What can we learn using computational methods about how potassium ions and water molecules move through the narrowest part of a potassium channel?
In this paper, we calculate the average force experienced by three potassium ions as they move through the selectivity filter of a voltage-gated potassium channel. This allows us to identify the most probably mechanism, which includes two “knock-on” events, just like a Newton’s cradle. By examining the behaviour of the conducting waters and the protein in detail we can see how the waters rotate to coordinate one or other of the conducting potassium ions, and even get squeezed between two potassium ions during a knock-on event. We also see how the coordination number of each potassium ion changes.
This article is published in the Journal of Physical Chemistry Letters and is free to download (open access). There is an accompanying paper that is published in the Journal of Chemical Theory and Computation.