骨架构象的细节是至关重要的许多生物医学上重要的新的角色被发现的大小RNA分子：特异性的适体结合，剪接的控制，特异性的蛋白质相互作用的系统中，从SiRNA核糖体，特别是一个机制的理解核酶催化。然而，在RNA或RNP晶体结构的典型分辨率下，将RNA骨架原子正确地拟合到电子密度图中是非常困难的：即使用简化的糖皱褶描述，每个残基也有6个可变的二面角，并且只有磷酸和碱基可以真正清楚地看到。如果添加氢原子，则当前沉积的结构中的相当大百分比的寡核苷酸残基显示物理上不可能的空间冲突，表明细化从错误的角度组合开始。RNA骨架的多维搜索问题将通过Snoeyink小组使用的逆运动学和相关方法来解决，以改善蛋白质设计中蛋白质骨架替代品的搜索，修改以允许由磷酸盐和碱基位置和方向的相当精确但部分知识提供的约束的不寻常性质。Richardson小组的全原子接触分析和质量过滤数据库统计将提供筛选分子合理性的可能的几何解决方案的必要步骤，以前在评估和改进蛋白质晶体结构和RNA结构生物信息学方面取得了成功。实用工具将建立在现有的KiNG和/或法师系统上，这些系统已经具有模型和地图显示以及模型操作和分析的能力。可用性将受益于Richardson实验室的晶体学和模型校正经验，以及感兴趣的RNA晶体学家的β测试;速度和鲁棒性将受益于Snoeyink小组在算法和良好编程实践方面的专业知识。