{"id":2196,"date":"2017-05-04T09:30:15","date_gmt":"2017-05-04T16:30:15","guid":{"rendered":"http:\/\/blogs.oregonstate.edu\/psquared\/?p=2196"},"modified":"2017-05-04T09:47:37","modified_gmt":"2017-05-04T16:47:37","slug":"modeling-hemagglutinin","status":"publish","type":"post","link":"https:\/\/blogs.oregonstate.edu\/psquared\/2017\/05\/04\/modeling-hemagglutinin\/","title":{"rendered":"Modeling Hemagglutinin"},"content":{"rendered":"<p><strong>The Protein:\u00a0<\/strong><a href=\"https:\/\/pdb101.rcsb.org\/motm\/76\">Hemagglutinin<\/a>\u00a0(HA), a protein involved in the viral infection process. Specifically, HA helps cells internalize the virus and eventually the viral RNA.<\/p>\n<p><strong>Structure:\u00a0<\/strong>Hemagglutinin is a trimeric transmembrane protein that extends from the surface of viruses. There are two types of chains in the\u00a0enzyme, which we can call HA I and HA II. HA I (shown in blue) sits on the top of the protein while HA II (shown in yellow) is partially covered by\u00a0HA I at first. There are also various carbohydrates on the Hemagglutinin surface. The viral strain (H1,H2, etc) can change if the location of the carbohydrate chains on the HA surface changes.<\/p>\n<div id=\"attachment_2197\" style=\"width: 202px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/05\/Hemagglutinin1.gif\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2197\" class=\"wp-image-2197 size-medium\" src=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/05\/Hemagglutinin1-192x300.gif\" alt=\"\" width=\"192\" height=\"300\" \/><\/a><p id=\"caption-attachment-2197\" class=\"wp-caption-text\"><em>Hemagglutinin\u00a0extending from virus surface<\/em><\/p><\/div>\n<p>You can view the various hemagglutinin structures on PYMOL using the following PDB IDs:<\/p>\n<ul>\n<li>1RD8 &#8211; uncleaved hemagglutinin from\u00a0the 1918 influenza virus<\/li>\n<li>1RUZ &#8211; the active form of hemagglutinin from\u00a0the 1918 influenza virus<\/li>\n<\/ul>\n<p><strong>Mechanism of Action:\u00a0<\/strong><\/p>\n<p><a href=\"https:\/\/www.youtube.com\/watch?v=YSgkoldBNkI\">Video 1<\/a> shows the whole influenza virus infection process<\/p>\n<p><a href=\"https:\/\/www.youtube.com\/watch?v=zP4xbcqJ2CY\">Video 2 <\/a>(skip to minute 4) shows the membrane fusion process<\/p>\n<p>The blue portion of the protein targets sialic acids, which are part of some glycoproteins found on the cell membrane. Once the virus is docked on the cell membrane surface the cell internalizes the entire virus via endocytosis and begins releasing acids meant to digest the endosomal contents. However, the acids actually help activate conformational changes in Hemagglutinin, which allow the red portion of the protein\u00a0to attach to the endosomal membrane. The yellow portion of the protein then moves up the the protein and\u00a0brings the viral and endosomal membranes together.\u00a0The viral RNA can enter the cell after\u00a0the two membranes fuse together.<\/p>\n<div id=\"attachment_2198\" style=\"width: 405px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/05\/Hemagglutinin2.gif\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2198\" class=\"wp-image-2198 \" src=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/05\/Hemagglutinin2-300x151.gif\" alt=\"\" width=\"395\" height=\"199\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Hemagglutinin2-300x151.gif 300w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Hemagglutinin2-400x202.gif 400w\" sizes=\"auto, (max-width: 395px) 100vw, 395px\" \/><\/a><p id=\"caption-attachment-2198\" class=\"wp-caption-text\"><em>Hemagglutinin conformational changes<\/em><\/p><\/div>\n<p><strong>Modeling Ideas:<\/strong><\/p>\n<p>Some combination of these<\/p>\n<p>1.Different colored flowers made of tissue to represent the different parts of the protein joined together by pipe cleaners or wire or something similar since the protein looks like a flower bouquet from certain angles. And tissues are the only cold\/flu related\u00a0material I can think of.<\/p>\n<p>2. Tissue flowers for the HA I portion and then spiral bracelets to represent the alpha helices on the inside. Show conformational changes by moving the different pieces. Use a safety pin\/bobby pin structure to pull two &#8220;membranes&#8221; (pieces of cloth?) together to represent the fusion of the viral and cell membranes.<\/p>\n<p>3. Play-doh model of the three different stages?<\/p>\n<div id=\"attachment_2202\" style=\"width: 310px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/05\/Tissue-carnations.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2202\" class=\"wp-image-2202 size-medium\" src=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/05\/Tissue-carnations-300x300.jpg\" alt=\"\" width=\"300\" height=\"300\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations-300x300.jpg 300w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations-150x150.jpg 150w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations-768x768.jpg 768w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations-1024x1024.jpg 1024w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations-120x120.jpg 120w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations-400x400.jpg 400w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/05\/Tissue-carnations.jpg 2048w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><p id=\"caption-attachment-2202\" class=\"wp-caption-text\">Tissue carnations<\/p><\/div>\n<div id=\"attachment_2168\" style=\"width: 310px\" class=\"wp-caption alignleft\"><a href=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/04\/DNA-bracelet.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2168\" class=\"wp-image-2168 size-medium\" src=\"http:\/\/blogs.oregonstate.edu\/psquared\/files\/2017\/04\/DNA-bracelet-300x223.jpg\" alt=\"\" width=\"300\" height=\"223\" srcset=\"https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/04\/DNA-bracelet-300x223.jpg 300w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/04\/DNA-bracelet-400x297.jpg 400w, https:\/\/osu-wams-blogs-uploads.s3.amazonaws.com\/blogs.dir\/150\/files\/2017\/04\/DNA-bracelet.jpg 570w\" sizes=\"auto, (max-width: 300px) 100vw, 300px\" \/><\/a><p id=\"caption-attachment-2168\" class=\"wp-caption-text\">Spiral bracelet<\/p><\/div>\n<p style=\"text-align: center\">\n","protected":false},"excerpt":{"rendered":"<p>The Protein:\u00a0Hemagglutinin\u00a0(HA), a protein involved in the viral infection process. Specifically, HA helps cells internalize the virus and eventually the viral RNA. Structure:\u00a0Hemagglutinin is a trimeric transmembrane protein that extends from the surface of viruses. There are two types of &hellip; <a href=\"https:\/\/blogs.oregonstate.edu\/psquared\/2017\/05\/04\/modeling-hemagglutinin\/\">Continue reading <span class=\"meta-nav\">&rarr;<\/span><\/a><\/p>\n","protected":false},"author":8430,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[840433,4797],"tags":[],"class_list":["post-2196","post","type-post","status-publish","format-standard","hentry","category-2017-posts","category-student-posts"],"_links":{"self":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/posts\/2196","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/users\/8430"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/comments?post=2196"}],"version-history":[{"count":5,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/posts\/2196\/revisions"}],"predecessor-version":[{"id":2204,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/posts\/2196\/revisions\/2204"}],"wp:attachment":[{"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/media?parent=2196"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/categories?post=2196"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.oregonstate.edu\/psquared\/wp-json\/wp\/v2\/tags?post=2196"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}