Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study
Fuente:
arXiv
Saved in:
| Main Authors: | , , |
|---|---|
| Format: | Preprint |
| Published: |
2018
|
| Subjects: | |
| Online Access: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1866915555832758272 |
|---|---|
| author | Nathalie, Basdevant Delphine, Dessaux Rosa, Ramirez |
| author_facet | Nathalie, Basdevant Delphine, Dessaux Rosa, Ramirez |
| contents | 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 $\pm~350$~mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_1810_09918 |
| institution | arXiv |
| publishDate | 2018 |
| record_format | arxiv |
| spellingShingle | Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study Nathalie, Basdevant Delphine, Dessaux Rosa, Ramirez Biological Physics 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 $\pm~350$~mV. We also discuss the time to reach a stationary regime and the role of the protein flexibility in our CG simulations. |
| title | Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study |
| topic | Biological Physics |
| url | https://arxiv.org/abs/1810.09918 |