Fig. 3: Molecular dynamics simulations of CC-Type2-(L_aI_dG_e)₄.

a, b Conformational free-energy landscape calculated from multiple MD simulations. These were initiated from the open and closed crystal structures in the absence (a) and presence (b) of isopropanol, for a total simulation time of 54.7 μs and 83.5 μs, respectively. The root-mean-square deviations (RMSD) to the closed and open crystal structures (marked on the axes) provide conformational coordinates. Regions for the metastable states (S and S’) identified by clustering are shown as insets. c Superimposition of the free-energy minima in the absence (blue) and presence (red) of isopropanol. Each contour corresponds to 0.25 kcal/mol and their colour changes from dark to light as the energy increases. d, e Superimposed poses from each metastable state in the absence (d, S) and presence (e, S’) of isopropanol, with their relative population indicated in percentage. State S'₃ is also shown from the side to highlight its slipped helices. f, g Mean channel radii of the metastable states in the absence (f) and presence (g) of isopropanol. The thin black lines are for the radius of the open channel in the crystal structure (the closed X-ray crystal structure is too collapsed to compute a channel radius).