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 alpha(IIb) subunit of integrin alpha(IIb)beta(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 alpha(IIb)beta(3) activation due to disruption of the helix-helix interactions between the transmembrane domains of the alpha(IIb) and beta(3) subunits. In this paper, we show the direct interaction of the designed anti-alpha(IIb) CHAMP peptide with isolated full-length integrin alpha(IIb)beta(3) 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 alpha-helical conformation that does not disrupt bilayer integrity. The activity and selectivity of the CHAMP peptides were further explored in platelets, comfirming that anti-alpha(IIb) activates wild-type alpha(IIb)beta(3) in whole cells as a result of its disruption of the protein-protein interactions between the alpha and beta 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.