Break CDK2/Cyclin E1 Interface Allosterically with Small Peptides
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{"title"=>"Break CDK2/Cyclin E1 interface allosterically with small peptides", "type"=>"journal", "authors"=>[{"first_name"=>"Hao", "last_name"=>"Chen", "scopus_author_id"=>"55553726648"}, {"first_name"=>"Yunjie", "last_name"=>"Zhao", "scopus_author_id"=>"37000276500"}, {"first_name"=>"Haotian", "last_name"=>"Li", "scopus_author_id"=>"55829141800"}, {"first_name"=>"Dongyan", "last_name"=>"Zhang", "scopus_author_id"=>"56379179700"}, {"first_name"=>"Yanzhao", "last_name"=>"Huang", "scopus_author_id"=>"7501572309"}, {"first_name"=>"Qi", "last_name"=>"Shen", "scopus_author_id"=>"48663048900"}, {"first_name"=>"Rachel", "last_name"=>"Van Duyne", "scopus_author_id"=>"24167399800"}, {"first_name"=>"Fatah", "last_name"=>"Kashanchi", "scopus_author_id"=>"26643432100"}, {"first_name"=>"Chen", "last_name"=>"Zeng", "scopus_author_id"=>"7103181392"}, {"first_name"=>"Shiyong", "last_name"=>"Liu", "scopus_author_id"=>"57191659009"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84907854986", "pui"=>"600116586", "doi"=>"10.1371/journal.pone.0109154", "pmid"=>"25290691", "scopus"=>"2-s2.0-84907854986", "issn"=>"19326203", "isbn"=>"2011014212"}, "id"=>"b7823013-30ca-3fd9-867e-032a258d0a5d", "abstract"=>"Most inhibitors of Cyclin-dependent kinase 2 (CDK2) target its ATP-binding pocket. It is difficult, however, to use this pocket to design very specific inhibitors because this catalytic pocket is highly conserved in the protein family of CDKs. Here we report some short peptides targeting a noncatalytic pocket near the interface of the CDK2/Cyclin complex. Docking and molecular dynamics simulations were used to select the peptides, and detailed dynamical network analysis revealed that these peptides weaken the complex formation via allosteric interactions. Our experiments showed that upon binding to the noncatalytic pocket, these peptides break the CDK2/Cyclin complex partially and diminish its kinase activity in vitro. The binding affinity of these peptides measured by Surface Plasmon Resonance can reach as low as 0.5 µM.", "link"=>"http://www.mendeley.com/research/break-cdk2cyclin-e1-interface-allosterically-small-peptides", "reader_count"=>10, "reader_count_by_academic_status"=>{"Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>1}, "reader_count_by_user_role"=>{"Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>4, "Student > Postgraduate"=>1, "Student > Master"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>4, "Chemistry"=>4, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>4}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>4}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}}, "reader_count_by_country"=>{"Brazil"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1707662"], "description"=>"<p>*With 60 µM ATP.</p><p>SPR-derived binding affinities of CDK2 for four peptides with and without 60 µM ATP.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196094, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.t004", "stats"=>{"downloads"=>1, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SPR_derived_binding_affinities_of_CDK2_for_four_peptides_with_and_without_60_181_M_ATP_/1196094", "title"=>"SPR-derived binding affinities of CDK2 for four peptides with and without 60 µM ATP.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707659"], "description"=>"<p>RANK: The rank of the protein-peptide model sorted by AutoDock binding energy. Methods: Frequency, Pmfscore and AutoDock (details see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109154#pone-0109154-t002\" target=\"_blank\">table 2</a>).</p><p>SET1, SET2 and SET3 have been defined as CDK2 with different T-loop conformation (see text).</p><p>CONTROL: The previous experimental result <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109154#pone.0109154-Chen1\" target=\"_blank\">[20]</a> shows that TAALS and LAALS bound to unphosplorylated form of CDK2, but TAALD not.</p><p>Stay: That means that the peptide is staying in the pocket during the MD simulation.</p><p>MD simulations of CDK2-peptide docking decoys.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196091, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.t001", "stats"=>{"downloads"=>2, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MD_simulations_of_CDK2_peptide_docking_decoys_/1196091", "title"=>"MD simulations of CDK2-peptide docking decoys.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707658"], "description"=>"<p>The blue lines are experimental data, and the red lines are fitted results. The binding affinities (K<sub>D</sub>) between CDK2 and TAALS (A) with and (B) without 60 µM ATP are 3.3 µM, 1.4 µM, respectively. The binding affinities (K<sub>D</sub>) between CDK2 and LAALS (C) with and (D) without 60 µM ATP are 61 µM, 8.0 µM, respectively. The binding affinities (K<sub>D</sub>) between CDK2 and DAALT (E) with and (F) without 60 µM ATP are 37 µM, 0.47 µM, respectively. The binding affinities (K<sub>D</sub>) between CDK2 and YAALQ (G) with and (H) without 60 µM ATP are 61 µM, 98 µM, respectively.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196090, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.g005", "stats"=>{"downloads"=>0, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_SPR_binding_assay_results_of_CDK2_and_peptides_with_and_without_ATP_/1196090", "title"=>"SPR binding assay results of CDK2 and peptides with and without ATP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707652"], "description"=>"<p>Left: the docked RAALF and CDK2 complex structure,as an initial structure for MD simulation; Right, after 5 ns MD simulation, the RAALF and CDK2 complex structure is shown. The green represent peptide RAALF, and the purple balls are atoms from the key residues: K178, Y180, and the red is the T-loop of CDK2. The MD simulation shows that after 5 ns, the peptide RAALF (Green) swam away from the key pocket sites of CDK2.