Graphene Nanopores for Protein Sequencing

Abstract

An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of individual proteins that can be sequenced, the time, and the cost of the sequencing procedures. Over the past decade, nanopores have emerged as an alternative platform for detection and characterization of nucleic acid polymers. Here, we report the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. We focus our study on the biologically significant phenylalanine-glycine repeat peptides (FG-nups) abundant in the nuclear pore complexes of eukaryotic cells. Surprisingly, we found FG-nups to behave similarly to single stranded DNA: the peptides adhere to graphene and exhibit step-wise translocation when subject to a transmembrane bias. Reducing the peptide's charge density or increasing the peptide's hydrophobicity was found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias was observed even when the ratio of charged to hydrophobic amino acids within the peptide was as low as 1:8. Neutral peptides were found to exhibit unidirectional and stepwise transport when driven by a gradient of hydrostatic pressure. Analysis of the ionic current blockade produced by the stepwise transport revealed stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore. All of the above suggests that protein sequencing by measuring ionic current blockades in a graphene nanopore may be possible.