Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates
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{"title"=>"Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates", "type"=>"journal", "authors"=>[{"first_name"=>"Michael F.", "last_name"=>"Chou", "scopus_author_id"=>"7201844108"}, {"first_name"=>"Sladjana", "last_name"=>"Prisic", "scopus_author_id"=>"8282602200"}, {"first_name"=>"Joshua M.", "last_name"=>"Lubner", "scopus_author_id"=>"55536439100"}, {"first_name"=>"George M.", "last_name"=>"Church", "scopus_author_id"=>"7005451318"}, {"first_name"=>"Robert N.", "last_name"=>"Husson", "scopus_author_id"=>"7005681135"}, {"first_name"=>"Daniel", "last_name"=>"Schwartz", "scopus_author_id"=>"55741211700"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"23300758", "doi"=>"10.1371/journal.pone.0052747", "pui"=>"366343858", "issn"=>"19326203", "sgr"=>"84871590810", "scopus"=>"2-s2.0-84871590810"}, "id"=>"e998c3b8-759e-3054-b197-16ae5db5d503", "abstract"=>"The identification of protein kinase targets remains a significant bottleneck for our understanding of signal transduction in normal and diseased cellular states. Kinases recognize their substrates in part through sequence motifs on substrate proteins, which, to date, have most effectively been elucidated using combinatorial peptide library approaches. Here, we present and demonstrate the ProPeL method for easy and accurate discovery of kinase specificity motifs through the use of native bacterial proteomes that serve as in vivo libraries for thousands of simultaneous phosphorylation reactions. Using recombinant kinases expressed in E. coli followed by mass spectrometry, the approach accurately recapitulated the well-established motif preferences of human basophilic (Protein Kinase A) and acidophilic (Casein Kinase II) kinases. These motifs, derived for PKA and CK II using only bacterial sequence data, were then further validated by utilizing them in conjunction with the scan-x software program to computationally predict known human phosphorylation sites with high confidence.", "link"=>"http://www.mendeley.com/research/using-bacteria-determine-protein-kinase-specificity-predict-target-substrates", "reader_count"=>31, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Librarian"=>2, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>5, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Librarian"=>2, "Researcher"=>11, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Master"=>5, "Student > Bachelor"=>1, "Lecturer > Senior Lecturer"=>1, "Professor"=>2}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>5, "Agricultural and Biological Sciences"=>22, "Neuroscience"=>1, "Chemistry"=>1, "Social Sciences"=>2}, "reader_count_by_subdiscipline"=>{"Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>1}, "Social Sciences"=>{"Social Sciences"=>2}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>22}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}}, "reader_count_by_country"=>{"United States"=>5, "Denmark"=>1, "India"=>1}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/519214"], "description"=>"<p>These motif extraction results illustrate the inter-residue correlations found among the phosphorylated peptides identified using the ProPeL methodology, and are highly consistent with the previously established consensus sequences for the PKA and CK II kinases.</p>", "links"=>[], "tags"=>["analyses", "pka", "ck", "ii"], "article_id"=>189709, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.g002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_motif_x_analyses_for_PKA_A_and_B_and_CK_II_C_and_D_/189709", "title"=>"<i>motif-x</i> analyses for PKA (A and B) and CK II (C and D).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-26 02:41:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/519601"], "description"=>"*<p>Out of 1,168,144 total serine and threonine residues.</p>**<p>From the PhosphoSitePlus database.</p>***<p>Tryptic peptide containing the predicted phosphorylation site greater than 35 residues in length.</p>****<p>Phosphorylated at homologous site in rat and cow.</p>", "links"=>[], "tags"=>["20", "ck", "ii", "phosphorylation", "predictions", "proteome", "motif", "propel"], "article_id"=>190087, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.t003", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_20_scan_x_CK_II_phosphorylation_predictions_based_on_a_human_whole_proteome_scan_with_the_CK_II_motif_obtained_using_the_ProPeL_methodology_/190087", "title"=>"Top 20 <i>scan-x</i> CK II phosphorylation predictions based on a human whole proteome scan with the CK II motif obtained using the ProPeL methodology.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-26 00:01:27"}
  • {"files"=>["https://ndownloader.figshare.com/files/519631"], "description"=>"*<p>Out of 1,168,144 total serine and threonine residues.</p>**<p>From the PhosphoSitePlus database.</p>***<p>Tryptic peptide containing the predicted phosphorylation site less than length 10 or greater than length 35.</p>", "links"=>[], "tags"=>["20", "pka", "phosphorylation", "predictions", "proteome", "motif", "propel"], "article_id"=>190118, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.t002", "stats"=>{"downloads"=>9, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Top_20_scan_x_PKA_phosphorylation_predictions_based_on_a_human_whole_proteome_scan_with_the_PKA_motif_obtained_using_the_ProPeL_methodology_/190118", "title"=>"Top 20 <i>scan-x</i> PKA phosphorylation predictions based on a human whole proteome scan with the PKA motif obtained using the ProPeL methodology.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-26 00:01:58"}
