Systematic identification of phosphorylation-mediated protein interaction switches
Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites...
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| Veröffentlicht in: | PLoS computational biology 2017-03, Vol.13 (3), p.e1005462-e1005462 |
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| container_title | PLoS computational biology |
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| creator | Betts, Matthew J Wichmann, Oliver Utz, Mathias Andre, Timon Petsalaki, Evangelia Minguez, Pablo Parca, Luca Roth, Frederick P Gavin, Anne-Claude Bork, Peer Russell, Robert B |
| description | Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions. We estimate that there are likely thousands of phosphorylation mediated switches yet to be uncovered, even among existing phosphorylation datasets. The results suggest that phosphorylation sites on globular, as distinct from disordered, parts of the proteome frequently function as switches, which might be one of the ancient roles for kinase phosphorylation. |
| doi_str_mv | 10.1371/journal.pcbi.1005462 |
| format | Article |
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Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions. We estimate that there are likely thousands of phosphorylation mediated switches yet to be uncovered, even among existing phosphorylation datasets. The results suggest that phosphorylation sites on globular, as distinct from disordered, parts of the proteome frequently function as switches, which might be one of the ancient roles for kinase phosphorylation.</description><identifier>ISSN: 1553-7358</identifier><identifier>ISSN: 1553-734X</identifier><identifier>EISSN: 1553-7358</identifier><identifier>DOI: 10.1371/journal.pcbi.1005462</identifier><identifier>PMID: 28346509</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Binding Sites ; Bioinformatics ; Biology and Life Sciences ; Computer Simulation ; Kinases ; Laboratories ; Models, Chemical ; Models, Molecular ; Molecular biology ; Mutation ; Observations ; Peptide mapping ; Phosphorylation ; Phosphotransferases - chemistry ; Phosphotransferases - ultrastructure ; Physical Sciences ; Protein Binding ; Protein Conformation ; Protein interaction ; Protein Interaction Mapping - methods ; Protein structure ; Protein-protein interactions ; Proteins ; Proteome - chemistry ; Proteome - ultrastructure ; Proteomics ; Research and Analysis Methods ; RNA polymerase ; Sequence Analysis, Protein - methods ; Structure-Activity Relationship ; Switches</subject><ispartof>PLoS computational biology, 2017-03, Vol.13 (3), p.e1005462-e1005462</ispartof><rights>COPYRIGHT 2017 Public Library of Science</rights><rights>2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, et al. (2017) Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Comput Biol 13(3): e1005462. https://doi.org/10.1371/journal.pcbi.1005462</rights><rights>2017 Betts et al 2017 Betts et al</rights><rights>2017 Public Library of Science. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited: Betts MJ, Wichmann O, Utz M, Andre T, Petsalaki E, Minguez P, et al. (2017) Systematic identification of phosphorylation-mediated protein interaction switches. PLoS Comput Biol 13(3): e1005462. https://doi.org/10.1371/journal.pcbi.1005462</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c633t-14ce6d48b4ff4974c2f64023168c4a8f1fedd684c4a196734f4bc99e41536fd33</citedby><cites>FETCH-LOGICAL-c633t-14ce6d48b4ff4974c2f64023168c4a8f1fedd684c4a196734f4bc99e41536fd33</cites><orcidid>0000-0002-8294-2995 ; 0000-0003-4583-9814</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386296/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386296/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2100,2926,23865,27923,27924,53790,53792,79371,79372</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28346509$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Iakoucheva, Lilia M.</contributor><creatorcontrib>Betts, Matthew J</creatorcontrib><creatorcontrib>Wichmann, Oliver</creatorcontrib><creatorcontrib>Utz, Mathias</creatorcontrib><creatorcontrib>Andre, Timon</creatorcontrib><creatorcontrib>Petsalaki, Evangelia</creatorcontrib><creatorcontrib>Minguez, Pablo</creatorcontrib><creatorcontrib>Parca, Luca</creatorcontrib><creatorcontrib>Roth, Frederick P</creatorcontrib><creatorcontrib>Gavin, Anne-Claude</creatorcontrib><creatorcontrib>Bork, Peer</creatorcontrib><creatorcontrib>Russell, Robert B</creatorcontrib><title>Systematic identification of phosphorylation-mediated protein interaction switches</title><title>PLoS computational biology</title><addtitle>PLoS Comput Biol</addtitle><description>Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions. We estimate that there are likely thousands of phosphorylation mediated switches yet to be uncovered, even among existing phosphorylation datasets. The results suggest that phosphorylation sites on globular, as distinct from disordered, parts of the proteome frequently function as switches, which might be one of the ancient roles for kinase phosphorylation.