Biophysical basis of the promiscuous binding of B‐cell lymphoma protein 2 apoptotic repressor to BH3 ligands

Abstract

Bcl2 apoptotic repressor carries out its function by virtue of its ability to bind to BH3 domains of various pro-apoptotic regulators in a highly promiscuous manner. Herein, we investigate the biophysical basis of such promiscuity of Bcl2 toward its cognate BH3 ligands. Our data show that while the BH3 ligands harboring the LXXXAD motif bind to Bcl2 with submicromolar affinity, those with the LXXX[G/S]D motif afford weak interactions. This implies that the replacement of alanine at the fourth position (A+4)—relative to the N-terminal leucine (L0) within the LXXXAD motif—to glycine/serine results in the loss of free energy of binding. Consistent with this notion, the A+4 residue within the BH3 ligands harboring the LXXXAD motif engages in key intermolecular van der Waals contacts with A149 lining the ligand binding groove within Bcl2, while A+4G/S substitution results in the disruption of such favorable binding interactions. Of particular interest is the observation that while increasing ionic strength has little or negligible effect on the binding of high-affinity BH3 ligands harboring the LXXXAD motif, the binding of those with the LXXX[G/S]D motif in general experiences a varying degree of enhancement. This salient observation is indicative of the fact that hydrophobic forces not only play a dominant but also a universal role in driving the Bcl2-BH3 interactions. Taken together, our study sheds light on the molecular basis of the factors governing the promiscuous binding of Bcl2 to pro-apoptotic regulators and thus bears important consequences on the development of rational therapeutic approaches.

Impact of lymphoma‐linked Asn11Tyr point mutation on the interaction between Bcl‐2 and a BH3 mimetic: Insights from molecular dynamics simulation

“…According to our results, the binding free energies of the wild‐type Bcl‐2/43B and N11Y mutant Bcl‐2/43B complexes are −7.7 and −5.6 kcal/mol, respectively (Table ). The computed values of the wild‐type Bcl‐2/43B complex is in good agreement with the experimental value, −7.0 kcal/mol, of the binding free energy of Bad to Bcl‐2 (Bhat et al, ), obtained from the dissociation constant, and that of other Bcl‐2‐BH3 mimetics (Acoca, Cui, Shore, & Purisima, ; Dalafave & Prisco, ; Guo, Thorarensen, Che, & Xing, ), confirming the reliability and robustness of our force field parameters and simulation protocol.…”

An evolutionary biochemist's perspective on promiscuity

“…Protein biochemists and molecular biologists often use the term “promiscuous” to describe broad-specificity proteins that bind to multiple interaction partners, which may be ligands, substrates or other macromolecules [1–3]. While this is a reasonable use of the term, evolutionary biochemists prefer to reserve the term “promiscuous” to refer to interactions that are not physiologically relevant [4].…”

Comparative Transcriptome Analysis of Bombyx mori (Lepidoptera) Larval Midgut Response to BmNPV in Susceptible and Near-Isogenic Resistant Strains

“…Amyloid precursor protein is a member of several signaling pathways that are involved in abnormal cell cycles, subsequently leading to apoptosis [54]. B-cell lymphoma protein 2 could bind to BH3 domains of various pro-apoptotic regulators to activate apoptosis [55]. The overexpression of cytochrome c in rabies virus showed a decreased pathogenicity in vitro and in vivo [56].…”