Web interface for brownian dynamics simulation of ion transport and its applications to beta-barrel pores

Authors

  • Kyu Il Lee,

    1. Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
    Search for more papers by this author
    • These authors contributed equally to this work.

  • Sunhwan Jo,

    1. Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
    Search for more papers by this author
    • These authors contributed equally to this work.

  • Huan Rui,

    1. Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
    Search for more papers by this author
  • Bernhard Egwolf,

    1. Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
    Search for more papers by this author
  • Benoît Roux,

    1. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois
    Search for more papers by this author
  • Richard W. Pastor,

    1. Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
    Search for more papers by this author
  • Wonpil Im

    Corresponding author
    1. Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas
    • Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kanas
    Search for more papers by this author
    • Fax: (+00) (785) (864) (5558)


Abstract

Brownian dynamics (BD) based on accurate potential of mean force is an efficient and accurate method for simulating ion transport through wide ion channels. Here, a web-based graphical user interface (GUI) is presented for carrying out grand canonical Monte Carlo (GCMC) BD simulations of channel proteins: http://www.charmm-gui.org/input/gcmcbd. The webserver is designed to help users avoid most of the technical difficulties and issues encountered in setting up and simulating complex pore systems. GCMC/BD simulation results for three proteins, the voltage dependent anion channel (VDAC), α-Hemolysin (α-HL), and the protective antigen pore of the anthrax toxin (PA), are presented to illustrate the system setup, input preparation, and typical output (conductance, ion density profile, ion selectivity, and ion asymmetry). Two models for the input diffusion constants for potassium and chloride ions in the pore are compared: scaling of the bulk diffusion constants by 0.5, as deduced from previous all-atom molecular dynamics simulations of VDAC, and a hydrodynamics based model (HD) of diffusion through a tube. The HD model yields excellent agreement with experimental conductances for VDAC and α-HL, while scaling bulk diffusion constants by 0.5 leads to underestimates of 10–20%. For PA, simulated ion conduction values overestimate experimental values by a factor of 1.5–7 (depending on His protonation state and the transmembrane potential), implying that the currently available computational model of this protein requires further structural refinement. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2012

Ancillary