Protein coevolution and physicochemical adaptation in the APAF-1/apoptosome: structural and functional implications

Abstract

The apoptosome is involved in the mitochondrial pathway of apoptosis, consisting of APAF-1, caspase 9 and cytochrome c, forming a heptamer that activates effector caspases, causing cell death. This protein complex has also been characterized in Drosophila melanogaster (DARK) and Caenorhabditis elegans (CED-4). Here we present an evolutionary guided in silico characterization of the APAF-1/apoptosome. The evolutionary history of the apoptosome was determined, taking the possible orthologs of the APAF-1 version, and executing a protein coevolution and a positive selection analysis, to make structural and functional inferences and identify residues under destabilizing changes, respectively. Results suggests that the APAF-1/apoptosome is not unique to vertebrates, but also some basal invertebrates could possess orthologous copies. New possible versions were also detected in other taxa. Not all insects and other arthropods have the DARK version, just as not all nematodes have the CED-4 version. In the APAF-1 version, amino acid clusters with coevolution signal located in the interior, gave more insights on new potential interactions, allowing us to infer a more detailed model that includes allosterism, of how cytochrome c associates with {beta} propellers during APAF-1 activation, as well as interactions essential for nucleotide exchange, activation of CASP9, the molecular timer and other pathways in mitochondria to induce apoptosis. Residues on the surface under destabilizing changes have guided the protein complex in adaptations necessary for conformational changes, interactions and folding.