The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc
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{"title"=>"The impact of small molecule binding on the energy landscape of the intrinsically disordered protein C-Myc", "type"=>"journal", "authors"=>[{"first_name"=>"Julien", "last_name"=>"Michel", "scopus_author_id"=>"15520146800"}, {"first_name"=>"Rémi", "last_name"=>"Cuchillo", "scopus_author_id"=>"55316945200"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84864018938", "pmid"=>"22815918", "isbn"=>"0950-9232 (Print)\\r0950-9232 (Linking)", "pui"=>"365274113", "issn"=>"19326203", "scopus"=>"2-s2.0-84864018938", "doi"=>"10.1371/journal.pone.0041070"}, "id"=>"eba95437-64ca-3eea-9cb4-332a0a74c044", "abstract"=>"Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (1), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to 1 were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule 1 was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding 1 are already partially formed in the apo ensemble, suggesting that 1 binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins.", "link"=>"http://www.mendeley.com/research/impact-small-molecule-binding-energy-landscape-intrinsically-disordered-protein-cmyc-2", "reader_count"=>70, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>23, "Student > Ph. D. Student"=>29, "Other"=>1, "Student > Master"=>4, "Student > Bachelor"=>5, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>4, "Researcher"=>23, "Student > Ph. D. Student"=>29, "Other"=>1, "Student > Master"=>4, "Student > Bachelor"=>5, "Professor"=>1, "Student > Postgraduate"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>8, "Materials Science"=>1, "Agricultural and Biological Sciences"=>26, "Medicine and Dentistry"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>2, "Chemistry"=>24, "Psychology"=>1, "Computer Science"=>2}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>24}, "Physics and Astronomy"=>{"Physics and Astronomy"=>2}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>26}, "Computer Science"=>{"Computer Science"=>2}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>8}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Canada"=>1, "United States"=>1, "Ireland"=>1, "Italy"=>2, "Lithuania"=>1, "Australia"=>1, "Germany"=>2, "Spain"=>1}, "group_count"=>6}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/609444"], "description"=>"<p>The conformations depicted are those closest to the center of the most populated clusters. The fractional cluster populations are: 0.101±0.018 (A), 0.075±0.034 (B), 0.060±0.040 (C), 0.059±0.027 (D), 0.055±0.016 (E), 0.043±0.004 (F), 0.030±0.017 (G), 0.021±0.009 (H), 0.021±0.003 (I). Figure prepared with the software VMD <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041070#pone.0041070-Humphrey1\" target=\"_blank\">[78]</a>.</p>", "links"=>[], "tags"=>["conformations", "computed", "equilibrium", "ensemble", "apo"], "article_id"=>279936, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g005", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_conformations_from_the_computed_equilibrium_ensemble_for_apo_c_Myc_402_8211_412_/279936", "title"=>"Representative conformations from the computed equilibrium ensemble for apo c-Myc<sub>402–412</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 02:45:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/317865", "https://ndownloader.figshare.com/files/317903", "https://ndownloader.figshare.com/files/317935", "https://ndownloader.figshare.com/files/317971", "https://ndownloader.figshare.com/files/317996"], "description"=>"<div><p>Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (<b>1</b>), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to <b>1</b> were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule <b>1</b> was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding <b>1</b> are already partially formed in the apo ensemble, suggesting that <b>1</b> binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins.</p> </div>", "links"=>[], "tags"=>["binding", "intrinsically", "disordered", "c-myc"], "article_id"=>122747, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041070.s001", "https://dx.doi.org/10.1371/journal.pone.0041070.s002", "https://dx.doi.org/10.1371/journal.pone.0041070.s003", "https://dx.doi.org/10.1371/journal.pone.0041070.s004", "https://dx.doi.org/10.1371/journal.pone.0041070.s005"], "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/The_Impact_of_Small_Molecule_Binding_on_the_Energy_Landscape_of_the_Intrinsically_Disordered_Protein_C_Myc/122747", "title"=>"The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-16 00:45:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/609167"], "description"=>"<p>The small molecule 10058-F4 (<b>1</b>, purple star) disrupts heterodimerization of the bHLHZip domains in c-Myc (blue) and Max (red) by stabilizing conformations in monomeric c-Myc incompatible with c-Myc/Max dimerizaton.</p>", "links"=>[], "tags"=>["inhibition"], "article_id"=>279660, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g001", "stats"=>{"downloads"=>0, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Small_molecule_inhibition_of_the_c_Myc_Max_interaction_/279660", "title"=>"Small molecule inhibition of the c-Myc/Max interaction.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 02:41:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/609637"], "description"=>"<p>A) Probability distribution of backbone RMSD of conformations from the apo (black curve) and holo (red curve) ensembles to: A) holo cluster center 7A, B) holo cluster center 7B, C) holo cluster center 7C, D) apo cluster center 5A. The inset shows the low-RMSD regions. Each panel also shows an overlay of the lowest RMSD apo or holo structure to cluster centers from panels A–D. For clarity only the peptide backbone (tube representation, apo conformations in blue, holo conformations in orange) and ligand atoms (CPK) are shown. Figure prepared using VMD <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041070#pone.0041070-Humphrey1\" target=\"_blank\">[78]</a>.</p>", "links"=>[], "tags"=>["holo", "apo", "conformations"], "article_id"=>280137, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g008", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_selected_holo_and_apo_conformations_to_the_apo_and_holo_ensembles_/280137", "title"=>"Comparison of selected holo and apo conformations to the apo and holo ensembles.