Fundamental Studies of RNA Conformational Thermodynamics

摘要 非编码(NC)RNA是生物学中的关键角色，越来越被认为是治疗的靶点 传染病、癌症和遗传疾病，以及作为生物工程和合成的分子工具 生物学。功能和调控RNA在多步生化循环中经历构象转变， 配基结合和信号传递。重要的是要了解这些RNA结构是如何形成的，以及它们是如何形成的 对细胞和化学信号的动态变化，因为这些信号在生物学上的重要性 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是生命的一个基本分子，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，我们缺乏一个预测rna三级构象的能量模型。 热力学，它最终是理解和操纵RNA的形式和功能所必需的 生物过程。与RNA二级结构能量学的碱基对步骤的能量性不同， RNA三级结构能量学需要构象系综的统计力学模型 以及确定描绘形成不同构象的概率的配分函数。 RNA的分子特性--分层折叠、重复的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更简单和更容易处理。从… 在这些性质的基础上，一个重构模型已经被开发出来，它可以允许构象热力学 根据组成结构元素的构象集成进行预测：螺旋、连接和 第三方联系合作伙伴。这一提议的中心假设是，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 确定数千种RNA元素的构象系综是一项巨大的挑战。要做到这一点， 将使用‘RNA-map’-这是一项新技术，它提供数百万热力学测量和 数万个RNA螺旋、连接和三次接触的定量“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)建立一个 RNA元素的构象热力学图谱；(2)定义了一个构象系综名册 这些要素；然后(3)在重构模型中使用这些信息来合理地设计和 设计ncRNAs的构象和能量特性。该项目还将提供免费提供的 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，帮助指导社区范围的模型开发。

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.