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id="toc-Electron_transfer_proteins" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Electron_transfer_proteins"> <div class="vector-toc-text"> <span class="vector-toc-numb">1.1</span> <span>Electron transfer proteins</span> </div> </a> <ul id="toc-Electron_transfer_proteins-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Signal_transduction" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Signal_transduction"> <div class="vector-toc-text"> <span class="vector-toc-numb">1.2</span> <span>Signal transduction</span> </div> </a> <ul id="toc-Signal_transduction-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Membrane_transport" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Membrane_transport"> <div class="vector-toc-text"> <span class="vector-toc-numb">1.3</span> <span>Membrane transport</span> </div> </a> <ul id="toc-Membrane_transport-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Cell_metabolism" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Cell_metabolism"> <div class="vector-toc-text"> <span class="vector-toc-numb">1.4</span> <span>Cell metabolism</span> </div> </a> <ul id="toc-Cell_metabolism-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Muscle_contraction" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Muscle_contraction"> <div class="vector-toc-text"> <span class="vector-toc-numb">1.5</span> <span>Muscle contraction</span> </div> </a> <ul id="toc-Muscle_contraction-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Types" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Types"> <div class="vector-toc-text"> <span class="vector-toc-numb">2</span> <span>Types</span> </div> </a> <button aria-controls="toc-Types-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Types subsection</span> </button> <ul id="toc-Types-sublist" class="vector-toc-list"> <li id="toc-Homo-oligomers_vs._hetero-oligomers" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Homo-oligomers_vs._hetero-oligomers"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.1</span> <span>Homo-oligomers vs. hetero-oligomers</span> </div> </a> <ul id="toc-Homo-oligomers_vs._hetero-oligomers-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Stable_interactions_vs._transient_interactions" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Stable_interactions_vs._transient_interactions"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.2</span> <span>Stable interactions vs. transient interactions</span> </div> </a> <ul id="toc-Stable_interactions_vs._transient_interactions-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Covalent_vs._non-covalent" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Covalent_vs._non-covalent"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.3</span> <span>Covalent vs. non-covalent</span> </div> </a> <ul id="toc-Covalent_vs._non-covalent-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Role_of_water" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Role_of_water"> <div class="vector-toc-text"> <span class="vector-toc-numb">2.4</span> <span>Role of water</span> </div> </a> <ul id="toc-Role_of_water-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Structure" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Structure"> <div class="vector-toc-text"> <span class="vector-toc-numb">3</span> <span>Structure</span> </div> </a> <button aria-controls="toc-Structure-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Structure subsection</span> </button> <ul id="toc-Structure-sublist" class="vector-toc-list"> <li id="toc-Protein-protein_interaction_domains" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Protein-protein_interaction_domains"> <div class="vector-toc-text"> <span class="vector-toc-numb">3.1</span> <span>Protein-protein interaction domains</span> </div> </a> <ul id="toc-Protein-protein_interaction_domains-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Properties_of_the_interface" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Properties_of_the_interface"> <div class="vector-toc-text"> <span class="vector-toc-numb">4</span> <span>Properties of the interface</span> </div> </a> <ul id="toc-Properties_of_the_interface-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Regulation" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Regulation"> <div class="vector-toc-text"> <span class="vector-toc-numb">5</span> <span>Regulation</span> </div> </a> <ul id="toc-Regulation-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Experimental_methods" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Experimental_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">6</span> <span>Experimental methods</span> </div> </a> <button aria-controls="toc-Experimental_methods-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Experimental methods subsection</span> </button> <ul id="toc-Experimental_methods-sublist" class="vector-toc-list"> <li id="toc-Yeast_two-hybrid_screening" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Yeast_two-hybrid_screening"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.1</span> <span>Yeast two-hybrid screening</span> </div> </a> <ul id="toc-Yeast_two-hybrid_screening-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Affinity_purification_coupled_to_mass_spectrometry" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Affinity_purification_coupled_to_mass_spectrometry"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.2</span> <span>Affinity purification coupled to mass spectrometry</span> </div> </a> <ul id="toc-Affinity_purification_coupled_to_mass_spectrometry-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Nucleic_acid_programmable_protein_array_(NAPPA)" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Nucleic_acid_programmable_protein_array_(NAPPA)"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.3</span> <span>Nucleic acid programmable protein array (NAPPA)</span> </div> </a> <ul id="toc-Nucleic_acid_programmable_protein_array_(NAPPA)-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Intragenic_complementation" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Intragenic_complementation"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.4</span> <span>Intragenic complementation</span> </div> </a> <ul id="toc-Intragenic_complementation-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Other_potential_methods" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Other_potential_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">6.5</span> <span>Other potential methods</span> </div> </a> <ul id="toc-Other_potential_methods-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Computational_methods" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Computational_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">7</span> <span>Computational methods</span> </div> </a> <button aria-controls="toc-Computational_methods-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Computational methods subsection</span> </button> <ul id="toc-Computational_methods-sublist" class="vector-toc-list"> <li id="toc-Computational_prediction_of_protein–protein_interactions" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Computational_prediction_of_protein–protein_interactions"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.1</span> <span>Computational prediction of protein–protein interactions</span> </div> </a> <ul id="toc-Computational_prediction_of_protein–protein_interactions-sublist" class="vector-toc-list"> <li id="toc-Genomic_context_methods" class="vector-toc-list-item vector-toc-level-3"> <a class="vector-toc-link" href="#Genomic_context_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.1.1</span> <span>Genomic context methods</span> </div> </a> <ul id="toc-Genomic_context_methods-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Text_mining_methods" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Text_mining_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.2</span> <span>Text mining methods</span> </div> </a> <ul id="toc-Text_mining_methods-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Machine_learning_methods" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Machine_learning_methods"> <div class="vector-toc-text"> <span class="vector-toc-numb">7.3</span> <span>Machine learning methods</span> </div> </a> <ul id="toc-Machine_learning_methods-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-Databases" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Databases"> <div class="vector-toc-text"> <span class="vector-toc-numb">8</span> <span>Databases</span> </div> </a> <ul id="toc-Databases-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Interaction_networks" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Interaction_networks"> <div class="vector-toc-text"> <span class="vector-toc-numb">9</span> <span>Interaction networks</span> </div> </a> <button aria-controls="toc-Interaction_networks-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle Interaction networks subsection</span> </button> <ul id="toc-Interaction_networks-sublist" class="vector-toc-list"> <li id="toc-Signed_interaction_networks" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Signed_interaction_networks"> <div class="vector-toc-text"> <span class="vector-toc-numb">9.1</span> <span>Signed interaction networks</span> </div> </a> <ul id="toc-Signed_interaction_networks-sublist" class="vector-toc-list"> <li id="toc-RNA_interference_screens" class="vector-toc-list-item vector-toc-level-3"> <a class="vector-toc-link" href="#RNA_interference_screens"> <div class="vector-toc-text"> <span class="vector-toc-numb">9.1.1</span> <span>RNA interference screens</span> </div> </a> <ul id="toc-RNA_interference_screens-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> </ul> </li> <li id="toc-As_therapeutic_targets" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#As_therapeutic_targets"> <div class="vector-toc-text"> <span class="vector-toc-numb">10</span> <span>As therapeutic targets</span> </div> </a> <button aria-controls="toc-As_therapeutic_targets-sublist" class="cdx-button cdx-button--weight-quiet cdx-button--icon-only vector-toc-toggle"> <span class="vector-icon mw-ui-icon-wikimedia-expand"></span> <span>Toggle As therapeutic targets subsection</span> </button> <ul id="toc-As_therapeutic_targets-sublist" class="vector-toc-list"> <li id="toc-Examples_2" class="vector-toc-list-item vector-toc-level-2"> <a class="vector-toc-link" href="#Examples_2"> <div class="vector-toc-text"> <span class="vector-toc-numb">10.1</span> <span>Examples</span> </div> </a> <ul id="toc-Examples_2-sublist" class="vector-toc-list"> </ul> </li> </ul> </li> <li id="toc-See_also" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#See_also"> <div class="vector-toc-text"> <span class="vector-toc-numb">11</span> <span>See also</span> </div> </a> <ul id="toc-See_also-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-References" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#References"> <div class="vector-toc-text"> <span class="vector-toc-numb">12</span> <span>References</span> </div> </a> <ul id="toc-References-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-Further_reading" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#Further_reading"> <div class="vector-toc-text"> <span class="vector-toc-numb">13</span> <span>Further reading</span> </div> </a> <ul id="toc-Further_reading-sublist" class="vector-toc-list"> </ul> </li> <li id="toc-External_links" class="vector-toc-list-item vector-toc-level-1"> <a class="vector-toc-link" href="#External_links"> <div class="vector-toc-text"> <span class="vector-toc-numb">14</span> <span>External links</span> </div> </a> <ul id="toc-External_links-sublist" class="vector-toc-list"> </ul> </li> </ul> </div> </div> </nav> </div> </div> <div class="mw-content-container"> <main id="content" class="mw-body"> <header class="mw-body-header vector-page-titlebar"> <nav aria-label="Contents" class="vector-toc-landmark"> <div id="vector-page-titlebar-toc" class="vector-dropdown vector-page-titlebar-toc vector-button-flush-left" > <input type="checkbox" id="vector-page-titlebar-toc-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-vector-page-titlebar-toc" class="vector-dropdown-checkbox " aria-label="Toggle the table of contents" > <label id="vector-page-titlebar-toc-label" for="vector-page-titlebar-toc-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--icon-only " aria-hidden="true" ><span class="vector-icon mw-ui-icon-listBullet mw-ui-icon-wikimedia-listBullet"></span> <span class="vector-dropdown-label-text">Toggle the table of contents</span> </label> <div class="vector-dropdown-content"> <div id="vector-page-titlebar-toc-unpinned-container" class="vector-unpinned-container"> </div> </div> </div> </nav> <h1 id="firstHeading" class="firstHeading mw-first-heading"><span class="mw-page-title-main">Protein–protein interaction</span></h1> <div id="p-lang-btn" class="vector-dropdown mw-portlet mw-portlet-lang" > <input type="checkbox" id="p-lang-btn-checkbox" role="button" aria-haspopup="true" data-event-name="ui.dropdown-p-lang-btn" class="vector-dropdown-checkbox mw-interlanguage-selector" aria-label="Go to an article in another language. Available in 21 languages" > <label id="p-lang-btn-label" for="p-lang-btn-checkbox" class="vector-dropdown-label cdx-button cdx-button--fake-button cdx-button--fake-button--enabled cdx-button--weight-quiet cdx-button--action-progressive mw-portlet-lang-heading-21" aria-hidden="true" ><span class="vector-icon mw-ui-icon-language-progressive mw-ui-icon-wikimedia-language-progressive"></span> <span class="vector-dropdown-label-text">21 languages</span> </label> <div class="vector-dropdown-content"> <div class="vector-menu-content"> <ul class="vector-menu-content-list"> <li class="interlanguage-link