Modeling of interaction between cytochrome c and the WD domains of Apaf-1: bifurcated salt bridges underlying apoptosome assembly

Table 3 Salt bridges between Apaf-1 and cytochrome c in the PatchDock’ model

Amino acid pair	Distance, Å		Contact time during simulation
Amino acid pair	after energy minimization	during MD simulation	<3 Å	<4 Å	<5 Å	<6 Å
Lys7-Asp902	2.65	7.55 ± 2.44	12 %	13 %	17 %	24 %
Lys7-Asp903	2.77	6.34 ± 1.48	0 %	1 %	32 %	47 %
Lys8-Asp1147	2.65	3.51 ± 0.75	29 %	78 %	97 %	98 %
Lys25-Asp877	2.63	6.80 ± 1.48	3 %	4 %	11 %	25 %
Lys25-Asp941	11.37	6.87 ± 1.85	0 %	0 %	14 %	34 %
Lys27-Glu925	3.8	3.98 ± 0.89	28 %	34 %	99 %	100 %
Lys39-Glu791	2.67	21.52 ± 5.12	1 %	1 %	2 %	2 %
Lys39-Asp792	12.44	21.25 ± 5.99	0 %	0 %	2 %	3 %
Lys72-Asp1024	4.57	7.37 ± 1.02	0 %	0 %	1 %	8 %
Lys72-Asp1023	2.64	3.32 ± 0.77	57 %	69 %	100 %	100 %
Lys79-Glu981	2.63	4.06 ± 1.57	40 %	53 %	78 %	88 %
Lys86-Glu1045	7.01	4.37 ± 2.26	38 %	60 %	77 %	81 %
Lys86-Asp1064	8.95	5.67 ± 1.73	9 %	23 %	37 %	47 %
Lys87-Asp1106	9.56	5.11 ± 2.29	27 %	41 %	56 %	69 %

Distances between amino group nitrogens and the nearest of two carboxyl group oxygens are given for the structure after energy minimization (static parameter) and in the course of the MD simulation (dynamic parameter)

ISSN: 1745-6150