Homodimerization of the Death-Associated Protein Kinase Catalytic Domain: Development of a New Small Molecule Fluorescent Reporter
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{"title"=>"Homodimerization of the death-associated protein kinase catalytic domain: Development of a new small molecule fluorescent reporter", "type"=>"journal", "authors"=>[{"first_name"=>"Michael", "last_name"=>"Zimmermann", "scopus_author_id"=>"7201476475"}, {"first_name"=>"Cédric", "last_name"=>"Atmanene", "scopus_author_id"=>"23487960200"}, {"first_name"=>"Qingyan", "last_name"=>"Xu", "scopus_author_id"=>"57199200013"}, {"first_name"=>"Laetitia", "last_name"=>"Fouillen", "scopus_author_id"=>"25636809500"}, {"first_name"=>"Alain", "last_name"=>"van Dorsselaer", "scopus_author_id"=>"7007142561"}, {"first_name"=>"Dominique", "last_name"=>"Bonnet", "scopus_author_id"=>"57193153340"}, {"first_name"=>"Claire", "last_name"=>"Marsol", "scopus_author_id"=>"6603352949"}, {"first_name"=>"Marcel", "last_name"=>"Hibert", "scopus_author_id"=>"7003355569"}, {"first_name"=>"Sarah", "last_name"=>"Sanglier-Cianferani", "scopus_author_id"=>"7801640947"}, {"first_name"=>"Claire", "last_name"=>"Pigault", "scopus_author_id"=>"6603304999"}, {"first_name"=>"Laurie K.", "last_name"=>"McNamara", "scopus_author_id"=>"22835689100"}, {"first_name"=>"D.", "last_name"=>"Martin Watterson", "scopus_author_id"=>"7006284890"}, {"first_name"=>"Jacques", "last_name"=>"Haiech", "scopus_author_id"=>"7006038601"}, {"first_name"=>"Marie Claude", "last_name"=>"Kilhoffer", "scopus_author_id"=>"6604039914"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-78649798970", "sgr"=>"78649798970", "pui"=>"360095074", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"21152427", "doi"=>"10.1371/journal.pone.0014120"}, "id"=>"569c2ad5-039b-3596-9085-270b7f7710ac", "abstract"=>"BACKGROUND: Death-Associated Protein Kinase (DAPK) is a member of the Ca2+/calmodulin regulated serine/threonine protein kinases. Its biological function has been associated with induced cell death, and in vivo use of selective small molecule inhibitors of DAPK catalytic activity has demonstrated that it is a potential therapeutic target for treatment of brain injuries and neurodegenerative diseases.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: In the in vitro study presented here, we describe the homodimerization of DAPK catalytic domain and the crucial role played by its basic loop structure that is part of the molecular fingerprint of death protein kinases. Nanoelectrospray ionization mass spectrometry of DAPK catalytic domain and a basic loop mutant DAPK protein performed under a variety of conditions was used to detect the monomer-dimer interchange. A chemical biological approach was used to find a fluorescent probe that allowed us to follow the oligomerization state of the protein in solution.\\n\\nCONCLUSIONS/SIGNIFICANCE: The use of this combined biophysical and chemical biology approach facilitated the elucidation of a monomer-dimer equilibrium in which the basic loop plays a key role, as well as an apparent allosteric conformational change reported by the fluorescent probe that is independent of the basic loop structure.", "link"=>"http://www.mendeley.com/research/homodimerization-deathassociated-protein-kinase-catalytic-domain-development-new-small-molecule-fluo-2", "reader_count"=>16, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>2, "Researcher"=>5, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>3, "Student > Bachelor"=>1, "Professor"=>3}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>2, "Researcher"=>5, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>3, "Student > Bachelor"=>1, "Professor"=>3}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>13, "Chemistry"=>1}, "reader_count_by_subdiscipline"=>{"Chemistry"=>{"Chemistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/815620"], "description"=>"<p>s<sub>20,w</sub>  =  sedimentation coefficient of major species observed corrected to 20°C; SD s<sub>20,w</sub>  =  standard deviation of s<sub>20,w</sub>; Calc. M  =  calculated molecular mass of species.</p>", "links"=>[], "tags"=>["centrifugation", "dapkwt", "ammonium", "acetate", "buffer", "ph", "concentrations"], "article_id"=>485968, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014120.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analytical_centrifugation_of_DAPKwt_in_ammonium_acetate_buffer_NH_4_Ac_pH_8_8_at_different_concentrations_pH_8_8_/485968", "title"=>"Analytical centrifugation of DAPKwt in ammonium acetate buffer (NH<sub>4</sub>Ac, pH 8.8) at different concentrations (pH 8.8).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-11-30 01:39:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/815125"], "description"=>"<p>Proteins were diluted to 5 µM in NH<sub>4</sub>Ac buffer at (A, E) 5 mM, (B, F) 50 mM, (C, G) 120 mM and (D, H) 250 mM. (○) and () are related to monomeric and dimeric DAPK, respectively.</p>", "links"=>[], "tags"=>["spectrometry", "dapkwt"], "article_id"=>485473, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014120.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Noncovalent_mass_spectrometry_analysis_of_A_8211_D_DAPKwt_and_E_8211_H_DAPKdel_/485473", "title"=>"Noncovalent mass spectrometry analysis of (A–D) DAPKwt and (E–H) DAPKdel.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-30 01:31:13"}
