Prediction of Protein Binding Regions in Disordered Proteins
Publication Date
May 01, 2009
Journal
PLOS Computational Biology
Authors
Bálint Mészáros, István Simon & Zsuzsanna Dosztányi
Volume
5
Issue
5
Pages
e1000376
DOI
http://doi.org/10.1371/journal.pcbi.1000376
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1000376
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/19412530
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2671142
Europe PMC
http://europepmc.org/abstract/MED/19412530
Web of Science
000267081300021
Scopus
67049119327
Mendeley
http://www.mendeley.com/research/prediction-protein-binding-regions-disordered-proteins-7
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CiteULike | Further Information

Mendeley | Further Information

{"title"=>"Prediction of protein binding regions in disordered proteins", "type"=>"journal", "authors"=>[{"first_name"=>"Bálint", "last_name"=>"Mészáros", "scopus_author_id"=>"18836694000"}, {"first_name"=>"István", "last_name"=>"Simon", "scopus_author_id"=>"7102610581"}, {"first_name"=>"Zsuzsanna", "last_name"=>"Dosztányi", "scopus_author_id"=>"6602651849"}], "year"=>2009, "source"=>"PLoS Computational Biology", "identifiers"=>{"issn"=>"1553734X", "sgr"=>"67049119327", "arxiv"=>"1203.2655", "doi"=>"10.1371/journal.pcbi.1000376", "scopus"=>"2-s2.0-67049119327", "pui"=>"354725653", "isbn"=>"0011-3891", "pmid"=>"19412530"}, "id"=>"70e42d61-c2c9-39a0-bc0d-fc09c57bbf77", "abstract"=>"Many disordered proteins function via binding to a structured partner and undergo a disorder-to-order transition. The coupled folding and binding can confer several functional advantages such as the precise control of binding specificity without increased affinity. Additionally, the inherent flexibility allows the binding site to adopt various conformations and to bind to multiple partners. These features explain the prevalence of such binding elements in signaling and regulatory processes. In this work, we report ANCHOR, a method for the prediction of disordered binding regions. ANCHOR relies on the pairwise energy estimation approach that is the basis of IUPred, a previous general disorder prediction method. In order to predict disordered binding regions, we seek to identify segments that are in disordered regions, cannot form enough favorable intrachain interactions to fold on their own, and are likely to gain stabilizing energy by interacting with a globular protein partner. The performance of ANCHOR was found to be largely independent from the amino acid composition and adopted secondary structure. Longer binding sites generally were predicted to be segmented, in agreement with available experimentally characterized examples. Scanning several hundred proteomes showed that the occurrence of disordered binding sites increased with the complexity of the organisms even compared to disordered regions in general. Furthermore, the length distribution of binding sites was different from disordered protein regions in general and was dominated by shorter segments. These results underline the importance of disordered proteins and protein segments in establishing new binding regions. Due to their specific biophysical properties, disordered binding sites generally carry a robust sequence signal, and this signal is efficiently captured by our method. Through its generality, ANCHOR opens new ways to study the essential functional sites of disordered proteins.", "link"=>"http://www.mendeley.com/research/prediction-protein-binding-regions-disordered-proteins-7", "reader_count"=>119, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>26, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>48, "Student > Postgraduate"=>8, "Student > Master"=>21, "Student > Bachelor"=>6, "Professor"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Researcher"=>26, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>48, "Student > Postgraduate"=>8, "Student > Master"=>21, "Student > Bachelor"=>6, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Unspecified"=>1, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>13, "Agricultural and Biological Sciences"=>86, "Neuroscience"=>1, "Chemistry"=>5, "Computer Science"=>7, "Earth and Planetary Sciences"=>1, "Psychology"=>3}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>5}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Psychology"=>{"Psychology"=>3}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>86}, "Computer Science"=>{"Computer Science"=>7}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>13}, "Unspecified"=>{"Unspecified"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Argentina"=>1, "Hungary"=>1, "United States"=>2, "Japan"=>1, "United Kingdom"=>4, "Malaysia"=>1, "Spain"=>1, "India"=>2, "Canada"=>1, "Sweden"=>1, "Ireland"=>1, "Poland"=>1, "Germany"=>1}, "group_count"=>5}

CrossRef

