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

TL;DR

This work uses polarizable-water MARTINI coarse-grained MD to study ionic transport through the α-hemolysin pore under external fields, reproducing key features of current rectification and anion selectivity observed experimentally. By systematically neutralizing specific trans-side and constriction residues and analyzing ~100 1.5 μs simulations, the authors identify D128 as the principal driver of rectification and K147 as the primary contributor to anion selectivity, with the phenomena arising from local electrostatics rather than global pore charge. Ionic-density maps corroborate these roles by showing concentration patterns of cations near the trans end (affecting rectification) and anions near the constriction (affecting selectivity). The study demonstrates that coarse-grained, polarizable-solvent simulations can capture nanopore transport behavior at voltages closer to experimental conditions, enabling broad mutational screening and applicability to other nanopores.

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 $α$-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.

Figures (7)

• Figure 1: Representation of $\alpha$-hemolysin in cartoon mode. The five charged amino acids in the stem are highlighted in different colors. At the pore constriction (E111 and K147) and at the trans side (D127, D128 and K131). On the right, view from the trans side.
• Figure 2: $IV$ curves for the WT pore (A) and neutral constrained $\alpha$HL (B). We show in green the lines resulting from linear regression either on the positive or the negative potentials.
• Figure 3: Ionic density maps for the WT $\alpha$-hemolysin, in the presence of a positive electric field $E_z=+0.03$ V/nm (A) and negative electric field $E_z=-0.03$ V/nm (B).
• Figure 4: $IV$ curves for the constrained $\alpha$HL with a modified trans extremity: D128N* (A) and D127N-K131N* (B).
• Figure 5: Ionic density maps for the modified $\alpha$-hemolysins D128N* (A), D127N* (B) and D127N-K131N (C) in the presence of a negative electric field $E_z=-0.03$ V/nm.