Timme, M.; Holthuis, J. C. M.; Melo, M. N.

Ceramides bind voltage-dependent anion channels (VDACs) to promote mitochondrial apoptosis. However, the underlying mechanism is unclear. Ceramide binding relies on a charged, bilayer-facing glutamate that also controls complex formation between VDACs and pro-survival hexokinase HKI, suggesting that ceramides may exert their pro-apoptotic activity by displacing HKI from VDACs. Here, we challenged this model using coarse-grain molecular dynamics simulations. We show that ceramides impair VDAC-HKI complex assembly, but not via direct competition with HKI for binding to the crucial glutamate. Instead, we find that ceramides disrupt the membrane thinning capacity of polar channel residues adjacent to the glutamate, thereby congesting a low-energy passageway used by HKI for efficient complex formation. We also demonstrate that VDACs are tilted in the membrane and that ceramides act as modulators of channel tilt by neutralizing the hydrophobic mismatch imposed by the polar channel residues. We postulate that this ceramide action further modulates the oligomerization propensity of VDACs. Altogether, our data reveal a mechanistic basis for how ceramides may trigger apoptotic cell death.