Effect of Mg2+ Ions on TPP Riboswitch Aptamer Folding

Abstract

Riboswitch is an RNA molecule that can regulate transcription or translation by sensing ligands. In the thiamine pyrophosphate (TPP) riboswitch, the TPP ligand binds to the riboswitch to regulate gene expression. TPP riboswitch has two binding pockets: one for TPP ligand and other for Mg2+ ions. In the folded state, TPP aptamer has two arms composed of five helices. One arm is composed of P2-P3 helices and the other arm is composed of P4-P5 helices. P1 helix acts as base holding both arms from P2 and P4 helices. We have studied the effect of Mg2+ ions on the conformational transitions in the aptamer domain of TPP riboswitch using three-interaction-site (TIS) coarse-grained model and molecular dynamics simulation. In low [Mg2+] (< 4 mM), aptamer adopts unfolded conformation leading to the disruption of the TPP binding pocket, whereas in high [Mg2+] (> 6 mM), it adopts a folded conformation facilitating the formation and stabilization of TPP binding pocket. At intermediate [Mg2+] (4-6 mM), an intermediate is populated, where the P1 and P2 helices form. Formation of these helices allows the aptamer to adopt a Y-shaped conformation. In this concentration range, the aptamer displays transitions between a close arm Y-shaped conformation forming TPP binding pocket and the open arm Y-shaped conformation disrupting TPP binding pocket.