De novo design of a nanopore for single-molecule detection that incorporates a β-hairpin peptide

• Published in: Nature nanotechnology Vol. 17; no. 1; pp. 67 - 75
• Main Authors: Shimizu, Keisuke, Mijiddorj, Batsaikhan, Usami, Masataka, Mizoguchi, Ikuro, Yoshida, Shuhei, Akayama, Shiori, Hamada, Yoshio, Ohyama, Akifumi, Usui, Kenji, Kawamura, Izuru, Kawano, Ryuji
• Format: Journal Article
• Language: English
• Published: England Nature Publishing Group 01.01.2022; Nature Publishing Group UK
• Subjects: Amino Acid Sequence; Amino acids; Chains; Design; Diameters; DNA - chemistry; Glycine; Hydrophobic and Hydrophilic Interactions; Ion Channel Gating; Lipid Bilayers - chemistry; Lipids; Lysine - chemistry; Models, Molecular; Mutation; Nanopores; Peptides; Peptides - chemistry; Polynucleotides; Polypeptides; Pore formation; Protein Structure, Secondary; Proteins; Single Molecule Imaging
• ISSN: 1748-3387; 1748-3395
• DOI: 10.1038/s41565-021-01008-w

The amino-acid sequence of a protein encodes information on its three-dimensional structure and specific functionality. De novo design has emerged as a method to manipulate the primary structure for the development of artificial proteins and peptides with desired functionality. This paper describes the de novo design of a pore-forming peptide, named SV28, that has a β-hairpin structure and assembles to form a stable nanopore in a bilayer lipid membrane. This large synthetic nanopore is an entirely artificial device for practical applications. The peptide forms multidispersely sized nanopore structures ranging from 1.7 to 6.3 nm in diameter and can detect DNAs. To form a monodispersely sized nanopore, we redesigned the SV28 by introducing a glycine-kink mutation. The resulting redesigned peptide forms a monodisperse pore with a diameter of 1.7 nm leading to detection of a single polypeptide chain. Such de novo design of a β-hairpin peptide has the potential to create artificial nanopores, which can be size adjusted to a target molecule.