title: Folding of SAM-II riboswitch explored by replica-exchange molecular dynamics simulation.
abstract: Riboswitches are cis-acting RNA fragments that function via a conformational transition mechanism when a specific target molecule binds to its binding pocket, representing an inviting new class of biomolecular target for the development of antibiotics. To understand the folding mechanism of SAM-II riboswitch, occurring predominantly in proteobacteria, a 100ns replica-exchange molecular dynamics simulation in explicit solvent is performed. Our results show that this RNA pseudoknot has multiple folding pathways, and various intermediate structures. The resultant riboswitch conformational transition map is well consistent with the recent fluorescence measurement, which confirms the dynamical properties of this pseudoknot. Moreover, a novel transition pathway is predicted. The global folding dynamics is mainly coupled with the helix rather than the loop region. The potential folding pathways of the riboswitch presented here should lead to a deeper understanding of the folding mechanism of the riboswitch, as well as the conformational change of RNA pseudoknot.
authors.affiliation: Beijing University of Chinese Medicine, Beijing 100029, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Xue
authors.affiliation: Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China.
authors.forename: Wang
authors.initials: W
authors.lastname: Yongjun
authors.affiliation: First Clinical Medical College, Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing 100700, China. Electronic address: lzhh3610@sina.com.
authors.forename: Li
authors.initials: L
authors.lastname: Zhihong
mesh_terms: D008390:Markov Chains; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D058928:Riboswitch; D013696:Temperature
chemical_list: D058928:Riboswitch
keywords: Bacteria; Folding dynamics; REMD; Riboswitch