Molecular Basis for Bcl-2 Homology 3 Domain Recognition in the Bcl-2 Protein Family

Abstract

The proteins of the Bcl-2 family are important regulators of apoptosis, or programmed cell death. These proteins regulate this fundamental biological process via the formation of heterodimers involving both pro-and anti-apoptotic family members. Disruption of the balance between anti-and pro-apoptotic Bcl-2 proteins is the cause of numerous pathologies. Bcl-xl, an anti-apoptotic protein of this family, is known to form heterodimers with multiple pro-apoptotic proteins, such as Bad, Bim, Bak, and Bid. To elucidate the molecular basis of this recognition process, we used molecular dynamics simulations coupled with the Molecular Mechanics/Poisson-Boltzmann Surface Area approach to identify the amino acids that make significant energetic contributions to the binding free energy of four complexes formed between Bcl-xl and pro-apoptotic Bcl-2 homology 3 peptides. A fifth protein-peptide complex composed of another anti-apoptotic protein, Bcl-w, in complex with the peptide from Bim was also studied. The results identified amino acids of both the anti-apoptotic proteins as well as the Bcl-2 homology 3 (BH3) domains of the pro-apoptotic proteins that make strong, recurrent interactions in the protein complexes. The calculations show that the two anti-apoptotic proteins, Bcl-xl and Bcl-w, share a similar recognition mechanism. Our results provide insight into the molecular basis for the promiscuous nature of this molecular recognition process by members of the Bcl-2 protein family. These amino acids could be targeted in the design of new mimetics that serve as scaffolds for new antitumoral molecules.

Molecular Basis of Bcl-XL-p53 Interaction: Insights from Molecular Dynamics Simulations

“…Previous point mutation studies of these two Bad peptide residues (A5G and F23A) demonstrated ∼4 fold less binding affinity compared with wild type peptide also suggests the important role of these residues for binding [36]. Previous computational study also recognized these two residues as probable hot spots of BH3 peptides for Bcl-2 family proteins binding [44]. These strong interactions of A5 and F23 could be the possible reasons for the extended alpha helical nature of the Bad peptide appeared in the Bcl-XL/Bad peptide simulation (Figure S1B).…”

An Integrated Bioinformatics and Computational Biology Approach Identifies New BH3-Only Protein Candidates

“…The BH1 domain is part of the hydrophobic groove that binds BH3 motifs [32], suggesting a BH3-mediated interaction. N136 of BCL-xL forms a hydrogen bond with a carboxylate group of the conserved D in the BH3 motif [32]. Mutation of N136 to I eliminates this and leads to loss of a stabilizing interaction.…”

Targeting γ-Herpesvirus 68 Bcl-2-mediated Down-regulation of Autophagy

“…Of these residues, Leu 112 , Leu 116 , and Gly 120 are completely buried; Phe 123 is partially buried; the aliphatic part of the Lys 117 side chain hydrophobically packs against M11 residues Asp 81 and Arg 87 , whereas the amino group makes polar and charged interactions; and Gly 120 and Asp 121 interact with a Gly-Arg pair conserved in most Bcl-2 homologs, including Bcl-X L and M11 (21, 22, 36 -38). This Gly-Arg pair, especially the Arg, has been shown to contribute significantly to the interaction of many Bcl-2 homologs with diverse BH3 domains (19,48 The Beclin 1 BH3 domain binds with a very similar, moderate binding affinity of ϳ1.5 M to both M11 and Bcl-X L (see Table 3). Further, for both interactions, the favorable free energy of association (⌬G) is due to enthalpic contributions (⌬H app ) rather than due to entropic contributions (⌬S app ), which are negative in each case (see Table 3).…”