{"id":6992,"date":"2018-02-20T15:09:00","date_gmt":"2018-02-20T15:09:00","guid":{"rendered":"https:\/\/website.prod.unilu.spikeseed.cloud\/en\/news\/metabolic-modelling-becomes-three-dimensional\/"},"modified":"2018-02-20T15:09:00","modified_gmt":"2018-02-20T15:09:00","slug":"metabolic-modelling-becomes-three-dimensional","status":"publish","type":"news","link":"https:\/\/www.uni.lu\/en\/news\/metabolic-modelling-becomes-three-dimensional\/","title":{"rendered":"Metabolic modelling becomes three-dimensional"},"content":{"rendered":"<section class=\"wp-block-unilux-blocks-free-section section\"><div class=\"container xl:max-w-screen-xl\"><p>An international research consortium has developed, with significant involvement of Luxembourg Centre for Systems Biomedicine (LCSB) scientists, the first computer model to include 3D in the representation of human metabolic processes.<\/p><p>To this end, the researchers integrated the three-dimensional structures of over 4,000 metabolic products, or metabolites as they are known, and nearly 13,000 proteins into an existing computer model. They also added an enormous volume of genetic and chemical information to the model on which the simulation runs. The name of this new computer-based tool, which has been made available to the biomedical research community recently, is Recon3D. The researchers\u2019 results on Recon3D appear in the journal <a href=\"https:\/\/www.nature.com\/nbt\/\" target=\"_blank\" title=\"\" rel=\"noopener\">Nature Biotechnology<\/a> (<a href=\"http:\/\/www.nature.com\/articles\/nbt.4072\" target=\"_blank\" title=\"Recon3D enables a three-dimensional view of gene variation in human metabolism\" rel=\"noopener\">doi:10.1038\/nbt.4072<\/a>).<\/p><figure class=\"wp-block-dev4-reusable-blocks-image  object-fit--contain\">\n    \n<img decoding=\"async\" class=\"wp-block-image unilux-custom-image-block\"\n                alt=\"\"\n            src=\"https:\/\/www.uni.lu\/wp-content\/uploads\/sites\/9\/2023\/07\/recon3d.jpg\"\n                srcset=\"https:\/\/www.uni.lu\/wp-content\/uploads\/sites\/9\/2023\/07\/recon3d-300x103.jpg 300w, https:\/\/www.uni.lu\/wp-content\/uploads\/sites\/9\/2023\/07\/recon3d.jpg 500w\"\n                style=\"object-position: 50.00% 50.00%; font-family: &quot;object-fit: contain; object-position: 50.00% 50.00%;&quot;; aspect-ratio: 21\/9; object-fit: contain; width: 100%;\"\n        loading=\"lazy\"\n\/>            <p class=\"wp-block-dev4-reusable-blocks-image-caption\">\n            Recon3D est disponible sur vmh.live, Virtual Metabolic Human database.        <\/p>\n    <\/figure><p>The importance of scientific computer models continues to increase. They make the existing knowledge tangible and thereby help scientists to accurately formulate and work on targeted problems in research. To create such models, researchers analyse all the publications and databases they can find on a topic and feed this information into their model.<\/p><p>Human metabolism research is one example, as Prof. Ines Thiele, head of the\u00a0Molecular Systems Physiology group at the LCSB of the University of Luxembourg and an ATTRACT fellow of the Luxembourg National Research Fund (FNR), says: \u201cfor the predecessor of Recon3D, Recon 2, a large team of research groups in different fields aggregated an enormous volume of data on the genome, chemical metabolic activities and physiological properties of the human organism.\u201d <strong>This data basis has now been considerably expanded yet again for Recon3D<\/strong>, Thiele reports.<\/p>\n<h2 class=\"has-text-align-left wp-block-unilux-blocks-heading\"        id=\"computer-model-of-human-metabolic-processes\"\n    >\nComputer model of human metabolic processes<\/h2>\n<p>What is unique about the new computer model, however, is the integrated three-dimensional structural data of proteins and metabolites. Dr Ronan Fleming, head of the LCSB\u00a0Systems Biochemistry group which was responsible for integrating the structural data of the metabolites into Recon3D, says \u201cso far, we have been able to say of a given metabolic reaction that substance A and B turn into substances C and D. Now, <strong>we know precisely which atoms each substance consists of, how the atoms are arranged in the starting materials and where those very same atoms can be found again in the products of the chemical reaction<\/strong>.