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

Abstract

BackgroundBinding of cytochrome c, released from the damaged mitochondria, to the apoptotic protease activating factor 1 (Apaf-1) is a key event in the apoptotic signaling cascade. The binding triggers a major domain rearrangement in Apaf-1, which leads to oligomerization of Apaf-1/cytochrome c complexes into an apoptosome. Despite the availability of crystal structures of cytochrome c and Apaf-1 and cryo-electron microscopy models of the entire apoptosome, the binding mode of cytochrome c to Apaf-1, as well as the nature of the amino acid residues of Apaf-1 involved remain obscure.ResultsWe investigated the interaction between cytochrome c and Apaf-1 by combining several modeling approaches. We have applied protein-protein docking and energy minimization, evaluated the resulting models of the Apaf-1/cytochrome c complex, and carried out a further analysis by means of molecular dynamics simulations. We ended up with a single model structure where all the lysine residues of cytochrome c that are known as functionally-relevant were involved in forming salt bridges with acidic residues of Apaf-1. This model has revealed three distinctive bifurcated salt bridges, each involving a single lysine residue of cytochrome c and two neighboring acidic resides of Apaf-1. Salt bridge-forming amino acids of Apaf-1 showed a clear evolutionary pattern within Metazoa, with pairs of acidic residues of Apaf-1, involved in bifurcated salt bridges, reaching their highest numbers in the sequences of vertebrates, in which the cytochrome c-mediated mechanism of apoptosome formation seems to be typical.ConclusionsThe reported model of an Apaf-1/cytochrome c complex provides insights in the nature of protein-protein interactions which are hard to observe in crystallographic or electron microscopy studies. Bifurcated salt bridges can be expected to be stronger than simple salt bridges, and their formation might promote the conformational change of Apaf-1, leading to the formation of an apoptosome. Combination of structural and sequence analyses provides hints on the evolution of the cytochrome c-mediated apoptosis.ReviewersThis article was reviewed by Andrei L. Osterman, Narayanaswamy Srinivasan, Igor N. Berezovsky, and Gerrit Vriend (nominated by Martijn Huynen).Electronic supplementary materialThe online version of this article (doi:10.1186/s13062-015-0059-4) contains supplementary material, which is available to authorized users.

Increased dynamics in the 40–57 Ω-loop of the G41S variant of human cytochrome c promote its pro-apoptotic conformation

“…This has been highlighted recently through the discovery of a species-dependent interaction between cyt and Apaf-1 in cytosolic extracts, which is proposed to arise due to sequence variation between mitochondrial species in the 40–57 Ω-loop 45 . Further to this discovery, residues flanking Pro44 have for some time been associated with a conformational change in cells undergoing apoptosis 46 and recent modelling studies suggest H-cyt interacts with Apaf-1 through contact via the 40–57 Ω-loop 45 47 . Thus based on the present work we propose that the dynamics of 40–57 Ω-loop may be species-specific and tuned to regulate interaction with the cognate Apaf-1.…”

Resveratrol protects retinal ganglion cells against ischemia induced damage by increasing Opa1 expression

“…Opa1 is well known for its role in the regulation of mitochondrial dynamics, where it inhibits mitochondrial cristae remodeling and cytochrome c release (13,51). cytochrome c released into the cytosol can recruit pro-apoptotic signals and trigger downstream apoptotic events by binding between the two tryptophan (W) and aspartate (d)-rich Wd domains of the apoptotic protease activating factor (Apaf-1), thereby irreversibly activating the apoptotic cascade (52). cristae morphogenesis, which is induced by the reduction of Opa1 expression, may increase the probability of cytochrome c release (53,54).…”

The Evolution of Tau Phosphorylation and Interactions

“…This binding causes a major conformational change that eventually could lead to the assembly of apoptosome. Molecular modeling predicted that cytochrome c binds owing to the interaction of its lysine residues with conserved Asp residues of Apaf-1 (Shalaeva et al, 2015). The recently resolved apoptosome structure confirmed the involvement of conserved Asp residues in cytochrome c binding (Zhou et al, 2015).…”