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. 2024 Dec 4;53(1):gkae1120. doi: 10.1093/nar/gkae1120

Figure 3.

Figure 3.

TF interactions with nucleosomes. (A) Schematic of TFs: Gal4–VP16 and Gal4-DBD. Gal4–VP16 contains the DNA binding domain and dimerization domain of Gal4 fused to the VP16 AD from the herpes simplex virus. Gal4-DBD contains the DNA binding domain and dimerization domain of Gal4. (B) Schematic of Gal4–VP16 binding equilibrium to a partially unwrapped nucleosome. (C) Normalized ΔFRET (the asymptote of the beginning of the Hill plot fit is set to 1 and the asymptote of the ending of the fit is set to 0) of Gal4–VP16 (dark gray squares) and Gal4-DBD (light gray circles) binding nucleosomes at increasing amounts. Gal4–VP16 binds with an S1/2 of 55 ± 2 nM and Gal4-DBD binds with an S1/2 of 19 ± 1 nM. (D) Bar plot of S1/2 is determined from the weighted fits to binding isotherms in panel (C). Each FRET value was determined in triplicate and the uncertainty is determined from the standard error of the three measurements. The uncertain of each S1/2 value was determined from the covariance matrix of the weighted fit.