\u201d<\/p><p>To make this possible, the researchers first had to find out which computational program \u2013 or algorithm as scientists call it \u2013 imports the three-dimensional structures of the molecules most accurately from the literature into Recon3D. To find this out, Fleming\u2019s team researched the molecular structure of the starting materials of a series of chemical reactions and determined the whereabouts of every single atom after the metabolic reaction was completed. They then tested various algorithms on the same reactions to identify those with the best predictive power. Fleming reports \u201cwith these results, we were then able to import very accurate structures of more than 4,000 metabolites into the computer model.\u201d Fleming\u2019s colleagues from the University of California in the United States expanded Recon3D with data on almost 13,000 protein structures, thereby <strong>bridging the research fields of structural biology and systems biology<\/strong>.<\/p>\n<h2 class=\"has-text-align-left wp-block-unilux-blocks-heading\"        id=\"an-expanded-computer-model-available-to-all-researchers\"\n    >\nAn expanded computer model available to all researchers<\/h2>\n<p>\u201cRecon3D now allows us to study metabolic processes that run differently, for example, in Parkinson\u2019s patients than in healthy people, much better and with more accuracy,\u201d Thiele sums up <strong>the possibilities that the new computer model offers<\/strong>. Dr Andreas Dr\u00e4ger from the Center for Bioinformatics at the University of T\u00fcbingen (ZBIT) has put it into a standardised format so that other researchers can use the model for their scientific questions. &#8220;Recon3D lays the foundations for creating cell-type-specific models that could be used to simulate the function of tissues through to entire organs in the computer,&#8221; explains Dr\u00e4ger and continues \u201cit could help to better understand the interplay between pathogens, such as bacteria or viruses, and the human host.\u201d Fleming also adds that, thanks to the three-dimensional structures of the metabolites and proteins in Recon3D, it is now possible to follow, at atomic resolution, how a genetic mutation could affect the development of certain diseases. \u201cThis can open up entirely new avenues for research on therapeutic approaches,\u201d Fleming concludes.<\/p><\/div><\/section>","protected":false},"excerpt":{"rendered":"<p>An international research consortium has developed, with significant involvement of Luxembourg Centre for Systems Biomedicine (LCSB) scientists, the first computer model to include 3D in the representation of human metabolic processes.<\/p>\n","protected":false},"author":0,"featured_media":6993,"template":"","format":"standard","meta":{"featured_image_focal_point":[],"show_featured_caption":false,"ulux_newsletter_groups":"","uluxPostTitle":"","uluxPrePostTitle":"","_trash_the_other_posts":false,"_price":"","_stock":"","_tribe_ticket_header":"","_tribe_default_ticket_provider":"","_tribe_ticket_capacity":"0","_ticket_start_date":"","_ticket_end_date":"","_tribe_ticket_show_description":"","_tribe_ticket_show_not_going":false,"_tribe_ticket_use_global_stock":"","_tribe_ticket_global_stock_level":"","_global_stock_mode":"","_global_stock_cap":"","_tribe_rsvp_for_event":"","_tribe_ticket_going_count":"","_tribe_ticket_not_going_count":"","_tribe_tickets_list":"[]","_tribe_ticket_has_attendee_info_fields":false},"news-category":[11,10],"news-topic":[26],"organisation":[209,233],"authorship":[],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v22.3 (Yoast SEO v22.3) - 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