In Silico Adoption of an Orphan Nuclear Receptor NR4A1
Publication Date
August 13, 2015
Journal
PLOS ONE
Authors
Harald Lanig, Felix Reisen, David Whitley, Gisbert Schneider, et al
Volume
10
Issue
8
Pages
e0135246
DOI
https://dx.plos.org/10.1371/journal.pone.0135246
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0135246
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/26270486
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535767
Europe PMC
http://europepmc.org/abstract/MED/26270486
Web of Science
000359492800044
Scopus
84942939433
Mendeley
http://www.mendeley.com/research/silico-adoption-orphan-nuclear-receptor-nr4a1
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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/2211123"], "description"=>"<p>Putative ligands for the newly found binding site in NR4A1.</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1509996, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g005", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Putative_ligands_for_the_newly_found_binding_site_in_NR4A1_/1509996", "title"=>"Putative ligands for the newly found binding site in NR4A1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211119"], "description"=>"<p>Each vertex represents one pocket. Vertices are connected if the pockets are located in similar regions of the protein surface and have a mutual overlap of at least 30%. Vertex labels consist of the cluster number (0–14, c = crystal) and the pocket number (as identified by PocketPicker,<sup>36</sup> sorted by size in ascending order). Vertex colors and sizes correspond to the number of the snapshots (red: crystal) and the pocket sizes, respectively. Clusters <b>1</b>–<b>3</b> contain pockets that are present both in the crystal structure and in some snapshots. Pockets of clusters <b>4–10</b> are not present or smaller than 100 Å<sup>3</sup> in the crystal structure. Cluster <b>4</b> (light green) represents a potential binding site. Clusters <b>5–10</b> represent pockets whose shapes or sizes render ligand binding unlikely.</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1509992, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g003", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_of_pockets_that_occur_in_the_crystal_structure_and_different_snapshots_of_the_MD_simulation_/1509992", "title"=>"Clustering of pockets that occur in the crystal structure and different snapshots of the MD simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211117"], "description"=>"<p>The clustering results are color-coded to indicate the population of the cluster in the given time period. The blue vertical dashed lines indicate transitions detected by DASH. The red dashed boxes indicate the clusters/conformations in which the binding pocket discussed below was found.</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1509990, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g002", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Clustering_above_and_DASH_35_below_analyses_of_the_4_1_s_simulation_of_NR4A1_/1509990", "title"=>"Clustering (above) and DASH, [35] (below) analyses of the 4.1 μs simulation of NR4A1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211128"], "description"=>"<p>The blue double headed arrows indicate the axes of the helices 1 and 9 in the apo-structure. The regions of the protein that rearrange on ligand binding are denoted by the ellipses (Red; adjacent to the binding site. Violet; remote loop <sup>25</sup>F FQELVLPHFGKEDAGD-D<sup>40</sup>).</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1510001, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g007", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Apo_NR4A1_blue_PDB_2QW4_compared_to_a_snapshot_of_NR4A1_after_45ns_simulation_in_the_presence_of_1_green_/1510001", "title"=>"Apo-NR4A1 (blue, PDB:2QW4) compared to a snapshot of NR4A1 after 45ns simulation in the presence of 1 (green).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211125"], "description"=>"<p>Representative snapshots taken from the MD simulation of ligand 1 within the new binding pocket (cyan, after 100 ns; magenta, after 800ns), fitted onto the starting geometry of the docked complex (green).</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1509998, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g006", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_snapshots_taken_from_the_MD_simulation_of_ligand_1_within_the_new_binding_pocket_cyan_after_100_ns_magenta_after_800ns_fitted_onto_the_starting_geometry_of_the_docked_complex_green_/1509998", "title"=>"Representative snapshots taken from the MD simulation of ligand 1 within the new binding pocket (cyan, after 100 ns; magenta, after 800ns), fitted onto the starting geometry of the docked complex (green).