{"id":28497,"date":"2015-10-05T13:47:08","date_gmt":"2015-10-05T11:47:08","guid":{"rendered":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/"},"modified":"2021-06-16T14:40:44","modified_gmt":"2021-06-16T14:40:44","slug":"part-4-topological-and-structural-analysis-of-proteins","status":"publish","type":"teachingbase","link":"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/?lang=cs","title":{"rendered":"\u010c\u00e1st 4: Topologick\u00e1 a strukturn\u00ed anal\u00fdza protein\u016f"},"content":{"rendered":"\n<div class=\"vf-tabs\"><ul class=\"vf-tabs__list\" data-vf-js-tabs=\"true\"><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-feeb5d9b-3c8d-4306-b0e3-a7aaf182833d\">Overview<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a825691f-52a3-4fdb-ad2b-e746a1da8a8c\">Va\u0161e \u00faloha<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a06ebf8a-83a2-4f49-a96a-4f17cb2ab058\">Uniprot e PDBe<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-a68c550e-908c-4c46-8c0b-6e40d1090e49\">Ot\u00e1zky<\/a><\/li><li class=\"vf-tabs__item\"><a class=\"vf-tabs__link\" href=\"#vf-tabs__section-ff1dedb3-2691-46d2-9e4d-5d2ff1cc3fba\">Activity navigation<\/a><\/li><\/ul><div class=\"vf-tabs-content\" data-vf-js-tabs-content=\"true\">\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-feeb5d9b-3c8d-4306-b0e3-a7aaf182833d\"><h2>Overview<\/h2>\n<p>Krom\u011b anal\u00fdzy prim\u00e1rn\u00ed aminokyselinov\u00e9 sekvence opsin\u016f se v t\u00e9to \u010d\u00e1sti zam\u011b\u0159\u00edme na prostorovou strukturu proteinov\u00fdch molekul a uk\u00e1\u017eeme si, jak u\u017eite\u010dn\u00e9 jsou pro tyto \u00fa\u010dely bioinformatick\u00e9 datab\u00e1ze.Budeme pracovat s hov\u011bz\u00edm rhodopsinem, kter\u00fd jsme ji\u017e identifikovali v prvn\u00ed \u010d\u00e1sti a v datab\u00e1zi Uniprot vyhled\u00e1me jeho sekund\u00e1rn\u00ed strukturu a membr\u00e1nov\u00e9 topologie (tj. jak je protein situov\u00e1n vzhledem k bun\u011b\u010dn\u00e9 membr\u00e1n\u011b atd.). Pot\u00e9 pou\u017eijeme datab\u00e1zi Protein Data Bank in Europe (PDBe), abychom se pod\u00edvali na celkovou prostorovou strukturu.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a825691f-52a3-4fdb-ad2b-e746a1da8a8c\"><h2>Va\u0161e \u00faloha<\/h2>\n<p><strong>\u0158i\u010fte se n\u00e1sleduj\u00edc\u00edmi pokyny:<\/strong><\/p>\n\n\n\n<p><strong>1. <\/strong>Pou\u017eijte Uniprot Protein Knowledgebase k vyhled\u00e1n\u00ed a zobrazen\u00ed sekund\u00e1rn\u00edch struktur hov\u011bz\u00edho rhodopsinu.<br><strong>2.<\/strong> Prozkoumejte prostorovou strukturu hov\u011bz\u00edho rhodopsinu pomoc\u00ed Protein Data Bank in Europe (PDBe).<br><strong>3.<\/strong> Pokuste se odpov\u011bd\u011bt na ot\u00e1zky.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a06ebf8a-83a2-4f49-a96a-4f17cb2ab058\"><h2>Uniprot e PDBe<\/h2>\n<p><strong>1.<\/strong> Otev\u0159ete odkaz v nov\u00e9m okn\u011b prohl\u00ed\u017ee\u010de: <a href=\"https:\/\/www.uniprot.org\/\" target=\"_blank\" rel=\"noreferrer noopener\">https:\/\/www.uniprot.org\/<\/a><\/p>\n\n\n\n<p><strong>2.