Thermodynamics and kinetics of the hairpin ribozyme from atomistic folding/unfolding simulations.

ABSTRACT: We report a set of atomistic folding/unfolding simulations for the hairpin ribozyme using a Monte Carlo algorithm. The hairpin ribozyme folds in solution and catalyzes self-cleavage or ligation via a specific two-domain structure. The minimal active ribozyme has been studied extensively, showing stabilization of the active structure by cations and dynamic motion of the active structure. Here, we introduce a simple model of tertiary-structure formation that leads to a phase diagram for the RNA as a function of temperature and tertiary-structure strength. We then employ this model to capture many folding/unfolding events and to examine the transition-state ensemble (TSE) of the RNA during folding to its active "docked" conformation. The TSE is compact but with few tertiary interactions forme

SUBMITTER: Nivon LG 

PROVIDER: S-EPMC3508787 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature