title: Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation.
abstract: A 120 ns replica-exchange molecular dynamics simulation in explicit solvent is performed to probe the conformational transitions in 5'-GGGCGCAAGCCU-3' RNA GCAA tetraloop. The ample structural transition information of the loop is detected on the basis of extensive clustering analysis. The resultant loop structural transition map nicely agrees with the recent ultrafast fluorescence measurement, which confirms the dynamical properties of this tetraloop. Moreover, a new transition pattern that was not disclosed previously is predicted. Meanwhile, the folding free energy landscapes were characterized: the global folding dynamics is coupled mainly with the stem rather than the loop part.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, Singapore 637551, and State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P.R. China.
authors.forename: Yufen
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: School of Biological Sciences, Nanyang Technological University, Singapore 637551, and State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P.R. China.
authors.forename: Xian
authors.initials: X
authors.lastname: Zhao
authors.affiliation: School of Biological Sciences, Nanyang Technological University, Singapore 637551, and State Key Laboratory of Crystal Materials, Shandong University, Jinan 250100, P.R. China.
authors.forename: Yuguang
authors.initials: Y
authors.lastname: Mu