Next-generation computational/chemical methods for complex RNA structures

用于复杂 RNA 结构的下一代计算/化学方法

• 批准号: 9765345
• 负责人: Rhiju Das
• 金额: $ 68.01万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-01 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9765345
• 关键词: 3-Dimensional; Address; Adoption; Anti-Bacterial Agents; Antiviral Agents; Bacteria; Behavior; Biochemical; Biological; Biomedical Engineering; Biomedical Research; Biophysics; Chemicals; Communities; Complex; Cryoelectron Microscopy; Crystallography; Development; Disease; Engineering; HIV; Heterogeneity; Life; Medical; Methods; Modification; Molecular Conformation; Mutation; Organism; Phylogenetic Analysis; Play; Proteins; RNA; RNA Folding; Regulation; Research; Retroviridae; Role; Savings; Software Tools; Structure; Technology; Testing; Untranslated RNA; Viral; Work; biochemical tools; blind; computerized tools; design; experimental study; genetic information; model design; molecular modeling; neoplastic cell; next generation; novel; prospective; structural biology; success; targeted treatment; therapeutic genome editing; three dimensional structure; tool

PROJECT SUMMARY The continuing discoveries of non-coding RNAs and their critical roles in cellular and viral machinery are inspiring novel antibacterial, antitumor, antiviral, and genome-editing therapies based on disabling, manipulating, and repurposing the RNAs involved. Unfortunately, our poor biophysical understanding of `how RNAs work' hinders the development of these potentially life-saving efforts. A critical bottleneck has been the inapplicability of crystallography, NMR, cryoelectron microscopy, phylogenetic analysis, and biochemical methods to determine the partly ordered conformations of non-coding RNAs in all their functional states. To resolve this bottleneck, we are developing experimental methods and complementary computational approaches that give rich information sufficient to infer and engineer RNA secondary and tertiary structures and their heterogeneous ensembles, evaluated through community-wide blind trials, prospective compensatory mutation/rescue experiments, and global RNA design challenges. Here, we outline expansions of our research that will rigorously address four biomedically significant problems that have so far seen limited progress in molecular modeling efforts: the heterogeneity of RNA structures within their native cellular and viral contexts; modeling and design of RNA's biological interactions with proteins and other molecules, modulated by chemical modification; high-accuracy calculation of RNA folding energetics; and the automated design of dynamic 3D RNA structures for eventual medical applications. We will evaluate success through continuing blind trials, independent tests by more than a dozen expert biological and bioengineering collaborators, and through adoption of our methods and software tools by the broader research community. In the same way that specialized structural biology tools and computational design are establishing a firm understanding of protein behavior and regulation, we propose that the technologies outlined here will transform our understanding of structure in non-coding RNAs, providing a stronger basis for their biomedical activation or disruption.

项目摘要 持续发现非编码RNA及其在细胞和中的关键作用 病毒机械鼓舞了新颖的抗菌，抗肿瘤，抗病毒和基因组编辑 基于禁用，操纵和重新利用所涉及的RNA的疗法。 不幸的是，我们对“ RNA如何工作”的生物物理不良理解阻碍了 发展这些潜在的挽救生命的努力。关键的瓶颈是 晶体学，NMR，冷冻电子显微镜，系统发育分析的不适用性， 和生化方法来确定非编码的部分有序构象 RNA在其所有功能状态下。为了解决这种瓶颈，我们正在发展 实验方法和互补的计算方法，可提供丰富 足以推断和设计RNA二级和第三级结构以及 他们的异构合奏，通过社区范围的盲试验评估， 前瞻性补偿性突变/救援实验和全球RNA设计 挑战。在这里，我们概述了研究的扩展，这些扩展将严格解决四个 迄今为止的生物医学意义问题，分子的进展有限 建模工作：其天然细胞和病毒中RNA结构的异质性 上下文； RNA与蛋白质和其他的生物学相互作用的建模和设计 分子，通过化学修饰调节； RNA的高准确计算 折叠能量学；以及最终动态3D RNA结构的自动设计 医疗应用。我们将通过持续的盲试验评估成功， 十多个专家生物学和生物工程的独立测试 合作者，以及通过更广泛的方法和软件工具采用我们的方法和软件工具 研究社区。以专门的结构生物学工具和 计算设计正在建立对蛋白质行为和 法规，我们建议这里概述的技术将改变我们 了解非编码RNA中的结构，为其提供更强的依据 生物医学激活或破坏。