</description><subject>Binding Sites</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Computer Simulation</subject><subject>Kinases</subject><subject>Laboratories</subject><subject>Models, Chemical</subject><subject>Models, Molecular</subject><subject>Molecular biology</subject><subject>Mutation</subject><subject>Observations</subject><subject>Peptide mapping</subject><subject>Phosphorylation</subject><subject>Phosphotransferases - chemistry</subject><subject>Phosphotransferases - ultrastructure</subject><subject>Physical Sciences</subject><subject>Protein Binding</subject><subject>Protein Conformation</subject><subject>Protein interaction</subject><subject>Protein Interaction Mapping - methods</subject><subject>Protein structure</subject><subject>Protein-protein interactions</subject><subject>Proteins</subject><subject>Proteome - chemistry</subject><subject>Proteome - ultrastructure</subject><subject>Proteomics</subject><subject>Research and Analysis Methods</subject><subject>RNA polymerase</subject><subject>Sequence Analysis, Protein - methods</subject><subject>Structure-Activity Relationship</subject><subject>Switches</subject><issn>1553-7358</issn><issn>1553-734X</issn><issn>1553-7358</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><sourceid>DOA</sourceid><recordid>eNqVkk1v1DAQhiMEoqXwDxBE4lIOWeL4I_alUlUVWKkCqYWz5TjjXa-SONgOsP8e725adREXZEW2J8_MeF69WfYalQuEa_Rh4yY_qG4x6sYuUFlSwqon2SmiFBc1pvzpo_NJ9iKETVmmo2DPs5OKY8JoKU6z27ttiNCraHVuWxiiNVanmxtyZ_Jx7UL6_Lbbh4oeWqsitPnoXQQ75HaI4JXe8-GXjXoN4WX2zKguwKt5P8u-f7z-dvW5uPn6aXl1eVNohnEsENHAWsIbYgwRNdGVYaSsMGJcE8UNMtC2jJN0QYLVmBjSaCGAIIqZaTE-y94e6o6dC3KWI0jEOWcMlYInYnkgWqc2cvS2V34rnbJyH3B-JZVPk3cgG1ohQxXUzAhiWtJQaEpGmaioqKtm1-1i7jY1SQadpPKqOyp6_Gewa7lyPyXFnFWCpQLncwHvfkwQouxt0NB1agA37d-N6hpRtuv17i_039MtDtRKpQHsYFzqq9NqobfaDWBsil8SkdxCECYp4f1RQmIi_I4rNYUgl3e3_8F-OWbJgdXeheDBPKiCSrnz6v3z5c6rcvZqSnvzWNGHpHtz4j-XTObr</recordid><startdate>20170301</startdate><enddate>20170301</enddate><creator>Betts, Matthew J</creator><creator>Wichmann, Oliver</creator><creator>Utz, Mathias</creator><creator>Andre, Timon</creator><creator>Petsalaki, Evangelia</creator><creator>Minguez, Pablo</creator><creator>Parca, Luca</creator><creator>Roth, Frederick P</creator><creator>Gavin, Anne-Claude</creator><creator>Bork, Peer</creator><creator>Russell, Robert B</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISN</scope><scope>ISR</scope><scope>3V.</scope><scope>7QO</scope><scope>7QP</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AL</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>JQ2</scope><scope>K7-</scope><scope>K9.</scope><scope>LK8</scope><scope>M0N</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-8294-2995</orcidid><orcidid>https://orcid.org/0000-0003-4583-9814</orcidid></search><sort><creationdate>20170301</creationdate><title>Systematic identification of phosphorylation-mediated protein interaction switches</title><author>Betts, Matthew J ; Wichmann, Oliver ; Utz, Mathias ; Andre, Timon ; Petsalaki, Evangelia ; Minguez, Pablo ; Parca, Luca ; Roth, Frederick P ; Gavin, Anne-Claude ; Bork, Peer ; Russell, Robert B</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c633t-14ce6d48b4ff4974c2f64023168c4a8f1fedd684c4a196734f4bc99e41536fd33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Binding Sites</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Computer Simulation</topic><topic>Kinases</topic><topic>Laboratories</topic><topic>Models, Chemical</topic><topic>Models, Molecular</topic><topic>Molecular biology</topic><topic>Mutation</topic><topic>Observations</topic><topic>Peptide mapping</topic><topic>Phosphorylation</topic><topic>Phosphotransferases - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PLoS computational biology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Betts, Matthew J</au><au>Wichmann, Oliver</au><au>Utz, Mathias</au><au>Andre, Timon</au><au>Petsalaki, Evangelia</au><au>Minguez, Pablo</au><au>Parca, Luca</au><au>Roth, Frederick P</au><au>Gavin, Anne-Claude</au><au>Bork, Peer</au><au>Russell, Robert B</au><au>Iakoucheva, Lilia M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Systematic identification of phosphorylation-mediated protein interaction switches</atitle><jtitle>PLoS computational biology</jtitle><addtitle>PLoS Comput Biol</addtitle><date>2017-03-01</date><risdate>2017</risdate><volume>13</volume><issue>3</issue><spage>e1005462</spage><epage>e1005462</epage><pages>e1005462-e1005462</pages><issn>1553-7358</issn><issn>1553-734X</issn><eissn>1553-7358</eissn><abstract>Proteomics techniques can identify thousands of phosphorylation sites in a single experiment, the majority of which are new and lack precise information about function or molecular mechanism. Here we present a fast method to predict potential phosphorylation switches by mapping phosphorylation sites to protein-protein interactions of known structure and analysing the properties of the protein interface. We predict 1024 sites that could potentially enable or disable particular interactions. We tested a selection of these switches and showed that phosphomimetic mutations indeed affect interactions. We estimate that there are likely thousands of phosphorylation mediated switches yet to be uncovered, even among existing phosphorylation datasets. The results suggest that phosphorylation sites on globular, as distinct from disordered, parts of the proteome frequently function as switches, which might be one of the ancient roles for kinase phosphorylation.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28346509</pmid><doi>10.1371/journal.pcbi.1005462</doi><orcidid>https://orcid.org/0000-0002-8294-2995</orcidid><orcidid>https://orcid.org/0000-0003-4583-9814</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Binding Sites Bioinformatics Biology and Life Sciences Computer Simulation Kinases Laboratories Models, Chemical Models, Molecular Molecular biology Mutation Observations Peptide mapping Phosphorylation Phosphotransferases - chemistry Phosphotransferases - ultrastructure Physical Sciences Protein Binding Protein Conformation Protein interaction Protein Interaction Mapping - methods Protein structure Protein-protein interactions Proteins Proteome - chemistry Proteome - ultrastructure Proteomics Research and Analysis Methods RNA polymerase Sequence Analysis, Protein - methods Structure-Activity Relationship Switches |
| title | Systematic identification of phosphorylation-mediated protein interaction switches |
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