The Manipulation of the Internal Hydrophobicity of FraC Nanopores Augments Peptide Capture and Recognition

The detection of analytes and the sequencing of DNA using biological nanopores have seen major advances over recent years. The analysis of proteins and peptides with nanopores, however, is complicated by the complex physico-chemical structure of polypeptides and the lack of understanding of the mechanism of capture and recognition of polypeptides by nanopores. In this work, we show that introducing aromatic amino acids at precise positions within the lumen of alpha-helical fragaceatoxin C (FraC) nanopores increased the capture frequency of peptides and largely improved the discrimination among peptides of similar size. Molecular dynamics simulations determined the sensing region of the nanopore, elucidated the microscopic mechanism enabling accurate characterization of the peptides via ionic current blockades in FraC, and characterized the effect of the pore modification on peptide discrimination. This work provides insights to improve the recognition and to augment the capture of peptides by nanopores, which is important for developing a real-time and single-molecule size analyzer for peptide recognition and identification.

Automated summary

This study enhanced the capture frequency and discrimination of peptides by introducing aromatic amino acids into nanopores. Molecular dynamics simulations identified the sensing region and microscopic mechanisms of nanopores, as well as the effects of pore modification on peptide discrimination in FraC.