Mechanism of polypeptide translocation through gold nanopores in view of sequencing applications

A crucial aspect of the label-free sequencing of peptides and single proteins in solid-state nanopores via optical methods is the ability to control the translocation dynamics of the biomolecule, especially its speed. Very often, this dynamics is studied in terms of its effect on ionic currents through the nanopore. Herein, with attention to label-free optical sequencing methods, we directly study the translocation motion of (poly)peptides by molecular dynamics. By analysis of a vast set of simulations of polyglutamic acids, we show that the peptide elongation is determined by the electrostatic repulsion between the side chains, with less dependence on ionic strength and a more prominent effect of ion type, which emerges as a factor to control the peptide elongation for sequential amino acid detection. Instead, the ionic strength influences the speed of translocation under driving electrostatic fields. Through comparative analysis of simulations with and without confinement of the peptide in a gold nanopore, we quantify the influence of the nanopore on the sequential transit of amino acids and clarify the role of the peptide-pore interaction in promoting the peptide elongation and slowing down their translocation. We identify a stop-and-go translocation mechanism that can be controlled by lateral electric fields, such as in experimental "hot spots", to achieve translocation velocities adequate for single-amino acid detection, while the use of appropriate ions also favors elongated peptide poses suitable for single-amino acid detection. We also present experiments on polyglutamic acid translocation which, compared with the theoretical results, turn out to be compatible with the stop-and-go translocation mechanism. The translocation mechanism, which is characterized by the proximity of the peptide to the nanopore surface, raises expectations for the promising use of plasmonic hot spots in single-amino acid detection.