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Table 2 Validation of predictions made by assuming modular mode of binding and mutations from a small consensus pool of amino acids (Approach 1)

From: Exploiting the recognition code for elucidating the mechanism of zinc finger protein-DNA interactions

Validation with DNA targets binding to QNK Validation with DNA targets binding to Zif-268
Target DNA 5' - 3' Predicted H-bond Energy Finger 2 (QDK) Kd value Jameison et al. 1996 [32] Target DNA Predicted H-bond Energy Finger 2 (RHR) ΔG value Rebar et al. 1994 [33]
GGG GCG GAA 2.867 16 GCG TGG GCG 0 0
GGG GCA GAA 1.064 24 GCG TAG GCG 2.18 0.5
GGG TCA GAA 0.8568 142 GCG GGG GCG 2.15 1.3
GGG TCG GAA 0.8477 990 GCG AGG GCG 2.77 1.7
GGG GTC GAA 0.228 7500 GCG TTG GCG 3.22 1.9
GGG ATC GAA 0.033 25000 GCG GAG GCG 1.19 1.9
  1. The trend of the predicted H-bond energies is similar to the reported Kd values for QNK that bind well to various DNA targets. The trend of the predicted H-bond energies is similar to the reported ΔG values for Zif-268 that binds well to various DNA targets