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.

项目概要 非编码 RNA 及其在细胞和细胞中的关键作用的不断发现 病毒机制正在激发新型抗菌、抗肿瘤、抗病毒和基因组编辑的灵感 基于禁用、操纵和重新利用相关 RNA 的疗法。 不幸的是，我们对“RNA如何工作”的生物物理学理解不足，阻碍了 发展这些可能挽救生命的努力。一个关键的瓶颈是 晶体学、核磁共振、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 处于所有功能状态的 RNA。为了解决这个瓶颈，我们正在开发 实验方法和互补的计算方法提供了丰富的 足以推断和设计 RNA 二级和三级结构的信息， 他们的异质整体，通过社区范围的盲试验进行评估， 前瞻性补偿突变/拯救实验和全局RNA设计 挑战。在这里，我们概述了我们研究的扩展，将严格解决四个问题 迄今为止，分子生物学领域进展有限的生物医学重大问题 建模工作：天然细胞和病毒内 RNA 结构的异质性 上下文； RNA与蛋白质和其他生物相互作用的建模和设计 分子，通过化学修饰进行调节； RNA的高精度计算 折叠能量学；以及最终的动态 3D RNA 结构的自动化设计 医疗应用。我们将通过持续的盲目试验来评估成功， 由十几位生物和生物工程专家独立测试 合作者，并通过更广泛的人采用我们的方法和软件工具 研究社区。就像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的牢固理解 监管，我们建议这里概述的技术将改变我们的 理解非编码RNA的结构，为它们的研究提供更坚实的基础 生物医学激活或破坏。