Inverse Kinematics, Sterics & Data - To Fit RNA Backbone

逆运动学、立体学

• 批准号: 7426852
• 负责人: JANE Shelby RICHARDSON
• 金额: $ 19.76万
• 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 2010-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7426852
• 关键词: Address; Algorithms; Binding; Bioinformatics; Biology; Catalysis; Catalytic RNA; Crystallography; Data; Databases; Deposition; Diagnosis; Hydrogen; Investigation; Knowledge; Maps; Mathematics; Methods; Modeling; Molecular; Molecular Conformation; Nature; Nucleic Acids; Oligonucleotides; Phase; Positioning Attribute; Procedures; Proteins; R-factor; RNA; RNA Splicing; Relative (related person); Resolution; Ribose; Ribosomes; Role; Screening procedure; Small RNA; Solutions; Specificity; Speed; Structure; System; Techniques; Testing; Vertebral column; aptamer; base; density; design; electron density; experience; improved; inorganic phosphate; interest; kinematics; programs; resistance factors; statistics; sugar; tool; usability

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）：该项目建议通过结合数学、分子图学、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简单、更准确的工具，以将 RNA 主链拟合到密度中。 RNA骨架构象的细节对于大小RNA分子发现的许多生物医学重要的新作用至关重要：特异性适体结合、剪接控制、从SiRNA到核糖体的系统中蛋白质相互作用的特异性，尤其是对核酶催化机制的理解。然而，以 RNA 或 RNP 晶体结构的典型分辨率将 RNA 主链原子正确拟合到电子密度图中是非常困难的：即使使用简化的糖褶皱描述，每个残基也有 6 个可变的二面角，并且只能真正清楚地看到磷酸盐和碱基。如果添加氢原子，则当前沉积结构中很大一部分寡核苷酸残基显示出物理上不可能的空间冲突，表明精炼是从错误的角度组合开始的。 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，以改进蛋白质设计中蛋白质骨架替代品的搜索，并进行修改以允许由相当精确但部分的磷酸盐和碱基位置和方向的知识提供的约束的不寻常性质。理查森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可能的分子合理性几何解决方案的必要步骤，此前这些分析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。实用工具将构建在现有的 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作和分析的功能。可用性将受益于理查森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 beta 测试；速度和稳健性将受益于 Snoeyink 团队在算法方面的专业知识和良好的编程实践。