<\/strong> Prohledejte Unitprot \u201cProtein Knowledgebase (UniProtKB)\u201d zad\u00e1n\u00edm p\u0159\u00edstupov\u00e9ho \u010d\u00edsla (Uniprot accession number) nebo n\u00e1zvu hov\u011bz\u00edho rhodopsinu v pol\u00ed\u010dku query a kliknut\u00edm na &#8220;Search&#8221;. <strong>Uniprot name: OPSD_BOVIN, accession number: P02699<\/strong><br>Na str\u00e1nce v\u00fdsledk\u016f najdete souhrn v\u0161ech v\u011bdeck\u00fdch informac\u00ed t\u00fdkaj\u00edc\u00edch se tohoto proteinu. Projd\u011bte tento p\u0159ehled a pokuste se odpov\u011bd\u011bt na zadan\u00e9 ot\u00e1zky.<\/p>\n\n\n\n<p><strong>3.<\/strong> Pro vstup do PDBe (Protein Data Bank in Europe) sje\u010fte dol\u016f k pol\u00ed\u010dku &#8220;Sequences&#8221; a klikn\u011bte na &#8220;UniParc&#8221; vedle p\u0159\u00edstupov\u00e9ho \u010d\u00edsla. Tak se dostanete k arch\u00edvu sekvenc\u00ed, kter\u00fd obsahuje odkazy na rozmanit\u00e9 datab\u00e1ze a jejich \u00fadaje relevantn\u00ed k dan\u00e9mu proteinu. Vyhledejte jak\u00fdkoliv odkaz propojen\u00fd s PDB (ve sloupci &#8220;Database&#8221;) a najd\u011bte nejnov\u011bj\u0161\u00ed z\u00e1znam (\u0161est\u00fd sloupec ukazuje naposledy vid\u011bn\u00fd z\u00e1znam &#8211; &#8220;last seen&#8221;).<\/p>\n\n\n\n<p><strong>4.<\/strong> Nyn\u00ed jste p\u0159esm\u011brov\u00e1ni na \u00fadaje o hov\u011bz\u00edm rhodopsinu v datab\u00e1zi PDBe.<\/p>\n\n\n\n<p><strong>5.<\/strong> Klikn\u011bte na &#8220;View in 3D&#8221; a n\u00e1sledn\u011b vyberte &#8220;Astex Viewer&#8221;. M\u016f\u017eete b\u00fdt op\u011bt dot\u00e1z\u00e1ni na povolen\u00ed ke spu\u0161t\u011bn\u00ed Javy ve va\u0161em po\u010d\u00edta\u010di.<\/p>\n\n\n\n<p><strong>6.<\/strong> Jestli\u017ee v\u0161e funguje spr\u00e1vn\u011b, d\u00edv\u00e1te se pr\u00e1v\u011b na trojrozm\u011brnou strukturu hov\u011bz\u00edho rhodopsinu zobrazenou jako stuhy (ribbon-cartoon). Pomoc\u00ed kurzoru m\u016f\u017eete strukturu libovoln\u011b ot\u00e1\u010det v prostoru. Zp\u016fsob zobrazen\u00ed (nap\u0159. zp\u016fsob zobrazen\u00ed struktury \u010di barva) m\u016f\u017eete zm\u011bnit bu\u010f v nab\u00eddce po lev\u00e9 stran\u011b, nebo kliknut\u00edm prav\u00e9ho tla\u010d\u00edtka my\u0161i. Prohl\u00e9dn\u011bte si prostorovou strukturu hov\u011bz\u00edho rhodopsinu a pokuste se odpov\u011bd\u011bt na uveden\u00e9 ot\u00e1zky.<\/p>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-a68c550e-908c-4c46-8c0b-6e40d1090e49\"><h2>Ot\u00e1zky<\/h2>\n<p><strong>1.<\/strong> Za pou\u017eit\u00ed informac\u00ed poskytnut\u00fdch v datab\u00e1zi Uniprot se pokuste odpov\u011bd\u011bt na tyto ot\u00e1zky:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Kolik transmembr\u00e1nov\u00fdch dom\u00e9n m\u00e1 hov\u011bz\u00ed rhodopsin a jak jsou distribuov\u00e1ny v r\u00e1mci proteinu?<\/li><li>Kter\u00e9 aminokyselinov\u00e9 zbytky tvo\u0159\u00ed vazebn\u00e9 m\u00edsto pro chromofor?<\/li><li>Jak vypad\u00e1 sekund\u00e1rn\u00ed struktura hov\u011bz\u00edho rhodopsinu? (Obsahuje v\u00edce alfa-helix\u016f nebo beta-skl\u00e1dan\u00fdch list\u016f)?<\/li><\/ul>\n\n\n\n<p><strong>2. <\/strong>Za pou\u017eit\u00ed trojrozm\u011brn\u00e9 struktuy se pokuste odpov\u011bd\u011bt na tyto ot\u00e1zky:<\/p>\n\n\n\n<ul class=\"wp-block-list\"><li>Jak\u00fd je celkov\u011b tvar hov\u011bz\u00edho rhodopsinu?<\/li><li>Dok\u00e1\u017eete rozpoznat jednotliv\u00e9 alfa helixy a beta skl\u00e1dan\u00e9 listy? Tento protein byl vykrystalizov\u00e1n jako dimer, tzn. \u017ee obsahuje dv\u011b polypeptidov\u00e9 podjednotky. Vid\u00edte dv\u011b skupiny transmembr\u00e1nov\u00fdch helix\u016f?<\/li><li>Dok\u00e1\u017eete lokalizovat vazebn\u00e9 m\u00edsto chromoforu uvnit\u0159 stuhov\u00e9ho modelu proteinov\u00e9 struktury?<\/li><\/ul>\n<\/section>\n\n\n\n<section class=\"vf-tabs__section\" id=\"vf-tabs__section-ff1dedb3-2691-46d2-9e4d-5d2ff1cc3fba\"><h2>Activity navigation<\/h2>\n<ul class=\"wp-block-list\"><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28420\">P\u00e1tr\u00e1n\u00ed po evoluci sv\u011btlo\u010divn\u00fdch protein\u016f<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-1-search-for-protein-identity\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28440\">\u010c\u00e1st 1: Hled\u00e1n\u00ed identity nezn\u00e1m\u00e9ho proteinu<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-2-multiple-sequence-alignment-of-protein-sequences\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28454\">Part 2: Multiple sequence alignment of protein sequences<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-3-phylogenetic-analysis-of-aligned-protein-sequences\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28474\">\u010c\u00e1st 3: Fylogenetick\u00e1 anal\u00fdza proteinov\u00fdch sekvenc\u00ed<\/a><\/li><li><a href=\"https:\/\/www.embl.org\/ells\/teachingbase\/opsins-bioinformatics\/part-4-topological-and-structural-analysis-of-proteins\/?lang=cs\" data-type=\"teachingbase\" data-id=\"28497\">\u010c\u00e1st 4: Topologick\u00e1 a strukturn\u00ed anal\u00fdza protein\u016f<\/a><\/li><\/ul>\n<\/section>\n<\/div><\/div>\n\n\n\n<p><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"featured_media":28498,"parent":28420,"menu_order":1,"template":"","class_list":["post-28497","teachingbase","type-teachingbase","status-publish","has-post-thumbnail","hentry"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28497","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase"}],"about":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/types\/teachingbase"}],"up":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/teachingbase\/28420"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media\/28498"}],"wp:attachment":[{"href":"https:\/\/www.embl.org\/ells\/wp-json\/wp\/v2\/media?parent=28497"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}