Many bacterial genes are controlled by metabolite sensing motifs known as riboswitches that are located in the 5' un-translated region of their mRNAs. Small molecular metabolites bind to riboswitches with amazing specificity, modulating gene regulation in a feedback loop. We have used computational simulations to study the mechanism of action of glmS and SAM-II riboswitches, two riboswitches with very different mechanisms of action. The glmS riboswitch is believed to exploit a general acid-base catalytic mechanism in the presence of glucosamine-6-phosphate (GlcN6P) to accelerate self-cleavage by ~6 orders of magnitude, while the SAM-II riboswitch is allosterically regulated upon binding S-adenosylmethionine (SAM). Our results suggest that GlcN6P is acting as the general acid. We show that binding of SAM to the SAM-II riboswitch alters the curvature and base-pairing of the expression platform. The specificity of the metabolites will also be discussed.

Atomistic basis for the on-off signaling mechanism in riboswitches

245th National Meeting (2013)

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