Fig. 2.

MD simulations of Sox2 and Oct4 binding to naked DNAs (see Table 1 for DNA sequences). (A) A representative trajectory of the Sox2 binding and induced bending of DNA. The DNA binding position b_Sox2 (see Methods for definition) of Sox2 (purple dots in Middle) and the bending angle η of DNA (see SI Appendix, Supplementary Methods for definition; gray dots in Lower) are plotted as functions of MD steps. The cyan region in Middle (DNA indices 7 to 13) represents the consensus sequence for Sox2 binding. The black line in Lower is the moving average of the DNA bending angle data. (Upper) Snapshots of Sox2-DNA sequence-nonspecific (Left, MD step $5\times {10}^6$) and specific binding (Right, MD step $4\times {10}^7$). The dashed lines on the structures show the direction of DNA double helix axes. (B) Representative time series of the Oct4 POU_S (orange) and POU_HD (red) binding positions on DNA. The consensus sequences for POU_S and POU_HD are marked by blue and green bars on the right vertical axis. (C) The 2D free energy surface of binding positions of the POU_S $\left(b_{{\text{POU}}_{\text{S}}}\right)$ and POU_HD $\left(b_{{\text{POU}}_{\text{HD}}}\right)$ domains. (D) Representative structures of the two free energy minima (S₁ and S₂). The color scheme of the structures is the same as Fig. 1.