Fig. 3: Structural ensembles and dynamics of AflR-DBD in complex with different promoter DNAs.
a–c MD-derived structural ensembles showing binding modes of ver1, vbs, and norA complex. Major conformational clusters are shown with their relative populations. In each panel, two AflR-DBD molecules bind to DNA (gray) in an inverted orientation, with binding sites labeled as A and B (blue letters). Cyan arrows indicate regions of conformational variability. d–f NMR relaxation dynamics of AflR-DBD bound to ver1, vbs, and norA promoter (pink). NMR relaxation dynamics of AflR-DBD in free state (gray, from Fig. 1j, k) are shown for comparison. T₁ and T₂ relaxation rates were estimated by fitting the peak intensities to single exponential decays, with error bars representing the uncertainty derived from the fitting procedure. NOE values were determined as the ratio of peak intensities in spectra recorded with and without proton saturation, with error bars calculated based on the standard deviation of noise in the saturated and unsaturated spectra using error propagation45. Cyan arrows highlight residues with differential binding-induced changes in dynamics.
