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Table 4 Validation of predictions by assuming modular mode of binding and mutations using all 20 amino acids (Approach 3)

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' Kd value Predicted H-bond Energy Finger 2 (QDK) Jameison et al. 1996 [32] Predicted H-bond Energy Finger 2 (QDK) Rebar et al. 1994 [33] ΔG value Hydrogen bond energy (RERRHRRER)
   Pre Minimization Post Minimization    
GCG TGG GCG 16 1.3 6.7 GCG TGG GCG 0 32
GCG TAG GCG 24 1.3 5.3 GCG TAG GCG 0.5 30.9
GCG GGG GCG 142 1.3 3.4 GCG GGG GCG 1.3 39.3
GCG AGG GCG 990 1.3 1.4 GCG AGG GCG 1.7 44
GCG TTG GCG 7500 1.3 1.3 GCG GAG GCG 1.9 37
GCG GAG GCG 250000 3.7 1.17 GCG TTG GCG 1.9 62
  1. A) The predicted H-bond energies after minimization follow the same trend as the Kd values reported in literature of various ZFP (QDK)-DNA pairs. Without the minimization, the results are inconsistent with experimental data. B) For DNA targets reported in literature binding with Zif-268 helix, the trend of predicted H-bond energies by this approach has too many outliers for the reported ΔG values for the various DNA-ZFP pairs in literature, rendering this approach unreliable