Addition of a transcription factor site to a simple promoter and its effect on the P_bound graph. (A) Illustrations of the promoters considered and the associated binding affinities for nucleosomes and transcription factors. (B) Shown are transcription factor binding probabilities to a low-affinity binding site for a simple promoter with a single low-affinity site (green), and for promoters with an additional high-affinity site located at various distances from the low-affinity site at increasing transcription factor concentrations. The addition of a transcription factor binding site can have both a cooperative effect (light purple and pink curves) and a destructive effect (yellow and cyan curves). Note that the addition of a transcription factor site results in a change in the shape of the activation curve. (C) Shown is the ratio between the probability of transcription factor binding to the low affinity site in a promoter with two transcription factor sites (P_bound,_2sites) and in a promoter with one transcription factor site (P_bound,1site) at increasing transcription factor concentrations. This ratio can be viewed as the strength of the cooperative/destructive binding effect between the transcription factors (see main text). The ratio obtained changes as concentration increases and can be larger or smaller than one indicating a cooperative/destructive effect, respectively. (D–F) Examination of the cooperative effect generated by adding an adjacent high-affinity site to a promoter with a single, either low- or high-affinity, transcription factor site. (D) Illustrations of the promoters considered and the associated binding affinities for nucleosomes and transcription factors. (E) Transcription factor binding probability graphs for promoters with one high-affinity site (pink curve), two high-affinity sites (red curve), one low-affinity site (light blue), or one low-affinity and one high-affinity site (blue). The energetic contribution () from binding is set to 1200 for a high-affinity site, and 200 for a low-affinity site. (F) Shown is the ratio between the probability of transcription factor binding to the left site (marked as site 1) in a promoter with two transcription factor sites (P_bound,2sites) and in a promoter with one transcription factor site (P_bound,1site) at increasing transcription factor concentrations. Note that the cooperative effect between a low-affinity site and a high-affinity site is larger than the cooperative effect between two high-affinity sites.