Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA

Abstract

Significance Ribosomes are complexes between ribosomal RNA (rRNA) and a number of proteins. Because ribosome assembly begins with rRNA folding, we simulated the molecular details of Mg 2+ -driven folding of the central domain of the bacterial rRNA. Good agreement with experiments on the folding of the three-way junction in the center of the rRNA validates the model. Coupling of rRNA folding and Mg 2+ binding shows that ions interact with rRNA segments in a coordinated manner. The shape of rRNA changes from a sphere in the unfolded state to a prolate ellipsoid at high Mg 2+ concentration, which is the opposite of what transpires when a globular protein folds. Our study provides the needed framework for undertaking ion-driven folding of large RNA molecules.