Potassium ions in the cavity of a KcsA channel model

The high rate of ion flux and selectivity of potassium channels has been attributed to the conformation and dynamics of the ions in the filter which connects the channel cavity and the extracellular environment. The cavity serves as the reservoir for potassium ions diffusing from the intracellular medium. The cavity is believed to decrease the dielectric barrier for the ions to enter the filter. We study here the equilibrium and dynamic properties of potassium ions entering the water-filled cavity of a KcsA channel model. Atomistic molecular dynamics simulations that are supplemented by electrostatic calculations reveal the important role of water molecules and the partially charged protein helices at the bottom of the cavity in overcoming the energy barrier and stabilizing the potassium ion in the cavity. We further show that the average time for a potassium ion to enter the cavity is much shorter than the conduction rate of a potassium passing through the filter, and this time duration is insensitive over a wide range of the membrane potential. The conclusions drawn from the study of the channel model are applicable in generalized contexts, including the entry of ions in artificial ion channels and other confined geometries.