  • {"files"=>["https://ndownloader.figshare.com/files/280807"], "description"=>"<div><p>The identification of protein kinase targets remains a significant bottleneck for our understanding of signal transduction in normal and diseased cellular states. Kinases recognize their substrates in part through sequence motifs on substrate proteins, which, to date, have most effectively been elucidated using combinatorial peptide library approaches. Here, we present and demonstrate the ProPeL method for easy and accurate discovery of kinase specificity motifs through the use of native bacterial proteomes that serve as <em>in vivo</em> libraries for thousands of simultaneous phosphorylation reactions. Using recombinant kinases expressed in <em>E. coli</em> followed by mass spectrometry, the approach accurately recapitulated the well-established motif preferences of human basophilic (Protein Kinase A) and acidophilic (Casein Kinase II) kinases. These motifs, derived for PKA and CK II using only bacterial sequence data, were then further validated by utilizing them in conjunction with the <em>scan-x</em> software program to computationally predict known human phosphorylation sites with high confidence.</p> </div>", "links"=>[], "tags"=>["kinase", "specificity", "substrates"], "article_id"=>115380, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Using_Bacteria_to_Determine_Protein_Kinase_Specificity_and_Predict_Target_Substrates__/115380", "title"=>"Using Bacteria to Determine Protein Kinase Specificity and Predict Target Substrates", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-26 01:29:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/519076"], "description"=>"<p>pLogos for Protein Kinase A (A, B), Casein Kinase II (C, D), and control (E, F) illustrate preferred residues by position. Note, pLogos are derived from phosphorylation sites in <i>E. coli</i> obtained using the ProPeL methodology (after subtraction of endogenous phosphorylation sites). In each pLogo, residue heights are proportional to their log binomial probabilities in the context of the <i>E. coli</i> background with residues above the x-axis indicating overrepresentation and residues below the x-axis indicating underrepresentation. The central residue in each pLogo is fixed and denotes the modification site. The pLogos and corresponding extracted motifs (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052747#pone-0052747-g002\" target=\"_blank\">Figure 2</a>) are highly consistent with the known basophilic specificity of PKA and acidophilic specificity of CK II. Additionally, the control phosphorylation sites (i.e., endogenous <i>E. coli</i> phosphorylation sites) do not conform to a motif and lack any statistically significant residues.</p>", "links"=>[], "tags"=>["representations", "substrate"], "article_id"=>189570, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.g001", "stats"=>{"downloads"=>3, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_pLogo_representations_of_substrate_sequence_specificities_/189570", "title"=>"pLogo representations of substrate sequence specificities.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-26 02:39:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/519317"], "description"=>"<p>Average pLogo position weight matrix scores of CK II (red) and PKA (blue) pLogos when scanned against known human substrates from the PhosphoSitePlus database compared to average scores obtained from scanning CK II and PKA pLogos against an equivalent number of random human serine and threonine residues. Error bars represent 95% confidence intervals.</p>", "links"=>[], "tags"=>["plogos", "derived", "propel", "kinase", "substrates"], "article_id"=>189803, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.g003", "stats"=>{"downloads"=>5, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Goodness_of_fit_of_the_pLogos_derived_from_ProPeL_and_actual_known_kinase_substrates_versus_random_substrates_/189803", "title"=>"Goodness-of-fit of the pLogos derived from ProPeL and actual known kinase substrates versus random substrates.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-26 02:43:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/519468"], "description"=>"<p>These curves illustrate the tradeoff between sensitivity and specificity achieved by the ProPeL based <i>scan-x</i> (red) and combinatorial peptide library based Scansite (blue) predictors, and indicate the similarity of results achieved using these experimentally orthogonal approaches. Panels (A) and (B) are based on PKA serine and threonine predictions, respectively, while panels (C) and (D) are based on CK II serine and threonine predictions, respectively. The Scansite web server does not score all phosphorylatable residues in a given sequence, which results in partial ROC curves.</p>", "links"=>[], "tags"=>["curves", "scansite", "pka", "ck", "ii", "kinase"], "article_id"=>189957, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.g004", "stats"=>{"downloads"=>2, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Receiver_Operating_Characteristic_ROC_curves_for_the_scan_x_and_Scansite_PKA_and_CK_II_kinase_specific_predictors_/189957", "title"=>"Receiver Operating Characteristic (ROC) curves for the <i>scan-x</i> and Scansite PKA and CK II kinase specific predictors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-12-26 02:45:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/519559"], "description"=>"*<p>Phosphorylatable residues (Ser and Thr) and Cys are not included in combinatorial peptide libraries used for kinase specificity determination.</p>**<p>In proteome-derived libraries motif width limits depend on whether the kinase reaction is performed before or after proteolytic peptide digestion.</p>", "links"=>[], "tags"=>["combinatorial", "peptide", "proteome-derived", "propel", "motif"], "article_id"=>190049, "categories"=>["Microbiology", "Biochemistry", "Information And Computing Sciences", "Cancer", "Biological Sciences", "Genetics"], "users"=>["Michael F. Chou", "Sladjana Prisic", "Joshua M. Lubner", "George M. Church", "Robert N. Husson", "Daniel Schwartz"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0052747.t001", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_combinatorial_peptide_library_screening_proteome_derived_library_and_ProPeL_motif_discovery_methodologies_/190049", "title"=>"Comparison of combinatorial peptide library screening, proteome-derived library, and ProPeL motif discovery methodologies.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-12-26 00:00:49"}

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Relative Metric

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