Structure-based Simulation of Riboswitches: Electrostatic Effects

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：它们对细菌代谢施加强大的控制，并且在细菌中发现，但在人类中没有。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述了一个中间的、决策的状态，显示出形成良好的二级结构，但缺乏三级接触，并且相对于完全形成的配体结合状态进行了扩展。我们和其他人发现，镁离子对于将系统从开放的、决策的整体移动到完全封闭的配体结合状态至关重要。这个过程包括三级接触的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获了扩散和外球镁对RNA的影响，但需要更长的时间尺度来研究从决策到完全致密形式的开放到封闭的转变。基于结构的模型极大地改善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天然相互作用的重要影响，由SAXS和SHAPE探测SAM- I， SAM- II和腺嘌呤核开关的数据支持。我们将使用hamilton复制交换来结合螯合的、特定位点结合的镁相互作用，并计划替代策略来支持我们的研究。我们将研究漫射的作用，外球面，

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.