On the selectivity of the NaChBac channel: an integrated computational and experimental analysis of sodium and calcium permeation

Ion channel selectivity is essential for their function, yet the molecular basis of a channel’s ability to select between ions is still rather controversial. In this work, using a combination of molecular dynamics simulations and electrophysiological current measurements we analyze the ability of the NaChBac channel to discriminate between calcium and sodium. Our simulations show that a single calcium ion can access the Selectivity Filter (SF) interacting so strongly with the glutamate ring so as to remain blocked inside. This is consistent with the tiny calcium currents recorded in our patch-clamp experiments. Two reasons explain this scenario. The first is the higher free energy of ion/SF binding of Ca 2+ with respect to Na + . The second is the strong electrostatic repulsion exerted by the resident ion that turns back a second potentially incoming Ca 2+ , preventing the knock-on permeation mechanism. Finally, we analyzed the possibility of the Anomalous Mole Fraction Effect (AMFE), i.e. the ability of micromolar Ca 2+ concentrations to block Na + currents. Current measurements in Na + /Ca 2+ mixed solutions excluded the AMFE, in agreement with metadynamics simulations showing the ability of a sodium ion to by-pass and partially displace the resident calcium. Our work supports a new scenario for Na + /Ca 2+ selectivity in the bacterial sodium channel, challenging the traditional notion of an exclusion mechanism strictly confining Ca 2+ ions outside the channel.