Figure 4.

Structural basis of enhanced facilitated diffusion in the presence of crowding agents. Horizontally, the figures portray 1) the time evolution of distances between the center of recognition helix of Sap-1 and the center of the closest DNA basepair (bp), 2) ${\text{E}}_{protein-DNA}^{el}$-${\text{R}}_{protein-DNA}$ contour plots indicating the differences in various search modes, and 3) their corresponding snapshots showing the protein position during these search modes for nonspecific crowder interaction strengths, ε = 0.0 (A–C), 0.2 (D–F), and 0.5 (G–I), respectively. For simplicity in representation, the crowder molecules in the front and back of the DNA are not shown in the plot. To see this figure in color, go online.