Fig. 7: The proposed folding free-energy landscape for flaviviral xrRNAs.

The folding is cooperatively sculpted by Mg²⁺ and PK2 length variations. In the absence of Mg²⁺, unfolded state (U) is the most stable conformation. The addition of Mg²⁺ stabilizes the intermediate (I_C) and folded state (F). Long PK2 further stabilizes F state and enhances the native state formation. Disruption of tertiary interactions including PK1 or J2/3 destabilizes the I_C and F state significantly, while long PK2 at high Mg²⁺ can compensate for the destabilization effect. However, the complete disruption of PK2 (PK2-L3) results in the formation of nonnative intermediates (I_M) and misfolded conformation (F_M).