interwiki-ar mw-list-item"><a href="https://ar.wikipedia.org/wiki/%D8%AA%D8%A2%D8%AB%D8%B1%D8%A7%D8%AA_%D8%A7%D9%84%D8%A8%D8%B1%D9%88%D8%AA%D9%8A%D9%86-%D8%A8%D8%B1%D9%88%D8%AA%D9%8A%D9%86" title="تآثرات البروتين-بروتين – Arabic" lang="ar" hreflang="ar" data-title="تآثرات البروتين-بروتين" data-language-autonym="العربية" data-language-local-name="Arabic" class="interlanguage-link-target"><span>العربية</span></a></li><li class="interlanguage-link interwiki-bs mw-list-item"><a href="https://bs.wikipedia.org/wiki/Interakcija_protein-protein" title="Interakcija protein-protein – Bosnian" lang="bs" hreflang="bs" data-title="Interakcija protein-protein" data-language-autonym="Bosanski" data-language-local-name="Bosnian" class="interlanguage-link-target"><span>Bosanski</span></a></li><li class="interlanguage-link interwiki-ca mw-list-item"><a href="https://ca.wikipedia.org/wiki/Interacci%C3%B3_prote%C3%AFna-prote%C3%AFna" title="Interacció proteïna-proteïna – Catalan" lang="ca" hreflang="ca" data-title="Interacció proteïna-proteïna" data-language-autonym="Català" data-language-local-name="Catalan" class="interlanguage-link-target"><span>Català</span></a></li><li class="interlanguage-link interwiki-de mw-list-item"><a href="https://de.wikipedia.org/wiki/Protein-Protein-Interaktion" title="Protein-Protein-Interaktion – German" lang="de" hreflang="de" data-title="Protein-Protein-Interaktion" data-language-autonym="Deutsch" data-language-local-name="German" class="interlanguage-link-target"><span>Deutsch</span></a></li><li class="interlanguage-link interwiki-el mw-list-item"><a href="https://el.wikipedia.org/wiki/%CE%94%CE%AF%CE%BA%CF%84%CF%85%CE%B1_%CF%80%CF%81%CF%89%CF%84%CE%B5%CF%8A%CE%BD%CE%B9%CE%BA%CF%8E%CE%BD_%CE%B1%CE%BB%CE%BB%CE%B7%CE%BB%CE%B5%CF%80%CE%B9%CE%B4%CF%81%CE%AC%CF%83%CE%B5%CF%89%CE%BD" title="Δίκτυα πρωτεϊνικών αλληλεπιδράσεων – Greek" lang="el" hreflang="el" data-title="Δίκτυα πρωτεϊνικών αλληλεπιδράσεων" data-language-autonym="Ελληνικά" data-language-local-name="Greek" class="interlanguage-link-target"><span>Ελληνικά</span></a></li><li class="interlanguage-link interwiki-es mw-list-item"><a href="https://es.wikipedia.org/wiki/Interacciones_prote%C3%ADna-prote%C3%ADna" title="Interacciones proteína-proteína – Spanish" lang="es" hreflang="es" data-title="Interacciones proteína-proteína" data-language-autonym="Español" data-language-local-name="Spanish" class="interlanguage-link-target"><span>Español</span></a></li><li class="interlanguage-link interwiki-fa mw-list-item"><a href="https://fa.wikipedia.org/wiki/%D8%AA%D8%B9%D8%A7%D9%85%D9%84_%D9%BE%D8%B1%D9%88%D8%AA%D8%A6%DB%8C%D9%86-%D9%BE%D8%B1%D9%88%D8%AA%D8%A6%DB%8C%D9%86" title="تعامل پروتئین-پروتئین – Persian" lang="fa" hreflang="fa" data-title="تعامل پروتئین-پروتئین" data-language-autonym="فارسی" data-language-local-name="Persian" class="interlanguage-link-target"><span>فارسی</span></a></li><li class="interlanguage-link interwiki-fr mw-list-item"><a href="https://fr.wikipedia.org/wiki/Interaction_prot%C3%A9ine-prot%C3%A9ine" title="Interaction protéine-protéine – French" lang="fr" hreflang="fr" data-title="Interaction protéine-protéine" data-language-autonym="Français" data-language-local-name="French" class="interlanguage-link-target"><span>Français</span></a></li><li class="interlanguage-link interwiki-gl mw-list-item"><a href="https://gl.wikipedia.org/wiki/Interacci%C3%B3ns_prote%C3%ADna-prote%C3%ADna" title="Interaccións proteína-proteína – Galician" lang="gl" hreflang="gl" data-title="Interaccións proteína-proteína" data-language-autonym="Galego" data-language-local-name="Galician" class="interlanguage-link-target"><span>Galego</span></a></li><li class="interlanguage-link interwiki-ko mw-list-item"><a href="https://ko.wikipedia.org/wiki/%EB%8B%A8%EB%B0%B1%EC%A7%88-%EB%8B%A8%EB%B0%B1%EC%A7%88_%EC%83%81%ED%98%B8%EC%9E%91%EC%9A%A9" title="단백질-단백질 상호작용 – Korean" lang="ko" hreflang="ko" data-title="단백질-단백질 상호작용" data-language-autonym="한국어" data-language-local-name="Korean" class="interlanguage-link-target"><span>한국어</span></a></li><li class="interlanguage-link interwiki-it mw-list-item"><a href="https://it.wikipedia.org/wiki/Interazione_proteina-proteina" title="Interazione proteina-proteina – Italian" lang="it" hreflang="it" data-title="Interazione proteina-proteina" data-language-autonym="Italiano" data-language-local-name="Italian" class="interlanguage-link-target"><span>Italiano</span></a></li><li class="interlanguage-link interwiki-he mw-list-item"><a href="https://he.wikipedia.org/wiki/%D7%90%D7%99%D7%A0%D7%98%D7%A8%D7%90%D7%A7%D7%A6%D7%99%D7%99%D7%AA_%D7%97%D7%9C%D7%91%D7%95%D7%9F-%D7%97%D7%9C%D7%91%D7%95%D7%9F" title="אינטראקציית חלבון-חלבון – Hebrew" lang="he" hreflang="he" data-title="אינטראקציית חלבון-חלבון" data-language-autonym="עברית" data-language-local-name="Hebrew" class="interlanguage-link-target"><span>עברית</span></a></li><li class="interlanguage-link interwiki-ja mw-list-item"><a href="https://ja.wikipedia.org/wiki/%E3%82%BF%E3%83%B3%E3%83%91%E3%82%AF%E8%B3%AA%E9%96%93%E7%9B%B8%E4%BA%92%E4%BD%9C%E7%94%A8" title="タンパク質間相互作用 – Japanese" lang="ja" hreflang="ja" data-title="タンパク質間相互作用" data-language-autonym="日本語" data-language-local-name="Japanese" class="interlanguage-link-target"><span>日本語</span></a></li><li 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<div class="vector-body-before-content"> <div class="mw-indicators"> </div> <div id="siteSub" class="noprint">From Wikipedia, the free encyclopedia</div> </div> <div id="contentSub"><div id="mw-content-subtitle"><span class="mw-redirectedfrom">(Redirected from <a href="/w/index.php?title=Protein-protein_interaction&redirect=no" class="mw-redirect" title="Protein-protein interaction">Protein-protein interaction</a>)</span></div></div> <div id="mw-content-text" class="mw-body-content"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr"><div class="shortdescription nomobile noexcerpt noprint searchaux" style="display:none">Physical interactions and constructions between multiple proteins</div> <p class="mw-empty-elt"> </p> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:1dfj_RNAseInhibitor-RNAse_complex.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/5/56/1dfj_RNAseInhibitor-RNAse_complex.jpg/220px-1dfj_RNAseInhibitor-RNAse_complex.jpg" decoding="async" width="220" height="233" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/5/56/1dfj_RNAseInhibitor-RNAse_complex.jpg/330px-1dfj_RNAseInhibitor-RNAse_complex.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/5/56/1dfj_RNAseInhibitor-RNAse_complex.jpg/440px-1dfj_RNAseInhibitor-RNAse_complex.jpg 2x" data-file-width="725" data-file-height="768" /></a><figcaption>The horseshoe shaped ribonuclease inhibitor (shown as wireframe) forms a protein–protein interaction with the ribonuclease protein. The contacts between the two proteins are shown as coloured patches.</figcaption></figure> <p><b>Protein–protein interactions</b> (<b>PPIs</b>) are physical contacts of high specificity established between two or more <a href="/wiki/Protein" title="Protein">protein</a> molecules as a result of biochemical events steered by interactions that include <a href="/wiki/Electrostatic_forces" class="mw-redirect" title="Electrostatic forces">electrostatic forces</a>, <a href="/wiki/Hydrogen_bond" title="Hydrogen bond">hydrogen bonding</a> and the <a href="/wiki/Hydrophobic_effect" title="Hydrophobic effect">hydrophobic effect</a>. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. </p><p>Proteins rarely act alone as their functions tend to be regulated. Many molecular processes within a cell are carried out by <a href="/wiki/Molecular_machine" title="Molecular machine">molecular machines</a> that are built from numerous protein components organized by their PPIs. These physiological interactions make up the so-called <a href="/wiki/Interactome" title="Interactome">interactomics</a> of the organism, while aberrant PPIs are the basis of multiple aggregation-related diseases, such as <a href="/wiki/Creutzfeldt%E2%80%93Jakob_disease" title="Creutzfeldt–Jakob disease">Creutzfeldt–Jakob</a> and <a href="/wiki/Alzheimer%27s_disease" title="Alzheimer's disease">Alzheimer's diseases</a>. </p><p>PPIs have been studied with <a href="/wiki/Methods_to_investigate_protein%E2%80%93protein_interactions" title="Methods to investigate protein–protein interactions">many methods</a> and from different perspectives: <a href="/wiki/Biochemistry" title="Biochemistry">biochemistry</a>, <a href="/wiki/Quantum_chemistry" title="Quantum chemistry">quantum chemistry</a>, <a href="/wiki/Molecular_dynamics" title="Molecular dynamics">molecular dynamics</a>, <a href="/wiki/Signal_transduction" title="Signal transduction">signal transduction</a>, among others.<sup id="cite_ref-Titeca_2019_1-0" class="reference"><a href="#cite_note-Titeca_2019-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-2" class="reference"><a href="#cite_note-2"><span class="cite-bracket">[</span>2<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-3" class="reference"><a href="#cite_note-3"><span class="cite-bracket">[</span>3<span class="cite-bracket">]</span></a></sup> All this information enables the creation of large protein interaction networks<sup id="cite_ref-Mashaghi,_A._2004_113–121_4-0" class="reference"><a href="#cite_note-Mashaghi,_A._2004_113–121-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> – similar to <a href="/wiki/Metabolic_network" title="Metabolic network">metabolic</a> or <a href="/wiki/Genetic_networks" class="mw-redirect" title="Genetic networks">genetic/epigenetic networks</a> – that empower the current knowledge on <a href="/wiki/Biochemical_cascade" title="Biochemical cascade">biochemical cascades</a> and molecular etiology of disease, as well as the discovery of putative protein targets of therapeutic interest. </p> <meta property="mw:PageProp/toc" /> <div class="mw-heading mw-heading2"><h2 id="Examples">Examples</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=1" title="Edit section: Examples"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <div class="mw-heading mw-heading3"><h3 id="Electron_transfer_proteins">Electron transfer proteins</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=2" title="Edit section: Electron transfer proteins"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1236090951">.mw-parser-output .hatnote{font-style:italic}.mw-parser-output div.hatnote{padding-left:1.6em;margin-bottom:0.5em}.mw-parser-output .hatnote i{font-style:normal}.mw-parser-output .hatnote+link+.hatnote{margin-top:-0.5em}@media print{body.ns-0 .mw-parser-output .hatnote{display:none!important}}</style><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Electron_transfer_protein" class="mw-redirect" title="Electron transfer protein">Electron transfer protein</a></div> <p>In many metabolic reactions, a protein that acts as an electron carrier binds to an enzyme that acts as its <a href="/wiki/Reductase" class="mw-redirect" title="Reductase">reductase</a>. After it receives an electron, it dissociates and then binds to the next enzyme that acts as its <a href="/wiki/Oxidase" title="Oxidase">oxidase</a> (i.e. an acceptor of the electron). These interactions between proteins are dependent on highly specific binding between proteins to ensure efficient electron transfer. Examples: mitochondrial oxidative phosphorylation chain system components cytochrome c-reductase / <a href="/wiki/Cytochrome_c" title="Cytochrome c">cytochrome c</a> / cytochrome c oxidase; microsomal and mitochondrial P450 systems.<sup id="cite_ref-1996-Hanukoglu_5-0" class="reference"><a href="#cite_note-1996-Hanukoglu-5"><span class="cite-bracket">[</span>5<span class="cite-bracket">]</span></a></sup> </p><p>In the case of the mitochondrial P450 systems, the specific residues involved in the binding of the electron transfer protein <a href="/wiki/Adrenodoxin" class="mw-redirect" title="Adrenodoxin">adrenodoxin</a> to its reductase were identified as two basic Arg residues on the surface of the reductase and two acidic Asp residues on the adrenodoxin.<sup id="cite_ref-pmid8349601_6-0" class="reference"><a href="#cite_note-pmid8349601-6"><span class="cite-bracket">[</span>6<span class="cite-bracket">]</span></a></sup> More recent work on the phylogeny of the reductase has shown that these residues involved in protein–protein interactions have been conserved throughout the evolution of this enzyme.<sup id="cite_ref-2017-Hanukoglu-JME_7-0" class="reference"><a href="#cite_note-2017-Hanukoglu-JME-7"><span class="cite-bracket">[</span>7<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Signal_transduction">Signal transduction</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=3" title="Edit section: Signal transduction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Signal_transduction" title="Signal transduction">Signal transduction</a></div> <p>The activity of the cell is regulated by extracellular signals. Signal propagation inside and/or along the interior of cells depends on PPIs between the various signaling molecules. The recruitment of signaling pathways through PPIs is called <a href="/wiki/Signal_transduction" title="Signal transduction">signal transduction</a> and plays a fundamental role in many biological processes and in many diseases including <a href="/wiki/Parkinson%27s_disease" title="Parkinson's disease">Parkinson's disease</a> and cancer. </p> <div class="mw-heading mw-heading3"><h3 id="Membrane_transport">Membrane transport</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=4" title="Edit section: Membrane transport"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Membrane_transport" title="Membrane transport">Membrane transport</a></div> <p>A protein may be carrying another protein (for example, from <a href="/wiki/Cytoplasm" title="Cytoplasm">cytoplasm</a> to <a href="/wiki/Cell_nucleus" title="Cell nucleus">nucleus</a> or vice versa in the case of the <a href="/wiki/Nuclear_pore" title="Nuclear pore">nuclear pore</a> importins).