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/899600"], "description"=>"<p><i>Top:</i> Number of atomic contacts (green) and prediction\n output (blue) and for the N-terminal binding region of human p27.\n “D1”and “D2” denote the two\n strongly interacting domains (red boxes) and “LH”\n denotes the weakly interacting linker domain between them (yellow box).\n <i>Bottom:</i> Crystal structure of human p27 (red and\n yellow) complexed with CDK2 (magenta) and Cyclin A (blue) (PDB ID: 1jsu\n <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000376#pcbi.1000376-Russo1\" target=\"_blank\">[62]</a>). Red parts denote regions that are\n predicted to bind by the predictor. These regions correspond to the\n experimentally verified strongly binding regions of p27. The figure was\n generated by PyMOL.</p>", "links"=>[], "tags"=>["biochemistry/bioinformatics", "biochemistry/theory and simulation", "Computational biology", "computational biology/macromolecular sequence analysis", "computational biology/systems biology", "evolutionary biology/bioinformatics", "molecular biology/bioinformatics"], "article_id"=>570048, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ANCHOR_prediction_for_human_p27_/570048", "title"=>"ANCHOR prediction for human p27.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-01 00:00:48"}
  • {"files"=>["https://ndownloader.figshare.com/files/900195"], "description"=>"<p><i>N<sub>int</sub></i> shows the number of interacting\n residues in the short disordered binding sites,\n <i>N<sub>found</sub></i> shows the amount of these\n that are correctly found by the predictor. As there are types of\n amino acids that are rare, Fisher's exact test was used to\n calculate (two-tailed) <i>p</i> values to determine if the\n predictor works significantly better or worse for certain amino acid\n types with high p values corresponding to no significant\n difference.</p>", "links"=>[], "tags"=>["anchor", "amino", "acid", "binding"], "article_id"=>570654, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.t005", "stats"=>{"downloads"=>2, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_independence_of_the_efficiency_of_ANCHOR_from_the_amino_acid____composition_of_the_binding_sites_/570654", "title"=>"The independence of the efficiency of ANCHOR from the amino acid\n composition of the binding sites.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-01 00:10:54"}
  • {"files"=>["https://ndownloader.figshare.com/files/899704"], "description"=>"<p>Red bars mark known interaction sites, green box marks the globular WH1\n domain, blue boxes mark the GBD and VCA domains. Light red boxes\n indicate the regions with putative SH3 domain interaction sites.</p>", "links"=>[], "tags"=>["biochemistry/bioinformatics", "biochemistry/theory and simulation", "Computational biology", "computational biology/macromolecular sequence analysis", "computational biology/systems biology", "evolutionary biology/bioinformatics", "molecular biology/bioinformatics"], "article_id"=>570156, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.g007", "stats"=>{"downloads"=>4, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_ANCHOR_prediction_for_human_WASp_/570156", "title"=>"ANCHOR prediction for human WASp.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-01 00:02:36"}
  • {"files"=>["https://ndownloader.figshare.com/files/900160"], "description"=>"<p>The number and fraction of amino acids in different secondary\n structures in the disordered chains of the complexes. The three\n groups show these data for all the amino acids in the PDB\n structures, the ones in interaction and the ones that are correctly\n identified as part of binding site by ANCHOR.</p>", "links"=>[], "tags"=>["distributions", "disordered", "binding"], "article_id"=>570618, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.t006", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Secondary_structure_distributions_in_the_short_disordered_binding____site_dataset_/570618", "title"=>"Secondary structure distributions in the short disordered binding\n site dataset.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-01 00:10:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/900093"], "description"=>"<p>Optimal parameters of the predictor determined during training.\n <i>w<sub>1</sub></i>,\n <i>w<sub>2</sub></i>, <i>p<sub>1</sub></i>,\n <i>p<sub>2</sub></i> and\n <i>p<sub>3</sub></i> are the optimized parameters,\n <i>F</i> is the fraction of the residues in the\n disordered regions in the Disprot database that are predicted to be\n in binding sites, <i>TRP</i> and <i>FPR</i> are\n the True- and False Positive Rates, respectively.</p>", "links"=>[], "tags"=>["the", "optimization"], "article_id"=>570554, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.t002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Parameter_and_prediction_accuracy_values_obtained_during_the____optimization_of_ANCHOR_/570554", "title"=>"Parameter and prediction accuracy values obtained during the\n optimization of ANCHOR.