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[{"key": "dc.contributor.author", "value": "Kalikka, Janne", "language": null, "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2013-03-25T10:23:37Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2013-03-25T10:23:37Z", "language": null, "element": "date", "qualifier": "available", "schema": "dc"}, {"key": "dc.date.issued", "value": "2008", "language": null, "element": "date", "qualifier": "issued", "schema": "dc"}, {"key": "dc.identifier.other", "value": "oai:jykdok.linneanet.fi:1257198", "language": null, "element": "identifier", "qualifier": "other", "schema": "dc"}, {"key": "dc.identifier.uri", "value": "https://jyx.jyu.fi/handle/123456789/41109", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "T\u00e4ss\u00e4 ty\u00f6ss\u00e4 tutkittiin DigA16- ja 1KT7-proteiineja. Proteiineille suoritettiin klassisia MD-simulaatioita k\u00e4ytt\u00e4m\u00e4ll\u00e4 Orac4.0-ohjelmistoa. DigA16-proteiinin kokeellisesti mitattu rakenne t\u00e4ydennettiin tietokoneella ja kokonaisesta proteiinista simuloitiin kolmea eri rakennetta. 1KT7-proteiinin simulaation l\u00e4ht\u00f6rakenteena oli kokeellisesti mitattu rakenne, jota ei tarvinnut t\u00e4ydent\u00e4\u00e4. Simulaatioita suoritettiin kutakin 10,751 nanosekunnin verran, joista 0,751 ns oli alustusta ja 10 ns simulointia 300 Kelviniss\u00e4. T\u00e4st\u00e4 10 ns vaiheesta ker\u00e4ttiin analysoitu data. Simulaation aikana kokonaisenergia kasvoi tasaisesti. Kasvu oli niin pient\u00e4, ett\u00e4 sen voidaan katsoa johtuneen t\u00e4ysin MD-simulaatiossa kumuloituvasta py\u00f6ristysvirheest\u00e4. T\u00e4m\u00e4 on tavallista MD-simulaatioille. Kahdesta DigA16-proteiinin simulaatioista l\u00f6ytyi pieni konformaatiomuutos, jonka aikaskaala on noin 2 ns. T\u00e4ss\u00e4 konformaatiomuutoksessa proteiinin aminohappoketjun p\u00e4\u00e4n 4-5 reunimmaista aminohappoa muuttavat selv\u00e4sti asentoaan. Lis\u00e4ksi tutkittiin miten DigA16-proteiinissa aminohappojen 42 ja 170 v\u00e4lill\u00e4 olevan rikki-rikki-sidoksen puuttuminen vaikutti proteiinin k\u00e4ytt\u00e4ytymiseen. Tuloksista voidaan p\u00e4\u00e4tell\u00e4, ett\u00e4 rikki-rikki-sidoksen puuttuminen aiheuttaa loppup\u00e4\u00e4n h\u00e4nn\u00e4n vaeltamisen kauemmas muusta proteiinista. Kuitenkin sidoksen puuttuminen aiheutti vain lokaaleja asennonmuutoksia proteiinin reunalla ja esimerkiksi proteiinin tunnusomaiseen \u03b2-tynnyriin sidoksen puuttuminen ei vaikuttanut. Edell\u00e4 mainittu konformaatiomuutos tapahtui aminohappoketjun toisessa p\u00e4\u00e4ss\u00e4, mutta kuitenkin muutos tapahtui vain niiss\u00e4 simulaatioissa, joissa rikki-rikki-sidos oli irti. Kahdessa simulaatiossa oli mukana vierasmolekyyli, joka oli proteiinin onkalossa. DigA16:n vierasmolekyylin\u00e4 oli digoksigeniini ja 1KT7:n vierasmolekyylin\u00e4 retinoli. Kumpikaan vierasmolekyyli ei kokenut asennonmuutosta. Pient\u00e4 heilumista tapahtui, mutta t\u00e4m\u00e4 on tavallista simulaatioissa. DigA16:n hydrolisi\u00e4 sivuryhmi\u00e4 on l\u00e4hell\u00e4 digoksigeniini\u00e4 ja ne todenn\u00e4k\u00f6isesti muodostavat sen kanssa vetysidoksia. 1KT7 puolestaan pit\u00e4\u00e4 hydrofobisia fenyylirenkaita ja metyyliryhmi\u00e4 retinolin l\u00e4hell\u00e4, mik\u00e4 oli odotettavissa.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted using Plone Publishing form by Janne Kalikka (jalajoka) on 2013-03-25 10:23:36.714819. Form: Pro gradu -lomake (1 tekij\u00e4) (https://kirjasto.jyu.fi/julkaisut/julkaisulomakkeet/pro-gradu-lomake-1-tekijae). JyX data:", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by jyx lomake-julkaisija (jyx-julkaisija@noreply.fi) on 2013-03-25T10:23:37Z\nNo. of bitstreams: 2\nURN:NBN:fi:jyu-201303251370.pdf: 3573118 bytes, checksum: 48f85adffe5a08bbcf54cd947798b0c9 (MD5)\nlicense.html: 107 bytes, checksum: a7d86e598caa500b1b433bbb9dc8ef1c (MD5)", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2013-03-25T10:23:37Z (GMT). No. of bitstreams: 2\nURN:NBN:fi:jyu-201303251370.pdf: 3573118 bytes, checksum: 48f85adffe5a08bbcf54cd947798b0c9 (MD5)\nlicense.html: 107 bytes, checksum: a7d86e598caa500b1b433bbb9dc8ef1c (MD5)\n Previous issue date: 2008", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "60 sivua", "language": null, "element": "format", "qualifier": "extent", "schema": "dc"}, {"key": "dc.format.mimetype", "value": "application/pdf", "language": null, "element": "format", "qualifier": "mimetype", "schema": "dc"}, {"key": "dc.language.iso", "value": "fin", "language": null, "element": "language", "qualifier": "iso", "schema": "dc"}, {"key": "dc.rights", "value": "In Copyright", "language": "en", "element": "rights", "qualifier": null, "schema": "dc"}, {"key": "dc.subject.other", "value": "biofysiikka", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "proteiinit", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "simulointi", "language": "", "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "Vierasmolekyylien sitoutumisen mallintaminen lipokaliiniproteiineissa", "language": null, "element": "title", "qualifier": null, "schema": "dc"}, {"key": "dc.type", "value": "master thesis", "language": null, "element": "type", "qualifier": null, "schema": "dc"}, {"key": "dc.identifier.urn", "value": "URN:NBN:fi:jyu-201303251370", "language": null, "element": "identifier", "qualifier": "urn", "schema": "dc"}, {"key": "dc.type.dcmitype", "value": "Text", "language": "en", "element": "type", "qualifier": "dcmitype", "schema": "dc"}, {"key": "dc.type.ontasot", "value": "Pro gradu -tutkielma", "language": "fi", "element": "type", "qualifier": "ontasot", "schema": "dc"}, {"key": "dc.type.ontasot", "value": "Master\u2019s thesis", "language": "en", "element": "type", "qualifier": "ontasot", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Matemaattis-luonnontieteellinen tiedekunta", "language": "fi", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.faculty", "value": "Faculty of Sciences", "language": "en", "element": "contributor", "qualifier": "faculty", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Fysiikan laitos", "language": "fi", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Department of Physics", "language": "en", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "University of Jyv\u00e4skyl\u00e4", "language": "en", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.contributor.organization", "value": "Jyv\u00e4skyl\u00e4n yliopisto", "language": "fi", "element": "contributor", "qualifier": "organization", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Fysiikka", "language": "fi", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Physics", "language": "en", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.date.updated", "value": "2013-03-25T10:23:37Z", "language": null, "element": "date", "qualifier": "updated", "schema": "dc"}, {"key": "dc.type.coar", "value": "http://purl.org/coar/resource_type/c_bdcc", "language": null, "element": "type", "qualifier": "coar", "schema": "dc"}, {"key": "dc.rights.accesslevel", "value": "openAccess", "language": "fi", "element": "rights", "qualifier": "accesslevel", "schema": "dc"}, {"key": "dc.type.publication", "value": "masterThesis", "language": null, "element": "type", "qualifier": "publication", "schema": "dc"}, {"key": "dc.subject.oppiainekoodi", "value": "4021", "language": null, "element": "subject", "qualifier": "oppiainekoodi", "schema": "dc"}, {"key": "dc.subject.yso", "value": "biofysiikka", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "proteiinit", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.subject.yso", "value": "simulointi", "language": null, "element": "subject", "qualifier": "yso", "schema": "dc"}, {"key": "dc.format.content", "value": "fulltext", "language": null, "element": "format", "qualifier": "content", "schema": "dc"}, {"key": "dc.rights.url", "value": "https://rightsstatements.org/page/InC/1.0/", "language": null, "element": "rights", "qualifier": "url", "schema": "dc"}, {"key": "dc.type.okm", "value": "G2", "language": null, "element": "type", "qualifier": "okm", "schema": "dc"}]
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