title: Modeling ion permeation through a bacterial voltage-gated calcium channel CaVAb using molecular dynamics simulations.
abstract: 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 (CaVAb) 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 CaVAb 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 CaVAb channel in the absence of Ca2+, while Cl-ions lack this ability.
authors.affiliation: Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. rafii-tabar@nano.ipm.ac.ir.
authors.forename: Jamal
authors.initials: J
authors.lastname: Adiban
authors.affiliation: Department of Applied Mathematics, School of Mathematical Sciences, Tarbiat Modares University, Tehran, Iran.
authors.forename: Yousef
authors.initials: Y
authors.lastname: Jamali
authors.affiliation: Department of Medical Physics and Biomedical Engineering, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran. rafii-tabar@nano.ipm.ac.ir.
authors.forename: Hashem
authors.initials: H
authors.lastname: Rafii-Tabar
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D002118:Calcium / Q000737:chemistry / Q000378:metabolism; D015220:Calcium Channels / Q000737:chemistry* / Q000378:metabolism; D007477:Ions / Q000737:chemistry* / Q000378:metabolism; D008051:Lipid Bilayers / Q000737:chemistry / Q000378:metabolism; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D010539:Permeability; D011485:Protein Binding; D013329:Structure-Activity Relationship
chemical_list: D001426:Bacterial Proteins; D015220:Calcium Channels; D007477:Ions; D008051:Lipid Bilayers; D002118:Calcium