Thermodynamics of the Hairpin Ribozyme from All-Atom Simulations

Abstract

The structure of the self-cleaving hairpin ribozyme is well characterized, and its folding has been examined in bulk and by single-molecule fluorescence, establishing the importance of cations, especially magnesium in the stability of the native fold. Here we describe the first all-atom folding simulations of the hairpin ribozyme, using a version of a Go potential with separate secondary and tertiary structure energetic contributions. The ratio of tertiary/secondary interaction energies serves as a proxy for non-specific cation binding: a high ratio corresponds to a high concentration, while a low one mimics low concentration. By studying the unfolding behavior of the RNA over a range of temperature and tertiary/secondary energies, a three-state phase diagram emerges, with folded, unfolded (coil) and transient folding/unfolding tertiary structure species. The thermodynamics were verified by paired folding simulations in each region of the phase diagram. The three phase behaviors correspond with experimentally observed states, so this simple model captures the essential aspect of thermodynamics in RNA folding.