Potassium ion permeation mechanism revealed by a novel MD simulation approach

The 2D PMF has revealed a general pattern that is in consistent with the results from umbrella sampling approach. The knock-on mechanism derived is the well known S₂-S₄ or S₁-S₃ configurations of permeation.

In addition, we are also able to extract 1D PMFs, which allow us to analyze the permeation pathways in details that are not easily reachable by 2D PMF. From 1D PMFs, we observed three possible permeation mechanisms. Beside the widely accepted S₂-S₄ or S₁-S₃ configurations, there are possibilities that four K⁺ ions occupy all four binding sites, or three K⁺ ions occupy S₄-S₃-S₂ at the same time.