Design guidelines for α-helical peptides that self-assemble into transmembrane barrel pores killing antibiotic-resistant bacteria

Abstract

De novo design of peptides that self-assemble into transmembrane barrel-like nanopore structures is challenging due to the complexity of several competing interactions involving peptides, lipids, water, and ions. Here, we develop a computational approach for the de novo design of -helical peptides that self-assemble into stable and large transmembrane barrel pores with a central nano-sized functional channel. We address the lack of existing design guidelines for the de novo pore-forming peptides and propose 52 sequence patterns, each of which can be tailored for different applications using the identified role of its residues. Atomic force microscopy, channel electrical recording, leakage of small fluorescent molecule and transport of macromolecule experiments confirm that the designed peptides form stable, large, and functional barrel-shaped nanopores in model membranes. The custom-designed peptides act as potent antimicrobial agents able to kill even antibiotic-resistant ESKAPE bacteria at micromolar concentrations, while exhibiting low toxicity to human cells. Peptides and their assembled nanopore structures can be similarly fine-tuned for other medical and biotechnological applications.