SDS-assisted protein transport through solid-state nanopores

Abstract

Using nanopores for the single-molecule sequencing of proteins – similar to nanopore-based sequencing of DNA – faces multiple challenges, including unfolding of the complex tertiary structure of the proteins and enforcing their unidirectional translocation through nanopores. Here, we combine molecular dynamics (MD) simulations with single-molecule experiments to investigate the utility of SDS (Sodium Dodecyl Sulfate) to unfold proteins for solid-state nanopore translocation, while simultaneously endowing them with a stronger electrical charge. Our simulations and experiments probe that SDS-treated proteins show considerable loss of protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force fue to the negative charge impaired by SDS. In summary, our results suggest that SDS causes protein unfolding while facilitating protein translocation in the direction of the electrophoretic force, both characteristics could bring great advantages for future protein sequencing applications using solid-state nanopores.

Mechanical characterization of HIV‐1 with a solid‐state nanopore sensor

“…A recent molecular dynamic modelling of micelle translocation through nanopores showed a stretching effect similar to what we have proposed for liposomes and viruses, which confirms soft particle deformation in nanopores. The larger dimensions and longer time‐scale of virus translocation experiments in this work, however, is beyond the limits of molecular dynamics modelling and therefore molecular dynamics was not suitable to simulate virus translocations.…”

Paving the way to single-molecule protein sequencing

“…Multiple chemical and physical methods have been proposed for protein unfolding in nanopore analysis. Several groups have shown the successful unfolding and translocation of proteins through solid-state nanopores using strong denaturants such as urea, sodium dodecyl sulphate (SDS), or guanidine hydrochloride (GdnHCl) [75][76][77] . Translocation of proteins through biological nanopores using denaturants has also been achieved [78][79][80] .…”

Application of Solid-State Nanopore in Protein Detection

“…Another solution is using denaturants. SDS [105], guanidium chloride [106], urea [75], and other denaturants can destroy protein spatial structure to allow it to translocate through nanopores in the unfolded state. SDS denatures proteins and negatively electrifies linear peptide chains.…”

“…SDS denatures proteins and negatively electrifies linear peptide chains. Restrepo-Pérez et al revealed that SDS could cause significant unfolding of proteins by molecular dynamics (MD) simulations combined with experiments [105]. As proteins have more negative electrical charge after being treated with SDS, their translocation is mainly determined by electrophoresis.…”