Conservation, Variability and the Modeling of Active Protein Kinases
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{"title"=>"Conservation, variability and the modeling of active protein kinases", "type"=>"journal", "authors"=>[{"first_name"=>"James D R", "last_name"=>"Knight", "scopus_author_id"=>"7401751432"}, {"first_name"=>"Bin", "last_name"=>"Qian", "scopus_author_id"=>"7102420676"}, {"first_name"=>"David", "last_name"=>"Baker", "scopus_author_id"=>"55463548900"}, {"first_name"=>"Rashmi", "last_name"=>"Kothary", "scopus_author_id"=>"7004475559"}], "year"=>2007, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"42049095895", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0000982", "pmid"=>"17912359", "pui"=>"351516170", "scopus"=>"2-s2.0-42049095895", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)"}, "id"=>"4aedbe70-12be-3cff-9bb8-b49288bdde15", "abstract"=>"The human proteome is rich with protein kinases, and this richness has made the kinase of crucial importance in initiating and maintaining cell behavior. Elucidating cell signaling networks and manipulating their components to understand and alter behavior require well designed inhibitors. These inhibitors are needed in culture to cause and study network perturbations, and the same compounds can be used as drugs to treat disease. Understanding the structural biology of protein kinases in detail, including their commonalities, differences and modes of substrate interaction, is necessary for designing high quality inhibitors that will be of true use for cell biology and disease therapy. To this end, we here report on a structural analysis of all available active-conformation protein kinases, discussing residue conservation, the novel features of such conservation, unique properties of atypical kinases and variability in the context of substrate binding. We also demonstrate how this information can be used for structure prediction. Our findings will be of use not only in understanding protein kinase function and evolution, but they highlight the flaws inherent in kinase drug design as commonly practiced and dictate an appropriate strategy for the sophisticated design of specific inhibitors for use in the laboratory and disease therapy.", "link"=>"http://www.mendeley.com/research/conservation-variability-modeling-active-protein-kinases-8", "reader_count"=>56, "reader_count_by_academic_status"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>1, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>3, "Professor > Associate Professor"=>2, "Researcher"=>16, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>19, "Student > Postgraduate"=>1, "Student > Master"=>6, "Other"=>2, "Student > Bachelor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>5, "Mathematics"=>1, "Agricultural and Biological Sciences"=>28, "Medicine and Dentistry"=>2, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Business, Management and Accounting"=>1, "Chemistry"=>10, "Computer Science"=>4}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>2}, "Chemistry"=>{"Chemistry"=>10}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>28}, "Computer Science"=>{"Computer Science"=>4}, "Business, Management and Accounting"=>{"Business, Management and Accounting"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>5}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>3}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "United States"=>1, "United Kingdom"=>2, "France"=>1, "Germany"=>1, "Estonia"=>1, "India"=>1}, "group_count"=>1}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/943606"], "description"=>"<p>The fifteen active-conformation kinase structures listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#pone-0000982-t001\" target=\"_blank\">Table 1</a> were aligned using our modified Procrustes approach. Shown in green sticks is the ATP or ATP analog molecule of each structure. Each kinase is colored uniquely.</p>", "links"=>[], "tags"=>["kinase"], "article_id"=>614012, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g002", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Multiple_kinase_alignment_/614012", "title"=>"Multiple kinase alignment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:06:52"}
  • {"files"=>["https://ndownloader.figshare.com/files/943685"], "description"=>"<p>Each sphere represents a conserved residue. Red indicates full conservation of a particular amino acid in all fifteen kinase structures; orange, conservation in thirteen or fourteen structures; and yellow, conservation in eleven or twelve structures. Blue spheres indicate full conservation of an amino-acid category. The ATP molecule of protein kinase A is shown in green sticks. (A) The consensus structure consisting of the forty-four points listed in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#pone-0000982-t002\" target=\"_blank\">Table 2</a>. (B) The consensus structure overlaid on the multiple alignment.</p>", "links"=>[], "tags"=>["kinase"], "article_id"=>614084, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g003", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_kinase_consensus_structure_/614084", "title"=>"A kinase consensus structure.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:08:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/943787"], "description"=>"<p>The atypical kinases (A) Rio2 and (B) transient receptor potential channel kinase (ChaK).