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    Multistep Current Signal in Protein Translocation through Graphene Nanopores

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    Type
    Article
    Authors
    Bonome, Emma Letizia
    Lepore, Rosalba
    Raimondo, Domenico
    Cecconi, Fabio
    Tramontano, Anna
    Chinappi, Mauro
    KAUST Grant Number
    KUK-I1-012-43
    Date
    2015-04-28
    Online Publication Date
    2015-04-28
    Print Publication Date
    2015-05-07
    Permanent link to this record
    http://hdl.handle.net/10754/598919
    
    Metadata
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    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.
    Sponsors
    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
    ae974a485f413a2113503eed53cd6c53
    10.1021/acs.jpcb.5b02172
    Scopus Count
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