{"id":48846,"date":"2022-06-10T08:00:00","date_gmt":"2022-06-10T06:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?p=48846"},"modified":"2024-10-18T10:25:02","modified_gmt":"2024-10-18T08:25:02","slug":"puzzling-out-the-structure-of-a-molecular-giant","status":"publish","type":"post","link":"https:\/\/www.embl.org\/news\/science\/puzzling-out-the-structure-of-a-molecular-giant\/","title":{"rendered":"Puzzling out the structure of a molecular giant"},"content":{"rendered":"\n<figure class=\"vf-figure wp-block-video\"><video style=\"max-width: 100%;\" autoplay controls loop poster=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/06\/HumanNPC-1000x600-1.jpg\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/06\/HumanNPC-video-1000x600-2.mp4\"><\/video><figcaption class=\"vf-figure__caption\">The human nuclear pore complex (NPC) is a doughnut-shaped molecular complex consisting of 30 different proteins arranged in ca. 1000 copies. It weighs 120 MDa, which in the cellular scale is enormous. Credit: Agnieszka Obarska-Kosi\u0144ska\/EMBL and MPI of Biophysics<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"a1\"><strong>The molecular giant and its missing screws<\/strong><\/h2>\n\n\n\n<p>The human nuclear pore complex (NPC) is a true molecular giant, which sits on the membrane separating the nucleus from the cytoplasm. It\u2019s doughnut-shaped and works as both a gateway and a checkpoint for molecules that travel between the cytoplasm and the nucleus. Thereby, the NPC facilitates fundamental processes in the cell, such as gene expression and translation. The nuclear transport system also plays a role in several diseases, including neurodegenerative disorders, cancer and viral infections.<\/p>\n\n\n\n<p>What\u2019s the NPC\u2019s structure? How are its proteins glued together? How does it attach to the nuclear membrane? These and other questions have now been answered by the <a href=\"https:\/\/www.embl.org\/groups\/kosinski\/\">Kosinski Group<\/a> at EMBL Hamburg and <a href=\"https:\/\/www.cssb-hamburg.de\/research\/research_groups\/kosinski_group\/index_eng.html\">Centre for Structural Systems Biology (CSSB)<\/a>, the <a href=\"https:\/\/www.biophys.mpg.de\/molecular-sociology\">Beck<\/a> and <a href=\"https:\/\/www.biophys.mpg.de\/theoretical-biophysics\">Hummer<\/a> Labs at the Max Planck Institute of Biophysics, and collaborators. They created the most complete model of the human NPC to date by combining the protein structure prediction program AlphaFold2 with techniques such as cryo-electron tomography, single particle cryo-EM and integrative modelling.<\/p>\n\n\n\n<p>For structural biologists, the human NPC is a challenging yet exciting 3D puzzle, with around 30 different proteins each present in multiple copies. This amounts to around 1000 puzzle pieces, which form a round core with surrounding flexible parts. Until now, the most accurate models of the human NPC core only covered 46% of the structure. But now, building on two decades of previous research in the field, scientists have created a new model of the NPC structure that covers more than 90% of its core.<\/p>\n\n\n\n<p>While previously proposed NPC models had gaps and contained some proteins only in fragments, the new model removes much of this ambiguity.<\/p>\n\n\n\n<p>\u201cIt\u2019s like when you disassemble and reassemble an electronic device. There will be always some screws left, and you just don\u2019t know where they are supposed to be,\u201d said EMBL Group Leader Jan Kosinski, who co-lead the investigation. \u201cWe finally managed to fit most of them, and now, we know exactly where they are, what they do, and how.\u201d<\/p>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"a2\"><strong>Experimentation and artificial intelligence work together<\/strong><\/h2>\n\n\n\n<p>How did the scientists achieve this? The key was to combine several experimental and computational methods. This enabled the scientists to visualise the NPC at different scales and levels of detail.<\/p>\n\n\n\n<p>For example, to model the overall silhouette of the NPC, the researchers used cryo-electron tomography. With this technique, they were able to observe the NPC in its cellular environment, rather than in isolation. More details of the individual protein building blocks were revealed by <a href=\"https:\/\/www.embl.org\/news\/science\/thornton-alphafold\/\">AlphaFold2<\/a>, an artificial intelligence-based program that predicts protein structures, created by the company <a href=\"https:\/\/www.deepmind.com\/research\/highlighted-research\/alphafold\">DeepMind<\/a>.<\/p>\n\n\n\n<p>\u201cAlphaFold2 was a breakthrough moment for us,\u201d said Agnieszka Obarska-Kosi\u0144ska, postdoc who performed the molecular modelling. \u201cBefore, we didn\u2019t know the structure of many proteins within the NPC. You cannot assemble a puzzle when you don\u2019t know what the pieces look like. But AlphaFold2 combined with other approaches enabled us to predict those shapes.