How do metal ions direct ribozyme folding?

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 bacteriumAzoarcusform 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.