Fig. 4

Electrostatic properties of the interacting surfaces of Apaf-1 and cytochrome c as calculated with the APBS (Adaptive Poisson-Boltzmann Solver [77]) and PDB2PQR [75, 76] software packages. The linear color scale was set from −3 (red) to 3 (blue) kcal/mol. a, WD domains of Apaf-1 are shown in a surface representation colored according to electric charge (red, negative; blue, positive), other domains of Apaf-1 are not colored, cytochrome c is not shown to reveal the negative charge of the binding interface; b, Surfaces of cytochrome c and WD domains of Apaf-1 are shown simultaneously, the negatively charged spot (colored red) on the cytochrome c surface is facing the outside; c, cytochrome c is shown in a cartoon representation with lysine residues shown as sticks (conservative residues shown in blue) and conserved residues 62–65 matching the negatively charged spot shown in green; d, the cytochrome c/Apaf-1 complex is shown in a “back view”, rotated by 180° as compared to panels a–c. Apaf-1 is shown in a cartoon representation, the acidic surface residues of WD domains potentially accessible to cytochrome c are shown as red sticks, the conservative acidic residues that are remote from the cytochrome c binding interface of the WD domains are shown as black sticks