Characterizing the consensus residue specificity and surface of Bcl-2 binding to BH3 ligands using the knob-socket model

Cancer cells bypass cell death by changing the expression of the BCL-2
family of proteins, which are apoptotic pathway regulators. Upregulation
of pro-survival BCL-2 proteins or downregulation of cell death effectors
BAX and BAK interferes with the initiation of the intrinsic apoptotic
pathway. In normal cells, apoptosis can occur through pro-apoptotic
BH3-only proteins interacting and inhibiting pro-survival BCL-2 proteins.
When cancer cells over-express pro-survival BCL-2 proteins, a potential
remedy is the sequestration of these pro-survival proteins through a class
of anti-cancer drugs called BH3 mimetics that bind in the hydrophobic
groove of pro-survival BCL-2 proteins. To improve the design of these BH3
mimetics, the packing interface between BH3 domain ligands and
pro-survival BCL-2 proteins was analyzed using the Knob-Socket model to
identify the amino acid residues responsible for interaction affinity and
specificity. A Knob-Socket analysis organizes all the residues in a
binding interface into simple 4 residue units: 3-residue sockets defining
surfaces on a protein that pack a 4th residue knob from the other
protein. In this way, the position and composition of the knobs packing
into sockets across the BH3/BCL-2 interface can be classified. A
Knob-Socket analysis of 19 BCL-2 protein and BH3 helix co-crystals reveal
multiple conserved binding patterns across protein paralogs. Conserved
knob residues such as a Gly, Leu, Ala and Glu most likely define binding
specificity in the BH3/BCL-2 interface, whereas other residues such as
Asp, Asn, and Val are important for forming surface sockets that bind
these knobs. These findings can be used to inform the design of BH3
mimetics that are specific to pro-survival BCL-2 proteins for cancer
therapeutics.