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196084, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.g002", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MD_simulation_of_RAALF_CDK2_docking_decoy_/1196084", "title"=>"MD simulation of RAALF-CDK2 docking decoy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707661"], "description"=>"<p>RANK: The rank of the protein-peptide model sorted by AutoDock binding energy. Methods: Frequency, Pmfscore and AutoDock (details see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109154#pone-0109154-t002\" target=\"_blank\">table 2</a>).</p><p>SET1 and SET2 have been defined as CDK2 with different T-loop conformation (see text).</p>1<p>Stay: That means that the peptide is staying in the pocket during the MD simulation.</p>2<p>Key residue and T-loop: Key residues are that Y180, K178of CDK2.</p>3<p>The value in brackets is calculated by Pmfscore.</p><p>Selection based on MD simulation results.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196093, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.t003", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Selection_based_on_MD_simulation_results_/1196093", "title"=>"Selection based on MD simulation results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707660"], "description"=>"1<p>Frequency: Top 5 was selected according to the number of the peptide sequence in the top 1000 lowest energy docking decoys.</p>2<p>AutoDock: Top 5 was selected according to the calculated binding energy by AutoDock.</p>3<p>Pmfscore is a statistical potential developed by Jiang <i>et al.</i><a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0109154#pone.0109154-Jiang1\" target=\"_blank\">[37]</a>. Top 5 was selected according to the Pmfscore.</p><p>Designed peptides based on three scoring methods.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196092, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.t002", "stats"=>{"downloads"=>1, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Designed_peptides_based_on_three_scoring_methods_/1196092", "title"=>"Designed peptides based on three scoring methods.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707655"], "description"=>"<p>Monomers with highly (anti)correlated motion are orange or red (blue). Interface regions displaying high degree of (anti)correlation are marked in white rectangles.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196087, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.g003", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Correlation_analysis_of_the_motion_during_a_20_ns_MD_simulation_of_the_CDK2_Cyclin_peptide_complex_structures_/1196087", "title"=>"Correlation analysis of the motion during a 20-ns MD simulation of the CDK2/Cyclin/peptide complex structures.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707656"], "description"=>"<p>A) C81 fractionated cell extracts containing cdk2/Cyclin E complex were incubated with α-Cyclin E antibody in the presence of six designed peptides at 10 µM concentration. Following immunoprecipitation of Cyclin E, Western blot for CDK2 was shown here. α-IgG is included as a negative control. B) Immunoprecipitated Cyclin E samples in the presence of peptides were assessed for kinase activity. Histone H1 (1 µg/reaction) was added to each reaction tube along with 2 µl of (γ-32P) ATP (3000 Ci/mmol). Reactions were incubated at 37°C for 30 min and stopped by the addition Laemmli buffer. The samples were separated on a 4–20% Tris–Glycine gel. Samples were ran on a gel, dried, and exposed to a PhosphorImager cassette and analyzed using Molecular Dynamic’s ImageQuant Software.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196088, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.g004", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dissociation_of_CDK2_Cyclin_E_in_the_presence_of_designed_peptides_/1196088", "title"=>"Dissociation of CDK2/Cyclin E in the presence of designed peptides.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 02:43:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/1707650"], "description"=>"<p>Left: the docked TAALS and CDK2 complex structure, as an initial structure for MD simulation; Right, after 5 ns MD simulation, the TAALS and CDK2 complex structure is shown. The green represent peptide TAALS, and the purple balls are atoms from the key residues: K178, Y180, and the red is the T-loop of CDK2. The MD simulation shows that after 5 ns, the peptide TAALS (Green) induced the conformational change of the CDK2 and moved to the gap between purple and red.</p>", "links"=>[], "tags"=>["0.5 µ M", "peptide", "kinase", "binding", "surface plasmon resonance", "noncatalytic pocket", "cdk", "inhibitor"], "article_id"=>1196082, "categories"=>["Biological Sciences"], "users"=>["Hao Chen", "Yunjie Zhao", "Haotian Li", "Dongyan Zhang", "Yanzhao Huang", "Qi Shen", "Rachel Van Duyne", "Fatah Kashanchi", "Chen Zeng", "Shiyong Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0109154.g001", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MD_simulation_of_TAALS_CDK2_docking_decoy_/1196082", "title"=>"MD simulation of TAALS-CDK2 docking decoy.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-10-07 02:43:55"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences/Computational biology", "average_usage"=>[341, 529]}, {"subject_area"=>"/Computer and information sciences", "average_usage"=>[327, 511]}]}
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