Prediction of TF target sites based on atomistic models of protein-DNA complexes

BMC Bioinformatics

Table 5 Contribution of hydrogen bonds, hydrophobic contacts and water-mediated hydrogen bonds to specific DNA recognition in terms of interface binding score (A) and STAMP E-value of structure-based PWMs (B)

A) Fraction of interface binding score contributed by:
	H-bonds	Hydrophobic contacts	Water-mediated H-bonds	# atomic interactions
CRP	1.00	0.00	0.00	8
PurR	0.76	0.24	0.00	6
MetJ	0.89	0.00	0.11	6
NarL	0.61	0.34	0.05	11
LEU3	1.00	0.00	0.00	4
PHO4	1.00	0.00	0.00	7
RAP1	1.00	0.00	0.00	12
ZIF268	0.70	0.00	0.30	21
B) E -value of PWM derived from:
	H-bonds	Hydrophobic contacts	Water-mediated H-bonds	All atomic interactions
NarL	1.049E-02	4.837E-04	-	7.010E-07
ZIF268	1.359E-11	-	6.957E-05	1.998E-14

A) Transcription factors in Table 3 where further analyzed by assessing the fraction of the interface binding score, obtained after summing all log-likelihood atomic scores, contributed by each interaction type. The number of atomic interactions found by the DNAPROT protocol in the native PDB structure is indicated in the rightmost column. B) A further analysis of two notable examples, NarL with an important hydrophobic contribution and ZIF268 with a remarkable contribution of water-mediated hydrogen bonds, in which structurally derived PWMs that consider exclusively H-bonds, hydrophobic contacts or water-mediated H-bonds are compared with default DNAPROT PWMs, which integrate all three atomic interactions.

ISSN: 1471-2105