Several major diseases caused by microbes, such as Tuberculosis, are becoming increasingly more difficult to treat with commonly used drugs. According to the US Food and Drug Administration, the need for new antibiotics is imperative to the successful treatment of new resistant bacterial infections ( 1). Ligand binding to SAM-II alters the curvature and base-pairing of the expression platform that could affect the interaction of the latter with the ribosome.Īntibiotic resistance is viewed as one of the most pressing public health problems around the world. The rate of forming contacts in the unbound form that are similar to that in the bound form is fast.
We show that the ensemble of conformations of the unbound form of the SAM-II riboswitch is a loose pseudoknot structure that periodically visits conformations similar to the bound form, and the pseudoknot structure is only fully formed upon binding the metabolite, SAM. Here, we report the results of molecular dynamics simulation studies of the S-adenosylmethionine (SAM)-II riboswitch that is involved in regulating translation in sulfur metabolic pathways in bacteria. Small molecular metabolites bind to the aptamer domain of riboswitches with amazing specificity, modulating gene regulation in a feedback loop as a result of induced conformational changes in the expression platform. Many bacterial genes are controlled by metabolite sensing motifs known as riboswitches, normally located in the 5′ un-translated region of their mRNAs.
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