Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion
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{"title"=>"Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion", "type"=>"journal", "authors"=>[{"first_name"=>"Paraskevi", "last_name"=>"Gkeka", "scopus_author_id"=>"26321096200"}, {"first_name"=>"Panagiotis", "last_name"=>"Angelikopoulos", "scopus_author_id"=>"25821851000"}, {"first_name"=>"Lev", "last_name"=>"Sarkisov", "scopus_author_id"=>"6602131087"}, {"first_name"=>"Zoe", "last_name"=>"Cournia", "scopus_author_id"=>"8987210100"}], "year"=>2014, "source"=>"PLoS Computational Biology", "identifiers"=>{"sgr"=>"84919623600", "pmid"=>"25474252", "isbn"=>"10.1371/journal.pcbi.1003917", "pui"=>"601020358", "issn"=>"15537358", "scopus"=>"2-s2.0-84919623600", "doi"=>"10.1371/journal.pcbi.1003917"}, "id"=>"249b3627-188c-354a-a652-02618c325a26", "abstract"=>"Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained Molecular Dynamics (MD) simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC) phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the bilayer core reveal that the hydrophobic and hydrophilic ligands of the NP surface rearrange to form optimal contacts with the lipid bilayer, leading to the so-called snorkeling effect. Inside cholesterol-containing bilayers, the NP induces rearrangement of the structure of the lipid bilayer in its vicinity from the liquid-ordered to the liquid phase spanning a distance almost twice its core radius (8-10 nm). Based on the physical insights obtained in this study, we propose a mechanism of cellular anionic NP partitioning, which requires structural rearrangements of both the NP and the bilayer, and conclude that the translocation of anionic NPs through cholesterol-rich membranes must be accompanied by formation of cholesterol-lean regions in the proximity of NPs.", "link"=>"http://www.mendeley.com/research/membrane-partitioning-anionic-ligandcoated-nanoparticles-accompanied-ligand-snorkeling-local-disorde", "reader_count"=>39, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>7, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Master"=>9, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>3, "Researcher"=>7, "Student > Doctoral Student"=>4, "Student > Ph. D. Student"=>11, "Student > Master"=>9, "Student > Bachelor"=>2, "Professor"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>4, "Engineering"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Materials Science"=>2, "Agricultural and Biological Sciences"=>8, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>5, "Chemistry"=>12, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>3}, "Materials Science"=>{"Materials Science"=>2}, "Chemistry"=>{"Chemistry"=>12}, "Physics and Astronomy"=>{"Physics and Astronomy"=>5}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>8}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>4}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Czech Republic"=>1, "United States"=>2, "Italy"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1821779"], "description"=>"<p>The calculation was performed over the last 500 ns of the simulation for the different systems. The snapshots correspond to the final frame of the simulation and are depicted to indicate the relative position of the NP with respect to the lipid bilayer at the end of the simulation. White corresponds to zero density of the negatively-charged moieties, indicating the snorkeling effect, where charged-end terminal groups orient themselves towards the lipid head groups and outside of the bilayer core. A typical RGB color scale is used to show increasing occupancy. Only the NP core is shown for clarity. The coloring is the same as in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003917#pcbi-1003917-g001\" target=\"_blank\">Figure 1</a>.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260320, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.g002", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_density_maps_of_the_negatively_charged_end_terminal_groups_of_the_NP_ligands_/1260320", "title"=>"Number density maps of the negatively charged end-terminal groups of the NP ligands.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821805"], "description"=>"<p>Normalized interaction energies of the NP with the different components of the system in KJ/mol.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260346, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.t001", "stats"=>{"downloads"=>1, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Normalized_interaction_energies_of_the_NP_with_the_different_components_of_the_system_in_KJ_mol_/1260346", "title"=>"Normalized interaction energies of the NP with the different components of the system in KJ/mol.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-12-04 03:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821761"], "description"=>"<p>DPPC molecule (top, left), cholesterol molecule (bottom, left), nanoparticle simulated in the water phase (center), and nanoparticle simulated in a membrane containing 30% cholesterol (right) (final snapshots). The molecules or CG beads are not shown to scale. Colors: Negative beads bearing -1e charge = purple; hydrophobic beads = cyan; positive beads = blue; cholesterol hydroxyl bead = gray; glycerol backbone beads = white; cholesterol sterol body beads = lime. The core of the NP is shown in gray and surface representation, whereas the hydrophobic parts of NP surface ligands are shown in a bead-spring representation. Arrows indicate the tendency of the surface charged ligands to associate with the DPPC head groups and their hydrophobic parts to interact with the hydrophobic core, inducing a snorkeling effect.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260304, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.g001", "stats"=>{"downloads"=>0, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Coarse_grained_models_of_the_system_components_/1260304", "title"=>"Coarse-grained models of the system components.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1824707", "https://ndownloader.figshare.com/files/1824713"], "description"=>"<div><p>Intracellular uptake of nanoparticles (NPs) may induce phase transitions, restructuring, stretching, or even complete disruption of the cell membrane. Therefore, NP cytotoxicity assessment requires a thorough understanding of the mechanisms by which these engineered nanostructures interact with the cell membrane. In this study, extensive Coarse-Grained Molecular Dynamics (MD) simulations are performed to investigate the partitioning of an anionic, ligand-decorated NP in model membranes containing dipalmitoylphosphatidylcholine (DPPC) phospholipids and different concentrations of cholesterol. Spontaneous fusion and translocation of the anionic NP is not observed in any of the 10-µs unbiased MD simulations, indicating that longer timescales may be required for such phenomena to occur. This picture is supported by the free energy analysis, revealing a considerable free energy barrier for NP translocation across the lipid bilayer. 