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bioRxiv · 10.1101/2025.04.15.648943

Structural basis of apoptosis induction by the mitochondrial voltage dependent anion channel

Daniilidis, M.·Guensel, U.·Broutzakis, G.·Janowski, R.·Leitl, K.·Fredriksson, K.·Niessing, D.·Gatsogiannis, C.·Hagn, F. X.
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Abstract

The voltage-dependent anion channel (VDAC) is the main gateway for metabolites across the mitochondrial outer membrane1. In addition, VDAC oligomers have been associated with apoptosis at mitochondrial stress conditions2. However, the mechanistic and structural basis of VDACs capability to induce apoptosis pathways remains poorly understood. Here, we show with biochemical and structural methods that VDAC1 oligomerization triggers the dissociation of its N-terminal -helix (VDAC1-N) from the channel interior. We used advanced lipid nanodiscs as a tool to selectively trap VDAC1 in its canonical helix-inserted and helix-exposed state to facilitate a structural characterization of both conformations by cryo-electron microscopy. The results show that slight changes in the shape and dynamics of the VDAC1 {beta}-barrel suffice to release the N-terminal helix to the channel exterior. This conformational switch addresses the long-standing question how VDAC1 can regulate partner protein binding. To confirm this hypothesis, we performed interaction studies between VDAC1 in both conformational states and the anti-apoptotic partner protein BclxL using nuclear magnetic resonance spectroscopy and could detect binding only for the helix-exposed state. These insights enabled the X-ray structure determination of the BclxL-VDAC1-N complex at high resolution and provided atomistic details on the VDAC1-N binding mode at the BH3-groove in BclxL. Further biochemical assays showed that VDAC1-N promotes pore formation of the pro-apoptotic Bcl2 protein Bak by neutralizing BclxLs inhibitory activity. These findings suggest that stress-induced oligomerization of VDAC can trigger the exposure of its N-terminal -helix leading to the neutralization of anti-apoptotic Bcl2 proteins. This mode-of-action is reminiscent of BH3-only sensitizer Bcl2 proteins3 that are efficient inducers of Bax/Bak-mediated mitochondrial outer membrane permeabilization and ultimately apoptosis.

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Daniilidis, M., Guensel, U., Broutzakis, G., Janowski, R., Leitl, K., Fredriksson, K., Niessing, D., Gatsogiannis, C., Hagn, F. X.. 2025-04-17. Structural basis of apoptosis induction by the mitochondrial voltage dependent anion channel. https://doi.org/10.1101/2025.04.15.648943

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