{"id":38,"date":"2021-06-18T09:26:03","date_gmt":"2021-06-18T03:56:03","guid":{"rendered":"https:\/\/neelsb.com\/myblog\/?p=38"},"modified":"2025-08-16T22:16:55","modified_gmt":"2025-08-16T16:46:55","slug":"dnd1","status":"publish","type":"post","link":"https:\/\/neelsb.com\/myblog\/2021\/06\/18\/dnd1\/","title":{"rendered":"Observation of a novel domain swapped dimer in RRM domain"},"content":{"rendered":"\n<figure class=\"wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"558\" src=\"https:\/\/neelsb.com\/myblog\/wp-content\/uploads\/2021\/06\/2-1024x558.jpg\" alt=\"\" class=\"wp-image-94\" srcset=\"https:\/\/neelsb.com\/myblog\/wp-content\/uploads\/2021\/06\/2-1024x558.jpg 1024w, https:\/\/neelsb.com\/myblog\/wp-content\/uploads\/2021\/06\/2-300x164.jpg 300w, https:\/\/neelsb.com\/myblog\/wp-content\/uploads\/2021\/06\/2-768x419.jpg 768w, https:\/\/neelsb.com\/myblog\/wp-content\/uploads\/2021\/06\/2-1536x837.jpg 1536w, https:\/\/neelsb.com\/myblog\/wp-content\/uploads\/2021\/06\/2-2048x1116.jpg 2048w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"wp-element-caption\"><em>2.3 \u00c5 resolution structure of human DND1-RRM2(PDB id 6LE1). The work was done by Ms. Pooja Kumari<\/em><\/figcaption><\/figure>\n\n\n\n<p><a href=\"https:\/\/web.archive.org\/web\/20220811025059\/http:\/\/neelsb.com\/myblog\/?tag=x-ray-crystallography\"><\/a>Cell, the functional unit of life, stores codes of its functioning in long strings called DNA, which is made of different combinations of four chemicals, namely A, G, C, and T. Specific stretches of DNA are called genes or coding regions, and thus a cell contains many genes. These genes code specifically to make proteins through a messenger entity called mRNA, which decodes the code. The proteins take birth at ribosomes inside the cell as a string where each bead represents one amino acid selected out of 20 naturally occurring ones. The proteins immediately fold, assisted or unassisted, to form a distinct three-dimensional shape. The three-dimensional organization dictates the functions of proteins, which are the workhorses of the cell, performing all functions in a very well-orchestrated manner. Depending on time, type, and location of the cell, one gene can code for different variants of proteins, called isoforms, that can have different shapes and functions. As Francis Crick has said, \u201c<em>The ultimate aim of biology is in fact to explain all biology in terms of physics and chemistry. Eventually, one may hope to have the whole of biology \u2018explained\u2019 in terms of the level below it, and so on right down to the atomic level<\/em>\u201d. In order to understand the function of proteins at the atomic level, it is absolutely essential to see their three-dimensional structures at atomic resolution. X-ray crystallography, NMR spectroscopy, X-ray-free electron laser (XFEL), and single-particle Cryo-Electron Microscopy are used to determine the atomic-resolution three-dimensional structures of proteins.<\/p>\n\n\n\n<p>Our group has been working on a class of RNA-binding protein domains known as RNA Recognition Motif (RRM), or Ribonucleoprotein domain (RNP), which is found to be the most abundant nucleic acid-binding domain in higher vertebrates. In humans, about 2% of the genome codes for RRM, and more than 500 RRM-containing proteins have been annotated. They are found in single copies, multiple copies, or in conjunction with other domains in the same protein. Studies show that RRM domains not only recognize nucleic acid but are also engaged in protein-protein interactions and protein-lipid interactions, owing to their structural plasticity. RRMs typically have about 90 amino acids with a representative topology of \u03b21-\u03b11-\u03b22-\u03b23-\u03b12-\u03b24, wherein the four-stranded \u03b2-sheets are packed against the two \u03b1-helices. There have been several examples where the length of loops, \u03b1-helix, and \u03b2-sheet vary, and additional secondary structured elements at RRM extremities are well conserved. These are crucial for interaction, allowing longer RNA recognition. In our previous study, we discovered a novel mode of RNA interaction where an extended \u03b11\u03b22 loop of human TAF-15 protein recognised a stem-loop RNA.