Mg2+-Dependent Multistep Folding and Stabilization of the GAAA Tetraloop-Receptor Interaction in a Group I Intron

Group I Introns are non-coding regions of pre-mRNA that catalyze their splicing from the RNA sequence by folding to a specific structure. We used computer simulations to study the folding mechanism of the P4-P6 domain in the Tetrahymena thermophila group I intron, focusing on the GAAA tetraloop-receptor (TL-R) interaction, which is a ubiquitous tertiary interaction in RNA structures. We show that the intron folds via a multistep pathway, populating seven states with distinct tertiary contacts. Under physiological Mg2+ concentrations ([Mg2+]), the loop-bulge-P4 tertiary interaction is essential to stabilize the docked TL-R complex, whereas in high [Mg2+], the TL-R complex is stable by itself. The solvated Mg2+ ions modulate the TL-R docking-undocking dynamics and stabilize non-native intermediate states. The condensation of Mg2+ in the major grooves of the TL and R helices is critical for them to attain specific stiffness essential for their facile docking. The results highlight the critical role of Mg2+ ions in facilitating TL-R interaction formation, which stabilizes long-range tertiary contacts in RNA structures. For Table of Contents Use Only O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/700762v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@142852org.highwire.dtl.DTLVardef@1632ad1org.highwire.dtl.DTLVardef@190021aorg.highwire.dtl.DTLVardef@17a1261_HPS_FORMAT_FIGEXP M_FIG C_FIG