Correcting Pervasive Errors in RNA Crystallography with Rosetta

使用 Rosetta 纠正 RNA 晶体学中普遍存在的错误

• 批准号: 8355778
• 负责人: Rhiju Das
• 金额: $ 11.48万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2012
• 资助国家: 美国
• 起止时间: 2012-09-30 至 2014-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8355778
• 关键词: Active Sites; Algorithms; Anti-Bacterial Agents; Antiviral Therapy; Bacteria; Benchmarking; Binding; Binding Sites; Biological Process; Catalytic RNA; Collaborations; Computer software; Crystallography; Data; Data Set; Deposition; Disease; Ensure; Enzymes; Evaluation; Exhibits; Functional RNA; Funding; Future; Genetic; Goals; Grant; HIV; Hour; Image; Length; Letters; Libraries; Life; Ligand Binding; Ligands; Manuals; Maps; Methods; Modeling; Monitor; Nucleotides; Organism; Play; Positioning Attribute; Process; Protein Biosynthesis; Proteins; Publications; RNA; RNA Folding; Regulation; Renaissance; Research; Resolution; Retroviridae; Ribonucleoproteins; Ribosomes; Role; Small RNA; Source; Structure; United States National Institutes of Health; Validation; Vertebral column; Viral; Visual; Work; X ray diffraction analysis; X-Ray Diffraction; base; computerized tools; conformer; density; electron density; improved; inorganic phosphate; neoplastic cell; novel; success; sugar; three dimensional structure; tool

DESCRIPTION (provided by applicant): The continuing discoveries of non-coding RNAs and their critical roles in cellular and viral machinery are inspiring novel antibacterial, antitumor, nd antiviral therapies based on disrupting or manipulating the RNAs involved. Most of RNA's biological functions depend on the formation of intricate 3D structure and binding to ligands and proteins. Unfortunately, crystallographic models, our richest sources of RNA structural information, contain pervasive errors due to ambiguities in manually fitting RNA backbones into experimental density maps. We have recently brought Rosetta high- resolution RNA structure prediction together with PHENIX diffraction-based refinement and MolProbity validation, to create Enumerative Real-space Refinement ASsisted by Electron density under Rosetta. The ERRASER method corrects the majority of identifiable sugar pucker errors, steric clashes, suspicious backbone rotamers, and incorrect bond lengths/angles in a benchmark of RNA data sets, including a ribosomal subunit. Furthermore, the method, on average, improves Rfree factors to rigorously set- aside data. In this exploratory grant, we first aim to expand ERRASER to resolve ambiguities at RNA/ligand, RNA/protein, and RNA crystal contacts, as will be necessary for correcting RNA enzyme active sites, ligand binding sites, and ribonucleoprotein machines. Second, we aim to make ERRASER available as a fully automated server that will both refine all extant PDB-deposited RNA and ribonucleoprotein models and enable crystallographers to rapidly correct errors in their future data sets. By rapidly and systematicall disambiguating RNA model fitting, ERRASER will enable RNA crystallography with significantly fewer errors. PUBLIC HEALTH RELEVANCE: RNA molecules play fundamental roles in transmitting and regulating genetic information in all living systems, including disease-causing bacteria, retroviruses like HIV, and tumor cells. New potentially life-saving therapies that target these RNAs are being hindered by our imperfect understanding of how RNAs fold into intricate 3D structures. Our work aims to develop a new tool that corrects pervasive mistakes in RNA crystallographic models, which are our richest sources of 3D information.

描述（由申请人提供）：非编码RNA及其在细胞和病毒机制中的关键作用的不断发现正在激发基于破坏或操纵相关RNA的新型抗菌、抗肿瘤和抗病毒疗法。RNA的大部分生物学功能取决于复杂的3D结构的形成以及与配体和蛋白质的结合。不幸的是，结晶学模型，我们最丰富的RNA结构信息的来源，包含普遍的错误，由于在手动拟合RNA骨架到实验密度图的模糊性。我们最近将Rosetta高分辨率RNA结构预测与基于PHENIX衍射的细化和MolProbity验证结合在一起，以在Rosetta下创建由电子密度辅助的枚举实空间细化。ERRASER方法纠正了RNA数据集（包括核糖体亚基）基准中大多数可识别的糖皱褶错误、空间冲突、可疑的骨架旋转异构体和不正确的键长/角度。此外，平均而言，该方法改进了Rfree因子以严格地留出数据。在这项探索性资助中，我们首先旨在扩展ERRASER以解决RNA/配体，RNA/蛋白质和RNA晶体接触的模糊性，这对于纠正RNA酶活性位点，配体结合位点和核糖核蛋白机器是必要的。其次，我们的目标是使ERRASER作为一个全自动化的服务器，既可以完善所有现存的PDB沉积的RNA和核糖核蛋白模型，使晶体学家能够快速纠正他们未来数据集的错误。通过快速和系统地消除RNA模型拟合的歧义，ERRASER将使RNA晶体学具有显著更少的错误。 公共卫生相关性：RNA分子在传递和调节所有生命系统中的遗传信息方面发挥着重要作用，包括致病细菌、逆转录病毒（如HIV）和肿瘤细胞。针对这些RNA的新的潜在拯救生命的疗法受到我们对RNA如何折叠成复杂的3D结构的不完善理解的阻碍。我们的工作旨在开发一种新的工具，纠正RNA晶体学模型中普遍存在的错误，这是我们最丰富的3D信息来源。