Structure-based Simulation of Riboswitches: Electrostatic Effects

描述(申请人提供)：核糖开关是一种很有前途的潜在抗生素靶标：它们对细菌新陈代谢具有强大的控制作用，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。我们的实验研究描绘了一种中间的决策状态，具有良好的二级结构，但缺乏三级接触，并且相对于完全形成的配体结合状态而扩展。我们和其他人发现，镁离子对于将系统从开放的、决策的整体转移到完全封闭的配体结合状态是至关重要的。这个过程包括三次接触的形成和镁离子的定点螯合。虽然我们的显式溶剂模拟捕捉到了扩散和外球镁对RNA的影响，但需要更长的时间尺度来研究从决策到完全紧凑的从开放到封闭的转变。基于结构的模型显著改进了分子模拟的构象采样和时间尺度，但不包括静电学。在这里，我们增加了由SAXS和SHAPE探测数据支持的静电和非-天然相互作用对SAM-I、SAM-II和腺嘌呤核糖开关的重要影响。我们将使用哈密顿副本交换来结合螯合的、特定结合的镁相互作用，并计划了替代策略来支持我们的研究。我们将研究漫射，外层球体， 和螯合镁离子对核糖开关三次接触形成的影响。

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.