Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels

Abstract

Fundamental concepts governing ion selectivity in narrow pores are reviewed and the microscopic factors responsible for the lack of selectivity of the NaK channel, which is structurally similar to the K+-selective KcsA channel, are elucidated on the basis of all-atom molecular dynamics free energy simulations. The results on NaK are contrasted and compared with previous studies of the KcsA channel. Analysis indicates that differences in hydration of the cation in the pore of NaK is at the origin of the lack of selectivity of NaK.

Figure 1.

Illustration of fundamental concepts in ion selectivity. In the top, K⁺ and Na⁺ are pictured in bulk solution with their first hydration shell. The difference in hydration free energy ΔG_bulk between these two cations is ∼18 kcal/mol. Binding to a rigid host (B) with a cavity size matching precisely a K⁺ ion (left) does not provide a favorable environment for the smaller Na⁺ (right). In this case, selectivity arises from the poor coordination interaction free energy ΔG_int between the ion and its rigid host. This is the classical snug-fit mechanism (Bezanilla and Armstrong, 1972). However, selectivity may also be achieved by a flexible host (C) able to deform and adapt to both K⁺ and Na⁺ ion, as long as there is a sufficient buildup of strain energy ΔG_strain This situation is characteristic of an induced-fit mechanism.

Figure 2.

Molecular dynamics simulations of the NaK channel. (A) Atomic simulation system comprising the NaK channel and the DPPC bilayer solvated by a 150 mM NaCl aqueous solution (total of 56,001 atoms). (B and C) Superposition of 10 instantaneous configurations taken from MD simulations illustrating the coordination and partial hydration of Na⁺ (B) and K⁺ (C) in site S3 (Na⁺, yellow; K⁺, magenta; water oxygens, red dots). (D and E) Superposition of 10 frames from MD simulations illustrating K⁺ coordination and partial hydration in sites S2 (D) and S4 (E). The average number of water is 2.3 around Na⁺ in S3 (B), and is 2.5, 2.1, and 2.4 around K⁺ in S2 (D), S3 (C), and S4 (E).

Figure 3.

Relative free energy ΔΔG as a function of the average hydration number. The free energy results were taken from Table I for all the binding sites of KcsA and NaK and from Table II for the toy models with eight ligands (eight carbonyls, seven carbonyls and one water, six carbonyls and two water, etc.). The free energies correspond to the computations with the CHARMM force field. The average hydration numbers were taken from Table III in the case of K⁺ occupying the given binding sites. The dotted line is only a visual guide.

Figure 4.

Comparison of radial distribution functions for the selective site S2 in KcsA (left) and the permissive site S3 in NaK (right). (Top) Ion–carbonyl oxygen radial distribution function (solid line, axis label on the left) and integrated coordination number (dashed line, axis label on the right) for K⁺ (black) and Na⁺ (green). (Bottom) Oxygen–oxygen radial distribution function for the opposite diagonal sides of the carbonyl cage forming the binding site for K⁺ (black) Na⁺ (green); a similar analysis has been performed by Asthagiri et al. (2006).