Conduction and Selectivity in Na+ Channels Analyzed by Bias-Exchange Metadynamics Simulations

Abstract

Bacterial Na+ channels have been the subjects of numerous computational studies since the first experimental structure of a Na+ selective channel was solved in 2011. Molecular Dynamics simulations revealed the presence of 2 binding sites for Na+ ions, respectively at the intracellular and extracellular entrance of the selectivity filter, separated by low energy barriers. While there is a general agreement about these features, there are also important differences among the various computational studies. In particular, ion conduction has been described both as a 2-ions or a 3-ions process, and this difference has been correlated to the direction of conduction, or to the state of the intracellular gate. A current limit of the computational strategies usually adopted to estimate the energy profiles for permeation events, is that the number of permeating ions has to be defined in advance. As consequence, it is difficult to compare energetically conduction mechanisms characterized by different number of ions, and this could explain the lack of congruence in the literature. In order to overcome this limit, we tested a novel approach for the analysis of ion conduction based on bias-exchange metadynamics simulations. In bias-exchange, several replicas of the system are simulated in parallel. A metadynamics simulation is performed for each replica, along one or a few collective variable, and at fixed time intervals swaps of configurations between replicas are attempted. Using this approach it was possible to analyze by a single set of simulations the free energy for permeation events with different number of ions. The analysis revealed that several conduction mechanisms are indeed possible for Na+ channels. This computational strategy could find wide applications for the study of ion channels, in particular to characterize conduction of ion-mixtures, or channels that exhibit heterogeneous conduction events.