Unidirectional Single-File Transport of Full-Length Proteins Through a Nanopore

Abstract

Nanopore technology offers long, accurate sequencing of an DNA or RNA strand via enzymatic ratcheting of the strand through a nanopore in single nucleotide steps, producing stepwise modulations of the nanopore ion current. In contrast to nucleic acids, their daughter molecules, proteins, have neutral peptide backbones and side chains of varying charges. Further, proteins have stable secondary and higher order structures that obstruct protein linearization required for single file nanopore transport. Here, we describe a general approach for realizing unidirectional transport of proteins through a nanopore that neither requires the protein to be uniformly charged nor a pull from a biological enzyme. At high concentrations of guanidinium chloride, we find fulllength proteins to translocate unidirectionally through an a-hemolysin nanopore in a polymer-based membrane, provided that one of the protein ends is decorated with a short anionic peptide. Molecular dynamics simulations show that such surprisingly steady protein transport is driven by a giant electro-osmotic effect caused by binding of guanidinium cations to the inner surface of the nanopore. We show that ionic current signals produced by protein passage can be used to distinguish two biological proteins and the global orientation of the same protein (N-to-C vs. C-to-N terminus) during the nanopore transport. With the average transport rate of one amino acid per 10 μs, our method may enable direct enzyme-free protein fingerprinting or perhaps even sequencing when combined with a high-speed nanopore reader instrument.