Paper Citing NAMD - Abstract
Dixit, Purushottam D.; Merchant, Safir; Asthagiri, D.
Ion Selectivity in the KcsA Potassium Channel from the Perspective of the Ion Binding Site
BIOPHYSICAL JOURNAL, 96:2138-2145, MAR 18 2009
To understand the thermodynamic exclusion of Na(+) relative to K(+) from the S(2) site of the selectivity filter, the distribution P(X)(epsilon) (X = K(+) or Na(+)) of the binding energy (epsilon) of the ion with the channel is analyzed using the potential distribution theorem. By expressing the excess chemical potential of the ion as a sum of mean-field and fluctuation mu(ex)(flux,X) contributions, we find that selectivity arises from a higher value of mu(ex)(flux,Na+) relative to mu(ex)(flux,K+). To understand the role of site-site interactions on mu(ex)(flux,X) we decompose P(X)(epsilon) into n-dependent distributions, where n is the number of ion-coordinating ligands within a distance lambda from the ion. For lambda comparable to typical ion-oxygen bond distances, investigations building on this multistate model reveal an inverse correlation between favorable ion-site and site-site interactions: the ion-coordination states that most influence the thermodynamics of the ion are also those for which the binding site is energetically less strained and vice versa. This correlation motivates understanding entropic effects in ion binding to the site and leads to the finding that mu(ex)(flux,X) is directly proportional to the average site-site interaction energy, a quantity that is sensitive to the chemical type of the ligand coordinating the ion. Increasing the coordination number around Na(+) only partially accounts for the observed magnitude of selectivity; acknowledging the chemical type of the ion-coordinating ligand is essential.
DOI:10.1016/j.bpj.2008.12.3917
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