Rationale for Bcl‐X L /Bad peptide complex formation from structure, mutagenesis, and biophysical studies

Abstract

The three‐dimensional structure of the anti‐apoptotic protein Bcl‐X L complexed to a 25‐residue peptide from the death promoting region of Bad was determined using NMR spectroscopy. Although the overall structure is similar to Bcl‐X L bound to a 16‐residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl‐X L . However, based upon site‐directed mutagenesis experiments, these additional contacts do not account for the increased affinity of the Bad 25‐mer for Bcl‐X L compared to the Bad 16‐mer. Rather, the increased helix propensity of the Bad 25‐mer is primarily responsible for its greater affinity for Bcl‐X L . Based on this observation, a pair of 16‐residue peptides were designed and synthesized that were predicted to have a high helix propensity while maintaining the interactions important for complexation with Bcl‐X L . Both peptides showed an increase in helix propensity compared to the wild‐type and exhibited an enhanced affinity for Bcl‐X L .