Inverse Kinematics, Sterics & Data - To Fit RNA Backbone

逆运动学、立体学

• 批准号: 7931191
• 负责人: JANE Shelby RICHARDSON
• 金额: $ 7.89万
• 依托单位: DUKE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2010-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7931191
• 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）：本项目旨在结合数学、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简单、更准确的工具，以适应RNA主链的密度。RNA主干构象的细节对许多生物医学上重要的新作用至关重要，无论是大的还是小的RNA分子：特异性适配体结合，剪接控制，从SiRNA到核糖体系统中蛋白质相互作用的特异性，特别是对核糖酶催化的机制理解。然而，以典型的RNA或RNP晶体结构的分辨率将RNA主链原子正确地拟合到电子密度图中是非常困难的：即使使用简化的糖块描述，每个残基也有6个可变的二面角，而且只有磷酸基和碱基才能被清楚地看到。如果加入氢原子，那么目前沉积结构中相当大比例的寡核苷酸残基表现出物理上不可能的空间冲突，这表明改进是从错误的角度组合开始的。RNA主链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主链替代品的搜索，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知识提供的不寻常的约束性质。Richardson小组的全原子接触分析和质量过滤数据库统计将为筛选分子合理性的可能几何解决方案提供必要的步骤，之前在蛋白质晶体结构和RNA结构生物信息学的评估和改进上取得了成功。实用工具将建立在现有的国王和/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；速度和健壮性将受益于Snoeyink团队在算法和良好编程实践方面的专业知识。

项目成果

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids.

• DOI: 10.1093/nar/gkm216
• 发表时间: 2007-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Davis IW;Leaver-Fay A;Chen VB;Block JN;Kapral GJ;Wang X;Murray LW;Arendall WB 3rd;Snoeyink J;Richardson JS;Richardson DC
• 通讯作者: Richardson DC

Defining and computing optimum RMSD for gapped and weighted multiple-structure alignment.

定义和计算带间隙和加权多结构比对的最佳 RMSD。

• DOI: 10.1109/tcbb.2008.92
• 发表时间: 2008
• 期刊: IEEE/ACM transactions on computational biology and bioinformatics
• 作者: Wang,Xueyi;Snoeyink,Jack
• 通讯作者: Snoeyink,Jack