Fundamental Studies of RNA Conformational Thermodynamics

RNA构象热力学基础研究

基本信息

批准号：
10348772
负责人：
Hashim M Al-Hashimi
金额：
$ 61.68万
依托单位：
STANFORD UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-05-01 至 2024-02-29
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10348772
关键词：
3-Dimensional Affinity Atlases Base Pairing Behavior Biochemical Biological Biological Process Biology Biomedical Engineering Chemicals Communicable Diseases Communities Complex Computer Models Cues DNA Data Development Dimensions Elements Engineering Fingerprint Gene Expression Genetic Code Genetic Diseases Goals Individual Lead Life Life Cycle Stages Ligand Binding Maps Measurement Mechanics Modeling Molecular Molecular Conformation Mutation Participant Probability Property Proteins RNA RNA Conformation RNA Sequences Signal Transduction Structure System Testing Therapeutic Intervention Thermodynamics Untranslated RNA Variant alpha helix base blind cancer genetics computerized tools conformational conversion design experimental study human disease improved model development new technology pathogen predictive modeling protein structure receptor reconstitution response synthetic biology tool viral RNA

项目摘要

Abstract Non-coding (nc)RNAs are key players in biology and are increasingly recognized as targets to treat infectious diseases, cancer, and genetic disorders, and as molecular tools for bioengineering and synthetic biology. Functional and regulatory RNAs undergo conformational transitions in multi-step biochemical cycles, ligand binding, and signaling. It is important to understand how these RNA structures form and how they dynamically change in response to cellular and chemical cues because of the biological importance of these RNAs, because this understanding will provide tools for bio-engineering and may facilitate therapeutic intervention, and, most fundamentally, because RNA is an essential molecule of life, both present and past. The thermodynamics of RNA secondary structure formation can be predicted with reasonable accuracy from nearest neighbor rules, and there have been remarkable advances in determining 3D RNA and RNA·protein structures. However, we lack a predictive energetic model for RNA tertiary conformational thermodynamics, which is ultimately required to understand and manipulate RNA form and function in biological processes. Unlike the energetic additivity of base pair steps for RNA secondary structure energetics, RNA tertiary structure energetics requires the statistical mechanical modeling of conformational ensembles and determination of partition functions that delineate the probabilities of forming different conformations. RNA's molecular properties—hierarchical folding, repeating structural motifs, and sparse tertiary contact interfaces—render tertiary structure energetics far simpler and more tractable for RNA than for proteins. From these properties, a Reconstitution Model has been developed that could allow conformational thermodynamics to be predicted based on conformational ensembles of component structural elements: helices, junctions, and tertiary contact partners. The central hypothesis of this proposal is that, by characterizing conformational thermodynamics for the array of component parts, the conformational thermodynamics of any arbitrary RNA can be determined. The central goals of this proposal are to test and develop this model and to overcome the vast challenge of determining conformational ensembles for thousands of RNA element. To accomplish this, `RNA-MaP' will be used—a novel technology that provides millions of thermodynamic measurements and quantitative `thermodynamic fingerprints' for tens of thousands of RNA helix, junction, and tertiary contact elements and provides data to obtain conformational ensembles for each element. This project will (1) build an atlas of conformational thermodynamics for RNA elements; (2) define a roster of conformational ensembles for these elements; and then (3) use this information within the Reconstitution Model to design and rationally engineer the conformational and energetic properties of ncRNAs. This project will also provide a freely available computational tool, RNAMake-ΔG, to model and engineer dynamic RNA tertiary structures, and will provide a wealth of high-precision thermodynamic data to help guide community-wide model development.

抽象的非编码 (nc)RNA 是生物学中的关键角色，并且越来越多地被认为是治疗靶点传染病、癌症和遗传性疾病，以及作为生物工程和合成的分子工具生物学。功能性和调节性 RNA 在多步骤生化循环中经历构象转变，了解这些 RNA 结构如何形成以及它们如何形成非常重要。由于这些细胞和化学信号的生物学重要性，它们会动态变化 RNA，因为这种理解将为生物工程提供工具，并可能促进治疗干预，最根本的是，因为 RNA 是生命的重要分子，无论是现在还是过去。 RNA二级结构形成的热力学可以合理准确地预测根据最近邻规则，在确定 3D RNA 和 RNA·蛋白质结构然而，我们缺乏RNA三级构象的预测能量模型。热力学，最终需要理解和操纵 RNA 的形式和功能与 RNA 二级结构能量学的碱基对步骤的能量加和性不同， RNA 三级结构能量学需要构象系综的统计力学模型以及确定划分函数来描述形成不同构象的概率。 RNA 的分子特性——层次折叠、重复结构基序和稀疏的三级接触界面——使 RNA 的三级结构能量学比蛋白质的三级结构能量学更简单、更容易处理。这些特性，已经开发了一个重构模型，可以允许构象热力学根据组件结构元素的构象集合进行预测：螺旋、连接点和该提案的中心假设是，通过表征构象。组成部分阵列的热力学、任意 RNA 的构象热力学可以确定该提案的中心目标是测试和开发该模型并克服该模型。确定数千个 RNA 元件的构象集合是一项巨大的挑战。将使用“RNA-MaP”——一种提供数百万次热力学测量和数万个 RNA 螺旋、连接点和三级接触的“定量热力学指纹” 元素并提供数据以获得每个元素的构象集合。该项目将（1）构建一个。 RNA 元件的构象热力学图集；(2) 定义一个构象系综名册；这些元素；然后（3）在重构模型中使用这些信息来设计和合理地该项目还将免费提供 ncRNA 的构象和能量特性。计算工具 RNAMake-ΔG，用于建模和设计动态 RNA 三级结构，并将提供丰富的高精度热力学数据有助于指导整个社区的模型开发。