Decoding the Heterodimer Stability of Pro‐Apoptotic Effectors via Multiscale Simulations: Mutational Insights Into Mitochondrial Signaling

The BCL-2 protein family plays a central role in regulating mitochondrial apoptosis, with Bcl-2 antagonist killer 1 (BAK) and Bcl-2-associated X protein (BAX) acting as key effectors that oligomerize to disrupt the outer mitochondrial membrane. While the mechanisms behind their homo-oligomerization are well studied, much less is known about their heterodimer. In this work, we explored how specific point mutations at the BAK-BAX interface affect the heterodimer's structure, dynamics, and energetics. Using DUET, we identified stabilizing and destabilizing mutations from both subunits, which were then subjected to 1 μs molecular dynamics simulations. Across multiple structural metrics, the L78D mutation in BAK consistently appeared to enhance rigidity and compactness, while the D68I mutation in BAX led to increased flexibility and conformational drift. Steered MD shows that BAK-L78D strengthens the BAK-BAX interface, resisting separation, whereas BAX-D68I weakens it, leading to faster dissociation. Markov state modeling with Kullback-Leibler divergence indicates that BAK-L78D mirrors wild-type dynamics, while BAX-D68I deviates across key slow motions. Alchemical free energy calculations further delineates the cost of transformation from one amino acid to the other in case of both the mutations. Together, these results highlight BAK-L78D as a stabilizing mutation and BAX-D68I as a destabilizing variant that modulates complex integrity.