Rationale for Bcl-x(L)/Bad peptide complex formation from structure, mutagenesis, and biophysical studies

The three-dimensional structure of the anti-apoptotic protein Bcl-x(L) comp lexed to a 25-residue peptide from the death promoting region of Bad was de termined using NMR spectroscopy. Although the overall structure is similar to Bcl-x(L) hound to a 16-residue peptide from the Bak protein (Sattler et al., 1997), the Bad peptide forms additional interactions with Bcl-x(L). Ho wever, based upon site-directed mutagenesis experiments, these additional c ontacts 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).