<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2019)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Cell_metabolism">Cell metabolism</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=5" title="Edit section: Cell metabolism"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Cell_metabolism" class="mw-redirect" title="Cell metabolism">Cell metabolism</a></div> <p>In many biosynthetic processes <a href="/wiki/Enzymes" class="mw-redirect" title="Enzymes">enzymes</a> interact with each other to produce small compounds or other macromolecules.<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (April 2019)">citation needed</span></a></i>]</sup> </p> <div class="mw-heading mw-heading3"><h3 id="Muscle_contraction">Muscle contraction</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=6" title="Edit section: Muscle contraction"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Muscle_contraction" title="Muscle contraction">Muscle contraction</a></div> <p>Physiology of <a href="/wiki/Muscle_contraction" title="Muscle contraction">muscle contraction</a> involves several interactions. <a href="/wiki/Myosin" title="Myosin">Myosin</a> filaments act as <a href="/wiki/Molecular_motor" title="Molecular motor">molecular motors</a> and by binding to <a href="/wiki/Actin" title="Actin">actin</a> enables filament sliding.<sup id="cite_ref-8" class="reference"><a href="#cite_note-8"><span class="cite-bracket">[</span>8<span class="cite-bracket">]</span></a></sup> Furthermore, members of the <a href="/wiki/Skeletal_muscle" title="Skeletal muscle">skeletal muscle</a> <a href="/wiki/Lipid_droplet-associated_protein" class="mw-redirect" title="Lipid droplet-associated protein">lipid droplet-associated proteins</a> family associate with other proteins, as activator of <a href="/wiki/Adipose_triglyceride_lipase" title="Adipose triglyceride lipase">adipose triglyceride lipase</a> and its <a href="/wiki/Coactivator" class="mw-redirect" title="Coactivator">coactivator</a> comparative gene identification-58, to regulate <a href="/wiki/Lipolysis" title="Lipolysis">lipolysis</a> in skeletal muscle </p> <div class="mw-heading mw-heading2"><h2 id="Types">Types</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=7" title="Edit section: Types"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Multiprotein_complex" class="mw-redirect" title="Multiprotein complex">Multiprotein complex</a></div> <p>To describe the types of protein–protein interactions (PPIs) it is important to consider that proteins can interact in a "transient" way (to produce some specific effect in a short time, like signal transduction) or to interact with other proteins in a "stable" way to form complexes that become molecular machines within the living systems. A protein complex assembly can result in the formation of <a href="/wiki/Oligomer" title="Oligomer">homo-oligomeric or hetero-oligomeric complexes</a>. In addition to the conventional complexes, as enzyme-inhibitor and antibody-antigen, interactions can also be established between domain-domain and domain-peptide. Another important distinction to identify protein–protein interactions is the way they have been determined, since there are techniques that measure direct physical interactions between protein pairs, named “binary” methods, while there are other techniques that measure physical interactions among groups of proteins, without pairwise determination of protein partners, named “co-complex” methods. </p> <div class="mw-heading mw-heading3"><h3 id="Homo-oligomers_vs._hetero-oligomers">Homo-oligomers vs. hetero-oligomers</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=8" title="Edit section: Homo-oligomers vs. hetero-oligomers"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Homo-oligomers are macromolecular complexes constituted by only one type of <a href="/wiki/Protein_subunit" title="Protein subunit">protein subunit</a>. Protein subunits assembly is guided by the establishment of <a href="/wiki/Non-covalent_interactions" class="mw-redirect" title="Non-covalent interactions">non-covalent interactions</a> in the <a href="/wiki/Quaternary_structure" class="mw-redirect" title="Quaternary structure">quaternary structure</a> of the protein. Disruption of homo-oligomers in order to return to the initial individual <a href="/wiki/Monomers" class="mw-redirect" title="Monomers">monomers</a> often requires denaturation of the complex.<sup id="cite_ref-Jones_9-0" class="reference"><a href="#cite_note-Jones-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> Several <a href="/wiki/Enzymes" class="mw-redirect" title="Enzymes">enzymes</a>, <a href="/wiki/Carrier_proteins" class="mw-redirect" title="Carrier proteins">carrier proteins</a>, scaffolding proteins, and transcriptional regulatory factors carry out their functions as homo-oligomers. Distinct protein subunits interact in hetero-oligomers, which are essential to control several cellular functions. The importance of the communication between heterologous proteins is even more evident during cell signaling events and such interactions are only possible due to structural domains within the proteins (as described below). </p> <div class="mw-heading mw-heading3"><h3 id="Stable_interactions_vs._transient_interactions">Stable interactions vs. transient interactions</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=9" title="Edit section: Stable interactions vs. transient interactions"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Stable interactions involve proteins that interact for a long time, taking part of permanent complexes as subunits, in order to carry out functional roles. These are usually the case of homo-oligomers (e.g. <a href="/wiki/Cytochrome_c" title="Cytochrome c">cytochrome c</a>), and some hetero-oligomeric proteins, as the subunits of <a href="/wiki/ATPase" title="ATPase">ATPase</a>. On the other hand, a protein may interact briefly and in a <a href="/wiki/Reversible_process_(thermodynamics)" title="Reversible process (thermodynamics)">reversible</a> manner with other proteins in only certain cellular contexts – <a href="/wiki/Cell_type" title="Cell type">cell type</a>, <a href="/wiki/Cell_cycle" title="Cell cycle">cell cycle stage</a>, external factors, presence of other binding proteins, etc. – as it happens with most of the proteins involved in <a href="/wiki/Biochemical_cascade" title="Biochemical cascade">biochemical cascades</a>. These are called transient interactions. For example, some G protein–coupled receptors only transiently bind to G<sub>i/o</sub> proteins when they are activated by extracellular ligands,<sup id="cite_ref-pmid=18434433_10-0" class="reference"><a href="#cite_note-pmid=18434433-10"><span class="cite-bracket">[</span>10<span class="cite-bracket">]</span></a></sup> while some G<sub>q</sub>-coupled receptors, such as muscarinic receptor M3, pre-couple with G<sub>q</sub> proteins prior to the receptor-ligand binding.<sup id="cite_ref-pmid=21873996_11-0" class="reference"><a href="#cite_note-pmid=21873996-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> Interactions between intrinsically disordered protein regions to globular protein domains (i.e. <a href="/wiki/MoRFs" class="mw-redirect" title="MoRFs">MoRFs</a>) are transient interactions.<sup id="cite_ref-12" class="reference"><a href="#cite_note-12"><span class="cite-bracket">[</span>12<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Covalent_vs._non-covalent">Covalent vs. non-covalent</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=10" title="Edit section: Covalent vs. non-covalent"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main articles: <a href="/wiki/Covalent_bond" title="Covalent bond">Covalent bond</a> and <a href="/wiki/Non-covalent_interactions" class="mw-redirect" title="Non-covalent interactions">Non-covalent interactions</a></div> <p>Covalent interactions are those with the strongest association and are formed by <a href="/wiki/Disulphide_bonds" class="mw-redirect" title="Disulphide bonds">disulphide bonds</a> or <a href="/wiki/Atomic_orbital" title="Atomic orbital">electron sharing</a>. While rare, these interactions are determinant in some <a href="/wiki/Posttranslational_modifications" class="mw-redirect" title="Posttranslational modifications">posttranslational modifications</a>, as <a href="/wiki/Ubiquitination" class="mw-redirect" title="Ubiquitination">ubiquitination</a> and <a href="/wiki/SUMOylation" class="mw-redirect" title="SUMOylation">SUMOylation</a>. Non-covalent bonds are usually established during transient interactions by the combination of weaker bonds, such as <a href="/wiki/Hydrogen_bonds" class="mw-redirect" title="Hydrogen bonds">hydrogen bonds</a>, ionic interactions, <a href="/wiki/Van_der_Waals_force" title="Van der Waals force">Van der Waals forces</a>, or hydrophobic bonds.<sup id="cite_ref-Jukka_13-0" class="reference"><a href="#cite_note-Jukka-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Role_of_water">Role of water</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=11" title="Edit section: Role of water"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Water molecules play a significant role in the interactions between proteins.<sup id="cite_ref-14" class="reference"><a href="#cite_note-14"><span class="cite-bracket">[</span>14<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-15" class="reference"><a href="#cite_note-15"><span class="cite-bracket">[</span>15<span class="cite-bracket">]</span></a></sup> The crystal structures of complexes, obtained at high resolution from different but homologous proteins, have shown that some interface water molecules are conserved between homologous complexes. The majority of the interface water molecules make hydrogen bonds with both partners of each complex. Some interface amino acid residues or atomic groups of one protein partner engage in both direct and water mediated interactions with the other protein partner. Doubly indirect interactions, mediated by two water molecules, are more numerous in the homologous complexes of low affinity.<sup id="cite_ref-16" class="reference"><a href="#cite_note-16"><span class="cite-bracket">[</span>16<span class="cite-bracket">]</span></a></sup> Carefully conducted mutagenesis experiments, e.g. changing a tyrosine residue into a phenylalanine, have shown that water mediated interactions can contribute to the energy of interaction.<sup id="cite_ref-17" class="reference"><a href="#cite_note-17"><span class="cite-bracket">[</span>17<span class="cite-bracket">]</span></a></sup> Thus, water molecules may facilitate the interactions and cross-recognitions between proteins. </p> <div class="mw-heading mw-heading2"><h2 id="Structure">Structure</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=12" title="Edit section: Structure"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main articles: <a href="/wiki/X-ray_crystallography" title="X-ray crystallography">X-ray crystallography</a> and <a href="/wiki/Nuclear_magnetic_resonance_spectroscopy" title="Nuclear magnetic resonance spectroscopy">Nuclear magnetic resonance spectroscopy</a></div> <p>The <a href="/wiki/Molecular_structure" class="mw-redirect" title="Molecular structure">molecular structures</a> of many protein complexes have been unlocked by the technique of <a href="/wiki/X-ray_crystallography" title="X-ray crystallography">X-ray crystallography</a>.<sup id="cite_ref-pmid2204619_18-0" class="reference"><a href="#cite_note-pmid2204619-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Alberts_19-0" class="reference"><a href="#cite_note-Alberts-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup> The first structure to be solved by this method was that of <a href="/wiki/Sperm_whale" title="Sperm whale">sperm whale</a> <a href="/wiki/Myoglobin" title="Myoglobin">myoglobin</a> by <a href="/wiki/John_Cowdery_Kendrew" class="mw-redirect" title="John Cowdery Kendrew">Sir John Cowdery Kendrew</a>.<sup id="cite_ref-20" class="reference"><a href="#cite_note-20"><span class="cite-bracket">[</span>20<span class="cite-bracket">]</span></a></sup> In this technique the angles and intensities of a beam of X-rays diffracted by crystalline atoms are detected in a film, thus producing a three-dimensional picture of the density of electrons within the crystal.<sup id="cite_ref-21" class="reference"><a href="#cite_note-21"><span class="cite-bracket">[</span>21<span class="cite-bracket">]</span></a></sup> </p><p>Later, <a href="/wiki/Nuclear_magnetic_resonance" title="Nuclear magnetic resonance">nuclear magnetic resonance</a> also started to be applied with the aim of unravelling the molecular structure of protein complexes. One of the first examples was the structure of calmodulin-binding domains bound to <a href="/wiki/Calmodulin" title="Calmodulin">calmodulin</a>.<sup id="cite_ref-Alberts_19-1" class="reference"><a href="#cite_note-Alberts-19"><span class="cite-bracket">[</span>19<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-NMR_22-0" class="reference"><a href="#cite_note-NMR-22"><span class="cite-bracket">[</span>22<span class="cite-bracket">]</span></a></sup> This technique is based on the study of magnetic properties of atomic nuclei, thus determining physical and chemical properties of the correspondent atoms or the molecules. Nuclear magnetic resonance is advantageous for characterizing weak PPIs.