{"id":1935,"date":"2022-03-24T16:00:00","date_gmt":"2022-03-24T16:00:00","guid":{"rendered":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/?p=1935"},"modified":"2026-01-26T16:28:03","modified_gmt":"2026-01-26T16:28:03","slug":"newly-published-in-annual-reviews-of-biochemistry","status":"publish","type":"post","link":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/2022\/03\/24\/newly-published-in-annual-reviews-of-biochemistry\/","title":{"rendered":"Newly published in Annual Reviews of Biochemistry"},"content":{"rendered":"<h2 class=\"wp-block-heading\">Angus &amp; Alessio\u2019s review on E3 Ligase Substrate Specificity for Targeted Protein Degradation<\/h2>\n<\/p>\n<p><strong>Authors<\/strong>: Angus D. Cowan, Alessio Ciulli*<\/p>\n<p><strong>Title<\/strong>: Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory<\/p>\n<h2 class=\"wp-block-heading\">Abstract<\/h2>\n<p>Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin\u2013proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein\u2013protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics.<\/p>\n<h2 class=\"wp-block-heading\">Great reviews<\/h2>\n<ul>\n<li><a href=\"https:\/\/doi.org\/10.1146\/annurev-biochem-032620-104421\">Read full article on DOI website<\/a>.<\/li>\n<li>Read the article open access via the personalized ePrint URL\u00a0<a href=\"http:\/\/arjournals.annualreviews.org\/eprint\/24XIS2WFPSJDN6JMBPPZ\/full\/10.1146\/annurev-biochem-032620-104421\">here<\/a>\u00a0for the Review in Advance (RIA) version.<\/li>\n<\/ul>\n<div id='gallery-1' class='gallery galleryid-1935 gallery-columns-3 gallery-size-large'><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon landscape'>\n\t\t\t\t<a href='https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/ToC_0.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"617\" src=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/ToC_0-1024x617.jpg\" class=\"attachment-large size-large\" alt=\"ToC Graphic for paper on on E3 Ligase Substrate Specificity for Targeted Protein Degradation\" srcset=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/ToC_0-1024x617.jpg 1024w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/ToC_0-300x181.jpg 300w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/ToC_0-768x463.jpg 768w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/ToC_0.jpg 1260w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"1019\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0-1019x1024.jpg\" class=\"attachment-large size-large\" alt=\"Figure 1. Native activity and pharmacological hijacking of E3 ligases. Graphical representation of (a) natural, (b) PROTAC-induced, and (c) molecular glue\u2013induced protein degradation by the ubiquitin\u2013proteasome system\" srcset=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0-1019x1024.jpg 1019w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0-298x300.jpg 298w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0-150x150.jpg 150w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0-768x772.jpg 768w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0-1528x1536.jpg 1528w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-1-01_0.jpg 1890w\" sizes=\"auto, (max-width: 1019px) 100vw, 1019px\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"886\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0-886x1024.jpg\" class=\"attachment-large size-large\" alt=\"Figure 2 Types of substrate recognition by E3 ligases. Graphical representation of type 1, type 2, and type 3 substrate recognition. Modification of either the substrate (type 2), or the E3 ligase (type 3) may be either allosteric or interfacial. The modification may be covalent, noncovalent, or a proteolytic cleavage event\" srcset=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0-886x1024.jpg 886w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0-260x300.jpg 260w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0-768x887.jpg 768w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0-1329x1536.jpg 1329w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0-1772x2048.jpg 1772w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-2-01_0.jpg 1890w\" sizes=\"auto, (max-width: 886px) 100vw, 886px\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"819\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0-819x1024.jpg\" class=\"attachment-large size-large\" alt=\"Figure 3 Recognition of substrates by E3 ligases in nature. Substrate receptors and substrates are colored gray and tan, respectively. Hydrogen bonds and ionic interactions are represented as black dotted lines\" aria-describedby=\"gallery-1-1938\" srcset=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0-819x1024.jpg 819w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0-240x300.jpg 240w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0-768x960.jpg 768w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0-1229x1536.jpg 1229w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0-1638x2048.jpg 1638w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-3-new-01_0.jpg 1890w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><\/a>\n\t\t\t<\/div>\n\t\t\t\t<figcaption class='wp-caption-text gallery-caption' id='gallery-1-1938'>\n\t\t\t\tFigure 3\n\t\t\t\t<\/figcaption><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"995\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01-995x1024.jpg\" class=\"attachment-large size-large\" alt=\"Figure 4 Ternary cocrystal structures of molecular glue degraders (orange carbons, chemical structure depicted) bound to E3 ligases (gray) and neo-substrates (tan).\" srcset=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01-995x1024.jpg 995w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01-291x300.jpg 291w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01-768x791.jpg 768w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01-1492x1536.jpg 1492w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-4-new-01.jpg 1877w\" sizes=\"auto, (max-width: 995px) 100vw, 995px\" \/><\/a>\n\t\t\t<\/div><\/figure><figure class='gallery-item'>\n\t\t\t<div class='gallery-icon portrait'>\n\t\t\t\t<a href='https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0.jpg'><img loading=\"lazy\" decoding=\"async\" width=\"819\" height=\"1024\" src=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0-819x1024.jpg\" class=\"attachment-large size-large\" alt=\"Figure 5 Ternary complex cocrystal structures of heterobifunctional PROTAC degraders (orange carbons, chemical structure depicted) bound to E3 ligases and neo-substrate targets\" srcset=\"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0-819x1024.jpg 819w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0-240x300.jpg 240w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0-768x960.jpg 768w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0-1229x1536.jpg 1229w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0-1638x2048.jpg 1638w, https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-content\/uploads\/sites\/233\/2023\/12\/Figure-5-new-01_0.jpg 1890w\" sizes=\"auto, (max-width: 819px) 100vw, 819px\" \/><\/a>\n\t\t\t<\/div><\/figure>\n\t\t<\/div>\n\n","protected":false},"excerpt":{"rendered":"<p>Angus &amp; Alessio\u2019s review on E3 Ligase Substrate Specificity for Targeted Protein Degradation Authors: Angus D. Cowan, Alessio Ciulli* Title: Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory Abstract Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[13,4],"tags":[],"class_list":["post-1935","post","type-post","status-publish","format-standard","hentry","category-13","category-news"],"blocksy_meta":[],"_links":{"self":[{"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/posts\/1935","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/comments?post=1935"}],"version-history":[{"count":2,"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/posts\/1935\/revisions"}],"predecessor-version":[{"id":4844,"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/posts\/1935\/revisions\/4844"}],"wp:attachment":[{"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/media?parent=1935"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/categories?post=1935"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/sites.dundee.ac.uk\/alessio-ciulli\/wp-json\/wp\/v2\/tags?post=1935"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}