{"id":7037,"date":"2016-05-10T11:09:46","date_gmt":"2016-05-10T09:09:46","guid":{"rendered":"http:\/\/news.embl.de\/?p=7037"},"modified":"2024-03-25T10:26:12","modified_gmt":"2024-03-25T09:26:12","slug":"1605-dapk","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/1605-dapk\/","title":{"rendered":"Enzyme with a dual-purpose loop"},"content":{"rendered":"\n

\u201cI really thought I had done something wrong!\u201d says Bertrand Simon who has just completed his PhD in the group of Matthias Wilmanns<\/a> at EMBL in Hamburg. Simon was studying a group of enzymes known as Death Associated Protein Kinases (DAPK), trying to understand how their activity is regulated. These enzymes can trigger the death of cells, ensuring they die off if they get out of check.<\/p>\n\n\n\n

Simon was taking a closer look at the 3D molecular structure of several DAPK molecules. \u201cDAPK has an inactive form and an active form\u201d explains Simon, \u201cWe wanted to show exactly how two active DAPK molecules \u2013 each known as a ‘monomer’ \u2013 bind together to make up the inactive ‘dimer’ form of the enzyme.\u201d<\/p>\n\n\n\n

In the loop<\/h2>\n\n\n\n

The 3D structure of a protein arises when a string of amino acids folds together \u2013 much like a length of string can be scrunched together to form a ball in the palm of your hand. Although the string of amino acids is folded in and around itself, some parts of the string will still be exposed and can interact with other molecules.<\/p>\n\n\n\n

\u201cLooking at the structure, we identified a small loop of amino acids that we thought could be important for binding two DAPK molecules together,\u201d explains Simon, who set about collecting evidence to support this assumption. \u201cThis looked like a small and straightforward project that would have finished off my PhD thesis nicely and added important information to our understanding of how this enzyme is regulated,\u201d he states. But as so often in science, things didn\u2019t turn out quite as expected.<\/p>\n\n\n\n

This looked like a small and straightforward project that would have finished off my PhD thesis nicely<\/p><\/blockquote>\n\n\n\n

Several 3D molecular structures of DAPK had already been solved by previous group members and collaborators Andrew McCarthy<\/a> and Darren Hart<\/a> from EMBL in Grenoble using structural biology methods, and deposited in the Protein Data Bank Europe (PDBe)<\/a>. Using these structures, Simon was able to identify and then systematically mutate the amino acids found at and around the loop he was interested in, and so show exactly which parts are significant for molecule binding.<\/p>\n\n\n\n

New hypothesis<\/h2>\n\n\n\n

One by one Simon exchanged the arginine amino acids along and around the loop for a reverse-charged amino acid, glutamate. The project started off nicely with everything working as planned. \u201cAll my experiments were going really well \u2013 something I had never experienced before!\u201d says Simon with a smile. \u201cThe experiments showed that the monomers couldn\u2019t bind together to form dimers without this little loop intact,\u201d he adds.<\/p>\n\n\n\n

Encouraged by this, and validated by additional structural biology experiments carried out by the Small Angle X-ray Scattering group of Dmitri Svergun<\/a> in Hamburg, Simon introduced the mutated proteins into the cell environment to show that the effect was seen here too. \u201cA change in enzyme activity after we had mutated a part of the protein would indicate we\u2019d hit the right spot,\u201d explains Simon. And nothing. \u201cThe protein was dead! Zero activity. It wasn\u2019t even binding to its normal signaling partner, an activity regulator protein called calmodulin, which had been carefully prepared the Schultz group<\/a> at EMBL in Heidelberg,\u201d he says. \u201cI thought, oops, I must have done something wrong!\u201d<\/p>\n\n\n\n

In a paper published in Science Signaling<\/em> in 2010, Wilmanns and colleagues had already presented the 3D structure of a DAPK monomer bound to calmodulin<\/a>. \u201cThe binding site for calmodulin was somewhere completely different to this small loop I was manipulating \u2013 it just didn\u2019t make any sense that the calmodulin binding wasn\u2019t working anymore,\u201d he says.<\/p>\n\n\n\n

There was nothing in the scientific literature that might explain what we were seeing<\/p><\/blockquote>\n\n\n\n

Simon repeated the experiments again, and again and again. \u201cAfter about two months with no change in result, I decided I needed to start thinking in a different direction,\u201d he says. Simon developed a new hypothesis: \u201cI considered the results I had been collecting as statements, and built a hypothesis around them and other information we knew from previous work done on DAPK in our group.\u201d<\/p>\n\n\n\n

Simon presented his new hypothesis to his supervisor Wilmanns. \u201cThere was nothing in the scientific literature that might explain what we were seeing,\u201d explains Wilmanns, \u201cbut the effects were so strong it was clear something interesting was going on.”<\/p>\n\n\n\n

