Fig. 2: The binding mode of ZnF to LC domains is different from that to DNA.
From: Zinc finger domains bind low-complexity domain polymers
a 1H-15N NMR spectra of 15N-labeled ZEB2-ZnF8 (15N-ZnF8) with mCherry (mCh; left), mCherry-fused hnRNPA2 LC domain (mCh:A2-LC; middle), ZnF-binding DNA (right). Samples were prepared in 20 mM Tris-HCl pH 7.5, 200 mM NaCl, 20 mM β-ME, 0.1 mM PMSF, 0.12 mM ZnCl2, and 5% 2H2O. Signals labeled by amino acid type and residue number showed significant changes. b Change in signal intensity of 15N-ZnF8 upon LC-binding. The intensity ratio is the signal intensity of LC-bound ZnF8 divided by the signal intensity of LC-free ZnF8. Significantly changed residues (intensity ratios less than mean−0.5 SD and mean−SD) are indicated by orange and red bars, respectively. Residues for which no signal was detected in the absence of LC domains are indicated by asterisks. The cysteine (C) and histidine (H) residues forming the C2H2-type ZnF motif are indicated by outlines. Errors of intensity ratios were estimated based on the measured background noise level. c Changes in signal intensity (upper) and chemical shift (lower) of 15N-ZnF8 upon DNA-binding. In the graph of intensity ratios, significantly changed residues (intensity ratios less than mean−0.5 SD and mean−SD) are indicated by orange and red bars, respectively. Errors of intensity ratios were estimated based on the measured background noise level. In the graph of chemical shift perturbations (CSP), significantly changed residues (CSP greater than mean+0.5 SD and mean+SD) are indicated by orange and red bars, respectively. Residues for which no signal was detected in the absence of LC domains are indicated by asterisks. The cysteine (C) and histidine (H) residues forming the C2H2-type ZnF motif are indicated by outlines. d Surface model of ZEB2-ZnF8 predicted by AlphaFold2. In the upper panel, residues that were significantly changed by binding to mCh:A2-LC (intensity ratios less than mean−0.5 SD and mean−SD) are shown in orange and red, respectively. In the lower panel, residues that were significantly changed by DNA-binding (CSP greater than mean+0.5 SD and mean + SD) are indicated by orange and red bars, respectively.
