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

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.