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-01 00:09:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/900059"], "description"=>"<p>Results of the testing of ANCHOR on the three testing datasets.\n <i>TPR<sub>AA</sub></i> denotes the ratio of\n correctly identified amino acids belonging to binding sites.\n <i>TPR<sub>SEG</sub></i> denotes the ratio of\n binding sites found by the algorithm.</p>", "links"=>[], "tags"=>["anchor", "evaluated", "testing"], "article_id"=>570517, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.t003", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prediction_efficiency_of_ANCHOR_evaluated_on_the_testing____datasets_/570517", "title"=>"Prediction efficiency of ANCHOR evaluated on the testing\n datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-01 00:08:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/445071", "https://ndownloader.figshare.com/files/445127", "https://ndownloader.figshare.com/files/445173", "https://ndownloader.figshare.com/files/445247", "https://ndownloader.figshare.com/files/445305", "https://ndownloader.figshare.com/files/445358", "https://ndownloader.figshare.com/files/445495", "https://ndownloader.figshare.com/files/445532", "https://ndownloader.figshare.com/files/445563", "https://ndownloader.figshare.com/files/445585", "https://ndownloader.figshare.com/files/445604", "https://ndownloader.figshare.com/files/445622", "https://ndownloader.figshare.com/files/445644", "https://ndownloader.figshare.com/files/445672"], "description"=>"<div><p>Many disordered proteins function via binding to a structured partner and undergo a disorder-to-order transition. The coupled folding and binding can confer several functional advantages such as the precise control of binding specificity without increased affinity. Additionally, the inherent flexibility allows the binding site to adopt various conformations and to bind to multiple partners. These features explain the prevalence of such binding elements in signaling and regulatory processes. In this work, we report ANCHOR, a method for the prediction of disordered binding regions. ANCHOR relies on the pairwise energy estimation approach that is the basis of IUPred, a previous general disorder prediction method. In order to predict disordered binding regions, we seek to identify segments that are in disordered regions, cannot form enough favorable intrachain interactions to fold on their own, and are likely to gain stabilizing energy by interacting with a globular protein partner. The performance of ANCHOR was found to be largely independent from the amino acid composition and adopted secondary structure. Longer binding sites generally were predicted to be segmented, in agreement with available experimentally characterized examples. Scanning several hundred proteomes showed that the occurrence of disordered binding sites increased with the complexity of the organisms even compared to disordered regions in general. Furthermore, the length distribution of binding sites was different from disordered protein regions in general and was dominated by shorter segments. These results underline the importance of disordered proteins and protein segments in establishing new binding regions. Due to their specific biophysical properties, disordered binding sites generally carry a robust sequence signal, and this signal is efficiently captured by our method. Through its generality, ANCHOR opens new ways to study the essential functional sites of disordered proteins.</p> </div>", "links"=>[], "tags"=>["binding", "regions", "disordered", "proteins"], "article_id"=>147729, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1000376.s001", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s002", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s003", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s004", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s005", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s006", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s007", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s008", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s009", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s010", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s011", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s012", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s013", "https://dx.doi.org/10.1371/journal.pcbi.1000376.s014"], "stats"=>{"downloads"=>17, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Prediction_of_Protein_Binding_Regions_in_Disordered_Proteins/147729", "title"=>"Prediction of Protein Binding Regions in Disordered Proteins", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2009-05-01 02:08:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/899926"], "description"=>"<p>The length distribution of (A) the disordered protein segments determined\n by IUPred and (B) predicted disordered binding sites determined by\n ANCHOR for the 736 complete proteomes available, grouped according to\n the three kingdoms of life.