Modelling the impact of magnesium ions concentration on the folding of the SAM-II riboswitch

Abstract

Riboswitches are regulatory elements present in bacterial messenger RNA acting as sensors of small molecules and consequently playing a vital role in bacterial gene regulation. The SAM-II riboswitch is a class of riboswitches, that recognizes S-adenosyl methionine. It has been previously illustrated that the presence of Mg2+ ions stabilizes the pre-existing minor state of the riboswitch, which is structurally characterised by having a nucleated pseudoknot, leading to the increase of its probability. In this study, an analytical equilibrium model is developed to describe the impact of Mg2+ ions concentration on the folding of the SAM-II riboswitch, linking RNA folding and tertiary interactions energetics to ligand binding, and, hence enabling quantitative predictions. The method was used to study the role of the P1 helix sequence in determining the fraction of binding competent conformers of the SAM-II riboswitch, by simulating the Mg2+ titration curves of various mutants.

Modeling Riboswitches: The impact of SAM concentration on the folding of the SAM-II riboswitch

“…7A) and 2 mM Mg 2+ , increased the folded by ten-fold 6 . Since in the absence of both ligands, the fraction of conformers that forms a pseudoknot is ~ 9.3-9.5% (as reported in 8 , and ~ 9.34% after fitting to Mg 2+ data as discussed 10 ), then the expected fraction having a partially or fully formed pseudoknot (fraction folded) would be ~ 93-95 % (specifically, 93.4%). Fig.…”

“…ions. The probabilities and equilibrium constant can also be obtained from a two-step Mg 2+ binding model 10 .…”

“…To be able to apply this model, the equilibrium constants 𝐾 𝑐𝑜𝑛𝑣1 10 , at specific Mg 2+ concentrations (the total Mg 2+ concentration is assumed to be 2 mM). The accessible contacts in the above equation refer to the population with the correct secondary structure.…”

“…2 and 4), however, is much simpler and more straightforward compared to the other models. The two models generally resemble the 2 or 3 step equilibrium models 10 and their parameters a can be directly determined without the need to construct a thermodynamic cycle (as described in the Methods section). On the contrary, determining the parameters Models 3, 5 and 6 (Fig.…”

“…The SAM-II riboswitch is a class of riboswitches that binds to the metabolite; SAM (S-Adenosyl-Methionine), leading to termination of the ribosomal translation of the downstream genes that are involved in the metabolism of SAM 3,4 . The mechanism by which the RNA switches its conformation from ON to OFF and vice versa, in the absence and the presence of SAM, respectively, is yet to be fully understood [5][6][7][8][9][10] . Understanding such mechanism is crucial to be able to control the function of the riboswitch by means of SAM or other designed small molecules 11,12 .…”