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211122"], "description"=>"<p>The flexible loop that is stabilized by ligand binding is indicated by the red ellipse.</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1509995, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g004", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_predicted_binding_site_blue_blue_grey_spheres_is_located_close_to_the_N_terminus_of_NR4A1_/1509995", "title"=>"The predicted binding site (blue/blue grey spheres) is located close to the N-terminus of NR4A1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211134", "https://ndownloader.figshare.com/files/2211135", "https://ndownloader.figshare.com/files/2211136", "https://ndownloader.figshare.com/files/2211137", "https://ndownloader.figshare.com/files/2211138", "https://ndownloader.figshare.com/files/2211139", "https://ndownloader.figshare.com/files/2211140", "https://ndownloader.figshare.com/files/2211141", "https://ndownloader.figshare.com/files/2211142"], "description"=>"<div><p>A 4.1μs molecular dynamics simulation of the NR4A1 (hNur77) apo-protein has been undertaken and a previously undetected druggable pocket has become apparent that is located remotely from the ‘traditional’ nuclear receptor ligand-binding site. A NR4A1/bis-indole ligand complex at this novel site has been found to be stable over 1 μs of simulation and to result in an interesting conformational transmission to a remote loop that has the capacity to communicate with a NBRE within a RXR-α/NR4A1 heterodimer. Several features of the simulations undertaken indicate how NR4A1 can be affected by alternate-site modulators.</p></div>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1510007, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0135246.s001", "https://dx.doi.org/10.1371/journal.pone.0135246.s002", "https://dx.doi.org/10.1371/journal.pone.0135246.s003", "https://dx.doi.org/10.1371/journal.pone.0135246.s004", "https://dx.doi.org/10.1371/journal.pone.0135246.s005", "https://dx.doi.org/10.1371/journal.pone.0135246.s006", "https://dx.doi.org/10.1371/journal.pone.0135246.s007", "https://dx.doi.org/10.1371/journal.pone.0135246.s008", "https://dx.doi.org/10.1371/journal.pone.0135246.s009"], "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_Silico_Adoption_of_an_Orphan_Nuclear_Receptor_NR4A1/1510007", "title"=>"<i>In Silico</i> Adoption of an Orphan Nuclear Receptor NR4A1", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211116"], "description"=>"<p>The structures of known small-molecule modulators of NR4A1.</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1509989, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structures_of_known_small_molecule_modulators_of_NR4A1_/1509989", "title"=>"The structures of known small-molecule modulators of NR4A1.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/2211133"], "description"=>"<p>Model of the apo-NR4A1 (green cylinders) in dimerization with apo-RXR-α (blue cylinders) at the NBS of a cognate NBRE, DNA (CPK colors) indicates the NBS sequences (Red) and the location of the <i>bis</i>-indole 1 (CPK spheres) post-superimposition of the NR4A1 45ns complex.</p>", "links"=>[], "tags"=>["site", "NR 4A ligand", "nbre", "NR 4A", "Orphan Nuclear Receptor NR 4A", "rxr", "simulation"], "article_id"=>1510006, "categories"=>["Biological Sciences"], "users"=>["Harald Lanig", "Felix Reisen", "David Whitley", "Gisbert Schneider", "Lee Banting", "Timothy Clark"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0135246.g008", "stats"=>{"downloads"=>0, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Model_of_the_apo_NR4A1_green_cylinders_in_dimerization_with_apo_RXR_blue_cylinders_at_the_NBS_of_a_cognate_NBRE_DNA_CPK_colors_indicates_the_NBS_sequences_Red_and_the_location_of_the_bis_indole_1_CPK_spheres_post_superimposition_of_the_NR4A1_45ns_complex/1510006", "title"=>"Model of the apo-NR4A1 (green cylinders) in dimerization with apo-RXR-α (blue cylinders) at the NBS of a cognate NBRE, DNA (CPK colors) indicates the NBS sequences (Red) and the location of the <i>bis</i>-indole 1 (CPK spheres) post-superimposition of the NR4A1 45ns complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-08-13 02:46:35"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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