</p>", "links"=>[], "tags"=>["atypical", "kinases", "rio2", "transient", "receptor", "kinase"], "article_id"=>614184, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_atypical_kinases_A_Rio2_and_B_transient_receptor_potential_channel_kinase_ChaK_/614184", "title"=>"The atypical kinases (A) Rio2 and (B) transient receptor potential channel kinase (ChaK).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:09:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/944308"], "description"=>"*<p>ChaK was aligned directly onto the consensus generated from the other fifteen samples. See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#s2\" target=\"_blank\">Results</a> section.</p><p>The amino acid or amino-acid category of the conserved residue is listed under “type”. For each structure the residue identifier corresponding to the conserved point is indicated (listed as x if the point is absent). For category types the amino acid present in each structure is indicated before the identifier. If a sample is missing a conserved amino acid but has a similar residue in the same location then the shared category is listed after the identifier. a, acidic; l, aliphatic; r, aromatic; b, basic; c, charged; h, hydrophobic; p, polar; s, small; v, very small.</p>", "links"=>[], "tags"=>["residues", "active-conformation", "kinases", "listed"], "article_id"=>614697, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.t002", "stats"=>{"downloads"=>1, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Conserved_residues_found_in_the_active_conformation_kinases_listed_in_Table_1_/614697", "title"=>"Conserved residues found in the active-conformation kinases listed in Table 1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-10-03 01:18:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/944240"], "description"=>"<p>(A) The best model is in blue and the actual structure in red (PDB code: 1ZAO). Structures are shown aligned based on C<sub>α</sub> RMSD. Residues 128–142 from the model are hidden because they are disordered in the actual structure. (B) Residues 214–237 are highlighted as aligned on side-chains. ATP is shown in green sticks.</p>", "links"=>[], "tags"=>["atypical"], "article_id"=>614634, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g009", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modeling_an_atypical_kinase_Rio2_/614634", "title"=>"Modeling an atypical kinase, Rio2.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:17:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/944063"], "description"=>"<p>Cross-eyed stereo views of (A) protein kinase A and (B) Akt2. Bound substrate peptides are shown in red sticks. Atoms belonging to non-conserved residues within 10 Å of the substrate peptide are shown as colored spheres. Red: atoms within 2 Å of a conserved residue; orange: atoms between 2 and 4 Å of a conserved residue; yellow: atoms between 4 and 6 Å of a conserved residue; green: atoms between 6 and 8 Å of a conserved residue; cyan: atoms between 8 and 10 Å of a conserved residue; and blue: atoms more than 10 Å from a conserved residue.</p>", "links"=>[], "tags"=>["biochemistry/bioinformatics", "cell biology/cell signaling", "computational biology/macromolecular structure analysis", "computational biology/protein structure prediction", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>614445, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g007", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Substrate_specific_variability_/614445", "title"=>"Substrate-specific variability.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:14:05"}
  • {"files"=>["https://ndownloader.figshare.com/files/944161"], "description"=>"<p>PDK1 was modeled using the consensus guided approach outlined in the Results and Methods sections. (A) The best model is in blue and the actual structure in red (PDB code: 1H1W). Structures are shown aligned based on C<sub>α</sub> RMSD. (B) Residues 201–225, comprising the floor of the active site, are highlighted as aligned on side chains. (C) Residues from the non-conserved regions of the substrate binding groove (residues 166–175 and 278–305) are shown as aligned on side chains. ATP from the true structure of PDK1 is shown in green sticks.</p>", "links"=>[], "tags"=>["biochemistry/bioinformatics", "cell biology/cell signaling", "computational biology/macromolecular structure analysis", "computational biology/protein structure prediction", "molecular biology/bioinformatics", "molecular biology/molecular evolution"], "article_id"=>614543, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g008", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Modeling_a_typical_kinase_/614543", "title"=>"Modeling a typical kinase.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:15:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/944286"], "description"=>"*<p>The average pair-wise sequence identity between this set as computed by ClustalW using its default parameters is 17%.</p>†<p>Residues 304-541 constitute a large spacer within the kinase domain <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#pone.0000982-Nolen2\" target=\"_blank\">[59]</a>.</p>‡<p>ChaK lacks a divalent cation in its active site and was not used to generate an initial alignment (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#s2\" target=\"_blank\">Results</a> section).