</p>", "links"=>[], "tags"=>["disordered", "binding", "sites", "in"], "article_id"=>570382, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.g009", "stats"=>{"downloads"=>1, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Length_distribution_of_disordered_and_disordered_binding_sites_in____complete_proteomes_/570382", "title"=>"Length distribution of disordered and disordered binding sites in\n complete proteomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-01 00:06:22"}
  • {"files"=>["https://ndownloader.figshare.com/files/899813"], "description"=>"<p>The number of amino acids in disordered binding sites divided by the\n number of amino acids in disordered regions plotted as a function of the\n number of amino acids in disordered regions divided by the total number\n of residues in the proteome of the organism for the 736 complete\n proteomes deposited in the SwissProt database, colored according to the\n three kingdoms of life. The outlying points are marked with the name of\n the corresponding organism.</p>", "links"=>[], "tags"=>["disordered", "binding", "residues", "in"], "article_id"=>570268, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.g008", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Fraction_of_disordered_and_disordered_binding_site_residues_in____complete_proteomes_/570268", "title"=>"Fraction of disordered and disordered binding site residues in\n complete proteomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-01 00:04:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/899491"], "description"=>"<p>(A) The distribution of the number of binding segments predicted in short\n (white bars) and long (black bars) binding sites. It shows the segmented\n nature of longer binding sites. (B) The distribution of the fraction of\n correctly recovered interacting residues in both the short (white bars)\n and long (black bars) disordered binding sites.</p>", "links"=>[], "tags"=>["accuracies", "segmentation", "long", "disordered", "binding"], "article_id"=>569941, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.g005", "stats"=>{"downloads"=>0, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prediction_accuracies_and_segmentation_for_the_short_and_long____disordered_binding_sites_/569941", "title"=>"Prediction accuracies and segmentation for the short and long\n disordered binding sites.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2009-05-01 02:45:41"}
  • {"files"=>["https://ndownloader.figshare.com/files/900121"], "description"=>"<p>Amino acid composition of the reference globular protein dataset\n comprised of all the amino acids in the longer chains of the ordered\n complexes dataset. Amino acids are sorted by increasing\n hydrophobicity based on the Fauchere-Pliska hydrophobicity scale\n <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000376#pcbi.1000376-Fauchere1\" target=\"_blank\">[94]</a>. <i>AA</i> denotes\n amino acid codes and <i>f</i> denotes the fraction of the\n respective amino acid expressed as a percentage.</p>", "links"=>[], "tags"=>["amino", "globular"], "article_id"=>570579, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.t001", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reference_amino_acid_composition_of_globular_proteins_/570579", "title"=>"Reference amino acid composition of globular proteins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-01 00:09:39"}
  • {"files"=>["https://ndownloader.figshare.com/files/900231"], "description"=>"<p>Prediction results for the α-MoRFs dataset. SEG denotes\n segment based results where each binding site is considered one\n segment and one such segment is considered found if at least five of\n its amino acids are correctly identified.</p>", "links"=>[], "tags"=>["anchor", "evaluated", "dataset"], "article_id"=>570692, "categories"=>["Biochemistry", "Molecular Biology", "Evolutionary Biology", "Medicine", "Biological Sciences"], "users"=>["Bálint Mészáros", "István Simon", "Zsuzsanna Dosztányi"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1000376.t004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Prediction_efficiency_of_ANCHOR_evaluated_on_an_independent_dataset____945_MoRFs_dataset_/570692", "title"=>"Prediction efficiency of ANCHOR evaluated on an independent dataset\n (α-MoRFs dataset).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2009-05-01 00:11:32"}

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Relative Metric

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