Computationally designed peptide inhibitors of protein-protein interactions in membranes

We recently reported a computational method (CHAMP) for designing sequence-specific peptides that bind to the membrane-embedded portions of transmembrane proteins. We successfully applied this method to design membrane-spanning peptides targeting the transmembrane domains of the α_IIb subunit of integrin α_IIbβ ₃. Previously, we demonstrated that these CHAMP peptides bind specifically with reasonable affinity to isolated transmembrane helices of the targeted transmembrane region. These peptides also induced integrin α_IIbβ₃ activation due to disruption of the helix-helix interactions between the transmembrane domains of the α_IIb and β₃ subunits. In this paper, we show the direct interaction of the designed anti-α_IIb CHAMP peptide with isolated full-length integrin α_IIbβ₃ in detergent micelles. Further, the behavior of the designed peptides in phospholipid bilayers is essentially identical to their behavior in detergent micelles. In particular, the peptides assume a membrane-spanning α-helical conformation that does not disrupt bilayer integrity. The activity and selectivity of the CHAMP peptides were further explored in platelets, comfirming that anti-α_IIb activates wild-type α_IIbβ ₃ in whole cells as a result of its disruption of the protein-protein interactions between the α and β subunits in the transmembrane regions. These results demonstrate that CHAMP is a successful chemical biology approach that can provide specific tools for probing the transmembrane domains of proteins.