</p>", "links"=>[], "tags"=>["kinase"], "article_id"=>614674, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.t001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Active_conformation_kinase_structures_/614674", "title"=>"Active-conformation kinase structures.<sup>*</sup>", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-10-03 01:17:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/943962"], "description"=>"<p>(A) In almost all protein kinases (such as protein kinase A shown) a lysine residue originating from β-strand 3 interacts with the α- and β-phosphates of ATP. This lysine is required for catalytic activity and has been termed the catalytic lysine. (B) In channel kinase (ChaK), the homologous lysine interacts with the α-phosphate and the adenine ring of ATP. An unique arginine residue located on β-strand 2 instead interacts with the α- and β-phosphates. (C) In protein kinase with no lysine 1 (WNK1, PDB code: 1T4H <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#pone.0000982-Min1\" target=\"_blank\">[22]</a>), the catalytic lysine is present but originates from β-strand 2, much like the arginine from ChaK. ATP is shown in green sticks. Potential hydrogen bonds between the positively charged residues and ATP are shown as dashed lines, and nitrogen atoms are colored blue. The WNK structure has no ATP or ATP analog.</p>", "links"=>[], "tags"=>["catalytic"], "article_id"=>614355, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g006", "stats"=>{"downloads"=>1, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variations_in_the_catalytic_lysine_/614355", "title"=>"Variations in the catalytic lysine.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:12:35"}
  • {"files"=>["https://ndownloader.figshare.com/files/943548"], "description"=>"<p>PKA is shown in its active conformation with ATP in green sticks and Mn<sup>2+</sup> as black spheres. β-strands, helices and loops are labeled as in Knighton <i>et al</i>. <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000982#pone.0000982-Knighton1\" target=\"_blank\">[45]</a>. The active site is situated between the small and large lobes, located above and below ATP respectively. CL: catalytic loop; MPL: magnesium-positioning loop.</p>", "links"=>[], "tags"=>["kinase"], "article_id"=>613946, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g001", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_structure_of_protein_kinase_A_PKA_/613946", "title"=>"The structure of protein kinase A (PKA).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:05:46"}
  • {"files"=>["https://ndownloader.figshare.com/files/464612"], "description"=>"<div><p>The human proteome is rich with protein kinases, and this richness has made the kinase of crucial importance in initiating and maintaining cell behavior. Elucidating cell signaling networks and manipulating their components to understand and alter behavior require well designed inhibitors. These inhibitors are needed in culture to cause and study network perturbations, and the same compounds can be used as drugs to treat disease. Understanding the structural biology of protein kinases in detail, including their commonalities, differences and modes of substrate interaction, is necessary for designing high quality inhibitors that will be of true use for cell biology and disease therapy. To this end, we here report on a structural analysis of all available active-conformation protein kinases, discussing residue conservation, the novel features of such conservation, unique properties of atypical kinases and variability in the context of substrate binding. We also demonstrate how this information can be used for structure prediction. Our findings will be of use not only in understanding protein kinase function and evolution, but they highlight the flaws inherent in kinase drug design as commonly practiced and dictate an appropriate strategy for the sophisticated design of specific inhibitors for use in the laboratory and disease therapy.</p></div>", "links"=>[], "tags"=>["variability", "modeling", "kinases"], "article_id"=>151580, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982", "stats"=>{"downloads"=>3, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Conservation_Variability_and_the_Modeling_of_Active_Protein_Kinases/151580", "title"=>"Conservation, Variability and the Modeling of Active Protein Kinases", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2007-10-03 00:26:20"}
  • {"files"=>["https://ndownloader.figshare.com/files/943875"], "description"=>"<p>In each kinase the catalytic aspartic acid is shown in red and the positively-charged residue that interacts with the γ-phosphate of ATP is shown in yellow with nitrogen atoms colored blue. ATP is shown in green sticks. (A) Protein kinase A, (B) activated CDC42 kinase 1, (C) channel kinase, and (D) Rio2 kinase.</p>", "links"=>[], "tags"=>["variability", "positioning"], "article_id"=>614271, "categories"=>["Medicine", "Cell Biology", "Molecular Biology", "Biochemistry"], "users"=>["James D. R. Knight", "Bin Qian", "David Baker", "Rashmi Kothary"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0000982.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Residue_variability_in_positioning_the_947_phosphate_of_ATP_/614271", "title"=>"Residue variability in positioning the γ-phosphate of ATP.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2007-10-03 01:11:11"}

PMC Usage Stats | Further Information

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Relative Metric

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