A considerable body of evidence has amassed implicating aBH3 domains as being capable of triggering multidomain BCL-2 family protein activation. Putative activating residues in BAX have been proposed through mutational analysis and stabilization of BH3 domains using all hydrocarbon stapling has demonstrated the activating ability of BID BH3 domain. The ability of aBH3s to drive BAK conformation change and oligomerization strongly suggests that as yet unidentified trigger residues also resides in BAK. Because mitochondria can be isolated, and respond to aBH3 peptide domain in a manner observed in vivo, our model incorporates a rapid concentration jump of aBH3, leading to initiation of the reaction leading to B*. This is consistent with pharmacological exposure in a cell free system, and is relevant to modelling the action of small molecule BH3 peptidomimetics. Protein-protein crosslinking studies in isolated mitochondria clearly identify constitutively monomeric BAK in the outer mitochondrial membrane. BMH internally crosslinks BAK cysteine residues 14 and 166, leading to a fast mobilizing band on SDS PAGE. This fast band reflects MK-0683 HDAC inhibitor within-membrane, kinase inhibitors closed conformation BAK, and is lost in the presence of BID BH3 peptide, consistent with unfolding and activation at the level of a monomeric species. The existence of closed conformer BAK in the outer mitochondrial membrane of healthy isolated mitochondria also implicates a constitutively left-shifted equilibrium strongly towards a closed/inactive conformation. Therefore, a requirement for constitutive PBP repression alone in this compartment is unlikely. If BAK can reside in the outer mitochondrial membrane as an inactive monomer, collision with an aBH3 would be required for activation. This model is entirely inconsistent with BAK requiring constitutive repression only to prevent its activation as suggested from genetic studies. Conversely, robust genetic evidence has confirmed that BAK activation can proceed in the absence of known aBH3s, suggesting that in some systems, constitutive BAK-PBP interaction is necessary to prevent its activation. This raises the important question of how two seemingly contradictory models can be reconciled. Dynamical systems analysis provides a powerful tool to capable of providing important insights to explain these experimentally observed phenomena. Our results strongly suggest that stable complexes of BAK can only occur in the open conformation, and that disruption of complexes with PBPs will yield free B*, which is assumed to be capable of further activation. B* binding is observed for adenoviral E1B19K and BCL-2. A central paradox in this model, is how B* forms in the first place, when no aBH3s are present. This may be explained in at least two ways.