Towards solution of the RNA folding problem

致力于解决RNA折叠问题

• 批准号: 8233539
• 负责人: Michael D. Brenowitz
• 金额: $ 33.76万
• 依托单位: ALBERT EINSTEIN COLLEGE OF MEDICINE
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-05-01 至 2015-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8233539
• 关键词: Affect; Behavior; Biological Models; Biological Process; Catalytic Domain; Cations; Cell physiology; Cells; Chemicals; Complex; Coupling; Data; Development; Elements; Environment; Genetic Transcription; Goals; Human Pathology; In Vitro; Individual; Introns; Kinetics; Life; Link; Measures; Mediating; Messenger RNA; Methods; Microscopic; Modeling; Molecular Chaperones; Nature; Nucleotides; Pathology; Pathway interactions; Physical environment; Physiological; Polynucleotides; Population; Process; Protein Binding; Proteins; RNA; RNA Folding; Reaction; Regulatory Element; Resolution; Shipping; Ships; Solutions; Structural Models; Structure; Study models; Temperature; Testing; Time; group I ribozyme; in vivo; mRNA Expression; millisecond; protein structure; research study; simulation; three dimensional structure

Project Summary RNA molecules often must fold into distinct three-dimensional structures to exert their biological function. These folded structures may be large or small, long-lived or transient, and/or stable or unstable in nature. The kinetics of RNA folding is characterized by multiple pathways, the population of intermediates and often (but not always) on- and/or off-pathway kinetically trapped species. Our approach to understanding how the RNA is folded is to determine which folding pathways are possible in vitro with the goal of determining the subset that occur in vivo. We computationally integrate local and global measures of folding into `structural-kinetic' models that characterize folding reactions from their earliest steps. Our development of high-throughput methods for the acquisition of time progress curves with millisecond time and single nucleotide spatial resolution allows general hypotheses to be tested against experimental data that is both deep and broad. The proposed studies of group I introns seek to establish quantitative relationships between RNA structure, stability and folding kinetics by critically comparing the folding of phylogenetically related RNA molecules and gentle systematic perturbation of tertiary contacts. The folding of a riboswitch whose structure is homologous to the catalytic core of group I intron is analyzed to determine if these different regulatory elements possess a common folding mechanism. We explore the effect on the observed emergent folding behavior solution variables such as temperature and ionic conditions that affect the microscopic environment of RNA in order to understand the relationships between the physical environment and folding environment. Lastly, we seek to understand how transcription affects RNA folding.

项目摘要 RNA分子通常必须折叠成不同的三维结构才能发挥其生物学作用 功能。这些折叠的结构可能是大的或大的，长寿命或短暂的，并且/或稳定或 本质上不稳定。 RNA折叠的动力学以多种途径为特征 中间体，通常（但并非总是）在动力学上被捕获的物种（但并非总是）。我们的 理解RNA折叠方式的方法是确定可能的折叠途径 在体外，确定体内发生的子集的目的。我们计算本地集成 以及将折叠折叠成“结构运动”模型的全球测量方法，这些模型表征了折叠反应 他们最早的步骤。我们开发用于获取时间进度的高通量方法 具有毫秒的时间和单核苷酸空间分辨率的曲线允许一般假设为 对既有深度又广泛的实验数据进行了测试。 I组内含子的拟议研究 寻求通过RNA结构，稳定性和折叠动力学之间的定量关系 批判性地比较系统发育相关的RNA分子的折叠和柔和的系统 第三次接触的扰动。折叠的核糖开关，其结构与 分析了I组内含子的催化核心，以确定这些不同的调节元素是否拥有 一种常见的折叠机制。我们探索对观察到的新兴折叠行为的影响 溶液变量，例如影响微观环境的温度和离子条件 为了了解物理环境与折叠之间的关系 环境。最后，我们试图了解转录如何影响RNA折叠。

项目成果

Probing RNA-Protein Interactions and RNA Compaction by Sedimentation Velocity Analytical Ultracentrifugation.

通过沉降速度分析超速离心探测 RNA-蛋白质相互作用和 RNA 压实。

• DOI: 10.1007/978-1-0716-0278-2_19
• 发表时间: 2020
• 期刊: Methods in molecular biology (Clifton, N.J.)
• 作者: Mitra,Somdeb;Demeler,Borries
• 通讯作者: Demeler,Borries

Using analytical ultracentrifugation (AUC) to measure global conformational changes accompanying equilibrium tertiary folding of RNA molecules.

使用分析超速离心 (AUC) 测量伴随 RNA 分子平衡三级折叠的整体构象变化。

• DOI: 10.1016/s0076-6879(09)69010-8
• 发表时间: 2009
• 期刊: Methods in enzymology
• 作者: Mitra,Somdeb