Fig. 3

Interactions on the interface between cytochrome c and Apaf-1 in the PatchDock’ model (this work) and the cryo-EM based model [PDB:3J2T] [25]. Cytochrome c is shown in cyan, the WD domains of Apaf-1 in the PatchDock’ model are shown in pink, the WD domains in the cryo-EM based model [PDB:3J2T] [25] are shown in yellow. a, the network salt bridge formed by Lys72 of cytochrome c causes Asp1024 residue of Apaf-1 to rotate. b, residue Lys7 eliminates electrostatic repulsion between residues Asp902 and Asp903 of Apaf-1 by forming a bifurcated salt bridge. c, neighboring residues Lys7 and Lys8 create a link between two WD domains at the bottom of cytochrome c binding cleft. Other domains of Apaf-1 are shown in red