HOLE - A PROGRAM FOR THE ANALYSIS OF THE PORE DIMENSIONS OF ION-CHANNEL STRUCTURAL MODELS

A method (HOLE) that allows the analysis of the dimensions of the pore running through a structural model of an ion channel is presented. Th e algorithm uses a Monte Carlo simulated annealing procedure to find t he best route for a sphere with variable radius to squeeze through the channel. Results can be displayed in a graphical fashion or visualize d with most common molecular graphics packages. Advances include a met hod to analyze the anisotropy within a pore. The method can also be us ed to predict the conductance of channels using a simple empirically c orrected ohmic model. As an example the program is applied to the chol era toxin B-subunit pentamer. The compatibility of the crystal structu re and conductance data is established. (C) 1996 Elsevier Science Inc.