TY - JOUR
T1 - SDS-assisted protein transport through solid-state nanopores
AU - Restrepo-Pérez, Laura
AU - John, Shalini
AU - Aksimentiev, Aleksei
AU - Joo, Chirlmin
AU - Dekker, Cees
N1 - 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.
PY - 2017/8/28
Y1 - 2017/8/28
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85026305393&partnerID=8YFLogxK
U2 - 10.1039/c7nr02450a
DO - 10.1039/c7nr02450a
M3 - Article
C2 - 28776058
AN - SCOPUS:85026305393
SN - 2040-3364
VL - 9
SP - 11685
EP - 11693
JO - Nanoscale
JF - Nanoscale
IS - 32
ER -