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Current Rectification and Ionic Selectivity of α-Hemolysin: Coarse-Grained Molecular Dynamics Simulations.

Delphine Dessaux¹, Jérôme Mathé¹, Rosa Ramirez¹

¹Université Paris-Saclay, Univ Evry, CNRS, LAMBE UMR8587, Évry-Courcouronnes 91025, France.

The Journal of Physical Chemistry. B

|June 3, 2022

Summary

This summary is machine-generated.

Coarse-grained molecular dynamics simulations reveal the physical processes of ionic transport through the alpha-hemolysin protein nanopore. This study identifies charged amino acids responsible for observed current asymmetry and anion selectivity.

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Area of Science:

Biophysics
Computational Biology
Nanotechnology

Background:

Understanding molecular-level physical processes in nanopore experiments requires detailed microscopic information.
Coarse-grained (CG) models offer a computationally efficient alternative to all-atom simulations for studying complex biological systems.

Purpose of the Study:

To investigate ionic transport through the alpha-hemolysin (α-HL) protein nanopore using molecular dynamics (MD).
To identify the roles of charged amino acids in determining nanopore ionic current characteristics.

Main Methods:

Performed 1.5 μs coarse-grained molecular dynamics simulations using the MARTINI force field and polarizable water.
Simulated ionic transport through the α-HL nanopore embedded in a lipid bilayer under various applied electric fields.
Neutralized charged amino acids in 12 different systems and ran approximately 100 simulations with electric fields ranging from ±0.04 V/nm.

Main Results:

Observed characteristic nanopore behaviors, including current asymmetry and anion selectivity, consistent with experimental data.
Identified specific charged amino acids within the α-HL pore that influence ionic current properties.
Generated ionic density maps to provide microscopic explanations for the observed ionic current features.

Conclusions:

Validated the coarse-grain approach for accurately studying ionic transport through protein nanopores.
Provided a molecular-level understanding of the mechanisms underlying current asymmetry and ion selectivity in the α-HL nanopore.
Demonstrated the utility of CG-MD simulations in complementing experimental findings in nanopore science.