Abstract
Riboswitches, typically an integral part of several mRNAs, consist of two domains – a ‘cognate metabolite’ sensing aptamer domain and an expression platform – regulating gene expression at the transcription or in the translation level. Because of their small size and high discriminative ability, p urine riboswitches have been studied extensively both experimentally as well as computationally. Crystal structures of ligand bound aptamer domain of purine riboswitches (Fig. 1) reveal a compact three-way junction architecture consisting of two stem-loops (P2-L2 and P3-L3), held together in parallel orientation by tertiary base pairing interactions between the loops (L2 and L3), converging to a base stem (P1) which communicates with the expression platform. Nucleotides belonging to the three junction loops (J1-2, J2-3 and J3-1) constitute the binding pocket which is lined above and below with double layers of stacked base triples. Though crystal structures of corresponding ligand-free aptamer domains are not available, biophysical and computational studies, including our earlier MD simulations of the add adenine riboswitch1, have provided insights into the functional dynamics connecting the two mechanistic events: discriminative ligand binding and communication with the expression Fig. 1 Ligand bound add platform. Adenine riboswitch In order to gain better insights into the ligand binding induced conformational changes, at the molecular level, and an understanding of the general principles underlying the switching event, we have carried out all-atom explicit solvent molecular dynamics simulations of add adenine riboswitch and xpt-pbuX guanine riboswitch, in ligand-free (APO) state and ligand-bound (HOLO) state, using ff99parmbsc0. Detailed analysis, including principal component analysis and conformational clustering, of the trajectories, reveal interesting insights into changes in conformational dynamics accompanying ligand binding. While confirming the existence of a preformed and ‘binding ready’ APO form and ligand binding induced stabilization of the expression platform linking P1 helices in both aptamers, our studies indicate possible role of stronger L2-L3 interactions in giving rise to fine differences in the functional dynamics of the guanine riboswitch, vis-a-vis the adenine riboswitch.