A magnesium-induced triplex pre-organizes the SAM-II riboswitch
Fig 4
Probability distribution and free energy landscape of the SAM-II riboswitch as a function of the number of Mg2+ions in the ion solvation layer and Mg2+ mediated phosphate contacts (PHOSCont).
(a) The distribution of Mg2+ in the ion solvation layer shows gradual shift accommodating more number of Mg2+ with increasing Mg2+ concentration. Beyond 8.0 mM the first ion-solvation layer appears saturated. Subsequent additions of Mg2+ beyond 8.0 mM do not effectively participate in the 1st layer of solvation by ionic interaction. (b) Snapshot extracted from the simulation at buffer condition [Mg2+] = 0.4 mM has single phosphate coordinated Mg2+. (c) Snapshot extracted from the simulation at buffer condition [Mg2+] = 8.0 mM has multiple phosphate coordinated Mg2+. (d) Single phosphate coordinated Mg2+ as a function of Mg concentration. (e) Multiple phosphate coordinated Mg2+ as a function of [Mg2+]. The population shift of such multiple coordinated Mg2+ serves to connect negatively charged phosphate groups. (f) Free energy landscape as a function of Ncont and PHOSCont for [Mg2+] = 0.4 mM. (g) Same as (f) for [Mg2+] = 2.0 mM. (h) Same as (f) for [Mg2+] = 8.0 mM. Increasing [Mg2+] reshapes the landscape, shifting the equilibrium from a basin at lower Ncont to a basin at higher Ncont.