  • {"files"=>["https://ndownloader.figshare.com/files/815575"], "description"=>"<p>R<sub>He</sub> represents the hydrodynamic radius obtained from DLS data analysis. Hydrodynamic radii in the table can be compared to gyration (Rg) and Stockes (R<sub>Hc</sub>) radii calculated from the atomic coordinates using the HYDROPRO program as indicated under <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014120#s2\" target=\"_blank\">Materials and Methods</a>. Calculated gyration radii (R<sub>g</sub>) of the monomeric and dimeric forms of DAPKwt are 2.04 nm and 2.89 nm, respectively. Calculated Stockes radii (R<sub>Hc</sub>) for the monomer and dimer are 2.65 nm and 3.58 nm, respectively.</p>", "links"=>[], "tags"=>["scattering", "parameters", "dapkwt", "ammonium", "acetate", "ph", "hepes", "buffer", "mm", "150"], "article_id"=>485914, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014120.t002", "stats"=>{"downloads"=>3, "page_views"=>28, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamic_light_scattering_DLS_parameters_for_DAPKwt_in_ammonium_acetate_NH_4_Ac_pH_8_8_or_HEPES_Buffer_50_mM_HEPES_150_mM_KCl_1_mM_MgCl_2_pH_7_5_/485914", "title"=>"Dynamic light scattering (DLS) parameters for DAPKwt in ammonium acetate (NH<sub>4</sub>Ac, pH 8.8) or HEPES Buffer (50 mM HEPES, 150 mM KCl, 1 mM MgCl<sub>2</sub>, pH 7.5).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-11-30 01:38:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/406684", "https://ndownloader.figshare.com/files/406702"], "description"=>"<div><h3>Background</h3><p>Death-Associated Protein Kinase (DAPK) is a member of the Ca<sup>2+</sup>/calmodulin regulated serine/threonine protein kinases. Its biological function has been associated with induced cell death, and <em>in vivo</em> use of selective small molecule inhibitors of DAPK catalytic activity has demonstrated that it is a potential therapeutic target for treatment of brain injuries and neurodegenerative diseases.</p><h3>Methodology/Principal Findings</h3><p>In the <em>in vitro</em> study presented here, we describe the homodimerization of DAPK catalytic domain and the crucial role played by its basic loop structure that is part of the molecular fingerprint of death protein kinases. Nanoelectrospray ionization mass spectrometry of DAPK catalytic domain and a basic loop mutant DAPK protein performed under a variety of conditions was used to detect the monomer-dimer interchange. A chemical biological approach was used to find a fluorescent probe that allowed us to follow the oligomerization state of the protein in solution.</p><h3>Conclusions/Significance</h3><p>The use of this combined biophysical and chemical biology approach facilitated the elucidation of a monomer-dimer equilibrium in which the basic loop plays a key role, as well as an apparent allosteric conformational change reported by the fluorescent probe that is independent of the basic loop structure.</p></div>", "links"=>[], "tags"=>["homodimerization", "death-associated", "kinase", "catalytic", "fluorescent"], "article_id"=>140361, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0014120.s001", "https://dx.doi.org/10.1371/journal.pone.0014120.s002"], "stats"=>{"downloads"=>2, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Homodimerization_of_the_Death_Associated_Protein_Kinase_Catalytic_Domain_Development_of_a_New_Small_Molecule_Fluorescent_Reporter/140361", "title"=>"Homodimerization of the Death-Associated Protein Kinase Catalytic Domain: Development of a New Small Molecule Fluorescent Reporter", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-11-30 00:06:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/815310"], "description"=>"<p>mFP corresponds to the polarization degree of the fluorescent probe ×10<sup>3</sup>. Error bars indicating the standard deviation were calculated from four independent titrations. Error bars are only shown for the most outer curves for sake of figure clarity. A) ATP-titration at the following total concentrations of ATP: • 0 µM; from ▴ to ▴ 0.4, 0.8, 1.6, 3.2, 6.3, 12.5 µM and ▪ 25 µM. The graphs for ATP concentrations of 50 µM and 1000 µM are not shown, as they are congruent with the one at 25 µM. ADP titrations lead to similar results and are not shown. B) Substrate peptide titration. Analogous to the ATP-titration for peptide concentrations of: • 0 µM; 0.8 µM • 6.3 µM; ▪ 50 µM. Only a representative number of titration curves are shown to keep the graphs well distinguishable from each other. C) Fitted Kd values of the fluorescent probe as a function of the stoichiometric ratio of ATP/DAPK (–•–) and ADP/DAPK (- - ▪ - -), respectively.