Investigating dynamic and energetic determinants of protein nucleic acid recognition: analysis of the zinc finger zif268-DNA complexes

Table 2 Fluctuations and Specificity.

PDB Code	Aminoacid sequence at positions -1, 2, 3, 6	Kd (nM)	Total Protein Flexibility (RMSF sum (nm))	Total Complex Flexibility (RMSF sum (nm))
1A1F	DSNR	0.019	7.18	9.49
1A1G	DSNR	1.8	6.05	8.70
1A1I	RADR	0.068	7.72	9.03
1A1J	RADR	0.035	7.6	10.1
1A1K	RADR	9.3	5.87	8.38
1A1L	RDER (wild type)	5.6	6.10	7.97
1AAY	RDER (wild type)	2.7	6.47	8.68
	Correlation Log(Kd)/RMSF		-0.92	-0.88

The complexes simulated, the dissociation constants, the total flexibility of each system evaluated as a sum of the Root Mean Square Fluctuations (RMSFs) of the proteins and of the complexes are indicated. Correlations between Log(Kd) and RMSFs are indicated in the last row of the table.

ISSN: 1472-6807