Cation Blocking Mechanisms of the KcsA Potassium Channel Explored with All-atom Free Energy Simulations

We have carried out free energy simulations of multiple ion configurations in the KcsA potassium channel to understand experimentally observed Na and Li blocking and offer predictions that are supported by electrophysiological assays and X-ray crystallographic structures. Through free energy perturbation and potential of mean force calculations we find that Na and Li can bind either inside the aqueous cavity of the channel or deep into the S4 site, coordinated by a plane of 4 carbonyl oxygens rather than the usual 8-ligand cage of K. We have found good evidence to support this prediction with the existence of at least two distinct binding sites for Na and Li suggested by the experiments. We demonstrate that a different multiple-ion mechanism is required for Li and Na ion permeation, involving large energetic barriers that are not encountered by K. These studies shed light on how small monovalent cations block the KcsA channel and provide new insight into the selectivity mechanisms of potassium channels.