<\/p>\n\n\n\n<p>Due to its unique amino acid composition,&nbsp;we started working on human DND1 (Dead end protein homolog 1), also known as DND MicroRNA-Mediated Repression Inhibitor 1. DND1 is an RNA-binding protein&nbsp;containing two RRMs, RRM1 and RRM2 domains, in tandem, and a double-stranded RNA-binding domain at the C-terminal, separated by 40 40-residue flexible linker. In humans, reports of dysregulation at DND1 or mutation in the gene have been associated with testicular cancer and tongue squamous cell carcinoma. We have determined the atomic-resolution crystal structure of DND1-RRM2 and observed a novel domain-swapped dimer formation, like one seen in HIV-1 protease. We validated the domain-swapped dimer formation in solution using nOe and relaxation data from NMR spectroscopy. <strong>Ours is the first report of domain<\/strong><strong>-swapped dimer formation in any RRM<\/strong><strong>, and it also points to the limitation<\/strong><strong>s faced by structure prediction tools.<\/strong> In conclusion, there is no substitute for experimentally determined structure if we have to appreciate protein diversity.<\/p>\n\n\n\n<p>\u091c\u0940\u0935\u0928 \u0915\u0940 \u0915\u093e\u0930\u094d\u092f\u093e\u0924\u094d\u092e\u0915 \u0907\u0915\u093e\u0908 \u0915\u094b\u0936\u093f\u0915\u093e \u0905\u092a\u0928\u0947 \u092d\u0940\u0924\u0930 \u091c\u0940\u0935\u0928 \u0915\u0940 \u0938\u0902\u0939\u093f\u0924\u093e \u0915\u094b \u091a\u093e\u0930 \u0930\u0938\u093e\u092f\u0928\u094b\u0902, \u090f, \u091c\u0940, \u0938\u0940 \u0914\u0930 \u091f\u0940, \u0915\u0947 \u0935\u093f\u092d\u093f\u0928\u094d\u0928 \u0938\u0902\u092f\u094b\u091c\u0928\u094b\u0902 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\u0938\u0902\u0930\u091a\u0928\u093e \u0915\u093e \u0915\u094b\u0908 \u0935\u093f\u0915\u0932\u094d\u092a \u0928\u0939\u0940\u0902 \u0939\u0948\u0964<\/p>\n\n\n\n<p><strong>References<\/strong><\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>Kumari P* and Bhavesh NS* (2021) Human DND1-RRM2 forms a non-canonical domain swapped dimer. <a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/pro.4083\" target=\"_blank\" rel=\"noreferrer noopener\"><em>Protein Sci.<\/em><\/a> <strong>30<\/strong>, 1184-1195<\/li>\n\n\n\n<li><strong>Structure co-ordinate<\/strong>s: Protein Data Bank (PDB) accession numbers <a href=\"https:\/\/www.rcsb.org\/structure\/6LE1\" target=\"_blank\" rel=\"noreferrer noopener\">6LE1<\/a>.<\/li>\n<\/ol>\n","protected":false},"excerpt":{"rendered":"<p>Cell, the functional unit of life, stores codes of its functioning in long strings called DNA, which is made of different combinations of four chemicals, namely A, G, C, and T. Specific stretches of DNA are called genes or coding regions, and thus a cell contains many genes. These genes code specifically to make proteins &hellip; <a href=\"https:\/\/neelsb.com\/myblog\/2021\/06\/18\/dnd1\/\" class=\"more-link\">Continue reading <span class=\"screen-reader-text\">Observation of a novel domain swapped dimer in RRM domain<\/span> <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"pagelayer_contact_templates":[],"_pagelayer_content":"","footnotes":""},"categories":[3],"tags":[18,19,15,20,13],"class_list":["post-38","post","type-post","status-publish","format-standard","hentry","category-science","tag-dnd1","tag-domain-swapped-dimer","tag-nmr-spectroscopy","tag-rrm","tag-x-ray-crystallography"],"_links":{"self":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts\/38","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/comments?post=38"}],"version-history":[{"count":3,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts\/38\/revisions"}],"predecessor-version":[{"id":95,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/posts\/38\/revisions\/95"}],"wp:attachment":[{"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/media?parent=38"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/categories?post=38"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/neelsb.com\/myblog\/wp-json\/wp\/v2\/tags?post=38"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}