\u201d<\/p>\n\n\n\n<p>To refine the picture even further, the researchers used ColabFold, a version of AlphaFold2 modified by the scientific community to model interactions between proteins. This allowed them to visualise how the different puzzle pieces combine to form smaller subcomplexes, and how those subcomplexes are then glued together to form the NPC.<\/p>\n\n\n\n<p>Finally, they put all the pieces together using the software <a href=\"https:\/\/www.embl-hamburg.de\/Assembline\/\">Assembline<\/a> previously developed by the <a href=\"https:\/\/www.embl.org\/groups\/kosinski\/\">Kosinski Group<\/a>, and validated it against experimental data.<\/p>\n\n\n\n<p>The resulting model was so complete and detailed that it enabled the researchers to create time-resolved molecular simulations that explain how the NPC proteins and the nuclear membrane interact to create a stable pore and how it responds to mechanical cues.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"471\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/05\/NPC-before-and-after-AF2-1024x471.png\" alt=\"\" class=\"wp-image-49162\" srcset=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/05\/NPC-before-and-after-AF2-1024x471.png 1024w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/05\/NPC-before-and-after-AF2-300x138.png 300w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/05\/NPC-before-and-after-AF2-768x353.png 768w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\">Comparison of the of the models of human nuclear pore complex obtained before (left) and after the use of AlphaFold2 combined with cryo-ET (right). The human nuclear pore complex has the total weight of 120 MDa. The previous models covered only up to 35 MDa. The new model covers 70 MDa. Credit: Agnieszka Obarska-Kosi\u0144ska\/EMBL and MPI of Biophysics<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\" id=\"a3\"><strong>Future directions<\/strong><\/h2>\n\n\n\n<p>This work was a big leap forward for NPC research, but there is still a lot left to explore.<\/p>\n\n\n\n<p>\u201cThis work exemplifies how, in the future, structural biology will embrace cell biology to create atomic models of ever larger assemblies of molecules that perform different functions in different parts of the cell,\u201d said Martin Beck. Gerhard Hummer agrees: \u201cWe can now think of building a complete dynamic model of the NPC and simulate nuclear transport in atomic detail.\u201d<\/p>\n\n\n\n<p>The Kosinski Group will aim their future work at developing automatic methods for integrating structural and microscopy data using AlphaFold2 and their own software <a href=\"https:\/\/www.embl-hamburg.de\/Assembline\/\">Assembline<\/a>. They plan to apply these approaches to studying molecular processes driving viral infections.<\/p>\n\n\n\n<p>Studying the NPC in its cellular surroundings also aligns with the goals of the new EMBL Programme \u2018<a href=\"https:\/\/www.embl.org\/about\/programme\/\">Molecules to Ecosystems<\/a>\u2019, which aims to explore life in context.<\/p>\n\n\n\n<div class=\"vf-embed vf-embed--16x9 | vf-u-margin__bottom--400\">\n<iframe src=\"https:\/\/www.youtube.com\/embed\/ue1TypC7CYE\" frameborder=\"0\" controls allowfullscreen><\/iframe><\/div>\n\n  \n<figcaption class=\"vf-figure__caption vf-u-margin__top--200\">Scientists at EMBL Hamburg and MPI of Biophysics created the most complete model of the human nuclear pore complex (NPC) thanks to combining AI with experimental and computational techniques.<\/figcaption>\n\n\n","protected":false},"excerpt":{"rendered":"<p>Scientists have solved several mysteries around the structure and function of a true molecular giant: the human nuclear pore complex. They created the most complete model of the complex thanks to combining the program AlphaFold2 with cryo-electron tomography, integrative modelling, molecular&hellip;<\/p>\n","protected":false},"author":96,"featured_media":49972,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[2,17591],"tags":[12758,4718,350,712,775,53,43,876,540,1790,35],"embl_taxonomy":[9596,19307],"class_list":["post-48846","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-science","category-science-technology","tag-alphafold","tag-artificial-intelligence","tag-beck","tag-cryo-electron-tomography","tag-cssb","tag-hamburg","tag-heidelberg","tag-integrative-modelling","tag-kosinski","tag-nuclear-pore","tag-structural-biology","embl_taxonomy-embl-hamburg","embl_taxonomy-kosinski-group"],"acf":{"featured":true,"show_featured_image":true,"field_target_display":"embl","article_intro":"<p>Combining AlphaFold2 with experimental and computational techniques has