Fig. 1: Schematic diagram of the apoptotic process and illustration of nearest neighbor analysis.

A Schematic illustration of the apoptotic process governed by Bad, Bcl-xL, and Bax. All Bcl-2 family proteins contain at least one of the four Bcl-2 homology motifs (BH1–4), which are essential for their function. Pro-apoptotic BH3-only proteins (e.g., Bad, Bid, and Bik) only contain the BH3 domain, while pro-apoptotic pore-forming (Bax and Bak) and anti-apoptotic (Bcl-2, Bcl-xL, Bcl-w, Mcl-1, and Bfl-1/A1) proteins contain all four BH domains and are referred to as multi-domain proteins. In response to apoptotic stimuli, the BH3 domain of pro-apoptotic BH3-only proteins (Bad) binds to the BH3 domain-binding groove of anti-apoptotic Bcl-2 proteins (Bcl-xL). This disrupts binding between anti-apoptotic and pore-forming (Bax) proteins, causing activation of the pore-forming protein. Certain BH3-only proteins (Bid and Bim) can also induce apoptosis by directly binding to and activating pore-forming proteins on the outer mitochondrial membrane [15]. The point of no return in the apoptotic process occurs when apoptotic pore-forming proteins have accumulated on mitochondria and permeabilized the outer mitochondrial membrane, leading to the release of cytochrome c and activation of caspases present in the cytoplasm [19]. B Illustration of nearest neighbor analysis. The distances between two proteins, Bad (green) and Bcl-xL (magenta) in this example, are measured by super-resolution stimulated emission depletion (STED) microscopy and summarized in a histogram. The <50 nm distance fraction (red) between two species is indicative of molecular interaction. Scale bars = 500 nm.