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Optimization of 3D Poisson–Nernst-Planck model for fast evaluation of diverse protein channels

Authors

  • Witold Dyrka,

    Corresponding author
    1. Group of Bioinformatics and Biophysics of Nanopores, Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland
    • Correspondence to: Malgorzata Kotulska; Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, ul. Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland. E-mail: malgorzata.kotulska@pwr.wroc.pl; Witold Dyrka, Kotulska; Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, ul. Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland. E-mail: witold.dyrka@pwr.wroc.pl

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  • Maciej M. Bartuzel,

    1. Group of Bioinformatics and Biophysics of Nanopores, Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland
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  • Malgorzata Kotulska

    Corresponding author
    1. Group of Bioinformatics and Biophysics of Nanopores, Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, Wroclaw, Poland
    • Correspondence to: Malgorzata Kotulska; Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, ul. Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland. E-mail: malgorzata.kotulska@pwr.wroc.pl; Witold Dyrka, Kotulska; Institute of Biomedical Engineering and Instrumentation, Wroclaw University of Technology, ul. Wybrzeze Wyspianskiego 27, 50–370 Wroclaw, Poland. E-mail: witold.dyrka@pwr.wroc.pl

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  • Witold Dyrka's current address is MAGNOME Team, Inria Bordeaux- Sud-Ouest Research Centre, Talence, France.

ABSTRACT

We show the accuracy and applicability of our fast algorithmic implementation of a three-dimensional Poisson–Nernst–Planck (3D-PNP) flow model for characterizing different protein channels. Due to its high computational efficiency, our model can predict the full current-voltage characteristics of a channel within minutes, based on the experimental 3D structure of the channel or its computational model structure. Compared with other methods, such as Brownian dynamics, which currently needs a few weeks of the computational time, or even much more demanding molecular dynamics modeling, 3D-PNP is the only available method for a function-based evaluation of very numerous tentative structural channel models. Flow model tests of our algorithm and its optimal parametrization are provided for five native channels whose experimental structures are available in the protein data bank (PDB) in an open conductive state, and whose experimental current-voltage characteristics have been published. The channels represent very different geometric and structural properties, which makes it the widest test to date of the accuracy of 3D-PNP on real channels. We test whether the channel conductance, rectification, and charge selectivity obtained from the flow model, could be sufficiently sensitive to single-point mutations, related to unsignificant changes in the channel structure. Our results show that the classical 3D-PNP model, under proper parametrization, is able to achieve a qualitative agreement with experimental data for a majority of the tested characteristics and channels, including channels with narrow and irregular conductivity pores. We propose that although the standard PNP model cannot provide insight into complex physical phenomena due to its intrinsic limitations, its semiquantitative agreement is achievable for rectification and selectivity at a level sufficient for the bioinformatical purpose of selecting the best structural models with a great advantage of a very short computational time. Proteins 2013; 81:1802–1822. © 2013 Wiley Periodicals, Inc.

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