Ion channels bear the same relation to electrical signaling in nerve, muscle, and synapse as enzymes bear to metabolism. The potassium channel is one of the most important type. Potassium ion is at least 10,000 times more permeant than sodium ion, remaining to be an open question of potassium channels. To elucidate the mechanism of ion selectivity at atomic level, the authors performed density functional theory to calculate the position energy on the basis of the X-ray structure of the KcsA channel. In the viewpoint of statistic thermodynamics, the two most readily permeant ions, potassium and rubidium ions, can pass through the selectivity filter. In contrast, sodium ions are preferring to stay in site 2 which can not pass through the channel. The energy barrier difference between the potassium ion and sodium ion is 35.15 kcal mol{sup}(-1). The energy barrier difference between the potassium ion and rubidium ion is 14.44 kcal mol{sup}(-1). The energy barrier difference between the potassium ion and ammonium ion is 21.97 kcal mol{sup}(-1). The results are qualitatively consistent with the experimental data. It is remarkable that the system, involving in 269 atoms, is much lower than the system involved in MD simulation which is on the order of 41000 atoms.
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