How do metal ions direct ribozyme folding?

Abstract

Ribozymes, which carry out phosphoryl transfer reactions, often require Mg²⁺ ions for catalytic activity. The correct folding of the active site and ribozyme tertiary structure is also regulated by metal ions in a manner which is not fully understood. Here, we employ coarse-grained molecular simulations to show that individual structural elements of the group I ribozyme from the bacterium Azoarcus form spontaneously in the unfolded ribozyme even at very low Mg²⁺ concentrations, and are transiently stabilized by coordination of Mg2+ ions to specific nucleotides. However, competition for scarce Mg²⁺ and topological constraints arising from chain connectivity prevent complete folding of the ribozyme. A much higher Mg²⁺ concentration is required for complete folding of the ribozyme and stabilization of the active site. When Mg²⁺ is replaced by Ca2+ the ribozyme folds but the active site remains unstable. Our results suggest that group I ribozymes utilize the same interactions with specific metal ligands for both structural stability and chemical activity.