Na(+)/Ca(2+) selectivity in the bacterial voltage-gated sodium channel NavAb

Abstract

The recent publication of a number of high resolution bacterial voltage-gated sodium channel structures has opened the door for the mechanisms employed by these channels to distinguish between ions to be elucidated. The way these channels select between Na(+) and K(+) has been investigated in computational studies, but the selectivity for Na(+) over Ca(2+) has not yet been studied in this way. Here we use molecular dynamics simulations to calculate the energetics of Na(+) and Ca(2+) transport through the channel. Single ion profiles show that Ca(2+) experiences a large barrier midway through the selectivity filter that is not seen by Na(+). This barrier is caused by the need for Ca(2+) to partly dehydrate to pass through this region and the lack of compensating interactions with the protein. Multi-ion profiles show that ions can pass each other in the channel, which is why the presence of Ca(2+) does not block Na(+) conduction despite binding more strongly in the pore.

Keywords: Action potential; Bacterial channel; Calcium channel; Ion channel; Ion selectivity; Molecular dynamics; Simulation; Sodium channel.

Figure 1. Simulation system.

A cross section of the simulation system is shown, with two of the four protein chains shown in purple, lipid in brown, Na⁺ in yellow, Cl⁻ in green and the volume sampled by water molecules indicated by the transparent surface.

Figure 2. Single ion potential of mean force.

Single ion potential of mean force (PMF) for Na⁺(blue), Ca²⁺(red) and K⁺(black dashed line) is shown as a function of the axial position of the ion, zeroed at the centre of the selectivity filter. The ion is in bulk water at the right side of the graph and in the central cavity of the channel on the left hand side. For Ca²⁺ the PMF shown is the average of 3 independent sets of simulations, with the standard deviation in the three values shown shaded in grey.

Figure 3. Snapshots of ions in the channel.

Simulation snapshots showing the ion and coordinating water when either Na⁺ (A) or Ca²⁺ (C) is at the external binding site, or when the Na⁺ (B) and Ca²⁺ (D) is at the location of the largest barrier experienced by Ca²⁺.

Figure 4. Coordination numbers of ions in the channel.

Coordination numbers for (A) Na⁺ and (B) Ca²⁺ as a function of the axial position of the ion in the pore. The total coordination number is shown in black, while the contribution from water (blue), glutamate side chains (red) and other protein residues (green) are indicated. Standard errors in the mean are smaller than the data points and are not shown.

Figure 5. Interaction energies of the ions with water and protein when in the channel.

Ion–water and ion–protein interaction energies. (A) the Ca²⁺–protein (black) and Ca²⁺–water (blue) interaction is plotted as a function of the axial position of the ion in the pore. (B) The sum of the ion–water and ion–protein interaction energies is shown for both Na⁺ (blue) and Ca²⁺ (red) as a function of the axial position of the ion in the pore. As only changes in the total energy with position are important for the discussion presented, the curves on B have been vertically shifted to zero at the left hand side to allow for the results for Ca²⁺ and Na⁺ to be more easily compared.

Figure 6. Potential of mean force for two sodium ions in the channel.

The PMF is plotted as a function of the positions of two Na⁺ ions in the pore. Contours are at 1 kcal/mol intervals. Representative snapshots are shown in the insets for three low energy configurations, whose locations are shown on the plot. The approximate lowest energy pathway for ion permeation is shown by the dotted line.

Figure 7. Potential of mean force for two calcium ions in the channel.

Two ion potential of mean force for Ca²⁺. The PMF is plotted as a function of the positions of two Ca²⁺ ions in the pore. Contours are at 1 kcal/mol intervals. Representative snapshots are shown in the insets for four low energy configurations, whose locations are shown on the plot. The approximate lowest energy pathway for ion permeation is shown by the dotted line. A smaller range of coordinates is shown compared to the other two ion PMFs as the ions are unlikely to pass each other in the pore.

Figure 8. Potential of mean force for one calcium and one sodium ion in the channel.

Mixed ion potential of mean force. The PMF is plotted as a function of the position of one Ca²⁺ ion (x-axis) and one Na⁺ ion (y-axis). Contours are at 1 kcal/mol intervals. Representative snapshots are shown in the insets for six low energy configurations whose locations are shown on the plot. The approximate lowest energy pathway for Na⁺ to permeate through the pore by passing a resident Ca²⁺ ion is shown by the dotted line.