Rational combinatorial design of pore-forming β-sheet peptides

Exogenous polypeptides that self-assemble on biological membranes into pores are abundant and structurally diverse, functioning as transporters, toxins, ion channels, and antibiotics. A means for designing novel pore-forming sequences would unlock new opportunities for the development and engineering of protein function in membranes. Toward this goal, we designed a 9,604-member rational combinatorial peptide library based on the structural principles of known membrane-spanning beta-sheets. When the library was screened under stringent conditions for sequences with pore-forming activity, a single active motif was found, which is characterized by aromatic residues at the lipid-exposed interfacial positions and basic residues in the pore-lining portion of the sequence. Peptides with this motif assembled on bilayer membranes into beta-sheets and formed transient peptide/lipid pores of approximately 1-nm diameter. The mechanism of action is very similar to that of natural, pore-forming peptides. These methods provide a powerful means for selecting and engineering novel pore-forming sequences and will open prospects for designing peptide antibiotics, biosensors, and new membrane protein structures.