Modeling ion permeation through a bacterial voltage-gated calcium channel Ca_VAb using molecular dynamics simulations

Activation of voltage-gated calcium channels by action potentials leads to the influx of Ca²⁺ ions. In this study, the ion permeation characteristics in bacterial voltage-gated calcium (Ca_VAb) channels were investigated using molecular dynamics simulations. Furthermore, the potential of mean force (PMF) calculations was evaluated to determine the free energy profile for the permeation of cations (Ca²⁺ and Na⁺) and anions (Cl^-) in the Ca_VAb channel. The results showed that both Ca²⁺ and Na⁺ cations experienced a deep energy well, while the Cl^- anion experienced a relatively high energy barrier at the center of the selectivity filter (site 2). Consistent with the experimental data, the results obtained from this study demonstrate that sites 2 and 3 displayed the highest and lowest affinities to Ca²⁺, respectively. These findings also indicate that Na⁺ can easily and quickly pass through the Ca_VAb channel in the absence of Ca²⁺, while Cl^- ions lack this ability.