<sup id="cite_ref-23" class="reference"><a href="#cite_note-23"><span class="cite-bracket">[</span>23<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Protein-protein_interaction_domains">Protein-protein interaction domains</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=13" title="Edit section: Protein-protein interaction domains"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Protein_domain" title="Protein domain">Protein domain</a></div> <p>Some proteins have specific <a href="/wiki/Protein_domain" title="Protein domain">structural domains</a> or <a href="/wiki/Sequence_motifs" class="mw-redirect" title="Sequence motifs">sequence motifs</a> that provide binding to other proteins. Here are some examples of such domains: </p> <ul><li><i>Src homology 2 (SH2) domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/SH2_domain" title="SH2 domain">SH2 domain</a></div></li></ul> <dl><dd>SH2 domains are structurally composed by three-stranded twisted beta sheet sandwiched flanked by two alpha-helices. The existence of a deep binding pocket with high affinity for <a href="/wiki/Phosphotyrosine" class="mw-redirect" title="Phosphotyrosine">phosphotyrosine</a>, but not for <a href="/wiki/Phosphoserine" title="Phosphoserine">phosphoserine</a> or <a href="/wiki/Phosphothreonine" class="mw-redirect" title="Phosphothreonine">phosphothreonine</a>, is essential for the recognition of tyrosine phosphorylated proteins, mainly autophosphorylated <a href="/wiki/Growth_factor" title="Growth factor">growth factor</a> receptors. Growth factor receptor binding proteins and <a href="/wiki/Phospholipase_C" title="Phospholipase C">phospholipase C</a>γ are examples of proteins that have SH2 domains.<sup id="cite_ref-Berridge_24-0" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>Src homology 3 (SH3) domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/SH3_domain" title="SH3 domain">SH3 domain</a></div></li></ul> <dl><dd>Structurally, SH3 domains are constituted by a beta barrel formed by two orthogonal beta sheets and three anti-parallel beta strands. These domains recognize <a href="/wiki/Proline" title="Proline">proline</a> enriched sequences, as polyproline type II helical structure (PXXP motifs)<sup class="noprint Inline-Template" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Verifiability" title="Wikipedia:Verifiability"><span title="The material near this tag needs to be fact-checked with the cited source(s). (August 2014)">verification needed</span></a></i>]</sup> in cell signaling proteins like protein <a href="/wiki/Tyrosine_kinases" class="mw-redirect" title="Tyrosine kinases">tyrosine kinases</a> and the growth factor receptor bound protein 2 (<a href="/wiki/Grb2" class="mw-redirect" title="Grb2">Grb2</a>).<sup id="cite_ref-Berridge_24-1" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>Phosphotyrosine-binding (PTB) domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/PTB_domain" class="mw-redirect" title="PTB domain">PTB domain</a></div></li></ul> <dl><dd>PTB domains interact with sequences that contain a phosphotyrosine group. These domains can be found in the <a href="/wiki/Insulin_receptor_substrate" title="Insulin receptor substrate">insulin receptor substrate</a>.<sup id="cite_ref-Berridge_24-2" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>LIM domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/LIM_domain" title="LIM domain">LIM domain</a></div></li></ul> <dl><dd>LIM domains were initially identified in three <a href="/wiki/Homeodomain_transcription_factors" class="mw-redirect" title="Homeodomain transcription factors">homeodomain transcription factors</a> (lin11, is11, and mec3). In addition to this <a href="/wiki/Homeodomain_proteins" class="mw-redirect" title="Homeodomain proteins">homeodomain proteins</a> and other proteins involved in development, LIM domains have also been identified in non-homeodomain proteins with relevant roles in <a href="/wiki/Cellular_differentiation" title="Cellular differentiation">cellular differentiation</a>, association with <a href="/wiki/Cytoskeleton" title="Cytoskeleton">cytoskeleton</a> and <a href="/wiki/Senescence" title="Senescence">senescence</a>. These domains contain a tandem cysteine-rich <a href="/wiki/Zn-finger" class="mw-redirect" title="Zn-finger">Zn<sup>2+</sup>-finger motif</a> and embrace the <a href="/wiki/Consensus_sequence" title="Consensus sequence">consensus sequence</a> CX2CX16-23HX2CX2CX2CX16-21CX2C/H/D. LIM domains bind to PDZ domains, bHLH transcription factors, and other LIM domains.<sup id="cite_ref-Berridge_24-3" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>Sterile alpha motif (SAM) domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/SAM_domain" class="mw-redirect" title="SAM domain">SAM domain</a></div></li></ul> <dl><dd>SAM domains are composed by five helices forming a compact package with a conserved <a href="/wiki/Hydrophobic_core" class="mw-redirect" title="Hydrophobic core">hydrophobic core</a>. These domains, which can be found in the <a href="/wiki/Eph_receptor" class="mw-redirect" title="Eph receptor">Eph receptor</a> and the stromal interaction molecule (<a href="/wiki/STIM" title="STIM">STIM</a>) for example, bind to non-SAM domain-containing proteins and they also appear to have the ability to bind <a href="/wiki/RNA" title="RNA">RNA</a>.<sup id="cite_ref-Berridge_24-4" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>PDZ domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/PDZ_domain" title="PDZ domain">PDZ domain</a></div></li></ul> <dl><dd>PDZ domains were first identified in three guanylate kinases: PSD-95, DlgA and ZO-1. These domains recognize carboxy-terminal tri-peptide motifs (S/TXV), other <a href="/wiki/PDZ_domain" title="PDZ domain">PDZ domains</a> or <a href="/wiki/LIM_domain" title="LIM domain">LIM domains</a> and bind them through a short peptide sequence that has a <a href="/wiki/C-terminal" class="mw-redirect" title="C-terminal">C-terminal</a> hydrophobic residue. Some of the proteins identified as having PDZ domains are scaffolding proteins or seem to be involved in ion receptor assembling and receptor-enzyme complexes formation.<sup id="cite_ref-Berridge_24-5" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>FERM domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/FERM_domain" title="FERM domain">FERM domain</a></div></li></ul> <dl><dd>FERM domains contain basic residues capable of binding <a href="/wiki/Phosphatidylinositol_4,5-bisphosphate" title="Phosphatidylinositol 4,5-bisphosphate">PtdIns(4,5)P<sub>2</sub></a>. <a href="/wiki/Talin_protein" class="mw-redirect" title="Talin protein">Talin</a> and <a href="/wiki/Focal_adhesion_kinase" class="mw-redirect" title="Focal adhesion kinase">focal adhesion kinase</a> (FAK) are two of the proteins that present FERM domains.<sup id="cite_ref-Berridge_24-6" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>Calponin homology (CH) domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Calponin_homology_domain" title="Calponin homology domain">Calponin homology domain</a></div></li></ul> <dl><dd>CH domains are mainly present in cytoskeletal proteins as <a href="/wiki/PARVA" title="PARVA">parvin</a>.<sup id="cite_ref-Berridge_24-7" class="reference"><a href="#cite_note-Berridge-24"><span class="cite-bracket">[</span>24<span class="cite-bracket">]</span></a></sup></dd></dl> <ul><li><i>Pleckstrin homology domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Pleckstrin_homology_domain" title="Pleckstrin homology domain">Pleckstrin homology domain</a></div></li></ul> <dl><dd>Pleckstrin homology domains bind to phosphoinositides and acid domains in signaling proteins.</dd></dl> <ul><li><i>WW domain </i> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/WW_domain" title="WW domain">WW domain</a></div></li></ul> <dl><dd>WW domains bind to proline enriched sequences.</dd></dl> <ul><li><i>WSxWS motif </i></li></ul> <dl><dd>Found in cytokine receptors</dd></dl> <div class="mw-heading mw-heading2"><h2 id="Properties_of_the_interface">Properties of the interface</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=14" title="Edit section: Properties of the interface"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The study of the molecular structure can give fine details about the interface that enables the interaction between proteins. When characterizing PPI interfaces it is important to take into account the type of complex.<sup id="cite_ref-Jones_9-1" class="reference"><a href="#cite_note-Jones-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> </p><p>Parameters evaluated include size (measured in absolute dimensions <a href="/wiki/Angstrom" title="Angstrom">Å<sup>2</sup></a> or in <a href="/wiki/Solvent_accessible_surface_area" class="mw-redirect" title="Solvent accessible surface area">solvent-accessible surface area (SASA)</a>), shape, complementarity between surfaces, residue interface propensities, hydrophobicity, segmentation and secondary structure, and conformational changes on complex formation.<sup id="cite_ref-Jones_9-2" class="reference"><a href="#cite_note-Jones-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> </p><p>The great majority of PPI interfaces reflects the composition of protein surfaces, rather than the protein cores, in spite of being frequently enriched in hydrophobic residues, particularly in aromatic residues.<sup id="cite_ref-Yan_25-0" class="reference"><a href="#cite_note-Yan-25"><span class="cite-bracket">[</span>25<span class="cite-bracket">]</span></a></sup> PPI interfaces are dynamic and frequently planar, although they can be globular and protruding as well.<sup id="cite_ref-JonesJMB_26-0" class="reference"><a href="#cite_note-JonesJMB-26"><span class="cite-bracket">[</span>26<span class="cite-bracket">]</span></a></sup> Based on three structures – <a href="/wiki/Insulin" title="Insulin">insulin</a> dimer, <a href="/wiki/Trypsin" title="Trypsin">trypsin</a>-pancreatic trypsin inhibitor complex, and <a href="/wiki/Oxyhaemoglobin" class="mw-redirect" title="Oxyhaemoglobin">oxyhaemoglobin</a> – <a href="/wiki/Cyrus_Chothia" title="Cyrus Chothia">Cyrus Chothia</a> and Joel Janin found that between 1,130 and 1,720 Å<sup>2</sup> of surface area was removed from contact with water indicating that hydrophobicity is a major factor of stabilization of PPIs.<sup id="cite_ref-pmid1153006_27-0" class="reference"><a href="#cite_note-pmid1153006-27"><span class="cite-bracket">[</span>27<span class="cite-bracket">]</span></a></sup> Later studies refined the buried surface area of the majority of interactions to 1,600±350 Å<sup>2</sup>. However, much larger interaction interfaces were also observed and were associated with <a href="/wiki/Conformational_change" title="Conformational change">significant changes in conformation</a> of one of the interaction partners.<sup id="cite_ref-pmid2204619_18-1" class="reference"><a href="#cite_note-pmid2204619-18"><span class="cite-bracket">[</span>18<span class="cite-bracket">]</span></a></sup> PPIs interfaces exhibit both shape and electrostatic complementarity.<sup id="cite_ref-Jones_9-3" class="reference"><a href="#cite_note-Jones-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-pmid=21873996_11-1" class="reference"><a href="#cite_note-pmid=21873996-11"><span class="cite-bracket">[</span>11<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Regulation">Regulation</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=15" title="Edit section: Regulation"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li>Protein concentration, which in turn are affected by expression levels and degradation rates;</li> <li>Protein affinity for proteins or other binding ligands;</li> <li>Ligands concentrations (<a href="/wiki/Substrate_(biochemistry)" class="mw-redirect" title="Substrate (biochemistry)">substrates</a>, <a href="/wiki/Ions" class="mw-redirect" title="Ions">ions</a>, etc.);</li> <li>Presence of other <a href="/wiki/Proteins" class="mw-redirect" title="Proteins">proteins</a>, <a href="/wiki/Nucleic_acids" class="mw-redirect" title="Nucleic acids">nucleic acids</a>, and <a href="/wiki/Ions" class="mw-redirect" title="Ions">ions</a>;</li> <li><a href="/wiki/Electric_field" title="Electric field">Electric fields</a> around proteins.</li> <li>Occurrence of covalent modifications;</li></ul> <div class="mw-heading mw-heading2"><h2 id="Experimental_methods">Experimental methods</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=16" title="Edit section: Experimental methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Methods_to_investigate_protein%E2%80%93protein_interactions" title="Methods to investigate protein–protein interactions">Methods to investigate protein–protein interactions</a></div> <p>There are a multitude of methods to detect them.<sup id="cite_ref-Titeca_2019_1-1" class="reference"><a href="#cite_note-Titeca_2019-1"><span class="cite-bracket">[</span>1<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-pmid7708014_28-0" class="reference"><a href="#cite_note-pmid7708014-28"><span class="cite-bracket">[</span>28<span class="cite-bracket">]</span></a></sup> Each of the approaches has its own strengths and weaknesses, especially with regard to the <a href="/wiki/Sensitivity_and_specificity" title="Sensitivity and specificity">sensitivity and specificity</a> of the method. The most conventional and widely used high-throughput methods are <a href="/wiki/Yeast_two-hybrid_screening" class="mw-redirect" title="Yeast two-hybrid screening">yeast two-hybrid screening</a> and <a href="/wiki/Affinity_purification" class="mw-redirect" title="Affinity purification">affinity purification</a> coupled to <a href="/wiki/Mass_spectrometry" title="Mass spectrometry">mass spectrometry</a>. </p> <figure class="mw-default-size mw-halign-left" typeof="mw:File/Thumb"><a href="/wiki/File:Principles_of_yeast_and_mammalian_two-hybrid_systems.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Principles_of_yeast_and_mammalian_two-hybrid_systems.svg/220px-Principles_of_yeast_and_mammalian_two-hybrid_systems.svg.png" decoding="async" width="220" height="152" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Principles_of_yeast_and_mammalian_two-hybrid_systems.svg/330px-Principles_of_yeast_and_mammalian_two-hybrid_systems.