SDS-assisted protein transport through solid-state nanopores

Laura Restrepo-Pérez, Shalini John, Aleksei Aksimentiev, Chirlmin Joo, Cees Dekker

Research output: Contribution to journalArticlepeer-review

59 Scopus citations

Abstract

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.

Original languageEnglish
Pages (from-to)11685-11693
Number of pages9
JournalNanoscale
Volume9
Issue number32
DOIs
StatePublished - 28 Aug 2017

Bibliographical note

Funding Information:
The authors thank Malwina Szczepaniak, James Wilson, and Maxim Belkin for insightful discussions. We also would like to acknowledge Pawel Tulinski for his help during titin purification. Titin protein plasmids were a generous gift from Victor Muñoz and Jrg Schnfelder. This work was supported by the National Human Genome Research Institute of the National Institute of Health under Award Number R01-HG007406. The C. D. lab was further supported by the ERC Advanced Grant SynDiv (no. 669598). C. J. was funded by the Foundation for Fundamental Research on Matter (12PR3029). L. R., C. J. and C. D. were funded by The Netherlands Organization of Scientific Research (NWO/OCW) as part of the Frontiers of the Nanoscience Program. The supercomputer time provided through XSEDE Allocation Grant MCA05S028 and the Blue Waters petascale supercomputer system (UIUC).

Publisher Copyright:
© The Royal Society of Chemistry.

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