{"id":4006,"date":"2015-05-18T12:32:41","date_gmt":"2015-05-18T10:32:41","guid":{"rendered":"http:\/\/news.embl.de\/?p=4006"},"modified":"2024-11-29T16:53:33","modified_gmt":"2024-11-29T15:53:33","slug":"1505-protein-domains","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/","title":{"rendered":"Are protein domains indivisible?"},"content":{"rendered":"\n<p><a href=\"research\/bateman\">Researchers at EMBL-EBI<\/a> have shown that protein domains, previously thought to be indivisible, complete units that make up proteins, can exist and function despite having lost large parts of their structure. <a href=\"http:\/\/genomebiology.com\/2015\/16\/1\/88\">Published in <em>Genome Biology<\/em><\/a>, the research into \u2018domain atrophy\u2019 offers new insights into the evolution, molecular mechanism, stability and function of protein domains.<\/p>\n\n\n\n<p>Proteins are everywhere, performing an endless variety of tasks to keep life moving along. They are made up of independent units called protein domains, which can be assembled in different combinations to build full proteins to order. Protein domains are defined by core structural elements, much in the same way a gear on a bike, watch or car can be defined by the number, size and arrangement of its cogs.<\/p>\n\n\n\n<p>But are protein domains really indivisible? The researchers set out to answer this question computationally by searching and comparing millions of protein sequences and hundreds of protein structures in public databases. They identified a small percentage of protein domains that have been retained throughout evolution, functioning just like their ancestors, despite having undergone large-scale structural deletions.<\/p>\n\n\n\n<p>\u201cYou can think of protein domains like cogs in an engine, with all these teeth that interlock and make each other move,\u201d explains Ananth Prakash of EMBL-EBI. \u201cYou can assume that a cog will need all its teeth to make a good enough connection to work properly. But we found that with some protein domains, the engine parts keep moving even if a large number of those \u2018teeth\u2019 are missing.\u201d<\/p>\n\n\n\n<blockquote class=\"vf-blockquote\"><p>It is simply amazing that proteins can tolerate such extreme mutations.<\/p><\/blockquote>\n\n\n\n<p>\u201cNormally, you\u2019d expect large-scale deletions, which we call domain atrophy, to inhibit a domain\u2019s function and cause unfolding,\u201d adds Alex Bateman, head of Protein Sequence Resources at EMBL-EBI. \u201cGiven that a mutation in a single residue can lead to a human disease, it is simply amazing that proteins can tolerate such extreme mutations.\u201d<\/p>\n\n\n\n<p>The team started with two major public resources, <a href=\"http:\/\/www.uniprot.org\">UniProt<\/a> and <a href=\"http:\/\/pfam.xfam.org\/\">Pfam<\/a>, selecting only the most robust entries and using a new algorithm to identify cases of partial protein domains. By painstakingly sifting through the results, like panning for gold, they collected a small set of protein domains with large-scale deletions in their core structural elements.<\/p>\n\n\n\n<p>\u201cMost atrophied domains retain structural elements or catalytic residues that are crucial for the normal functioning of a protein, which only makes sense,\u201d says Ananth. \u201cInterestingly, most of them appear to compensate for those atrophied sections by forming complexes with other partners.\u201d<\/p>\n\n\n\n<p>At the <a href=\"http:\/\/www.iscb.org\/\">ISMB conference<\/a> in 2014, members of the Bateman team at EMBL-EBI and the <a href=\"http:\/\/www.medicine.virginia.edu\/clinical\/departments\/medicine\/divisions\/infectiousdisease\/faculty\/bios\/pearson-w\">Pearson group<\/a> at the University of Virginia discovered that they had both been working along the same lines. Both groups agree that domain atrophy is extremely rare and that for the most part, protein domains are indivisible, structural building blocks. But their findings reveal a fascinating phenomenon, and the shared terminologies developed by the groups will help future investigations into the molecular mechanisms that cause parts of these protein domains to disappear in the first place.<\/p>\n\n\n\n<p><em>This post was originally published on <a href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/are-protein-domains-indivisible\" target=\"_blank\" rel=\"canonical nofollow noopener noreferrer\" data-href=\"https:\/\/www.ebi.ac.uk\/about\/news\/press-releases\/are-protein-domains-indivisible\">EMBL-EBI News.<\/a><\/em><\/p>\n","protected":false},"excerpt":{"rendered":"<p>New research shows that some proteins domains can function even with big parts missing.<\/p>\n","protected":false},"author":13,"featured_media":4011,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[440,36,31,42,75,94],"embl_taxonomy":[],"class_list":["post-4006","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-bateman","tag-embl-ebi","tag-evolution","tag-genomics","tag-phd","tag-protein-synthesis"],"acf":{"article_intro":"<p>Protein domains are considered to be indivisible units \u2013 but new research from EMBL-EBI shows that some can function even with big parts missing.<\/p>\n","related_links":[{"link_description":"Prakash A and Bateman A (2015). Domain atrophy creates rare cases of functional partial protein domains. Genome Biol. (in press); DOI: 10.1186\/s13059-015-0655-8","link_url":"http:\/\/europepmc.org\/abstract\/MED\/25924720"},{"link_description":"Triant D and Pearson W (2015). Most partial domains in proteins are alignment and annotation artifacts. Genome Biol. (in press); DOI: 10.1186\/s13059-015-0656-7","link_url":"http:\/\/www.genomebiology.com\/2015\/16\/1\/99"}],"article_sources":false,"vf_locked":false,"featured":false,"color":"#007B53"},"embl_taxonomy_terms":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Are protein domains indivisible? | EMBL<\/title>\n<meta name=\"description\" content=\"Proteins are made up of indivisible units called protein domains \u2013 but new research shows that some domains can function even with big parts missing.\" \/>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Are protein domains indivisible? | EMBL\" \/>\n<meta property=\"og:description\" content=\"Proteins are made up of indivisible units called protein domains \u2013 but new research shows that some domains can function even with big parts missing.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:author\" content=\"www.facebook.com\/EMBLEBI\" \/>\n<meta property=\"article:published_time\" content=\"2015-05-18T10:32:41+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-11-29T15:53:33+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/05\/DomainAtrophy_EMBL-e1431944993423.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"620\" \/>\n\t<meta property=\"og:image:height\" content=\"424\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Mary Todd Bergman\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@EMBLEBI\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Mary Todd Bergman\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\/\/schema.org\",\"@graph\":[{\"@type\":\"NewsArticle\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/\"},\"author\":{\"name\":\"Mary Todd Bergman\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/052a43af2beb3860bffa67c0f0474875\"},\"headline\":\"Are protein domains indivisible?\",\"datePublished\":\"2015-05-18T10:32:41+00:00\",\"dateModified\":\"2024-11-29T15:53:33+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/\"},\"wordCount\":515,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2015\/05\/DomainAtrophy_EMBL-e1431944993423.jpg\",\"keywords\":[\"bateman\",\"embl-ebi\",\"evolution\",\"genomics\",\"phd\",\"protein synthesis\"],\"articleSection\":[\"Science\",\"Science &amp; Technology\"],\"inLanguage\":\"en-US\"},{\"@type\":\"WebPage\",\"@id\":\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/\",\"url\":\"https:\/\/www.embl.org\/news\/science\/1505-protein-domains\/\",\"name\":\"Are protein domains indivisible? 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