Thermodynamically Calibrated RNA Simulations to Decode Mechanisms of RNA Molecular Recognition

通过热力学校准的 RNA 模拟来解码 RNA 分子识别机制

• 批准号: 9797040
• 负责人: Alan Austin Chen
• 金额: $ 35.91万
• 依托单位: STATE UNIVERSITY OF NEW YORK AT ALBANY
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-09-01 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9797040
• 关键词: 3-Dimensional; Affect; Base Pairing; Behavior; Binding; Bioinformatics; Biological; Biosensing Techniques; Biosensor; Chemicals; Complex; Computer Simulation; Data; Development; Engineering; Free Energy; Genetic Transcription; Ligand Binding; Ligands; Measures; Messenger RNA; Methods; MicroRNAs; Modeling; Molecular; Nanotechnology; Nucleic Acids; Nucleosides; Nucleotides; Pathway interactions; Proteins; RNA; RNA Folding; Research; Resolution; Structure; Structure-Activity Relationship; Techniques; Technology; Therapeutic Intervention; Thermodynamics; aptamer; base; design; engineering design; experimental study; flexibility; improved; interest; molecular recognition; novel; programs; simulation; small molecule; structural biology; success; three dimensional structure; two-dimensional

This MIRA proposal details a research program that centers around the development and application of improved, thermodynamically accurate computer models for simulating RNA 3D structures at atomic resolution. These models differ from existing models for RNA in that they are calibrated to reproduce solution thermodynamic data on the physical behavior of nucleotides and nucleosides, an approach that is readily extended to include the effects of unnatural RNAs and RNA-ligand interactions. This technology is particularly important as many biomedically important RNAs are not amenable to traditional structural biology techniques, which makes it difficult to establish basic structure-function relationships that must be understood before potential therapeutic interventions could be designed. Often, the only available structural information on an RNA of interest are secondary structure estimates from bioinformatics or from SHAPE chemical probing experiments. This proposal builds on recent successes in using molecular simulations restrained by sparse SHAPE or NMR data to simulate the folding pathway of a co-transcriptionally folded RNA, as well as describe how the flexibility of microRNA/mRNA complexes affect how they bind the hAGO2 protein. Building on these recent results, a comprehensive research program is proposed in three major parts. The first is the use of alchemical free-energy calculations to measure the energetics of RNA base-pairing and recalibrate them against experiment. The second is a two-dimensional replica-exchange method for fully automated, adaptive RNA folding incorporating variable strength secondary structure constraints – a method that show promising results that we expect to scale to large (50-100 nt) RNAs including tertiary motifs. Lastly, we propose a novel multi-dimensional technique to simultaneously fold RNA aptamers while also binding small-molecule ligands using Hamiltonian replica-exchange combined with alchemical free energy calculations – which will be necessary to capture the “induced fit” of the RNA aptamer upon ligand binding. These calculations will be used to predict ligand binding modes and engineer optimal RNA biosensors through targeting incorporation of chemically modified nucleic acids.

该MIRA提案详细介绍了一项研究计划，该计划围绕开发 并应用改进的热力学精确计算机模型来模拟RNA 原子分辨率的3D结构。这些模型与现有的RNA模型不同，因为 对它们进行校准以复制解决方案的热力学数据，以了解 核苷酸和核苷，这种方法很容易扩展到包括 不自然的RNA和RNA - 配体相互作用。这项技术特别重要，因为 生物医学重要的RNA不适合传统的结构生物学技术， 这使得必须建立必须是的基本结构功能关系 在设计潜在的治疗干预措施之前，请先理解。 通常，有关RNA感兴趣的RNA的唯一可用的结构信息是次要的 从生物信息学或形状化学探测实验的结构估计。这 提案建立在最新的使用分子模拟的成功基础上 形状或NMR数据，以模拟共同折叠RNA的折叠途径，AS 并描述microRNA/mRNA复合物的灵活性如何影响它们的结合方式 Hago2蛋白。在这些最新结果的基础上，一项全面的研究计划是 提议分为三个主要部分。首先是使用酒精自由能计算 测量RNA碱基对的能量，并将其重新校准，以防止实验。这 第二是用于完全自动化的自适应RNA的二维复制方法 折叠结合了可变强度二级结构约束 - 一种显示的方法 我们期望将其扩展到包括三级基序在内的大型（50-100 nt）RNA。 最后，我们提出了一种新型的多维技术，以简单地折叠RNA适体 同时还使用汉密尔顿复制品 - 交换结合了小分子配体 炼金术自由能计算 - 捕获捕获的“诱发拟合”是必不可少的 RNA APATMER在配体结合上。这些计算将用于预测配体结合 模式和工程师通过靶向化学掺入的最佳RNA生物传感器 修饰的核酸。