Cooperation between Magnesium and Metabolite Controls Collapse of the SAM-I Riboswitch.

ABSTRACT: The S-adenosylmethionine (SAM)-I riboswitch is a noncoding RNA that regulates the transcription termination process in response to metabolite (SAM) binding. The aptamer portion of the riboswitch may adopt an open or closed state depending on the presence of metabolite. Although the transition between the open and closed states is critical for the switching process, its atomistic details are not well understood. Using atomistic simulations, we calculate the effect of SAM and magnesium ions on the folding free energy landscape of the SAM-I riboswitch. These molecular simulation results are consistent with our previous wetlab experiments and aid in interpreting the SHAPE probing measurements. Here, molecular dynamics simulations explicitly identify target RNA motifs sensitive to magnesium ion

SUBMITTER: Roy S 

PROVIDER: S-EPMC5529334 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature