title: Reversible-Switch Mechanism of the SAM-III Riboswitch.
abstract: Riboswitches are self-regulatory elements located at the 5' untranslated region of certain mRNAs. The Enterococcus faecalis SAM-III (SMK) 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 SMKriboswitch 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 P0 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 functional structures guaranteed that this riboswitch can act as a reversible riboswitch.
authors.affiliation: Department of Physics, Wuhan University , Wuhan, Hubei 430072, P. R. China.|College of Mathematics and Physics, Huanggang Normal University , Huanggang, Hubei 438000, P. R. China.
authors.forename: Sha
authors.initials: S
authors.lastname: Gong
authors.affiliation: Department of Physics, Wuhan University , Wuhan, Hubei 430072, P. R. China.
authors.forename: Yujie
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Physics, Wuhan University , Wuhan, Hubei 430072, P. R. China.
authors.forename: Zhen
authors.initials: Z
authors.lastname: Wang
authors.affiliation: Department of Physics, Wuhan University , Wuhan, Hubei 430072, P. R. China.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Wang
authors.affiliation: Department of Physics, Wuhan University , Wuhan, Hubei 430072, P. R. China.
authors.forename: Wenbing
authors.initials: W
authors.lastname: Zhang
mesh_terms: D013293:Enterococcus faecalis / Q000737:chemistry; D011487:Protein Conformation; D058928:Riboswitch; D012436:S-Adenosylmethionine / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D058928:Riboswitch; D012436:S-Adenosylmethionine