helped scientists figure out the human nuclear pore complex\u2019s architecture in greater detail than ever before<\/p>\n","related_links":[{"link_description":"Kosinski Group ","link_url":"https:\/\/www.embl.org\/groups\/kosinski\/"},{"link_description":"Accessible 3D protein models to accelerate scientific discovery ","link_url":"https:\/\/www.embl.org\/news\/science\/thornton-alphafold\/"},{"link_description":"Observing the secret life of molecules inside the cell ","link_url":"https:\/\/www.embl.org\/news\/science\/observing-the-secret-life-of-molecules-inside-the-cell\/"},{"link_description":"Nuclear pores in their natural context ","link_url":"https:\/\/www.embl.org\/news\/science\/nuclear-pores-in-their-natural-context\/"}],"source_article":[{"publication_title":"AI-based structure prediction empowers integrative structural analysis of human nuclear pores.","publication_link":{"title":"","url":"https:\/\/doi.org\/10.1126\/science.abm9506 ","target":""},"publication_authors":"Mosalaganti S, Obarska-Kosi\u0144ska A, Siggel M et al.","publication_source":"Science","publication_date":"10 June 2022","publication_doi":"10.1126\/science.abm9506 "}],"in_this_article":[{"heading_description":"The molecular giant and its missing screws","anchor":"#a1"},{"heading_description":"Experimentation and artificial intelligence work together","anchor":"#a2"},{"heading_description":"Future directions","anchor":"#a3"}],"press_contact":"EMBL Generic","vf_locked":false,"field_article_language":{"value":"english","label":"English"},"article_translations":false,"languages":""},"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 &gt; All EMBL sites &gt; EMBL Hamburg"},{"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:\"5cf17219-ae78-437e-85e4-aad17a7c5e0f\";}","parents":[],"name":["Kosinski Group"],"slug":"kosinski-group","description":"What &gt; Structural Biology (EMBL Hamburg) &gt; Kosinski Group"}],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v26.2 - https:\/\/yoast.com\/wordpress\/plugins\/seo\/ -->\n<title>Puzzling out the structure of a molecular giant | EMBL<\/title>\n<meta name=\"description\" content=\"Combining AlphaFold2, cryo-ET and other methods enabled scientists to reveal new secrets of the human nuclear pore complex.\" \/>\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\/puzzling-out-the-structure-of-a-molecular-giant\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Puzzling out the structure of a molecular giant | EMBL\" \/>\n<meta property=\"og:description\" content=\"Combining AlphaFold2, cryo-ET and other methods enabled scientists to reveal new secrets of the human nuclear pore complex.\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.embl.org\/news\/science\/puzzling-out-the-structure-of-a-molecular-giant\/\" \/>\n<meta property=\"og:site_name\" content=\"EMBL\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/embl.org\/\" \/>\n<meta property=\"article:published_time\" content=\"2022-06-10T06:00:00+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2024-10-18T08:25:02+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/06\/HumanNPC-1000x600-1.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1000\" \/>\n\t<meta property=\"og:image:height\" content=\"600\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Dorota Badowska\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@d_badowska\" \/>\n<meta name=\"twitter:site\" content=\"@embl\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Dorota Badowska\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"5 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\/puzzling-out-the-structure-of-a-molecular-giant\/#article\",\"isPartOf\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/puzzling-out-the-structure-of-a-molecular-giant\/\"},\"author\":{\"name\":\"Dorota Badowska\",\"@id\":\"https:\/\/www.embl.org\/news\/#\/schema\/person\/b8ae50efcd7533f0ab2ec368736b1d04\"},\"headline\":\"Puzzling out the structure of a molecular giant\",\"datePublished\":\"2022-06-10T06:00:00+00:00\",\"dateModified\":\"2024-10-18T08:25:02+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/puzzling-out-the-structure-of-a-molecular-giant\/\"},\"wordCount\":852,\"publisher\":{\"@id\":\"https:\/\/www.embl.org\/news\/#organization\"},\"image\":{\"@id\":\"https:\/\/www.embl.org\/news\/science\/puzzling-out-the-structure-of-a-molecular-giant\/#primaryimage\"},\"thumbnailUrl\":\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2022\/06\/HumanNPC-1000x600-1.jpg\",\"keywords\":[\"alphafold\",\"artificial intelligence\",\"beck\",\"cryo-electron tomography\",\"cssb\",\"hamburg\",\"heidelberg\",\"integrative modelling\",\"kosinski\",\"nuclear pore complex\",\"structural biology\"],\"articleSection\":[\"Science\",\"Science &amp; 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