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

TL;DR

This study uses coarse-grained molecular dynamics to simulate ionic transport through a protein nanopore, comparing results with experiments and analyzing factors affecting ionic current and transport behavior.

Contribution

It demonstrates the application of the MARTINI CG force field to model ionic transport in protein nanopores and explores the effects of electric fields and protein flexibility.

Findings

CG ionic conductivity aligns with experimental data

I-V curves are qualitatively consistent with experiments

Current saturation occurs at high potentials

Abstract

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 ($\alpha$-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 $\pm~350$~mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations.