Structure-based Simulation of Riboswitches: Electrostatic Effects

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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.