Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations
Publication Date
December 05, 2013
Journal
PLOS Computational Biology
Authors
Nevena Todorova, Adam J. Makarucha, Nicholas D. M. Hine, Arash A. Mostofi, et al
Volume
9
Issue
12
Pages
e1003360
DOI
https://dx.plos.org/10.1371/journal.pcbi.1003360
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003360
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/24339760
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3854483
Europe PMC
http://europepmc.org/abstract/MED/24339760
Web of Science
000329364800001
Scopus
84892770558
Mendeley
http://www.mendeley.com/research/dimensionality-carbon-nanomaterials-determines-binding-dynamics-amyloidogenic-peptides-multiscale-th
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1305735"], "description"=>"<p>Contact stability plot of apoC-II adsorbed to C60 (red), carbon nanotubes (green) and graphene (blue).</p>", "links"=>[], "tags"=>[], "article_id"=>870272, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Persistent_contacts_/870272", "title"=>"Persistent contacts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305733"], "description"=>"<p>Phenyl rings demonstrating the aromatic ring arrangement categorized in three groups: face-to-face π-stacking, offset π-stacking and no π-stacking. To help in the interpretation of the cut-offs applied to categorize each aromatic arrangement, only the angle between the plane normal of the rings is shown (image on the right), while all other distance cut-offs are pair-wise in nature.</p>", "links"=>[], "tags"=>[], "article_id"=>870270, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g001", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Aromatic_ring_arrangement_categories_/870270", "title"=>"Aromatic ring arrangement categories.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305738"], "description"=>"<p>Relative DFT vacuum binding energies of apoC-II(60-70) adsorbed to C60 (red), carbon nanotube (green) and graphene (blue) vs the total contact area between the peptide and nanomaterial surface. The solution PMF free energy range for each nanomaterial is also shown (right axis, higher energy = stronger binding) to illustrate the correlation in energies between the classical and electronic structure methods.</p>", "links"=>[], "tags"=>["vacuo", "binding"], "article_id"=>870275, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vacuo_binding_energies_/870275", "title"=>"In vacuo binding energies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305737"], "description"=>"<p>The free energy of dissociation of apoC-II(60-70) peptide from a) C60 (red); b) nanotube (green) and c) graphene (blue) surface. Different initial conformations of the peptide on the nanomaterials surface were examined to improve the conformational sampling. Screenshots depicting typical representative structures of important events on the free energy surface are shown as insets. For clarity the peptide structure is drawn as ribbon (iceblue) and the aromatic residues are shown as licorice (yellow).</p>", "links"=>[], "tags"=>[], "article_id"=>870274, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g005", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Peptide_nanomaterial_free_energy_of_dissociation_/870274", "title"=>"Peptide-nanomaterial free energy of dissociation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305740", "https://ndownloader.figshare.com/files/1305741", "https://ndownloader.figshare.com/files/1305742", "https://ndownloader.figshare.com/files/1305743", "https://ndownloader.figshare.com/files/1305744", "https://ndownloader.figshare.com/files/1305745"], "description"=>"<div><p>Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth.</p></div>", "links"=>[], "tags"=>["carbon", "Nanomaterials", "determines", "binding", "amyloidogenic", "multiscale"], "article_id"=>870277, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003360.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003360.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003360.s003", "https://dx.doi.org/10.1371/journal.pcbi.1003360.s004", "https://dx.doi.org/10.1371/journal.pcbi.1003360.s005", "https://dx.doi.org/10.1371/journal.pcbi.1003360.s006"], "stats"=>{"downloads"=>4, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dimensionality_of_Carbon_Nanomaterials_Determines_the_Binding_and_Dynamics_of_Amyloidogenic_Peptides_Multiscale_Theoretical_Simulations_/870277", "title"=>"Dimensionality of Carbon Nanomaterials Determines the Binding and Dynamics of Amyloidogenic Peptides: Multiscale Theoretical Simulations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305739"], "description"=>"<p>Electron density difference maps of representative frames from the clustering analysis shown by an isosurface with isovalues of Δρ = +0.005e/Å<sup>3</sup> and −0.005e/Å<sup>3</sup>. Red represents charge accumulation, and blue represents charge depletion. The aromatic rings are colored yellow for clarity. The respective structures' π-stacking arrangement, aromatic contact area and binding energy differences relative to the strongest bound state (face-to-face π arrangement on graphene, figure c) are also shown together with close-up insets of specific features to aid interpretations of the results for a) C60, b) nanotube and c) graphene.</p>", "links"=>[], "tags"=>[], "article_id"=>870276, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g007", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Electron_density_difference_maps_/870276", "title"=>"Electron density difference maps.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305736"], "description"=>"<p>RDFs of the water probability density, <i>g(r)</i>, as a function of the distance, <i>r</i>, of water (O) from the side chain (H) atoms of apoC-II(60-70). RDFs for the peptide in a free (unbound) and adsorbed (bound) to a) C60, b) nanotube and c) graphene are shown.</p>", "links"=>[], "tags"=>["functions"], "article_id"=>870273, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Radial_distribution_functions_of_water_/870273", "title"=>"Radial distribution functions of water.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}
  • {"files"=>["https://ndownloader.figshare.com/files/1305734"], "description"=>"<p>(a and b) C60, (c) nanotube and (d) graphene surface; Secondary structure color codes: magenta = α-helix; red = π-helix; cyan = turn; white = coil; yellow = extended conformation; green = hydrogen bridge. Screen shots depicting the favorable peptide structure and aromatic residues arrangement for each system are shown as insets.</p>", "links"=>[], "tags"=>["behaviors", "observed"], "article_id"=>870271, "categories"=>["Biological Sciences"], "users"=>["Nevena Todorova", "Adam J. Makarucha", "Nicholas D. M. Hine", "Arash A. Mostofi", "Irene Yarovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003360.g002", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Secondary_structure_evolution_plots_for_typical_behaviors_observed_of_apoC_II_60_70_in_the_presence_of_nanomaterials_/870271", "title"=>"Secondary structure evolution plots for typical behaviors observed of apoC-II(60-70) in the presence of nanomaterials.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-12-05 04:57:15"}

PMC Usage Stats | Further Information

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Relative Metric

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