SDS-assisted protein transport through solid-state nanopores

SDS-assisted protein transport through solid-state nanopores

Restrepo Perez, L. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft)
John, Shalini (University of Illinois)
Aksimentiev, Aleksei (University of Illinois)
Joo, C. (TU Delft BN/Chirlmin Joo Lab; Kavli institute of nanoscience Delft)
Dekker, C. (TU Delft BN/Cees Dekker Lab; Kavli institute of nanoscience Delft)

2017-08-28

Using nanopores for 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 prove that SDS-treated proteins show a considerable loss of the protein structure during the nanopore translocation. Moreover, SDS-treated proteins translocate through the nanopore in the direction prescribed by the electrophoretic force due 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 being advantageous for future protein sequencing applications using solid-state nanopores.

http://resolver.tudelft.nl/uuid:ea585f41-5a6a-4284-bf8a-cf6a5f9ec6dc

https://doi.org/10.1039/c7nr02450a

2040-3364

Nanoscale, 9 (32), 11685-11693

Institutional Repository

journal article

© 2017 L. Restrepo Perez, Shalini John, Aleksei Aksimentiev, C. Joo, C. Dekker