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A mathematical equivalence between the MacKinnon model and the association/dissociation model explains its apparent success in explaining ion channel permeation

After MacKinnon discovered the structure of the potassium channel he proposed a two‐step permeation mechanism. His detailed description of the mechanism was recently implemented as a quantitative model consisting of a knock‐off step and a translocation step. The model was successfully fitted to previously published data, but the value of the fitted knock‐off distance is essentially zero which does not make physical sense because it effectively eliminates the voltage dependence of the knock‐off step – the step that actually moves an ion from one side of the selectivity filter to the other. However, a modified association/dissociation (A/D) model results in an identical mathematical expression for the flux, and the fitted parameters have the same numerical values, but they do have a sensible physical meaning. In the A/D model the parameter that becomes zero is an electrical association distance. The physical consequence of this value being zero is that association is simply not an activated process, a conclusion that is supported by previous analysis of experimental data. Thus, even though the two mechanisms are mathematically identical, the A/D mechanism is preferred because it has a simple physical interpretation that is also directly observed in a large group of molecular dynamics simulations. Support from NSF Grant DUE‐0836833 is gratefully acknowledged.