Fig. 3: Unconventional binding modes and impact of the spacer and flanking sequences.
From: Hidden modes of DNA binding by human nuclear receptors
a–d Multiple modes of DNA binding of Glucocorticoid receptor (GR)—a canonical homo-dimer bound to IR3 site (spacer in red), b trimer (overlaid half site in purple), c two tetramers (overlaid IR3 half sites in purple), and d monomers bound to non-canonical everted repeats of GR (n-GRE1 motif). The left panel presents motif representations of binding. Black and purple arrows represent GR binding to monomers G-AC- and -GT-C. The right panel presents corresponding structural representations—the crystal structure of the dimer (PDBid: 3g6q), and energy-minimized models of the trimer, tetramer-1, and n-GRE1 complexes. e Steroid hormone receptors GR and androgen receptor (AR) bind similar motifs but exhibit unique preferences for spacer (in red) and flanking DNA (in yellow) sequences. f GR binding affinity is correlated with the electrostatic potential (EP) of the spacer region in the canonical GR binding site. Left panel: binding affinity of GR to DNA sequences matching known motif 5ʹGNACANNNTGTNC3ʹ plotted as a function of EP reveals a strong correlation at the spacer region (center). The color of lines from minima (white) to maxima (blue) indicates enrichment. Right panel: scatter plot of enrichment at nucleotide position 5 (central N of the spacer) plotted as a function of EP. g DNA counterpart of two GR-DNA co-crystal structures demonstrates GR binding site with more negative EP (red, PDBid: 3g9i) harbors an ordered spine of hydration while one with a less negative EP (blue, PDBid: 3g6q) does not. The ordered hydration spine in the minor groove alters GR-DNA binding dynamics, thereby impacting binding affinity. h PPARG+ligand #15 and COUP-TF2+ligand #17 appear to display identical preferences for a direct repeat of 5ʹRGGTCR3ʹ half-sites separated by a 1-nucleotide spacer (DR1). However, each ligand-bound heterodimer displays different preferences for the DNA shape in the spacer and the second half site. Base step Roll values of different DNA sequences within DR1 are plotted and colored white (minima) to blue (maxima) corresponding to the enrichment values. Roll (ρ, inset) describes the rotational relationship between two stacked base pairs, with a positive role indicating that the base pairs are opened towards the minor groove. (Source data are provided as a Source Data file. Designed by Laura Vanderploeg).
