A magnesium-induced triplex pre-organizes the SAM-II riboswitch
Fig 5
Thermodynamics of triplex formation.
Free energy landscape of the SAM-II riboswitch as a function of total native contacts (x-axis) and native contacts for an individual structural element (y-axis). (a)-(c) Free energy landscapes for helix P2b formation for increasing values of [Mg2+], without SAM. (d) Free energy landscapes for helix P2b formation for the case of [Mg2+] = 2.0 mM, with SAM. (e)-(g) Free energy landscapes for triplex formation (L1-P2b contacts) for increasing values of [Mg2+], without SAM. (h) Free energy landscapes for triplex formation for the case of [Mg2+] = 2.0 mM, with SAM. (a)-(c) and (e)-(g) Collective integrity of triplex interaction (involving both P2b and P2b-L1) appears most sensitive RNA element to [Mg2+].