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/0/0e/Principles_of_yeast_and_mammalian_two-hybrid_systems.svg/440px-Principles_of_yeast_and_mammalian_two-hybrid_systems.svg.png 2x" data-file-width="404" data-file-height="280" /></a><figcaption>Principles of yeast and mammalian two-hybrid systems</figcaption></figure> <div class="mw-heading mw-heading3"><h3 id="Yeast_two-hybrid_screening">Yeast two-hybrid screening</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=17" title="Edit section: Yeast two-hybrid screening"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Two-hybrid_screening" title="Two-hybrid screening">Two-hybrid screening</a></div> <p>This system was firstly described in 1989 by Fields and Song using <i>Saccharomyces cerevisiae</i> as biological model.<sup id="cite_ref-29" class="reference"><a href="#cite_note-29"><span class="cite-bracket">[</span>29<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-30" class="reference"><a href="#cite_note-30"><span class="cite-bracket">[</span>30<span class="cite-bracket">]</span></a></sup> Yeast two hybrid allows the identification of pairwise PPIs (binary method) <i>in vivo</i>, in which the two proteins are tested for biophysically direct interaction. The Y2H is based on the functional reconstitution of the yeast transcription factor Gal4 and subsequent activation of a selective reporter such as His3. To test two proteins for interaction, two protein expression constructs are made: one protein (X) is fused to the Gal4 DNA-binding domain (DB) and a second protein (Y) is fused to the Gal4 activation domain (AD). In the assay, yeast cells are transformed with these constructs. Transcription of reporter genes does not occur unless bait (DB-X) and prey (AD-Y) interact with each other and form a functional Gal4 transcription factor. Thus, the interaction between proteins can be inferred by the presence of the products resultant of the reporter gene expression.<sup id="cite_ref-Jukka_13-1" class="reference"><a href="#cite_note-Jukka-13"><span class="cite-bracket">[</span>13<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Wodak_31-0" class="reference"><a href="#cite_note-Wodak-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> In cases in which the reporter gene expresses enzymes that allow the yeast to synthesize essential amino acids or nucleotides, yeast growth under selective media conditions indicates that the two proteins tested are interacting. Recently, software to detect and prioritize protein interactions was published.<sup id="cite_ref-Banerjee_32-0" class="reference"><a href="#cite_note-Banerjee-32"><span class="cite-bracket">[</span>32<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Velásquez-Zapata_33-0" class="reference"><a href="#cite_note-Velásquez-Zapata-33"><span class="cite-bracket">[</span>33<span class="cite-bracket">]</span></a></sup> </p><p>Despite its usefulness, the yeast two-hybrid system has limitations. It uses yeast as main host system, which can be a problem when studying proteins that contain mammalian-specific post-translational modifications. The number of PPIs identified is usually low because of a high false negative rate;<sup id="cite_ref-34" class="reference"><a href="#cite_note-34"><span class="cite-bracket">[</span>34<span class="cite-bracket">]</span></a></sup> and, understates <a href="/wiki/Membrane_proteins" class="mw-redirect" title="Membrane proteins">membrane proteins</a>, for example.<sup id="cite_ref-Stelzl_35-0" class="reference"><a href="#cite_note-Stelzl-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Pets_36-0" class="reference"><a href="#cite_note-Pets-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> </p><p>In initial studies that utilized Y2H, proper controls for false positives (e.g. when DB-X activates the reporter gene without the presence of AD-Y) were frequently not done, leading to a higher than normal false positive rate. An empirical framework must be implemented to control for these false positives.<sup id="cite_ref-37" class="reference"><a href="#cite_note-37"><span class="cite-bracket">[</span>37<span class="cite-bracket">]</span></a></sup> Limitations in lower coverage of membrane proteins have been overcoming by the emergence of yeast two-hybrid variants, such as the membrane yeast two-hybrid (MYTH)<sup id="cite_ref-Pets_36-1" class="reference"><a href="#cite_note-Pets-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> and the split-ubiquitin system,<sup id="cite_ref-Wodak_31-1" class="reference"><a href="#cite_note-Wodak-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> which are not limited to interactions that occur in the nucleus; and, the bacterial two-hybrid system, performed in bacteria;<sup id="cite_ref-38" class="reference"><a href="#cite_note-38"><span class="cite-bracket">[</span>38<span class="cite-bracket">]</span></a></sup> </p> <figure class="mw-default-size mw-halign-left" typeof="mw:File/Thumb"><a href="/wiki/File:Principle_of_Tandem_Affinity_Purification.svg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/9/96/Principle_of_Tandem_Affinity_Purification.svg/220px-Principle_of_Tandem_Affinity_Purification.svg.png" decoding="async" width="220" height="160" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/9/96/Principle_of_Tandem_Affinity_Purification.svg/330px-Principle_of_Tandem_Affinity_Purification.svg.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/9/96/Principle_of_Tandem_Affinity_Purification.svg/440px-Principle_of_Tandem_Affinity_Purification.svg.png 2x" data-file-width="342" data-file-height="249" /></a><figcaption>Principle of tandem affinity purification</figcaption></figure> <div class="mw-heading mw-heading3"><h3 id="Affinity_purification_coupled_to_mass_spectrometry">Affinity purification coupled to mass spectrometry</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=18" title="Edit section: Affinity purification coupled to mass spectrometry"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Mass_spectrometry" title="Mass spectrometry">Mass spectrometry</a></div> <p>Affinity purification coupled to mass spectrometry mostly detects stable interactions and thus better indicates functional in vivo PPIs.<sup id="cite_ref-pmid23017156|noedit_39-0" class="reference"><a href="#cite_note-pmid23017156|noedit-39"><span class="cite-bracket">[</span>39<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Wodak_31-2" class="reference"><a href="#cite_note-Wodak-31"><span class="cite-bracket">[</span>31<span class="cite-bracket">]</span></a></sup> This method starts by purification of the tagged protein, which is expressed in the cell usually at <i>in vivo</i> concentrations, and its interacting proteins (affinity purification). One of the most advantageous and widely used methods to purify proteins with very low contaminating background is the <a href="/wiki/Tandem_affinity_purification" title="Tandem affinity purification">tandem affinity purification</a>, developed by Bertrand Seraphin and Matthias Mann and respective colleagues. PPIs can then be quantitatively and qualitatively analysed by mass spectrometry using different methods: chemical incorporation, biological or metabolic incorporation (SILAC), and label-free methods.<sup id="cite_ref-Jones_9-4" class="reference"><a href="#cite_note-Jones-9"><span class="cite-bracket">[</span>9<span class="cite-bracket">]</span></a></sup> Furthermore, <a href="/wiki/Network_theory" title="Network theory">network theory</a> has been used to study the whole set of identified protein–protein interactions in cells.<sup id="cite_ref-Mashaghi,_A._2004_113–121_4-1" class="reference"><a href="#cite_note-Mashaghi,_A._2004_113–121-4"><span class="cite-bracket">[</span>4<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Nucleic_acid_programmable_protein_array_(NAPPA)"><span id="Nucleic_acid_programmable_protein_array_.28NAPPA.29"></span>Nucleic acid programmable protein array (NAPPA)</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=19" title="Edit section: Nucleic acid programmable protein array (NAPPA)"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>This system was first developed by LaBaer and colleagues in 2004 by using in vitro transcription and translation system. They use DNA template encoding the gene of interest fused with GST protein, and it was immobilized in the solid surface. Anti-GST antibody and biotinylated plasmid DNA were bounded in aminopropyltriethoxysilane (APTES)-coated slide. BSA can improve the binding efficiency of DNA. Biotinylated plasmid DNA was bound by avidin. New protein was synthesized by using cell-free expression system i.e. rabbit reticulocyte lysate (RRL), and then the new protein was captured through anti-GST antibody bounded on the slide. To test protein–protein interaction, the targeted protein cDNA and query protein cDNA were immobilized in a same coated slide. By using in vitro transcription and translation system, targeted and query protein was synthesized by the same extract. The targeted protein was bound to array by antibody coated in the slide and query protein was used to probe the array. The query protein was tagged with hemagglutinin (HA) epitope. Thus, the interaction between the two proteins was visualized with the antibody against HA.<sup id="cite_ref-40" class="reference"><a href="#cite_note-40"><span class="cite-bracket">[</span>40<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-41" class="reference"><a href="#cite_note-41"><span class="cite-bracket">[</span>41<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Intragenic_complementation">Intragenic complementation</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=20" title="Edit section: Intragenic complementation"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>When multiple copies of a polypeptide encoded by a <a href="/wiki/Gene" title="Gene">gene</a> form a complex, this protein structure is referred to as a multimer. When a multimer is formed from polypeptides produced by two different <a href="/wiki/Mutant" title="Mutant">mutant</a> <a href="/wiki/Allele" title="Allele">alleles</a> of a particular gene, the mixed multimer may exhibit greater functional activity than the unmixed multimers formed by each of the mutants alone. In such a case, the phenomenon is referred to as <a href="/wiki/Complementation_(genetics)" title="Complementation (genetics)">intragenic complementation</a> (also called inter-allelic complementation). Intragenic complementation has been demonstrated in many different genes in a variety of organisms including the fungi <i><a href="/wiki/Neurospora_crassa" title="Neurospora crassa">Neurospora crassa</a></i>, <i><a href="/wiki/Saccharomyces_cerevisiae" title="Saccharomyces cerevisiae">Saccharomyces cerevisiae</a></i> and <i><a href="/wiki/Schizosaccharomyces_pombe" title="Schizosaccharomyces pombe">Schizosaccharomyces pombe</a></i>; the bacterium <i><a href="/wiki/Salmonella" title="Salmonella">Salmonella</a> typhimurium</i>; the virus <a href="/wiki/Escherichia_virus_T4" title="Escherichia virus T4">bacteriophage T4</a>,<sup id="cite_ref-42" class="reference"><a href="#cite_note-42"><span class="cite-bracket">[</span>42<span class="cite-bracket">]</span></a></sup> an RNA virus<sup id="cite_ref-pmid12504565_43-0" class="reference"><a href="#cite_note-pmid12504565-43"><span class="cite-bracket">[</span>43<span class="cite-bracket">]</span></a></sup> and humans.<sup id="cite_ref-pmid15949719_44-0" class="reference"><a href="#cite_note-pmid15949719-44"><span class="cite-bracket">[</span>44<span class="cite-bracket">]</span></a></sup> In such studies, numerous <a href="/wiki/Mutation" title="Mutation">mutations</a> defective in the same gene were often isolated and mapped in a linear order on the basis of <a href="/wiki/Genetic_recombination" title="Genetic recombination">recombination</a> frequencies to form a <a href="/wiki/Gene_mapping" title="Gene mapping">genetic map</a> of the gene. Separately, the mutants were tested in pairwise combinations to measure complementation. An analysis of the results from such studies led to the conclusion that intragenic complementation, in general, arises from the interaction of differently defective polypeptide monomers to form a multimer.<sup id="cite_ref-pmid14149958_45-0" class="reference"><a href="#cite_note-pmid14149958-45"><span class="cite-bracket">[</span>45<span class="cite-bracket">]</span></a></sup> Genes that encode multimer-forming polypeptides appear to be common. One interpretation of the data is that polypeptide monomers are often aligned in the multimer in such a way that mutant polypeptides defective at nearby sites in the genetic map tend to form a mixed multimer that functions poorly, whereas mutant polypeptides defective at distant sites tend to form a mixed multimer that functions more effectively. Direct interaction of two nascent proteins emerging from nearby <a href="/wiki/Ribosome" title="Ribosome">ribosomes</a> appears to be a general mechanism for homo-oligomer (multimer) formation.<sup id="cite_ref-Bertolini2021_46-0" class="reference"><a href="#cite_note-Bertolini2021-46"><span class="cite-bracket">[</span>46<span class="cite-bracket">]</span></a></sup> Hundreds of protein oligomers were identified that assemble in human cells by such an interaction.<sup id="cite_ref-Bertolini2021_46-1" class="reference"><a href="#cite_note-Bertolini2021-46"><span class="cite-bracket">[</span>46<span class="cite-bracket">]</span></a></sup> The most prevalent form of interaction is between the N-terminal regions of the interacting proteins. Dimer formation appears to be able to occur independently of dedicated assembly machines. The intermolecular forces likely responsible for self-recognition and multimer formation were discussed by Jehle.