Binding Leverage as a Molecular Basis for Allosteric Regulation
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{"title"=>"Binding leverage as a molecular basis for allosteric regulation", "type"=>"journal", "authors"=>[{"first_name"=>"Simon", "last_name"=>"Mitternacht", "scopus_author_id"=>"8843303700"}, {"first_name"=>"Igor N.", "last_name"=>"Berezovsky", "scopus_author_id"=>"7003302633"}], "year"=>2011, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"1553734X", "scopus"=>"2-s2.0-80053440006", "pui"=>"362681144", "doi"=>"10.1371/journal.pcbi.1002148", "isbn"=>"1553-734X", "sgr"=>"80053440006", "pmid"=>"21935347"}, "id"=>"2e052972-bc7c-38cc-b288-ef01d8eb5831", "abstract"=>"Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein. We use Monte Carlo simulations to generate potential binding sites and either normal modes or pairs of crystal structures to describe relevant motions. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. Furthermore, our analysis of the catabolite activator protein, which is allosteric without conformational change, shows that its regulation involves other types of motion than those modulated at sites with high binding leverage. Our results point to the importance of incorporating dynamic information when predicting functional sites. Because it is possible to calculate binding leverage from a single crystal structure it can be used for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design.", "link"=>"http://www.mendeley.com/research/binding-leverage-molecular-basis-allosteric-regulation", "reader_count"=>72, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Librarian"=>2, "Researcher"=>29, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>4}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Librarian"=>2, "Researcher"=>29, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>21, "Student > Postgraduate"=>2, "Student > Master"=>3, "Other"=>1, "Student > Bachelor"=>4, "Professor"=>4}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>10, "Materials Science"=>1, "Agricultural and Biological Sciences"=>38, "Medicine and Dentistry"=>4, "Pharmacology, Toxicology and Pharmaceutical Science"=>3, "Chemical Engineering"=>1, "Physics and Astronomy"=>1, "Chemistry"=>10, "Social Sciences"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Materials Science"=>{"Materials Science"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>4}, "Chemistry"=>{"Chemistry"=>10}, "Social Sciences"=>{"Social Sciences"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>38}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>10}, "Unspecified"=>{"Unspecified"=>2}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>3}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"United States"=>5, "Norway"=>4, "Japan"=>1, "United Kingdom"=>2, "South Africa"=>1, "Portugal"=>1, "Germany"=>1, "Russia"=>1}, "group_count"=>6}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/734265"], "description"=>"<p>The top left panel shows an enzyme that is allosterically inhibited by ligand binding: the inhibition takes place by stabilization of an inactive conformation. The top right panel shows a putative free energy landscape for this process. The transition from the active to inhibited state can follow one of two main paths, either induced fit (green) or conformational selection (red). The bottom panels show allosteric activation for the same protein. With the geometry of the illustration there will be a large barrier for induced fit, as indicated in the bottom right free energy landscape.</p>", "links"=>[], "tags"=>["Computational biology", "physics"], "article_id"=>404624, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g001", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_A_basic_model_for_allostery_/404624", "title"=>"A basic model for allostery.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:17:04"}
  • {"files"=>["https://ndownloader.figshare.com/files/734498"], "description"=>"<p>(A) Cartoon of protein structure. Protein coordinates are taken from PDB entry 1j3h and ligand coordinates from 1atp. (B) Residues colored by <i>f<sub>i</sub></i>(0.04), with cyan representing <i>f<sub>i</sub></i> = 0 and magenta the highest recorded <i>f<sub>i</sub></i>. (C) ROC curves obtained with the four measures in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002148#pcbi-1002148-t001\" target=\"_blank\">Table 1</a>.</p>", "links"=>[], "tags"=>["kinase"], "article_id"=>404859, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g005", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_protein_kinase_A_PKA_using_L_LF10_/404859", "title"=>"Analysis of protein kinase A (PKA) using <i>L</i><sub>LF10</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:20:59"}
