Pore Dimensions of Ion Channels
Electronic version of:
Smart, O.S., Neduvelil, J.G., Wang, X., Wallace, B.A. and Sansom, M.S.P. (1996) HOLE: A program for the analysis of the pore dimensions of ion channel structural models. J. Mol. Graph., 14, 354-360.

HOLE: A Program for the Analysis of the Pore Dimensions of Ion Channel Structural Models

Oliver S. Smarta*, Joseph G. Neduvelila$, Xiaonan Wanga, B. A. Wallacea and Mark S. P. Sansomb
a Department of Crystallography
  Birkbeck College
  Malet Street 
  London WC1E 7HX

b Laboratory of Molecular Biophysics
  The Rex Richards Building
  University of Oxford
  Oxford OX1 3QU

* Address for correspondence: o.smart@cryst.bbk.ac.uk,
                              (fax + 44 171 631 6803)
$ current address: Merck Sharp & Dohme Research Laboratories,
                   Neuroscience Research Centre, Terlings Park, 
                   Eastwick Road, Harlow CM20 2QR, Essex, England


A method (HOLE) which allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented. The algorithm uses a Monte Carlo Simulated Annealing procedure to find the best route for a sphere with variable radius to squeeze through the channel. Results can be displayed in a graphical fashion or visualized with most common molecular graphics packages. Recent advances include a method to analyse the anisotropy within a pore. The method can also be used to predict the conductance of channels using a simple empirically-corrected ohmic model. As an example the program is applied to the cholera toxin B-subunit pentamer. The compatibility of the crystal structure and conductance data is established. Further details can be found on the HOLE home page. The software is available free on request to workers at non-profit making organizations.


o 1. Introduction

Ion channel structural studies, available information and cavity analysis methods.

o 2. Methods

HOLE Monte Carlo Simulated Annealing, visualization methods and program compatibility, Predicting conductance properties using HOLE.

o 3. Example application to cholera toxin B subunit pentamer

o 4. Discussion and Conclusions

o 5. Obtaining the HOLE package

o Acknowledgments

o References

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Oliver S. Smart (last modified 20/12/96)