<sup id="cite_ref-Jehle_1963_47-0" class="reference"><a href="#cite_note-Jehle_1963-47"><span class="cite-bracket">[</span>47<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Other_potential_methods">Other potential methods</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=21" title="Edit section: Other potential methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Diverse techniques to identify PPIs have been emerging along with technology progression. These include co-immunoprecipitation, <a href="/wiki/Microarrays" class="mw-redirect" title="Microarrays">protein microarrays</a>, <a href="/wiki/Analytical_ultracentrifugation" title="Analytical ultracentrifugation">analytical ultracentrifugation</a>, <a href="/wiki/Light_scattering" class="mw-redirect" title="Light scattering">light scattering</a>, <a href="/wiki/Fluorescence_spectroscopy" title="Fluorescence spectroscopy">fluorescence spectroscopy</a>, luminescence-based mammalian interactome mapping (LUMIER), resonance-energy transfer systems, mammalian protein–protein interaction trap, <a href="/wiki/Electro-switchable_biosurfaces" class="mw-redirect" title="Electro-switchable biosurfaces">electro-switchable biosurfaces</a>, <a href="/w/index.php?title=Protein%E2%80%93fragment_complementation_assay&action=edit&redlink=1" class="new" title="Protein–fragment complementation assay (page does not exist)">protein–fragment complementation assay</a>, as well as real-time label-free measurements by <a href="/wiki/Surface_plasmon_resonance" title="Surface plasmon resonance">surface plasmon resonance</a>, and <a href="/wiki/Calorimetry" title="Calorimetry">calorimetry</a>.<sup id="cite_ref-Stelzl_35-1" class="reference"><a href="#cite_note-Stelzl-35"><span class="cite-bracket">[</span>35<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-Pets_36-2" class="reference"><a href="#cite_note-Pets-36"><span class="cite-bracket">[</span>36<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Computational_methods">Computational methods</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=22" title="Edit section: Computational methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Text_mining_protocol.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/2/21/Text_mining_protocol.png/220px-Text_mining_protocol.png" decoding="async" width="220" height="565" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/2/21/Text_mining_protocol.png 1.5x" data-file-width="237" data-file-height="609" /></a><figcaption><a href="/wiki/Text_mining" title="Text mining">Text mining</a> protocol.</figcaption></figure> <div class="mw-heading mw-heading3"><h3 id="Computational_prediction_of_protein–protein_interactions"><span id="Computational_prediction_of_protein.E2.80.93protein_interactions"></span><a href="/wiki/Protein%E2%80%93protein_interaction_prediction" title="Protein–protein interaction prediction">Computational prediction of protein–protein interactions</a></h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=23" title="Edit section: Computational prediction of protein–protein interactions"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>The experimental detection and characterization of PPIs is labor-intensive and time-consuming. However, many PPIs can be also predicted computationally, usually using experimental data as a starting point. However, methods have also been developed that allow the prediction of PPI de novo, that is without prior evidence for these interactions. </p> <div class="mw-heading mw-heading4"><h4 id="Genomic_context_methods">Genomic context methods</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=24" title="Edit section: Genomic context methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><i><a href="/wiki/Protein%E2%80%93protein_interaction_prediction" title="Protein–protein interaction prediction">The Rosetta Stone or Domain Fusion method</a></i> is based on the hypothesis that interacting proteins are sometimes fused into a single protein in another genome.<sup id="cite_ref-48" class="reference"><a href="#cite_note-48"><span class="cite-bracket">[</span>48<span class="cite-bracket">]</span></a></sup> Therefore, we can predict if two proteins may be interacting by determining if they each have non-overlapping sequence similarity to a region of a single protein sequence in another genome. </p><p><i><a href="/wiki/Protein%E2%80%93protein_interaction_prediction" title="Protein–protein interaction prediction">The Conserved Neighborhood method</a></i> is based on the hypothesis that if genes encoding two proteins are neighbors on a chromosome in many genomes, then they are likely functionally related (and possibly physically interacting).<sup id="cite_ref-Raman_2010_49-0" class="reference"><a href="#cite_note-Raman_2010-49"><span class="cite-bracket">[</span>49<span class="cite-bracket">]</span></a></sup> </p><p><i><a href="/wiki/Protein%E2%80%93protein_interaction_prediction" title="Protein–protein interaction prediction">The Phylogenetic Profile method</a></i> is based on the hypothesis that if two or more proteins are concurrently present or absent across several genomes, then they are likely functionally related.<sup id="cite_ref-Raman_2010_49-1" class="reference"><a href="#cite_note-Raman_2010-49"><span class="cite-bracket">[</span>49<span class="cite-bracket">]</span></a></sup> Therefore, potentially interacting proteins can be identified by determining the presence or absence of genes across many genomes and selecting those genes which are always present or absent together. </p> <div class="mw-heading mw-heading3"><h3 id="Text_mining_methods">Text mining methods</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=25" title="Edit section: Text mining methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Further information: <a href="/wiki/Text_mining" title="Text mining">Text mining</a></div><p>Publicly available information from biomedical documents is readily accessible through the internet and is becoming a powerful resource for collecting known protein–protein interactions (PPIs), PPI prediction and protein docking. Text mining is much less costly and time-consuming compared to other high-throughput techniques. Currently, text mining methods generally detect <a href="/wiki/Binary_relation" title="Binary relation">binary relations</a> between interacting proteins from individual sentences using rule/pattern-based information extraction and <a href="/wiki/Machine_learning" title="Machine learning">machine learning</a> approaches.<sup id="cite_ref-50" class="reference"><a href="#cite_note-50"><span class="cite-bracket">[</span>50<span class="cite-bracket">]</span></a></sup> A wide variety of text mining applications for PPI extraction and/or prediction are available for public use, as well as repositories which often store manually validated and/or computationally predicted PPIs. Text mining can be implemented in two stages: <i>information retrieval</i>, where texts containing names of either or both interacting proteins are retrieved and <i>information extraction,</i> where targeted information (interacting proteins, implicated residues, interaction types, etc.) is extracted. </p><p>There are also studies using <a href="/wiki/Phylogenetic_profiling" title="Phylogenetic profiling">phylogenetic profiling</a>, basing their functionalities on the theory that proteins involved in common pathways co-evolve in a correlated fashion across species. Some more complex text mining methodologies use advanced <a href="/wiki/Natural_Language_Processing" class="mw-redirect" title="Natural Language Processing">Natural Language Processing</a> (NLP) techniques and build knowledge networks (for example, considering gene names as nodes and verbs as edges). Other developments involve <a href="/wiki/Kernel_method" title="Kernel method">kernel methods</a> to predict protein interactions.<sup id="cite_ref-51" class="reference"><a href="#cite_note-51"><span class="cite-bracket">[</span>51<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Machine_learning_methods">Machine learning methods</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=26" title="Edit section: Machine learning methods"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Sarkar%26Saha_Figure1A.png" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/5/52/Sarkar%26Saha_Figure1A.png/220px-Sarkar%26Saha_Figure1A.png" decoding="async" width="220" height="98" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/5/52/Sarkar%26Saha_Figure1A.png/330px-Sarkar%26Saha_Figure1A.png 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/5/52/Sarkar%26Saha_Figure1A.png/440px-Sarkar%26Saha_Figure1A.png 2x" data-file-width="1217" data-file-height="542" /></a><figcaption>Machine-learning technique classification hierarchy.</figcaption></figure> <p>Many computational methods have been suggested and reviewed for predicting protein–protein interactions.<sup id="cite_ref-kotlyar_52-0" class="reference"><a href="#cite_note-kotlyar-52"><span class="cite-bracket">[</span>52<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-ding_53-0" class="reference"><a href="#cite_note-ding-53"><span class="cite-bracket">[</span>53<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-sarkar_54-0" class="reference"><a href="#cite_note-sarkar-54"><span class="cite-bracket">[</span>54<span class="cite-bracket">]</span></a></sup> Prediction approaches can be grouped into categories based on predictive evidence: protein sequence, <a href="/wiki/Comparative_genomics" title="Comparative genomics">comparative genomics</a>, protein domains, protein tertiary structure, and interaction network topology.<sup id="cite_ref-kotlyar_52-1" class="reference"><a href="#cite_note-kotlyar-52"><span class="cite-bracket">[</span>52<span class="cite-bracket">]</span></a></sup> The construction of a positive set (known interacting protein pairs) and a negative set (non-interacting protein pairs) is needed for the development of a computational prediction model.<sup id="cite_ref-ding_53-1" class="reference"><a href="#cite_note-ding-53"><span class="cite-bracket">[</span>53<span class="cite-bracket">]</span></a></sup> Prediction models using machine learning techniques can be broadly classified into two main groups: supervised and unsupervised, based on the labeling of input variables according to the expected outcome.<sup id="cite_ref-sarkar_54-1" class="reference"><a href="#cite_note-sarkar-54"><span class="cite-bracket">[</span>54<span class="cite-bracket">]</span></a></sup> </p><p>In 2005, integral membrane proteins of <a href="/wiki/Saccharomyces_cerevisiae" title="Saccharomyces cerevisiae">Saccharomyces cerevisiae</a> were analyzed using the mating-based ubiquitin system (mbSUS). The system detects membrane proteins interactions with extracellular signaling proteins<sup id="cite_ref-55" class="reference"><a href="#cite_note-55"><span class="cite-bracket">[</span>55<span class="cite-bracket">]</span></a></sup> Of the 705 integral membrane proteins 1,985 different interactions were traced that involved 536 proteins. To sort and classify interactions a support vector machine was used to define high medium and low confidence interactions. The split-ubiquitin membrane yeast two-hybrid system uses transcriptional reporters to identify yeast transformants that encode pairs of interacting proteins.<sup id="cite_ref-56" class="reference"><a href="#cite_note-56"><span class="cite-bracket">[</span>56<span class="cite-bracket">]</span></a></sup> In 2006, <a href="/wiki/Random_forest" title="Random forest">random forest</a>, an example of a supervised technique, was found to be the most-effective machine learning method for protein interaction prediction.<sup id="cite_ref-57" class="reference"><a href="#cite_note-57"><span class="cite-bracket">[</span>57<span class="cite-bracket">]</span></a></sup> Such methods have been applied for discovering protein interactions on human interactome, specifically the interactome of <a href="/wiki/Membrane_proteins" class="mw-redirect" title="Membrane proteins">Membrane proteins</a><sup id="cite_ref-58" class="reference"><a href="#cite_note-58"><span class="cite-bracket">[</span>58<span class="cite-bracket">]</span></a></sup> and the interactome of Schizophrenia-associated proteins.<sup id="cite_ref-mkgnpjS_59-0" class="reference"><a href="#cite_note-mkgnpjS-59"><span class="cite-bracket">[</span>59<span class="cite-bracket">]</span></a></sup> </p><p>As of 2020, a model using residue cluster classes (RCCs), constructed from the <a href="/wiki/3did" title="3did">3DID</a> and Negatome databases, resulted in 96-99% correctly classified instances of protein–protein interactions.<sup id="cite_ref-60" class="reference"><a href="#cite_note-60"><span class="cite-bracket">[</span>60<span class="cite-bracket">]</span></a></sup> RCCs are a computational vector space that mimics protein fold space and includes all simultaneously contacted residue sets, which can be used to analyze protein structure-function relation and evolution.<sup id="cite_ref-61" class="reference"><a href="#cite_note-61"><span class="cite-bracket">[</span>61<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading2"><h2 id="Databases">Databases</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=27" title="Edit section: Databases"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Large scale identification of PPIs generated hundreds of thousands of interactions, which were collected together in specialized <a href="/wiki/Biological_databases" class="mw-redirect" title="Biological databases">biological databases</a> that are continuously updated in order to provide complete <a href="/wiki/Interactomes" class="mw-redirect" title="Interactomes">interactomes</a>. The first of these databases was the <a href="/wiki/Database_of_Interacting_Proteins" title="Database of Interacting Proteins">Database of Interacting Proteins (DIP)</a>.