Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study

Nathalie Basdevant (1) , Delphine Dessaux (1) , Rosa Ramirez (1)

1 LAMBE - Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement

The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. the ionic conductivity of cG ions in solution was computed and compared with experimental results. Next, we studied the electrostatic behavior of a solvated CG lipid bilayer in salt solution under an external electric field. We showed this approach correctly describes the experimental conditions under a potential bias. Finally, we performed CG molecular dynamics simulations of the ionic transport through a protein nanopore (α-hemolysin) inserted in a lipid bilayer, under different electric fields, for 2-3 microseconds. The resulting I − V curve is qualitatively consistent with experiments, although the computed current is one order of magnitude smaller. current saturation was observed for potential biases over ±350 mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations.

Domains: Biophysics; Theoretical and/or physical chemistry; Biological Physics [physics.bio-ph]

Nathalie Basdevant, Delphine Dessaux, Rosa Ramirez. Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study. Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-51942-y⟩. ⟨hal-02395220⟩