5-µs unbiased MD simulations with the NP inserted in the bilayer core reveal that the hydrophobic and hydrophilic ligands of the NP surface rearrange to form optimal contacts with the lipid bilayer, leading to the so-called snorkeling effect. Inside cholesterol-containing bilayers, the NP induces rearrangement of the structure of the lipid bilayer in its vicinity from the liquid-ordered to the liquid phase spanning a distance almost twice its core radius (8–10 nm). Based on the physical insights obtained in this study, we propose a mechanism of cellular anionic NPpartitioning, which requires structural rearrangements of both the NP and the bilayer, and conclude that the translocation of anionic NPs through cholesterol-rich membranes must be accompanied by formation of cholesterol-lean regions in the proximity of NPs.</p></div>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1261591, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003917.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003917.s002"], "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Membrane_Partitioning_of_Anionic_Ligand_Coated_Nanoparticles_Is_Accompanied_by_Ligand_Snorkeling_Local_Disordering_and_Cholesterol_Depletion_/1261591", "title"=>"Membrane Partitioning of Anionic, Ligand-Coated Nanoparticles Is Accompanied by Ligand Snorkeling, Local Disordering, and Cholesterol Depletion", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-04 15:02:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821802"], "description"=>"<p>Bilayer thickness, defined as the distance between phosphate groups (PO4) of different bilayer leaflets, for different cholesterol concentrations as a function of the distance from the NP-center of mass.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260344, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.g006", "stats"=>{"downloads"=>3, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Bilayer_thickness_defined_as_the_distance_between_phosphate_groups_PO4_of_different_bilayer_leaflets_for_different_cholesterol_concentrations_as_a_function_of_the_distance_from_the_NP_center_of_mass_/1260344", "title"=>"Bilayer thickness, defined as the distance between phosphate groups (PO4) of different bilayer leaflets, for different cholesterol concentrations as a function of the distance from the NP-center of mass.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821801"], "description"=>"<p>The concentration values as a function of the distance from the NP center of mass, c(d), are normalized with respect to the bulk values, c<sub>bulk</sub>.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260342, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.g005", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_2D_Radial_concentration_of_DPPC_and_CHOL_from_the_NP_center_of_mass_/1260342", "title"=>"2D Radial concentration of DPPC and CHOL from the NP center of mass.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821798"], "description"=>"<p>The characteristic values P<sub>2</sub> order parameter for various bilayer phases are demarcated in the color bar on the right <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003917#pcbi.1003917-Waheed1\" target=\"_blank\">[35]</a>. The different box sizes are due to the gradual condensing effect of cholesterol on the bilayer.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260339, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.g004", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Spatially_averaged_lipid_order_parameters_for_bilayer_systems_with_different_cholesterol_concentrations_/1260339", "title"=>"Spatially averaged lipid order parameters for bilayer systems with different cholesterol concentrations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/1821783"], "description"=>"<p>The error bars represent standard deviations from two independent sets of Umbrella sampling calculations using the bootstrapping technique. Detailed analysis of the PMF convergence is provided in Text S1.</p>", "links"=>[], "tags"=>["NP cytotoxicity assessment", "Cholesterol Depletion Intracellular uptake", "lipid bilayer", "cell membrane", "MD simulations", "dppc"], "article_id"=>1260324, "categories"=>["Uncategorised"], "users"=>["Paraskevi Gkeka", "Panagiotis Angelikopoulos", "Lev Sarkisov", "Zoe Cournia"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003917.g003", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_PMF_for_NP_partitioning_in_a_cholesterol_free_DPPC_lipid_bilayer_/1260324", "title"=>"PMF for NP partitioning in a cholesterol-free DPPC lipid bilayer.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:09:39"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"11", "full-text"=>"10", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"8"}
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  • {"unique-ip"=>"1", "full-text"=>"1", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2017", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"4", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"3"}
  • {"unique-ip"=>"3", "full-text"=>"3", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"1"}
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  • {"unique-ip"=>"3", "full-text"=>"1", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"5"}
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  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2018", "month"=>"7"}
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  • {"unique-ip"=>"9", "full-text"=>"9", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2020", "month"=>"7"}
  • {"unique-ip"=>"2", "full-text"=>"2", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"8"}
  • {"unique-ip"=>"4", "full-text"=>"4", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"9"}
  • {"unique-ip"=>"5", "full-text"=>"4", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"10"}
  • {"unique-ip"=>"2", "full-text"=>"1", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"11"}
  • {"unique-ip"=>"1", "full-text"=>"0", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2020", "month"=>"12"}
  • {"unique-ip"=>"3", "full-text"=>"2", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2021", "month"=>"1"}

Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[]}
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