Dual purpose<\/h2>\n\n\n\n

The work published in Structure<\/em>, suggests that the small loop is crucial for both dimer formation and<\/em> calmodulin binding. A renewed look at the structure published in 2010 shows that the small loop plays a much more significant role there too, as Simon hypothesizes. \u201cWhen we published the structure in 2010, we assumed the loop we were seeing was just an artefact of the sample preparation process,\u201d says Wilmanns. \u201cNow we think this small loop is needed to recruit calmodulin to DAPK in preparation for binding, hence without it, calmodulin binding does not work,\u201d he adds.<\/p>\n\n\n\n

\"Regulation<\/a>
Regulation mechanism: step 1) from inactive dimer to active monomer; 2) recruitment of signaling partner Calmodulin (grey); 3) binding to Calmodulin via a Calmodulin-specific binding site (blue). Star shows available active site. IMAGE: Petra Riedinger\/EMBL<\/figcaption><\/figure><\/div>\n\n\n\n

\u201cThe new hypothesis is quite a complex idea, but it is the only logical explanation that brings all the results together,\u201d says Simon.<\/p>\n\n\n\n

\u201cThis is very satisfying and exciting,\u201d concludes Wilmanns, \u201cwhat started as a small side project, unearthed a complex and important signaling pathway within this group of kinases. It goes to show, you can\u2019t always plan science!\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

Unexpected results: structure of DAPK enzyme reveals dual-purpose loop<\/p>\n","protected":false},"author":18,"featured_media":7056,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[65,29,37,53,43,35,306],"embl_taxonomy":[9596,19039,19403],"class_list":["post-7037","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-biophysics","tag-crystallography","tag-grenoble","tag-hamburg","tag-heidelberg","tag-structural-biology","tag-wilmanns","embl_taxonomy-embl-hamburg","embl_taxonomy-matthias-wilmanns","embl_taxonomy-wilmanns-group"],"acf":{"article_intro":"

Unexpected results: structure of Death Associated Protein Kinases (DAPK)\u00a0reveals a dual-purpose loop<\/p>\n","related_links":[{"link_description":"Wilmanns Group at EMBL in Hamburg","link_url":"http:\/\/http:\/\/www.embl-hamburg.de\/research\/unit\/wilmanns\/index.html"},{"link_description":"3D structure of DAPK bound to Calmodulin \u2013 EMBL press release, 26 January 2010","link_url":"http:\/\/www.embl-hamburg.de\/aboutus\/communication_outreach\/media_relations\/2010\/100126_Hamburg\/index.html"},{"link_description":"Protein Data Bank Europe (PDBe)","link_url":"http:\/\/www.ebi.ac.uk\/pdbe\/"}],"article_sources":[{"source_description":"

Simon B, et al.\u00a0Structure<\/em> (28 April 28 2016). DOI:\u00a010.1016\/j.str.2016.03.020<\/p>\n","source_link_url":"http:\/\/dx.doi.org\/10.1016\/j.str.2016.03.020"}],"vf_locked":false,"featured":false,"color":"#007B53","link_color":"#fff","show_featured_image":false,"in_this_article":false,"youtube_url":"","mp4_url":"","video_caption":"","press_contact":"None","translations":false},"embl_taxonomy_terms":[{"uuid":"a:3:{i:0;s:36:\"b14d3f13-5670-44fb-8970-e54dfd9c921a\";i:1;s:36:\"89e00fee-87f4-482e-a801-4c3548bb6a58\";i:2;s:36:\"613c4de5-1775-447f-af71-4b07085318e9\";}","parents":[],"name":["EMBL Hamburg"],"slug":"embl-hamburg","description":"Where > All EMBL sites > EMBL Hamburg"},{"uuid":"a:2:{i:0;s:36:\"4428d1fd-441a-4d6d-a1c5-5dcf5665f213\";i:1;s:36:\"c1800a73-a9f4-4389-887c-f069f4ebf475\";}","parents":[],"name":["Matthias Wilmanns"],"slug":"matthias-wilmanns","description":"Who > Matthias Wilmanns"},{"uuid":"a:3:{i:0;s:36:\"302cfdf7-365b-462a-be65-82c7b783ebf7\";i:1;s:36:\"2dc39890-6c01-47bf-ac78-d42abdb10079\";i:2;s:36:\"b7081976-e7c1-4678-ab00-3e02d20e9e87\";}","parents":[],"name":["Wilmanns Group"],"slug":"wilmanns-group","description":"What > Structural Biology (EMBL Hamburg) > Wilmanns Group"}],"yoast_head":"\nStudy reveals unexpected dual-purpose loop in DAPK enzyme<\/title>\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\/1605-dapk\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Study reveals unexpected dual-purpose loop in DAPK enzyme\" \/>\n<meta property=\"og:description\" content=\"Unexpected results: structure of DAPK enzyme reveals dual-purpose loop\" \/>\n<meta property=\"og:url\" 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