Regional fluctuation analysis. (A) Average regional RMSD for different conditions at 300 K, eight replicas combined. At room temperature, helices have similar scale of fluctuation with the presence of ligand. When the ligand is unbound, the fluctuation of the P1 helix and junctions increase the most, and the stability of P3 helix is also influenced with the further removal of Mg2+. The PK (loops, red) is the most flexible motif with the presence of ligand, but its fluctuations are not sensitive to the change of conditions. (B) Structure of mlf-aptamer colored by heat map of root-mean-square-fluctuation (RMSF) of different conditions at 300 K with eight replicas combined. Consistent with the RMSD analysis, the fluctuation in the P1 helix and pocket region becomes larger with the removal of either ligand or Mg2+, and the fluctuation of the PK is rather independent of the ligand and Mg2+ condition.
