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

BMC Genomics

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

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)	K_d 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

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

ISSN: 1471-2164