</p>", "links"=>[], "tags"=>["curves", "changes", "fluorescence", "polarization", "dapkwt", "hepes", "buffer", "ph", "mm", "150"], "article_id"=>485658, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014120.g003", "stats"=>{"downloads"=>3, "page_views"=>15, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Titration_curves_showing_changes_in_fluorescence_polarization_degree_as_a_function_of_the_concentration_of_DAPKwt_in_HEPES_Buffer_pH_7_5_50_mM_HEPES_150_mM_KCl_1_mM_MgCl_2_pH_7_5_/485658", "title"=>"Titration curves showing changes in fluorescence polarization degree as a function of the concentration of DAPKwt in HEPES Buffer pH 7.5 (50 mM HEPES, 150 mM KCl, 1 mM MgCl<sub>2</sub>, pH 7.5).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-30 01:34:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/815404"], "description"=>"<p>A) Binding of the fluorescently tagged ATP (Atto-495-ATP) to the catalytic domain of DAPKwt. mFP corresponds to the polarization degree of the fluorescent probe ×10<sup>3</sup>. One binding curve corresponds to a constant concentration of NH<sub>4</sub>Ac, pH 8.8: • 5 mM; from ▴ to ▴ 25, 50 and 100 mM, ▪ 250 mM. The binding curve of ATP shifts towards the left when the monomeric form is induced by higher NH<sub>4</sub>Ac concentrations. B) Noncovalent mass spectrometry analysis of DAPKwt at 5 µM in 50 mM NH<sub>4</sub>Ac buffer at pH 8.8 either alone (top) or in the presence of 25 µM ADP-Mg (middle) or 100 µM ADP-Mg (bottom). Inserts correspond to enlargements of 11+ and 15+ charge states of monomeric and dimeric DAPKwt, respectively. are related to 1∶0, 1∶1, 2∶0, 2∶1 and 2∶2 DAPKwt: ADP-Mg complexes respectively. * represent non-specific ADP-Mg adducts. C) Fitted Kd values of the fluorescent probe as a function of ATP/DAPKdel and ADP/DAPKdel ratios. D) DAPKwt is assayed under conditions favoring monomers ( 250 mM NH<sub>4</sub>Ac, pH 8.8) or dimers ( 5 mM NH<sub>4</sub>Ac, pH 8.8).</p>", "links"=>[], "tags"=>["binding", "catalytic"], "article_id"=>485757, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014120.g004", "stats"=>{"downloads"=>0, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ATP_ADP_binding_to_the_catalytic_domain_of_DAPK_/485757", "title"=>"ATP/ADP binding to the catalytic domain of DAPK.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-30 01:35:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/815220"], "description"=>"<p>A) Chemical structure of CHPO 187-3 H11-para, which was selected as best hit in the primary and secondary screening assays (absorption and fluorescent spectra of the probe are provided in Supporting Information, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0014120#pone.0014120.s001\" target=\"_blank\">Figure S1</a>). B) Binding of CHPO 187-3 H11-para (0.1 µM) to DAPKwt at different concentrations of NH<sub>4</sub>Ac (• 5 mM, ▪ 100 mM and ▴ 250 mM). Fluorescence polarization (mFP) is plotted <i>versus</i> protein concentration. mFP corresponds to the polarization degree of the fluorescent probe ×10<sup>3</sup>. Error bars indicate the standard deviation of four independent titrations. C) Same than in B) but with DAPKdel.</p>", "links"=>[], "tags"=>["fluorescent", "probe", "dimerization", "dapk", "catalytic"], "article_id"=>485565, "categories"=>["Biochemistry", "Biophysics"], "users"=>["Michael Zimmermann", "Cédric Atmanene", "Qingyan Xu", "Laetitia Fouillen", "Alain Van Dorsselaer", "Dominique Bonnet", "Claire Marsol", "Marcel Hibert", "Sarah Sanglier-Cianferani", "Claire Pigault", "Laurie K. McNamara", "D. Martin Watterson", "Jacques Haiech", "Marie-Claude Kilhoffer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0014120.g002", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ability_of_the_fluorescent_probe_to_monitor_dimerization_of_DAPK_catalytic_core_/485565", "title"=>"Ability of the fluorescent probe to monitor dimerization of DAPK catalytic core.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-11-30 01:32:45"}

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