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械中的关键作用的持续发现激发了基于破坏或操纵涉及的RNA的抗病毒疗法的新型抗菌，抗病毒疗法。 RNA的大多数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，由于手动将RNA骨架拟合到实验密度图中的歧义性，我们最丰富的RNA结构信息来源包含了普遍的错误。最近，我们将Rosetta高分辨率RNA结构预测以及基于苯金衍射的细化和磨牙验证，创建了由Rosetta下电子密度辅助的枚举实空间改进。 Erraser方法在RNA数据集的基准中纠正了大多数可识别的糖冰球错误，空间冲突，可疑的骨干旋转旋转剂和不正确的键长/角度，包括核糖体亚基。此外，该方法平均可以改善无RF的因素，以严格抛弃数据。在这项探索性赠款中，我们首先要扩展Erraser，以解决RNA/配体，RNA/蛋白质和RNA晶体接触的歧义，这对于纠正RNA酶的活性位点，配体结合位点和核糖核蛋白蛋白机器将是必要的。其次，我们的目标是使Erraser作为全自动服务器可用，该服务器既可以完善所有现有的PDB沉积RNA和核糖核蛋白模型，又可以使Crystallographter能够快速纠正其未来数据集中的错误。通过快速和系统的歧义RNA模型拟合，Erraser将使RNA晶体学明显较少。 公共卫生相关性：RNA分子在传输和调节所有生物系统中的遗传信息中起着基本作用，包括引起疾病的细菌，HIV等逆转录病毒和肿瘤细胞。我们对RNA如何将其折叠成复杂的3D结构的不完善的理解阻碍了针对这些RNA的新的潜在挽救生命的疗法。我们的工作旨在开发一种新工具，以纠正RNA晶体学模型中普遍错误的错误，这是我们最丰富的3D信息来源。