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The selectivity of the sodium channel has been the subject of numerous experimental and theoretical studies. In this work, this problem is approached from a theoretical point of view based on a model built from the Selective Filter (SF) of the open structure of the voltage-activated channel of the bacterium Magnetococcus marinus. This approach has allowed us to calculate the interaction energies of the system (cation-water-SF-fragment), both for the sodium cation and the potassium cation. The results have highlighted the importance of differential dehydration of cations, as well as the environment where it occurs. Semi-empirical and ab initio methods have been applied to analyze and quantify the interaction energies when the cations are in the SF of the sodium channel, with the DFT (ab initio) methods giving us the key to the distribution of the interaction energies and therefore how dehydration occurs. [ABSTRACT FROM AUTHOR]

Numerous theoretical and experimental studies have attempted to determine the mechanisms of bacterial potassium channel selectivity (KcsA). However, there are still different aspects that remain uncovered. In this paper, we have built a model based on a selective filter (SF) for the KcsA, taking into account its structure and calculating the system interaction energy (cation–water–SF-fragment), using both sodium and potassium as cations. The results tell us which aspects could be responsible for the higher selectivity of the channel. All this reveals that there are two most important aspects: the dehydration of potassium in relation to sodium, and the environment where such dehydration occurs, in the entrance of the SF. Both semi-empirical and ab initio methods are applied to analyse and quantify the change of the interactions that take place when the cation K+ or Na+ crosses the SF. [ABSTRACT FROM AUTHOR]