Figure 2.

Yan occupancy spreads across the element at equilibrium and depends on both protein-DNA and protein-protein interactions. All plots show fractional occupancy of positions along a 24 site element as a function of concentration; insets plot the same data with concentration on a log scale. The ETS site is at position 1 in (A) and (C) and at position 13 in (B) and (D), as shown in the keys. (A) Site-by-site occupancy using the wild-type values for Yan binding parameters. Occupancy is highest at the ETS site (red) and progressively decreases at sites farther from the ETS, suggestive of a spreading profile. (B) Site-by-site occupancy for an element with the ETS site in the interior at position 13, using wild-type values for α, β, and γ. (C) Site-by-site occupancy when the specific DNA binding term is set equal to the wild-type value for non-specific binding, i.e., an element without any specific binding sites. Occupancy is highest in the center of the element (green) and decreases symmetrically from the center. (D) Site-by-site occupancy when the protein-protein interaction term (γ) is set to 0 kcal/mol. Significant occupancy is only observed at the ETS site for high concentrations (green curve at position 13). Note that identical lines are plotted on top of one another.