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: 8825309
• 负责人: Karissa Y Sanbonmatsu
• 金额: $ 30.44万
• 依托单位: LOS ALAMOS NAT SECTY-LOS ALAMOS NAT LAB
• 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 2019-02-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8825309
• 关键词: Address; Adenine; Agreement; Antibiotics; Bacteria; Binding; Biological Assay; Charge; Chelating Agents; Coupling; Data; Decision Making; Dependence; Diffuse; Dissociation; Electrostatics; Equilibrium; Fluorescence; Gene Expression; Genetic Transcription; Goals; Human; Ions; Letters; Ligand Binding; Ligands; Magnesium; Maps; Measures; Metabolism; Methods; Modeling; Molecular; Molecular Conformation; Mutation; Pathway interactions; Physical condensation; Play; Population Distributions; Process; Publishing; RNA; RNA Folding; Relative (related person); Role; Sampling; Site; Solvents; Structure; Sulfonic Acids; System; Testing; Time; Untranslated RNA; Vertebral column; Weight; aptamer; base; chelation; chemical group; improved; infectious disease treatment; magnesium ion; molecular dynamics; molecular scale; pathogenic bacteria; phosphorothioate; public health relevance; quinoline; research study; response; simulation; stereochemistry

DESCRIPTION (provided by applicant): Riboswitches are a promising potential antibiotic target: they exert powerful control over bacterial metabolism and are found in bacteria but not in humans. These RNAs make gene expression decisions in response to ligand concentration, alternating between two drastically different conformations depending on the presence of a specific metabolite. Our experimental studies have delineated an intermediate, decision---making state, shown to have well---formed secondary structure but lacking in tertiary contacts and extended relative to the fully---formed ligand---bound state. We and others find that magnesium ions are critical to move the system from the open, decision---making ensemble to the fully closed ligand---bound state. This process involves tertiary contact formation and site---specific chelation of magnesium ions. While our explicit solvent simulations capture the influence of diffuse and outer sphere magnesium over the RNA, longer time scales are needed to study the open--- to---closed transition from the decision---making to fully compact form. Structure--- based models dramatically improve conformational sampling and time scales of molecular simulations, but do not include electrostatics. Here, we add the important effects of electrostatics and non---native interactions, supported by SAXS and SHAPE probing data on the SAM---I, SAM---II and adenine riboswitches. We will use Hamiltonian replica exchange to incorporate chelated, site---specifically bound magnesium interactions and have planned alternative strategies to bolster our study. We will investigate the role of diffuse, outer sphere, and chelated magnesium ions on tertiary contact formation in riboswitches.

描述（由申请人提供）：核糖开关是一种很有前途的潜在抗生素靶点：它们对细菌代谢发挥强大的控制作用，存在于细菌中，但不存在于人类中。这些RNA根据配体浓度做出基因表达决定，根据特定代谢物的存在在两种截然不同的构象之间交替。我们的实验研究已经描绘了一个中间，决策-决策状态，具有良好的-形成的二级结构，但缺乏三级接触和扩展相对于完全-形成配体-结合状态。我们和其他人发现，镁离子是至关重要的移动系统从开放的，决策-使合奏的完全封闭的配体-绑定状态。这一过程涉及三级接触形成和镁离子的位点特异性螯合。 虽然我们明确的溶剂模拟捕捉扩散和外球镁的RNA的影响，需要更长的时间尺度来研究开放--基于结构的模型大大提高了分子模拟的构象采样和时间尺度，但不包括静电。在这里，我们添加了静电和非-本地相互作用的重要影响，支持SAXS和SHAPE探测数据的SAM-I，SAM-II和腺嘌呤核糖开关。我们将使用汉密尔顿副本交换纳入螯合，网站---具体绑定镁的相互作用，并计划替代策略，以支持我们的研究。我们将研究扩散的，外层的作用， 和螯合镁离子对核糖开关中三级接触形成的影响。