Role of charged residues in the protein membrane and protein-protein interaction during activation of the mitochondrial pathway of apoptosis

Abstract

The intrinsic pathway of apoptosis is activated by signals of cellu-lar stress and regulated at the mitochondrial level. Such regulationis carried out by members of the Bcl-2 protein family (B leukemiacell lymphoma 2). Protein-protein and membrane-protein interac-tions allow the exposure of hidden domains in the initial conforma-tion of pro-apoptotic members. Bax and Bid are members of theBcl-2 family of proteins that promote apoptosis by an external mi-tochondrial membrane permeabilization mechanism (MOMP). Theinteraction between Bax, Bid and membrane, triggers a series ofevents that include; opening of a pore in the external mitochondrialmembrane, release of apoptogenic factors from the intermembranespace and activation of caspases, to finally culminate in a processof cell death program by apoptosis. Although there is a broad knowl-edge at the structural level of proteins belonging to the Bcl-2 family,the mechanisms involved in MOMP require a better understandingof the conformational changes and specific contacts required to trig-ger apoptosis.In a previous work we demonstrated the influence of non-specificelectrostatic interactions in the first approach between Bax-mem-brane and between Bax-Bid. In the present work, we computational-ly model the interaction between Bid and membrane, determine theamino acids important for the interaction between Bax and mem-brane by in silico mutagenesis, and try to elucidate the mechanisminvolved in the formation of the apoptogenic pore in the externalmitochondrial membrane. Free Electrostatic Energy of Binding,was computed using Finite Difference Poisson Boltzmann Equation(FDPB) method as implemented in software APBS (Adaptive Pois-son Boltzmann Solver). This type of calculations provided a startingpoint for further computational analysis through molecular dynam-ics simulations (MD). To this end, we used GROMACS simulationpackage.