<sup id="cite_ref-pmid10592249_62-0" class="reference"><a href="#cite_note-pmid10592249-62"><span class="cite-bracket">[</span>62<span class="cite-bracket">]</span></a></sup> </p><p><i>Primary databases</i> collect information about published PPIs proven to exist via small-scale or large-scale experimental methods. Examples: <a href="/wiki/Database_of_Interacting_Proteins" title="Database of Interacting Proteins">DIP</a>, <a href="/wiki/Biomolecular_Interaction_Network_Database" class="mw-redirect" title="Biomolecular Interaction Network Database">Biomolecular Interaction Network Database</a> (BIND), Biological General Repository for Interaction Datasets (<a href="/wiki/BioGRID" title="BioGRID">BioGRID</a>), Human Protein Reference Database (HPRD), IntAct Molecular Interaction Database, Molecular Interactions Database (MINT), MIPS Protein Interaction Resource on Yeast (MIPS-MPact), and MIPS Mammalian Protein–Protein Interaction Database (MIPS-MPPI).< </p><p><i>Meta-databases</i> normally result from the integration of primary databases information, but can also collect some original data. </p><p><i>Prediction databases</i> include many PPIs that are predicted using several techniques (main article). Examples: Human Protein–Protein Interaction Prediction Database (PIPs),<sup id="cite_ref-McDowallScott2009_63-0" class="reference"><a href="#cite_note-McDowallScott2009-63"><span class="cite-bracket">[</span>63<span class="cite-bracket">]</span></a></sup> Interlogous Interaction Database (I2D), <a href="/wiki/STRING" title="STRING">Known and Predicted Protein–Protein Interactions (STRING-db)</a>, and Unified Human Interactive (UniHI). </p><p>The aforementioned computational methods all depend on source databases whose data can be extrapolated to predict novel protein–protein interactions<i>. Coverage</i> differs greatly between databases. In general, primary databases have the fewest total protein interactions recorded as they do not integrate data from multiple other databases, while prediction databases have the most because they include other forms of evidence in addition to experimental. For example, the primary database IntAct has 572,063 interactions,<sup id="cite_ref-64" class="reference"><a href="#cite_note-64"><span class="cite-bracket">[</span>64<span class="cite-bracket">]</span></a></sup> the meta-database APID has 678,000 interactions,<sup id="cite_ref-65" class="reference"><a href="#cite_note-65"><span class="cite-bracket">[</span>65<span class="cite-bracket">]</span></a></sup> and the predictive database STRING has 25,914,693 interactions.<sup id="cite_ref-66" class="reference"><a href="#cite_note-66"><span class="cite-bracket">[</span>66<span class="cite-bracket">]</span></a></sup> However, it is important to note that some of the interactions in the STRING database are only predicted by computational methods such as Genomic Context and not experimentally verified. </p> <div class="mw-heading mw-heading2"><h2 id="Interaction_networks">Interaction networks</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=28" title="Edit section: Interaction networks"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1236090951"><div role="note" class="hatnote navigation-not-searchable">Main article: <a href="/wiki/Interactome" title="Interactome">Interactome</a></div> <figure class="mw-default-size mw-halign-right" typeof="mw:File/Thumb"><a href="/wiki/File:Schziophrenia_PPI.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Schziophrenia_PPI.jpg/220px-Schziophrenia_PPI.jpg" decoding="async" width="220" height="201" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Schziophrenia_PPI.jpg/330px-Schziophrenia_PPI.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/1/1d/Schziophrenia_PPI.jpg/440px-Schziophrenia_PPI.jpg 2x" data-file-width="783" data-file-height="716" /></a><figcaption>Schizophrenia PPI.<sup id="cite_ref-mkgnpjS_59-1" class="reference"><a href="#cite_note-mkgnpjS-59"><span class="cite-bracket">[</span>59<span class="cite-bracket">]</span></a></sup></figcaption></figure> <p>Information found in PPIs databases supports the construction of interaction networks. Although the PPI network of a given query protein can be represented in textbooks, diagrams of whole cell PPIs are frankly complex and difficult to generate.<sup id="cite_ref-67" class="reference"><a href="#cite_note-67"><span class="cite-bracket">[</span>67<span class="cite-bracket">]</span></a></sup> </p><p>One example of a manually produced molecular interaction map is the Kurt Kohn's 1999 map of cell cycle control.<sup id="cite_ref-68" class="reference"><a href="#cite_note-68"><span class="cite-bracket">[</span>68<span class="cite-bracket">]</span></a></sup> Drawing on Kohn's map, Schwikowski et al. in 2000 published a paper on PPIs in yeast, linking 1,548 interacting proteins determined by two-hybrid screening. They used a layered graph drawing method to find an initial placement of the nodes and then improved the layout using a force-based algorithm.<sup id="cite_ref-69" class="reference"><a href="#cite_note-69"><span class="cite-bracket">[</span>69<span class="cite-bracket">]</span></a></sup> </p><p>Bioinformatic tools have been developed to simplify the difficult task of visualizing molecular interaction networks and complement them with other types of data. For instance, <a href="/wiki/Cytoscape" title="Cytoscape">Cytoscape</a> is an open-source software widely used and many plugins are currently available.<sup id="cite_ref-70" class="reference"><a href="#cite_note-70"><span class="cite-bracket">[</span>70<span class="cite-bracket">]</span></a></sup> Pajek software is advantageous for the visualization and analysis of very large networks.<sup id="cite_ref-Raman_2010_49-2" class="reference"><a href="#cite_note-Raman_2010-49"><span class="cite-bracket">[</span>49<span class="cite-bracket">]</span></a></sup> </p><p>Identification of functional modules in PPI networks is an important challenge in bioinformatics. Functional modules means a set of proteins that are highly <a href="/wiki/Connectivity_(graph_theory)" title="Connectivity (graph theory)">connected</a> to each other in PPI network. It is almost similar problem as community detection in <a href="/wiki/Social_network" title="Social network">social networks</a>. There are some methods such as Jactive<sup id="cite_ref-71" class="reference"><a href="#cite_note-71"><span class="cite-bracket">[</span>71<span class="cite-bracket">]</span></a></sup> modules and MoBaS.<sup id="cite_ref-72" class="reference"><a href="#cite_note-72"><span class="cite-bracket">[</span>72<span class="cite-bracket">]</span></a></sup> Jactive modules integrate PPI network and <a href="/wiki/Gene_expression" title="Gene expression">gene expression</a> data where as MoBaS integrate PPI network and <a href="/wiki/Genome-wide_association_study" title="Genome-wide association study">Genome Wide association Studies</a>. </p><p>protein–protein relationships are often the result of multiple types of interactions or are deduced from different approaches, including co-localization, direct interaction, suppressive genetic interaction, additive genetic interaction, physical association, and other associations.<sup id="cite_ref-73" class="reference"><a href="#cite_note-73"><span class="cite-bracket">[</span>73<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Signed_interaction_networks">Signed interaction networks</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=29" title="Edit section: Signed interaction networks"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <figure class="mw-default-size" typeof="mw:File/Thumb"><a href="/wiki/File:Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg" class="mw-file-description"><img src="//upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg/220px-Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg" decoding="async" width="220" height="93" class="mw-file-element" srcset="//upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg/330px-Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg 1.5x, //upload.wikimedia.org/wikipedia/commons/thumb/e/ea/Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg/440px-Genetic_interactions_between_Ras_signalling_and_chromatin_remodelling-A.jpg 2x" data-file-width="445" data-file-height="188" /></a><figcaption>The protein protein interactions are displayed in a signed network that describes what type of interactions that are taking place<sup id="cite_ref-74" class="reference"><a href="#cite_note-74"><span class="cite-bracket">[</span>74<span class="cite-bracket">]</span></a></sup></figcaption></figure> <p>Protein–protein interactions often result in one of the interacting proteins either being 'activated' or 'repressed'. Such effects can be indicated in a PPI network by "signs" (e.g. "activation" or "inhibition"). Although such attributes have been added to networks for a long time,<sup id="cite_ref-75" class="reference"><a href="#cite_note-75"><span class="cite-bracket">[</span>75<span class="cite-bracket">]</span></a></sup> Vinayagam et al. (2014) coined the term <i>Signed network</i> for them. Signed networks are often expressed by labeling the interaction as either positive or negative. A positive interaction is one where the interaction results in one of the proteins being activated. Conversely, a negative interaction indicates that one of the proteins being inactivated.<sup id="cite_ref-Vinayagam_2014_76-0" class="reference"><a href="#cite_note-Vinayagam_2014-76"><span class="cite-bracket">[</span>76<span class="cite-bracket">]</span></a></sup> </p><p>Protein–protein interaction networks are often constructed as a result of lab experiments such as yeast two-hybrid screens or 'affinity purification and subsequent mass spectrometry techniques.<sup id="cite_ref-77" class="reference"><a href="#cite_note-77"><span class="cite-bracket">[</span>77<span class="cite-bracket">]</span></a></sup> However these methods do not provide the layer of information needed in order to determine what type of interaction is present in order to be able to attribute signs to the network diagrams. </p> <div class="mw-heading mw-heading4"><h4 id="RNA_interference_screens">RNA interference screens</h4><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=30" title="Edit section: RNA interference screens"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p><a href="/wiki/RNA_interference" title="RNA interference">RNA interference</a> (RNAi) screens (repression of individual proteins between transcription and translation) are one method that can be utilized in the process of providing signs to the protein–protein interactions. Individual proteins are repressed and the resulting phenotypes are analyzed. A correlating phenotypic relationship (i.e. where the inhibition of either of two proteins results in the same phenotype) indicates a positive, or activating relationship. Phenotypes that do not correlate (i.e. where the inhibition of either of two proteins results in two different phenotypes) indicate a negative or inactivating relationship. If protein A is dependent on protein B for activation then the inhibition of either protein A or B will result in a cell losing the service that is provided by protein A and the phenotypes will be the same for the inhibition of either A or B. If, however, protein A is inactivated by protein B then the phenotypes will differ depending on which protein is inhibited (inhibit protein B and it can no longer inactivate protein A leaving A active however inactivate A and there is nothing for B to activate since A is inactive and the phenotype changes). Multiple <a href="/wiki/RNA_interference" title="RNA interference">RNAi</a> screens need to be performed in order to reliably appoint a sign to a given protein–protein interaction. Vinayagam et al. who devised this technique state that a minimum of nine <a href="/wiki/RNA_interference" title="RNA interference">RNAi</a> screens are required with confidence increasing as one carries out more screens.<sup id="cite_ref-Vinayagam_2014_76-1" class="reference"><a href="#cite_note-Vinayagam_2014-76"><span class="cite-bracket">[</span>76<span class="cite-bracket">]</span></a></sup> </p> <div style="clear:both;" class=""></div> <div class="mw-heading mw-heading2"><h2 id="As_therapeutic_targets">As therapeutic targets</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=31" title="Edit section: As therapeutic targets"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <p>Modulation of PPI is challenging and is receiving increasing attention by the scientific community.<sup id="cite_ref-78" class="reference"><a href="#cite_note-78"><span class="cite-bracket">[</span>78<span class="cite-bracket">]</span></a></sup> Several properties of PPI such as allosteric sites and hotspots, have been incorporated into drug-design strategies.<sup id="cite_ref-79" class="reference"><a href="#cite_note-79"><span class="cite-bracket">[</span>79<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-80" class="reference"><a href="#cite_note-80"><span class="cite-bracket">[</span>80<span class="cite-bracket">]</span></a></sup> Nevertheless, very few PPIs are directly targeted by <a href="/wiki/Food_and_Drug_Administration" title="Food and Drug Administration">FDA</a>-approved small-molecule PPI inhibitors, emphasizing a huge untapped opportunity for drug discovery. </p><p>In 2014, Amit Jaiswal and others were able to develop 30 peptides to inhibit recruitment of telomerase towards telomeres by utilizing protein–protein interaction studies.