Multistep Current Signal in Protein Translocation through Graphene Nanopores

Type
Article

Authors
Bonome, Emma Letizia
Lepore, Rosalba
Raimondo, Domenico
Cecconi, Fabio
Tramontano, Anna
Chinappi, Mauro

KAUST Grant Number
KUK-I1-012-43

Online Publication Date
2015-04-28

Print Publication Date
2015-05-07

Date
2015-04-28

Abstract
© 2015 American Chemical Society. In nanopore sensing experiments, the properties of molecules are probed by the variation of ionic currents flowing through the nanopore. In this context, the electronic properties and the single-layer thickness of graphene constitute a major advantage for molecule characterization. Here we analyze the translocation pathway of the thioredoxin protein across a graphene nanopore, and the related ionic currents, by integrating two nonequilibrium molecular dynamics methods with a bioinformatic structural analysis. To obtain a qualitative picture of the translocation process and to identify salient features we performed unsupervised structural clustering on translocation conformations. This allowed us to identify some specific and robust translocation intermediates, characterized by significantly different ionic current flows. We found that the ion current strictly anticorrelates with the amount of pore occupancy by thioredoxin residues, providing a putative explanation of the multilevel current scenario observed in recently published translocation experiments.

Citation
Bonome EL, Lepore R, Raimondo D, Cecconi F, Tramontano A, et al. (2015) Multistep Current Signal in Protein Translocation through Graphene Nanopores. J Phys Chem B 119: 5815–5823. Available: http://dx.doi.org/10.1021/acs.jpcb.5b02172.

Acknowledgements
This research used the resources of the Supercomputing Laboratory at King Abdullah University of Science & Technology (KAUST) in Thuwal, Saudi Arabia and of the CINECA (GRAPUNA project). Funding: KAUST Award No. KUK-I1-012-43 made by King Abdullah University of Science and Technology (KAUST).

Publisher
American Chemical Society (ACS)

Journal
The Journal of Physical Chemistry B

DOI
10.1021/acs.jpcb.5b02172

PubMed ID
25866995

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