Conformational Transition Map of an RNA GCAA Tetraloop Explored by Replica-Exchange Molecular Dynamics Simulation.

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.