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    Brownian Dynamics Simulations of Ion Transport through the VDAC

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    Wonpil_v100_p611-619.pdf (759.2Kb)
    Issue Date
    2011-02-02
    Author
    Lee, Kyu, II
    Rui, Huan
    Pastor, Richard W.
    Im, Wonpil
    Publisher
    Elsevier
    Type
    Article
    Article Version
    Scholarly/refereed, publisher version
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    Abstract
    It is important to gain a physical understanding of ion transport through the voltage-dependent anion channel (VDAC) because this channel provides primary permeation pathways for metabolites and electrolytes between the cytosol and mitochondria. We performed grand canonical Monte Carlo/Brownian dynamics (GCMC/BD) simulations to explore the ion transport properties of human VDAC isoform 1 (hVDAC1; PDB:2K4T) embedded in an implicit membrane. When the MD-derived, space-dependent diffusion constant was used in the GCMC/BD simulations, the current-voltage characteristics and ion number profiles inside the pore showed excellent agreement with those calculated from all-atom molecular-dynamics (MD) simulations, thereby validating the GCMC/BD approach. Of the 20 NMR models of hVDAC1 currently available, the third one (NMR03) best reproduces both experimental single-channel conductance and ion selectivity (i.e., the reversal potential). In addition, detailed analyses of the ion trajectories, one-dimensional multi-ion potential of mean force, and protein charge distribution reveal that electrostatic interactions play an important role in the channel structure and ion transport relationship. Finally, the GCMC/BD simulations of various mutants based on NMR03 show good agreement with experimental ion selectivity. The difference in ion selectivity between the wild-type and the mutants is the result of altered potential of mean force profiles that are dominated by the electrostatic interactions.
    Description
    This is the publisher's version. Copyright 2011 by Elsevier.
    URI
    http://hdl.handle.net/1808/17473
    DOI
    https://doi.org/10.1016/j.bpj.2010.12.3708
    Collections
    • Molecular Biosciences Scholarly Works [575]
    Citation
    Lee, Kyu Il, Huan Rui, Richard W. Pastor, and Wonpil Im. "Brownian Dynamics Simulations of Ion Transport through the VDAC." Biophysical Journal 100.3 (2011): 611-19. http://dx.doi.org/10.1016/j.bpj.2010.12.3708.

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    Lawrence, KS 66045
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    Contact KU ScholarWorks
    785-864-8983
    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    785-864-8983

    KU Libraries
    1425 Jayhawk Blvd
    Lawrence, KS 66045
    Image Credits
     

     

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