Fig. 4: In vivo binding energy landscape of transcription factors.
From: Effective in vivo binding energy landscape illustrates kinetic stability of RBPJ-DNA binding
a Sketch of binding energy landscapes of a thermodynamically stable and a kinetically stable binding interaction. In both cases, the energy barrier of unbinding and thus the residence time in the bound state is equal. Binding energy differences. Differences in b specific binding energies ΔΔGs and c unspecific binding energies ΔΔGs between HT-RBPJ-WT and mutants, calculated from data in Fig. 2f, g, Fig. 3e and data listed in Supplementary Table 7. Data represented as value ± s.d. (Gaussian error propagation). Statistics are provided in Supplementary Tables 3 and 5. d In vivo chromatin binding energy landscapes of HT-RBPJ variants. Energy differences between bound states or transition barriers and the free state as well as kinetic rates of the target site search process by facilitated diffusion are indicated. Dark gray shade: specific association via unspecific binding and subsequent transition to specific binding; bright gray shade: direct specific association. Only relative, but not absolute energy differences of transition barriers can be obtained. Dotted arrows indicate undetermined rates, limits of the relative transition barriers are given in Supplementary Fig. 9. In vivo chromatin binding energy landscapes of e TALE variants2, f SOX2 variants constructed from published kinetic rates14, and g GAF variants constructed from published kinetic rates15. Color code in b–d as in Fig. 1. Source Data are provided as a Source Data file for Fig. 4b–g.
