Structure-based Simulation of Riboswitches: Electrostatic Effects

基于结构的核糖开关模拟：静电效应

• 批准号: 10389070
• 负责人: Karissa Y Sanbonmatsu
• 金额: $ 15.99万
• 依托单位: TRIAD NATIONAL SECURITY, LLC
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-03-15 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10389070
• 关键词: 3-Dimensional; Address; Bacterial Genes; Biochemical; Biochemistry; Biological Models; Biology; Biophysics; Biotechnology; CRISPR/Cas technology; Development; Diffuse; Electrostatics; Environment; Gene Expression Regulation; Genes; Genetic Transcription; Magnesium; MicroRNAs; Modeling; Molecular; Molecular Conformation; Publishing; RNA; Role; SAM Domain; Small Interfering RNA; Small RNA; Solvents; Structure; Techniques; Work; antimicrobial; aptamer; base; experimental study; magnesium ion; molecular dynamics; operation; simulation

With new developments in RNA biology, RNA biotechnology and RNA biomedicine each year, there is an urgent need to understand RNA mechanism in as much detail as possible. Small RNA techniques (miRNAs and siRNAs), and CRISPR-Cas9 gene editing are changing the landscape of biotechnology and biomedicine. Riboswitch RNAs are (i) important in bacterial gene regulation, (ii) interesting antimicrobial targets, and (iii) have potential for optimizing biotechnologies such as CRISPR-Cas9. These RNAs are excellent model systems for studying the hallmarks of RNA mechanism: magnesium-driven electrostatic effects, large 3-D conformational changes, changes in secondary structure, and co-transcriptional effects. Since 2009, we have published a variety of explicit solvent molecular dynamics simulation, structure-based molecular simulation, and wetlab biochemistry studies of riboswitches to understand their operation and the effect of magnesium on riboswitch structure and function. Focusing mainly on the aptamer domain of the SAM-I riboswitch, we have established that magnesium and SAM work together to achieve the fully collapsed, native state. In addition, magnesium facilitates a partial collapse, leaving the aptamer in a state permissible to strand invasion by the expression platform. In this project, we will study the entire riboswitch (aptamer and expression platform), investigating the role of magnesium in riboswitch function. Using atomistic structure-based electrostatic potential models for RNA and magnesium, we will disentangle the roles of inner sphere, outer sphere and diffuse magnesium ion effects in riboswitch operation. Using experimentally determined intermediate configurations, we will study transitions between intermediates during various points of riboswitch function. Our modeling we be enhanced by constraints from a variety of biochemical and biophysical experiments. We will address the fundamental question, how does the ionic environment enable riboswitch RNAs to accomplish their function?

每年有RNA生物学，RNA生物技术和RNA生物医学的新发展， 迫切需要尽可能详细地了解RNA机制。小RNA 技术（miRNA和siRNA）以及CRISPR-CAS9基因编辑正在改变景观 生物技术和生物医学。核糖开关RNA（i）在细菌基因调节中很重要，（ii） 有趣的抗菌靶标，（iii）具有优化生物技术（例如）的潜力 CRISPR-CAS9。这些RNA是研究RNA标志的出色模型系统 机理：镁驱动的静电效应，大型3-D构象变化，变化 二级结构和共转录效应。自2009年以来，我们发表了各种各样的 显式溶剂分子动力学模拟，基于结构的分子模拟和Wetlab 核糖开关的生物化学研究，以了解其运作和镁对 核糖开关结构和功能。主要关注Sam-i Riboswitch的适体域， 我们已经确定镁和山姆共同努力以实现完全崩溃的本地 状态。此外，镁有助于部分崩溃，使适体处于允许的状态 通过表达平台的入侵。在这个项目中，我们将研究整个Riboswitch （适体和表达平台），研究镁在核糖开关功能中的作用。使用 基于原子结构的RNA和镁的基于原子结构的静电模型，我们将分离 内球，外球和弥漫性镁离子在核糖开关操作中的作用。 使用实验确定的中间配置，我们将研究 在核糖开关功能的各个点中中间。我们的建模我们得到了增强 来自多种生化和生物物理实验的约束。我们将解决 基本问题，离子环境如何使Riboswitch RNA能够完成他们的 功能？