  • {"files"=>["https://ndownloader.figshare.com/files/734958"], "description"=>"<p>Analysis of monomers. For each protein 1 000 simulations of 100 000 MC steps each were performed.</p>", "links"=>[], "tags"=>["000", "simulations", "100", "mc", "steps"], "article_id"=>405319, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.t002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_monomers_For_each_protein_1_000_simulations_of_100_000_MC_steps_each_were_performed_/405319", "title"=>"Analysis of monomers. For each protein 1 000 simulations of 100 000 MC steps each were performed.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-15 01:28:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/734585"], "description"=>"<p>(A) Cartoon of structure with the coenzyme PLP drawn with white spheres and the SAM molecules with grey spheres. Protein coordinates are taken from PDB entry 1e5x and ligand coordinates from 2c2b. (B) Rotated view showing the SAM binding site, colored according to <i>f<sub>i</sub></i>(0.42). (C) Same view as (A) showing <i>f<sub>i</sub></i>(0.42) for active site cleft. (D) ROC curves.</p>", "links"=>[], "tags"=>["threonine", "synthase"], "article_id"=>404948, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_threonine_synthase_ThrS_using_L_LF10_/404948", "title"=>"Analysis of threonine synthase (ThrS) using <i>L</i><sub>LF10</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:22:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/734674"], "description"=>"<p>(A) The hexameric structure of BDGH with ligand atoms drawn as spheres. Red ligands are NADP, blue GTP and green ADP. The individual chains are colored yellow, orange and white within each trimer. 1nr7 was used for protein coordinates, and NADP, GTP and ADP were taken from PDB entries 1hwz and 1nqt. The antenna helices of three of the chains are indicated with arrows. (B) Slightly rotated view showing the active and both allosteric sites, colored according to <i>f</i><sub>i</sub>(0.25). (C) When more probe locations are included in the analysis, latent sites emerge, as exemplified here by <i>f</i><sub>i</sub>(0.41). (D) ROC curves.</p>", "links"=>[], "tags"=>["bovine", "glutamate", "dehydrogenase"], "article_id"=>405041, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g007", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_bovine_glutamate_dehydrogenase_BGDH_using_L_LF10_/405041", "title"=>"Analysis of bovine glutamate dehydrogenase (BGDH) using <i>L</i><sub>LF10</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:24:01"}
  • {"files"=>["https://ndownloader.figshare.com/files/734363"], "description"=>"<p>(A) Illustration of binding leverage for one normal mode. The outline represents the protein surface and the grey dumbbells ligands. The curved arrow shows the general direction of motion in one normal mode and the small arrows the direction of motion for specific Ca atoms in the same mode. Dashed lines indicate pairs of atoms whose interconnecting line crosses the ligand. (B) Illustration of the residue count <i>f<sub>i</sub></i>(<i>x</i>) for three probe locations.</p>", "links"=>[], "tags"=>["Computational biology", "physics"], "article_id"=>404723, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Binding_leverage_/404723", "title"=>"Binding leverage.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:18:43"}
  • {"files"=>["https://ndownloader.figshare.com/files/734423"], "description"=>"<p>Histograms of AUC values based on catalytic site predictions using LC and <i>L</i><sub>LF10</sub> for 226 enzymes.</p>", "links"=>[], "tags"=>["catalytic"], "article_id"=>404785, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g003", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prediction_of_catalytic_sites_/404785", "title"=>"Prediction of catalytic sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:19:45"}
  • {"files"=>["https://ndownloader.figshare.com/files/370839", "https://ndownloader.figshare.com/files/370861", "https://ndownloader.figshare.com/files/370881", "https://ndownloader.figshare.com/files/370926"], "description"=>"<div><p>Allosteric regulation involves conformational transitions or fluctuations between a few closely related states, caused by the binding of effector molecules. We introduce a quantity called binding leverage that measures the ability of a binding site to couple to the intrinsic motions of a protein. We use Monte Carlo simulations to generate potential binding sites and either normal modes or pairs of crystal structures to describe relevant motions. We analyze single catalytic domains and multimeric allosteric enzymes with complex regulation. For the majority of the analyzed proteins, we find that both catalytic and allosteric sites have high binding leverage. Furthermore, our analysis of the catabolite activator protein, which is allosteric without conformational change, shows that its regulation involves other types of motion than those modulated at sites with high binding leverage. Our results point to the importance of incorporating dynamic information when predicting functional sites. Because it is possible to calculate binding leverage from a single crystal structure it can be used for characterizing proteins of unknown function and predicting latent allosteric sites in any protein, with implications for drug design.