Balance between asymmetry and abundance in multi-domain DNA-binding proteins may regulate the kinetics of their binding to DNA
Fig 9
Examples of C2H2-type zinc-finger proteins with low (left side of each panel) and high (right side of each panel) asymmetry. (A) The amino-acid sequences and net charges of the three zinc-finger domains of the constitutive transcription factor Sp1 (left) and the inducible transcription factor Egr-1 (right). The amino-acid sequence is shown for each zinc finger domain (as identified at the left of the box), with the net charge of each domain shown immediately above it. In the sequence, positively and negatively charged residues are coloured in blue and red, respectively, and shown in bold. The recognition helix sequences are enclosed in a box. The positions (-1, +2, +3 and +6) of the four residues involved in specific DNA binding are shown in bold. With respect to the net charge, a pair of adjacent zinc finger domains is considered electrostatically asymmetric if it bears a negative net charge (<2e) and/or if the difference in net charge between the two members of the pair is ≥3e. If all pairs of adjacent domains fail these criteria, then the electrostatic asymmetry of the zinc finger protein is 0%. At the bottom of each box, the abundance and the percent asymmetry values are given at the left and right ends, respectively, of the see-saw, which represents their relationship (i.e. negative correlation). The two asymmetry percentages shown refer to non-specific binding and specific binding, respectively. Panels (B) and (C) show examples for 4-domain and 5-domain zinc finger proteins, respectively.