Journal of Physical Chemistry B, Vol.120, No.48, 12305-12311, 2016
Reversible-Switch Mechanism of the SAM-III Riboswitch
Riboswitches are self-regulatory elements located at the 5' untranslated region of certain mRNAs. The Enterococcus faecalis SAM-III (S-MK) riboswitch regulates downstream gene expression through conformational change by sensing S-adenosylmethionine (SAM) at the translation level. Using the recently developed systematic helix-based computational method, we studied the co-transcriptional folding behavior of the S-MK riboswitch and its shortened construct lacking the first six nucleotides. We find that there are no obvious misfolded structures formed during the transcription and refolding processes for this riboswitch. The full-length riboswitch quickly folds into the ON-state in the absence of SAM, and the coupling between transcription and translation is not required for the riboswitch to function. The potential to form helix PO is necessary for the riboswitch to function as a switch. For this thermodynamically controlled reversible riboswitch, the fast helix-exchanging transition pathway between the two act as a reversible riboswitch. functional structures guaranteed that this riboswitch can act as a reversible riboswitch.