Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study
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...
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| Veröffentlicht in: | Scientific reports 2019-10, Vol.9 (1), p.15740-12, Article 15740 |
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| creator | Basdevant, Nathalie Dessaux, Delphine Ramirez, Rosa |
| description | 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. |
| doi_str_mv | 10.1038/s41598-019-51942-y |
| format | Article |
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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.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-019-51942-y</identifier><identifier>PMID: 31673049</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/57/2266 ; 639/766/747 ; Biochemistry, Molecular Biology ; Biological Physics ; Biophysics ; Chemical Sciences ; Electric Conductivity ; Electric fields ; Hemolysin Proteins - chemistry ; Hemolysin Proteins - metabolism ; Humanities and Social Sciences ; Ion Transport ; Ions - metabolism ; Life Sciences ; Lipid bilayers ; Lipid Bilayers - metabolism ; Molecular dynamics ; Molecular Dynamics Simulation ; multidisciplinary ; Nanopores ; or physical chemistry ; Physics ; Protein structure ; Protein transport ; Proteins ; Science ; Science (multidisciplinary) ; Static Electricity ; Theoretical and</subject><ispartof>Scientific reports, 2019-10, Vol.9 (1), p.15740-12, Article 15740</ispartof><rights>The Author(s) 2019</rights><rights>2019. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>Attribution</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c508t-848211885760e073a67ee0a447cd15f916d0fdcafd78e32558d2f7505bf1ad273</citedby><cites>FETCH-LOGICAL-c508t-848211885760e073a67ee0a447cd15f916d0fdcafd78e32558d2f7505bf1ad273</cites><orcidid>0000-0002-6541-1105 ; 0000-0002-6775-2907 ; 0000-0002-5214-8651</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6823379/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6823379/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,42189,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/31673049$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink><backlink>$$Uhttps://univ-evry.hal.science/hal-02395220$$DView record in HAL$$Hfree_for_read</backlink></links><search><creatorcontrib>Basdevant, Nathalie</creatorcontrib><creatorcontrib>Dessaux, Delphine</creatorcontrib><creatorcontrib>Ramirez, Rosa</creatorcontrib><title>Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>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. 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Dessaux, Delphine ; Ramirez, Rosa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c508t-848211885760e073a67ee0a447cd15f916d0fdcafd78e32558d2f7505bf1ad273</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>631/57/2266</topic><topic>639/766/747</topic><topic>Biochemistry, Molecular Biology</topic><topic>Biological Physics</topic><topic>Biophysics</topic><topic>Chemical Sciences</topic><topic>Electric Conductivity</topic><topic>Electric fields</topic><topic>Hemolysin Proteins - chemistry</topic><topic>Hemolysin Proteins - metabolism</topic><topic>Humanities and Social Sciences</topic><topic>Ion Transport</topic><topic>Ions - metabolism</topic><topic>Life Sciences</topic><topic>Lipid bilayers</topic><topic>Lipid Bilayers - metabolism</topic><topic>Molecular dynamics</topic><topic>Molecular Dynamics Simulation</topic><topic>multidisciplinary</topic><topic>Nanopores</topic><topic>or physical chemistry</topic><topic>Physics</topic><topic>Protein structure</topic><topic>Protein transport</topic><topic>Proteins</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Static Electricity</topic><topic>Theoretical and</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Basdevant, Nathalie</creatorcontrib><creatorcontrib>Dessaux, Delphine</creatorcontrib><creatorcontrib>Ramirez, Rosa</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central Basic</collection><collection>Hyper Article en Ligne (HAL)</collection><collection>Hyper Article en Ligne (HAL) (Open Access)</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Basdevant, Nathalie</au><au>Dessaux, Delphine</au><au>Ramirez, Rosa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2019-10-31</date><risdate>2019</risdate><volume>9</volume><issue>1</issue><spage>15740</spage><epage>12</epage><pages>15740-12</pages><artnum>15740</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><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.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>31673049</pmid><doi>10.1038/s41598-019-51942-y</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0002-6541-1105</orcidid><orcidid>https://orcid.org/0000-0002-6775-2907</orcidid><orcidid>https://orcid.org/0000-0002-5214-8651</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | 631/57/2266 639/766/747 Biochemistry, Molecular Biology Biological Physics Biophysics Chemical Sciences Electric Conductivity Electric fields Hemolysin Proteins - chemistry Hemolysin Proteins - metabolism Humanities and Social Sciences Ion Transport Ions - metabolism Life Sciences Lipid bilayers Lipid Bilayers - metabolism Molecular dynamics Molecular Dynamics Simulation multidisciplinary Nanopores or physical chemistry Physics Protein structure Protein transport Proteins Science Science (multidisciplinary) Static Electricity Theoretical and |
| title | Ionic transport through a protein nanopore: a Coarse-Grained Molecular Dynamics Study |
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