ArticleScientific reports2019
Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- A Coarse-Grained SPICA Makeover for Solvated and Bare Sodium and Chloride Ions.Journal of chemical theory and computation · 2024Article
- Recent Advances in Modeling Membrane β-Barrel Proteins Using Molecular Dynamics Simulations: From Their Lipid Environments to Their Assemblies.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Structure and dynamics of an archetypal DNA nanoarchitecture revealed via cryo-EM and molecular dynamics simulations.Nature communications · 2023Article
- Effect of cetrimonium carrier micelles on bacterial membranes and extracellular DNA, an in silico study.Scientific reports · 2023Article
- Article
- Transmembrane potential of physiologically relevant model membranes: Effects of membrane asymmetry.The Journal of chemical physics · 2020Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The MARTINI coarse-grained (CG) force field is used to test the ability of CG models to simulate ionic transport through protein nanopores. The ionic conductivity of CG ions in solution was computed and compared with experimental results. Next, we studied the electrostatic behavior of a solvated CG lipid bilayer in salt solution under an external electric field. We showed this approach correctly describes the experimental conditions under a potential bias. Finally, we performed CG molecular dynamics simulations of the ionic transport through a protein nanopore (α-hemolysin) inserted in a lipid bilayer, under different electric fields, for 2-3 microseconds. The resulting I - V curve is qualitatively consistent with experiments, although the computed current is one order of magnitude smaller. Current saturation was observed for potential biases over ±350 mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations.
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Registered trials
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