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Membrane Transport Processes Analyzed by a Highly Parallel Nanopore Chip System at Single Protein Resolution

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

Nathalie Basdevant¹, Delphine Dessaux¹, Rosa Ramirez²

¹LAMBE, Univ Evry, CNRS, CEA, Université Paris-Saclay, 91025, Evry, France.

Scientific Reports

|November 2, 2019

Summary

The MARTINI coarse-grained model simulates ion transport through protein nanopores, showing qualitative agreement with experimental ionic conductivity and current-voltage curves. Protein flexibility influences simulation dynamics.

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Area of Science:

Computational Biophysics
Molecular Dynamics Simulations
Nanopore Science

Background:

Coarse-grained (CG) models offer computational efficiency for large biomolecular systems.
Simulating ionic transport through protein nanopores is crucial for understanding biological processes and developing sensing technologies.
Accurate modeling of ion-protein-membrane interactions under electric fields is essential.

Purpose of the Study:

To evaluate the MARTINI coarse-grained force field for simulating ionic transport through protein nanopores.
To investigate the electrostatic behavior of lipid bilayers and ion conductivity in solution using CG models.
To compare simulation results with experimental data for ionic current through the α-hemolysin nanopore.

Main Methods:

Utilized MARTINI coarse-grained (CG) force field for molecular dynamics (MD) simulations.
Computed ionic conductivity of CG ions in solution and compared with experimental values.
Simulated ionic transport through the α-hemolysin nanopore embedded in a lipid bilayer under varying electric fields.

Main Results:

The CG model accurately reproduced experimental ionic conductivity of ions in solution.
Simulations showed qualitative agreement with experimental current-voltage (I-V) curves for the α-hemolysin nanopore.
Observed current saturation at high electric fields (±350 mV) and discussed protein flexibility's role.

Conclusions:

The MARTINI CG force field is a viable tool for simulating ionic transport in protein nanopores.
CG simulations provide valuable insights into nanopore electrophysiology, despite quantitative discrepancies in current magnitude.
Further studies incorporating protein flexibility are needed for more precise predictions.