</p> </div>", "links"=>[], "tags"=>["binding", "leverage", "molecular", "allosteric"], "article_id"=>133264, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002148.s001", "https://dx.doi.org/10.1371/journal.pcbi.1002148.s002", "https://dx.doi.org/10.1371/journal.pcbi.1002148.s003", "https://dx.doi.org/10.1371/journal.pcbi.1002148.s004"], "stats"=>{"downloads"=>8, "page_views"=>18, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Binding_Leverage_as_a_Molecular_Basis_for_Allosteric_Regulation/133264", "title"=>"Binding Leverage as a Molecular Basis for Allosteric Regulation", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-09-15 00:54:24"}
  • {"files"=>["https://ndownloader.figshare.com/files/734986"], "description"=>"<p>AUC averages were calculated without the outlier ATCase. Ligand names are taken from the PDB files. Italicized PDB codes indicate the pair of structures used to calculate RMSD and difference vector. The column labeled “# sim” indicates the total number of simulations performed. “Probed sites” indicates how many of the binding sites our probe managed to reproduce. The AUC values are averages over two independent runs with different random number seeds. The differences between the total averages (bottom row) of the two runs were in the range 0.005–0.015.</p>", "links"=>[], "tags"=>["parameters"], "article_id"=>405346, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.t001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Simulation_parameters_and_results_/405346", "title"=>"Simulation parameters and results.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-15 01:29:06"}
  • {"files"=>["https://ndownloader.figshare.com/files/734795"], "description"=>"<p>(A) Two views of the tetrameric structure. Blue spheres represent the activator ADP and red spheres the substrate F6P. Protein coordinates were taken from PDB entry 3pfk, coordinates for F6P from 4pfk, and for PGA from 6pfk. (B) Same views as in (A) but now showing the surface colored by <i>f<sub>i</sub></i>(0.22). (C) Latent sites can be seen in a slightly rotated version of the left half of (B). (D) ROC curves.</p>", "links"=>[], "tags"=>["phosphofructokinase"], "article_id"=>405157, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g008", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_phosphofructokinase_PFK_using_L_LF10_/405157", "title"=>"Analysis of phosphofructokinase (PFK) using <i>L</i><sub>LF10</sub>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:25:57"}
  • {"files"=>["https://ndownloader.figshare.com/files/734459"], "description"=>"<p>Comparison between AUC values obtained for analyses of oligomeric enzymes and single chains (monomers) taken from the oligomeric structure. ATCase, which has very poor prediction results in the oligomeric analysis, behaves well in the single chain analysis (see also <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002148#pcbi-1002148-t002\" target=\"_blank\">Table 2</a>).</p>", "links"=>[], "tags"=>["Computational biology", "physics"], "article_id"=>404819, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g004", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Analysis_of_single_chains_/404819", "title"=>"Analysis of single chains.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:20:19"}
  • {"files"=>["https://ndownloader.figshare.com/files/734902"], "description"=>"<p>(A) Binding analysis of CAP based on PDB entry 1g6n. The coloring is based on <i>f<sub>i</sub></i>(0.1). To help the eye the most important sites have been marked with circles. The dimer is symmetric; the sites hidden in this view have similar properties to the ones shown. The location of the cAMP ligand in the crystal structure is marked by black spheres. (B) Putative free energy landscape at an intermediate cAMP concentration. The <i>x</i>-axis indicates the number of cAMP molecules bound, and the <i>y</i>-axis conformational degrees of freedom. We indicate that the conformational entropy is highest when one cAMP is bound by the wider minimum.</p>", "links"=>[], "tags"=>["activator"], "article_id"=>405266, "categories"=>["Physics", "Biological Sciences"], "users"=>["Simon Mitternacht", "Igor N. Berezovsky"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1002148.g009", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Catabolite_activator_protein_CAP_/405266", "title"=>"Catabolite activator protein (CAP).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-15 01:27:46"}

PMC Usage Stats | Further Information

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Relative Metric

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