Current rectification and ionic selectivity of alpha-hemolysin: Coarse-Grained Molecular Dynamics simulations

TL;DR

This study uses coarse-grained molecular dynamics simulations to explore ionic transport, current asymmetry, and selectivity in alpha-hemolysin nanopores, providing insights consistent with experimental observations.

Contribution

First coarse-grained simulation study of alpha-hemolysin nanopore ionic transport under various electric fields, identifying key charged residues affecting current behavior.

Findings

Observed current asymmetry and anion selectivity in simulations

Identified charged amino acids responsible for current features

Validated coarse-grained approach against experimental data

Abstract

In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since they allow longer simulations and application of lower electric potentials, closer to the experimental ones. We performed coarse-grained molecular dynamics of the ionic transport through the $\alpha$-hemolysin protein nanopore, inserted into a lipid bilayer surrounded by solvent and ions. For this purpose, we used the MARTINI coarse-grained force field and its polarizable water solvent (PW). Moreover, the electric potential difference applied experimentally was mimicked by the application of an electric field to the system. We present, in this study, the results of 1.5 microsecond long-molecular dynamics simulations of twelve different systems for which different charged amino acids were neutralized, each of them in the presence of nine different electric fields ranging between +/- 0.04 V/nm (a total of around 100 simulations). We were able to observe several specific features of this pore, current asymmetry and anion selectivity, in agreement with previous studies and experiments, and identified the charged amino acids responsible for these current behaviors, therefore validating our coarse-grain approach to study ionic transport through nanopores. We also propose a microscopic explanation of these ionic current features using ionic density maps.