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 00:02:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/609369"], "description"=>"<p>A) <sup>1</sup>H<sub>α</sub> chemical shifts. B) <sup>13</sup>C<sub>α</sub> chemical shifts. C) <sup>1</sup>H backbone amide chemical shifts. D) <sup>13</sup>C<sub>β</sub> chemical shifts. Black: experimental data. Solid red and blue: predicted by reweighting the biased BEMD simulations apoA and apoB respectively. Dotted red and blue: predicted from the neutral replicas of the BEMD simulations apoA and apoB respectively. Not all experimental <sup>13</sup>C<sub>β</sub> chemical shifts were reported. Camshift does not report chemical shifts for terminal residues.</p>", "links"=>[], "tags"=>["computed", "observed", "shifts", "apo"], "article_id"=>279861, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_computed_and_observed_secondary_chemical_shifts_for_apo_c_Myc_402_8211_412_/279861", "title"=>"Comparison of computed and observed secondary chemical shifts for apo c-Myc<sub>402–412</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 02:44:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/609298"], "description"=>"<p>Black: Simulation holoA, Red: Simulation holoB. A) CV1, B) CV2, C) CV3, D) CV4, E) CV5, F) CV6, G) CV7, H) CV8. See the <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041070#s4\" target=\"_blank\">Methods</a> section in the main text for a definition of each CV.</p>", "links"=>[], "tags"=>["profiles", "holo", "simulations", "projected"], "article_id"=>279792, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Free_energy_profiles_for_the_c_Myc_402_8211_412_1_holo_simulations_projected_along_several_collective_variables_/279792", "title"=>"Free energy profiles for the c-Myc<sub>402–412</sub>/1 holo simulations projected along several collective variables.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 02:43:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/609564"], "description"=>"<p>The conformations depicted are those closest to the cluster center. The fractional cluster populations are: 0.021±0.008 (A), 0.019±0.002 (B), 0.018±0.005 (C), 0.015±0.010 (D), 0.014±0.003 (E), 0.011±0.008 (F), 0.011±0.005 (G), 0.011±0.001 (H), 0.010±0.003 (I). Figure prepared with the software VMD <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041070#pone.0041070-Humphrey1\" target=\"_blank\">[78]</a>.</p>", "links"=>[], "tags"=>["conformations", "computed", "equilibrium", "ensemble"], "article_id"=>280061, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g007", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Representative_conformations_from_the_computed_equilibrium_ensemble_for_the_c_Myc_402_8211_412_1_complex_/280061", "title"=>"Representative conformations from the computed equilibrium ensemble for the c-Myc<sub>402–412</sub>/1 complex.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 00:01:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/609716"], "description"=>"1<p>helix and sheet content computed according to the DSSP and STRIDE methods respectively. A helix was defined as G + H + I and a sheet as B + E using the 7 letter DSSP code. The polyproline II content was estimated using the software PROSS.</p>2<p>Secondary structure content estimated from measured chemical shifts, using the webserver δ2d.</p>", "links"=>[], "tags"=>["apo"], "article_id"=>280217, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.t001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Percentage_of_secondary_structure_content_of_apo_c_Myc_402_8211_412_1_/280217", "title"=>"Percentage of secondary structure content of apo c-Myc<sub>402–412</sub>.<sup>1</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-16 00:03:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/609223"], "description"=>"<p>Black: Simulation apoA, Red: Simulation apoB. A) CV1, B) CV2, C) CV3, D) CV4 E) CV5 F) CV6 G) CV7. See the <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0041070#s4\" target=\"_blank\">Methods</a> section in the main text for a definition of each CV.</p>", "links"=>[], "tags"=>["profiles", "apo", "simulations", "projected"], "article_id"=>279716, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g002", "stats"=>{"downloads"=>1, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Free_energy_profiles_for_the_c_Myc_402_8211_412_apo_simulations_projected_along_several_collective_variables_/279716", "title"=>"Free energy profiles for the c-Myc<sub>402–412</sub> apo simulations projected along several collective variables.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 02:41:56"}
  • {"files"=>["https://ndownloader.figshare.com/files/609494"], "description"=>"<p> A) Average number of <sup>1</sup>H contacts between different c-Myc<sub>402–412</sub> residues and <b>1.</b> Color coded from white (no contacts) to red (high number of contacts). The extreme values of this color scale range from 0.02 to 1.08. B) Difference in the average number of <sup>1</sup>H contacts between different c-Myc<sub>402–412</sub> residues in the holo and apo ensembles. Red/blue indicates an increased/decreased average number of contacts upon binding of <b>1</b>. The extreme values of this color scale range from −1.22 to +0.67.</p>", "links"=>[], "tags"=>["contacts"], "article_id"=>280001, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Biophysics"], "users"=>["Julien Michel", "Rémi Cuchillo"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041070.g006", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Average_number_of_contacts_between_1_and_c_Myc_402_8211_412_/280001", "title"=>"Average number of contacts between 1 and c-Myc<sub>402–412</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-16 00:00:01"}

PMC Usage Stats | Further Information

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  • {"unique-ip"=>"13", "full-text"=>"15", "pdf"=>"7", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"11", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"4"}
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  • {"unique-ip"=>"6", "full-text"=>"6", "pdf"=>"3", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
  • {"unique-ip"=>"8", "full-text"=>"18", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"1", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
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  • {"unique-ip"=>"8", "full-text"=>"16", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"1", "year"=>"2015", "month"=>"11"}
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Relative Metric

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