Single‐Molecule Study of Peptides with the Same Amino Acid Composition but Different Sequences by Using an Aerolysin Nanopore

Abstract

Nanopore is an original sensor employed for highly sensitive peptides/proteins detection. Here, we describe the use of aerolysin nanopore to identify two similar model peptides, YEQYEQQDDDRQQQ (YEQ2Q3) and QDDDRQQQYEQYEQ (Q3YEQ2), with the same amino acid composition but different sequences. All‐atom molecular dynamics (MD) simulations reveal that YEQ2Q3 possesses fewer hydrogen bonds and a more extended conformation than Q3YEQ2. These two peptides that fold differently exhibit obviously distinct mass‐independent current blockades with characteristic dwell times when entering the aerolysin nanopore. Typically, at +60 mV, the statistical dwell time of 0.630 ± 0.018 ms for peptide Q3YEQ2 is clearly 4 times longer than the value of 0.160 ± 0.001 ms for peptide YEQ2Q3, and yet peptide YEQ2Q3 induces ∼1.9% larger blockade current amplitude than peptide Q3YEQ2. The obtained results show a remarkable potential of aerolysin nanopore for peptides/proteins identification, characterization, sequencing and also demonstrate that the mass identification of non‐uniformly charged peptides/proteins using nanopore technique could be complicated by their folded structure and complex analyte‐pore interaction.