<sup id="cite_ref-81" class="reference"><a href="#cite_note-81"><span class="cite-bracket">[</span>81<span class="cite-bracket">]</span></a></sup><sup id="cite_ref-82" class="reference"><a href="#cite_note-82"><span class="cite-bracket">[</span>82<span class="cite-bracket">]</span></a></sup> <a href="/wiki/Michelle_R._Arkin" title="Michelle R. Arkin">Arkin</a> and others were able to develop antibody fragment-based inhibitors to regulate specific protein-protein interactions.<sup id="cite_ref-83" class="reference"><a href="#cite_note-83"><span class="cite-bracket">[</span>83<span class="cite-bracket">]</span></a></sup> </p><p>As the "modulation" of PPIs not only includes the inhibition, but also the stabilization of <a href="/wiki/Protein_quaternary_structure" title="Protein quaternary structure">quaternary protein complexes</a>, molecules with this mechanism of action (so called <a href="/wiki/Molecular_glue" title="Molecular glue">molecular glues</a>) are also intensively studied.<sup id="cite_ref-84" class="reference"><a href="#cite_note-84"><span class="cite-bracket">[</span>84<span class="cite-bracket">]</span></a></sup> </p> <div class="mw-heading mw-heading3"><h3 id="Examples_2">Examples</h3><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=32" title="Edit section: Examples"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <ul><li>Tirobifan, inhibitor of the glycoprotein IIb/IIIa, used as a cardiovascular drug<sup class="noprint Inline-Template Template-Fact" style="white-space:nowrap;">[<i><a href="/wiki/Wikipedia:Citation_needed" title="Wikipedia:Citation needed"><span title="This claim needs references to reliable sources. (May 2023)">citation needed</span></a></i>]</sup></li> <li><a href="/wiki/Maraviroc" title="Maraviroc">Maraviroc</a>, inhibitor of the CCR5-gp120 interaction, used as anti-HIV drug.<sup id="cite_ref-Ivanov_85-0" class="reference"><a href="#cite_note-Ivanov-85"><span class="cite-bracket">[</span>85<span class="cite-bracket">]</span></a></sup></li> <li>AMG-176, AZD5991, S64315, inhibitors of <a href="/wiki/MCL1" title="MCL1">myeloid cell leukemia 1</a> (Mcl-1) protein and its interactions<sup id="cite_ref-86" class="reference"><a href="#cite_note-86"><span class="cite-bracket">[</span>86<span class="cite-bracket">]</span></a></sup></li></ul> <div class="mw-heading mw-heading2"><h2 id="See_also">See also</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=33" title="Edit section: See also"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1184024115">.mw-parser-output .div-col{margin-top:0.3em;column-width:30em}.mw-parser-output .div-col-small{font-size:90%}.mw-parser-output .div-col-rules{column-rule:1px solid #aaa}.mw-parser-output .div-col dl,.mw-parser-output .div-col ol,.mw-parser-output .div-col ul{margin-top:0}.mw-parser-output .div-col li,.mw-parser-output .div-col dd{page-break-inside:avoid;break-inside:avoid-column}</style><div class="div-col" style="column-width: 22em;"> <ul><li><a href="/wiki/Glycan-protein_interactions" title="Glycan-protein interactions">Glycan-protein interactions</a></li> <li><a href="/wiki/3did" title="3did">3did</a></li> <li><a href="/wiki/Allostery" class="mw-redirect" title="Allostery">Allostery</a></li> <li><a href="/wiki/Biological_network" title="Biological network">Biological network</a></li> <li><a href="/wiki/Biological_machine" class="mw-redirect" title="Biological machine">Biological machines</a></li> <li><a href="/wiki/DIMA_(database)" title="DIMA (database)">DIMA (database)</a></li> <li><a href="/wiki/Enzyme_catalysis" title="Enzyme catalysis">Enzyme catalysis</a></li> <li><a href="/wiki/HitPredict" title="HitPredict">HitPredict</a></li> <li><a href="/wiki/Human_interactome" title="Human interactome">Human interactome</a></li> <li><a href="/wiki/IsoBase" title="IsoBase">IsoBase</a></li> <li><a href="/wiki/Multiprotein_complex" class="mw-redirect" title="Multiprotein complex">Multiprotein complex</a></li> <li><a href="/wiki/Protein_dynamics#Global_flexibility:_multiple_domains" title="Protein dynamics">Protein domain dynamics</a></li> <li><a href="/wiki/Protein_domain#Domains_and_protein_flexibility" title="Protein domain">Protein flexibility</a></li> <li><a href="/wiki/Protein_structure" title="Protein structure">Protein structure</a></li> <li><a href="/wiki/Protein%E2%80%93protein_interaction_prediction" title="Protein–protein interaction prediction">Protein–protein interaction prediction</a></li> <li><a href="/wiki/Protein%E2%80%93protein_interaction_screening" title="Protein–protein interaction screening">Protein–protein interaction screening</a></li> <li><a href="/wiki/Systems_biology" title="Systems biology">Systems biology</a></li></ul> </div> <div class="mw-heading mw-heading2"><h2 id="References">References</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=34" title="Edit section: References"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239543626">.mw-parser-output .reflist{margin-bottom:0.5em;list-style-type:decimal}@media screen{.mw-parser-output .reflist{font-size:90%}}.mw-parser-output .reflist .references{font-size:100%;margin-bottom:0;list-style-type:inherit}.mw-parser-output .reflist-columns-2{column-width:30em}.mw-parser-output .reflist-columns-3{column-width:25em}.mw-parser-output .reflist-columns{margin-top:0.3em}.mw-parser-output .reflist-columns ol{margin-top:0}.mw-parser-output .reflist-columns li{page-break-inside:avoid;break-inside:avoid-column}.mw-parser-output .reflist-upper-alpha{list-style-type:upper-alpha}.mw-parser-output .reflist-upper-roman{list-style-type:upper-roman}.mw-parser-output .reflist-lower-alpha{list-style-type:lower-alpha}.mw-parser-output .reflist-lower-greek{list-style-type:lower-greek}.mw-parser-output .reflist-lower-roman{list-style-type:lower-roman}</style><div class="reflist reflist-columns references-column-width reflist-columns-2"> <ol class="references"> <li id="cite_note-Titeca_2019-1"><span class="mw-cite-backlink">^ <a href="#cite_ref-Titeca_2019_1-0"><sup><i><b>a</b></i></sup></a> <a href="#cite_ref-Titeca_2019_1-1"><sup><i><b>b</b></i></sup></a></span> <span class="reference-text"><style data-mw-deduplicate="TemplateStyles:r1238218222">.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:rgba(0,127,255,0.133)}.mw-parser-output .id-lock-free.id-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/6/65/Lock-green.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-limited.id-lock-limited a,.mw-parser-output .id-lock-registration.id-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/d/d6/Lock-gray-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .id-lock-subscription.id-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/a/aa/Lock-red-alt-2.svg")right 0.1em center/9px no-repeat}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/4/4c/Wikisource-logo.svg")right 0.1em center/12px no-repeat}body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-free a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-limited a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-registration a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .id-lock-subscription a,body:not(.skin-timeless):not(.skin-minerva) .mw-parser-output .cs1-ws-icon a{background-size:contain;padding:0 1em 0 0}.mw-parser-output .cs1-code{color:inherit;background:inherit;border:none;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;color:var(--color-error,#d33)}.mw-parser-output .cs1-visible-error{color:var(--color-error,#d33)}.mw-parser-output .cs1-maint{display:none;color:#085;margin-left:0.3em}.mw-parser-output .cs1-kern-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right{padding-right:0.2em}.mw-parser-output .citation .mw-selflink{font-weight:inherit}@media screen{.mw-parser-output .cs1-format{font-size:95%}html.skin-theme-clientpref-night .mw-parser-output .cs1-maint{color:#18911f}}@media screen and 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</ol></div> <div class="mw-heading mw-heading2"><h2 id="Further_reading">Further reading</h2><span class="mw-editsection"><span class="mw-editsection-bracket">[</span><a href="/w/index.php?title=Protein%E2%80%93protein_interaction&action=edit&section=35" title="Edit section: Further reading"><span>edit</span></a><span class="mw-editsection-bracket">]</span></span></div> <style data-mw-deduplicate="TemplateStyles:r1239549316">.mw-parser-output .refbegin{margin-bottom:0.5em}.mw-parser-output .refbegin-hanging-indents>ul{margin-left:0}.mw-parser-output .refbegin-hanging-indents>ul>li{margin-left:0;padding-left:3.2em;text-indent:-3.2em}.mw-parser-output .refbegin-hanging-indents ul,.mw-parser-output .refbegin-hanging-indents ul li{list-style:none}@media(max-width:720px){.mw-parser-output .refbegin-hanging-indents>ul>li{padding-left:1.6em;text-indent:-1.6em}}.mw-parser-output .refbegin-columns{margin-top:0.3em}.mw-parser-output .refbegin-columns ul{margin-top:0}.mw-parser-output .refbegin-columns li{page-break-inside:avoid;break-inside:avoid-column}@media screen{.mw-parser-output .refbegin{font-size:90%}}</style><div class="refbegin refbegin-columns references-column-width" style="column-width: 33em"> <ul><li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFStarkBreitkreutzRegulyBoucher2006" class="citation journal cs1">Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M (January 2006). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347471">"BioGRID: a general repository for interaction datasets"</a>. <i>Nucleic Acids Research</i>. <b>34</b> (Database issue): D535–D539. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<a rel="nofollow" class="external text" href="https://doi.org/10.1093%2Fnar%2Fgkj109">10.1093/nar/gkj109</a>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347471">1347471</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/16381927">16381927</a>.</cite><span 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title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Bioinformatics&rft.atitle=The+MIPS+mammalian+protein-protein+interaction+database&rft.volume=21&rft.issue=6&rft.pages=832-834&rft.date=2005-03&rft_id=info%3Adoi%2F10.1093%2Fbioinformatics%2Fbti115&rft_id=info%3Apmid%2F15531608&rft.aulast=Pagel&rft.aufirst=P&rft.au=Kovac%2C+S&rft.au=Oesterheld%2C+M&rft.au=Brauner%2C+B&rft.au=Dunger-Kaltenbach%2C+I&rft.au=Frishman%2C+G&rft.au=Montrone%2C+C&rft.au=Mark%2C+P&rft.au=St%C3%BCmpflen%2C+V&rft.au=Mewes%2C+HW&rft.au=Ruepp%2C+A&rft.au=Frishman%2C+D&rft_id=https%3A%2F%2Fdoi.org%2F10.1093%252Fbioinformatics%252Fbti115&rfr_id=info%3Asid%2Fen.wikipedia.org%3AProtein%E2%80%93protein+interaction" class="Z3988"></span></li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFCasado-VelaMatthiesenSellésNaranjo2013" class="citation journal cs1">Casado-Vela J, Matthiesen R, Sellés S, Naranjo JR (May 2013). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314489">"Protein-Protein Interactions: Gene Acronym Redundancies and Current Limitations Precluding Automated Data Integration"</a>. <i>Proteomes</i>. <b>1</b> (1): 3–24. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.3390%2Fproteomes1010003">10.3390/proteomes1010003</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5314489">5314489</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/28250396">28250396</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Proteomes&rft.atitle=Protein-Protein+Interactions%3A+Gene+Acronym+Redundancies+and+Current+Limitations+Precluding+Automated+Data+Integration&rft.volume=1&rft.issue=1&rft.pages=3-24&rft.date=2013-05&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC5314489%23id-name%3DPMC&rft_id=info%3Apmid%2F28250396&rft_id=info%3Adoi%2F10.3390%2Fproteomes1010003&rft.aulast=Casado-Vela&rft.aufirst=J&rft.au=Matthiesen%2C+R&rft.au=Sell%C3%A9s%2C+S&rft.au=Naranjo%2C+JR&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC5314489&rfr_id=info%3Asid%2Fen.wikipedia.org%3AProtein%E2%80%93protein+interaction" class="Z3988"></span></li> <li><link rel="mw-deduplicated-inline-style" href="mw-data:TemplateStyles:r1238218222"><cite id="CITEREFRobinBodeinScott-BoyerLeclercq2022" class="citation journal cs1">Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A (2022). <a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC494275">"Overview of methods for characterization and visualization of a protein-protein interaction network in a multi-omics integration context"</a>. <i>Frontiers in Molecular Biosciences</i>. <b>9</b>: 962799. <a href="/wiki/Doi_(identifier)" class="mw-redirect" title="Doi (identifier)">doi</a>:<span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://doi.org/10.3389%2Ffmolb.2022.962799">10.3389/fmolb.2022.962799</a></span>. <a href="/wiki/PMC_(identifier)" class="mw-redirect" title="PMC (identifier)">PMC</a> <span class="id-lock-free" title="Freely accessible"><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC494275">494275</a></span>. <a href="/wiki/PMID_(identifier)" class="mw-redirect" title="PMID (identifier)">PMID</a> <a rel="nofollow" class="external text" href="https://pubmed.ncbi.nlm.nih.gov/36158572">36158572</a>.</cite><span title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.jtitle=Frontiers+in+Molecular+Biosciences&rft.atitle=Overview+of+methods+for+characterization+and+visualization+of+a+protein-protein+interaction+network+in+a+multi-omics+integration+context&rft.volume=9&rft.pages=962799&rft.date=2022&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC494275%23id-name%3DPMC&rft_id=info%3Apmid%2F36158572&rft_id=info%3Adoi%2F10.3389%2Ffmolb.2022.962799&rft.aulast=Robin&rft.aufirst=V&rft.au=Bodein%2C+A&rft.au=Scott-Boyer%2C+MP&rft.au=Leclercq%2C+M&rft.au=P%C3%A9rin%2C+O&rft.au=Droit%2C+A&rft_id=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpmc%2Farticles%2FPMC494275&rfr_id=info%3Asid%2Fen.wikipedia.org%3AProtein%E2%80%93protein+interaction" class="Z3988"></span></li></ul> </div> <div class="mw-heading mw-heading2"><h2 id="External_links">External links</h2><span 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