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[{"key": "dc.contributor.advisor", "value": "Ihalainen Janne", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.advisor", "value": "Lehtivuori Heli", "language": "", "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Kurkinen, Sami", "language": null, "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2017-03-29T16:23:04Z", "language": "", "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2017-03-29T16:23:04Z", "language": "", "element": "date", "qualifier": "available", "schema": "dc"}, {"key": "dc.date.issued", "value": "2017", "language": null, "element": "date", "qualifier": "issued", "schema": "dc"}, {"key": "dc.identifier.other", "value": "oai:jykdok.linneanet.fi:1690707", "language": null, "element": "identifier", "qualifier": "other", "schema": "dc"}, {"key": "dc.identifier.uri", "value": "https://jyx.jyu.fi/handle/123456789/53397", "language": "", "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Fytokromit ovat bakteereissa, leviss\u00e4 ja kasveissa esiintyvi\u00e4 valoaktiivisia proteiineja, jotka aistivat punaista ja kaukopunaista valoa. Ne toimivat valoreseptoreina solusignaloinnissa. Puna- sek\u00e4 kaukopuna-alueen valo muuttaa fytokromeja edestakaisin valottuneen tilan ja lepotilan v\u00e4lill\u00e4. Valoaktivaatiomekanismi lepotilalta valottuneelle tilalle on monivaiheinen tapahtuma, joka alkaa kovalenttisesti sitoutuneen kromoforin isomerisaatiolla. Bakteerifytokromeissa kromofori on useimmiten biliverdiini. Fytokromiproteiinit tarjoavat mahdollisuuksia kudosten kuvantamiseen, vaikkakin tyypillisesti niiden fluoresenssin kvanttisaanto on heikko. Kvanttisaantoa voidaan kuitenkin parantaa heikent\u00e4m\u00e4ll\u00e4 valoaktivaatioreittej\u00e4, jotka ajavat virittynytt\u00e4 proteiinia kohti valottunutta tilaa. N\u00e4in suositaan niit\u00e4 kanavia, jotka johtavat viritystilan vaimenemiseen tai proteiinin fluoresenssiin. Viritystilan ominaisuudet tulee tuntea, jotta fytokromien fluoresoivia ominaisuuksia voitaisiin parantaa.\r\n\r\nT\u00e4ss\u00e4 ty\u00f6ss\u00e4 tutkittiin Deinococcus radioduransin fytokromin kromoforia sitovan osan valoaktivaatiomekanismia. Ty\u00f6ss\u00e4 vertailtiin poolisten ja poolittomien subtituutioiden vaikutusta biliverdiinin l\u00e4heisyydess\u00e4 olevaan konservoituneeseen aminohappoon H260. H260:n ja biliverdiinin v\u00e4lill\u00e4 olevaa vetysidosverkostoa h\u00e4irittiin seriini-, alaniini- ja leusiinimutaatioilla. Kaikki variantit tuottuivat ja sitoivat biliverdiini\u00e4 kovalenttisesti. Niiden valoaktivaatiota tutkittiin steady-state ja aikaerotteisen spektroskopian menetelmin. Lepotilassa H260A ja H260S variantin absorptiospektri muistutti villityypin absorptiospektri\u00e4. H260L variantin absorptiospektri poikkesi villityypin absorptiospektrist\u00e4 merkitt\u00e4v\u00e4sti, mik\u00e4 viittaa poolittoman leusiinin muuttavan hyvin merkitt\u00e4v\u00e4sti proteiinin sitoutumistaskua. Ty\u00f6ss\u00e4 tutkittiin my\u00f6s kaikkien varianttien kyky\u00e4 siirty\u00e4 lepotilasta aktiiviseen tilaan. Punaisella valolla valottamisen j\u00e4lkeen kaikkien varianttien reaktiotuote poikkesi villityypin vastaavasta, eik\u00e4 yksik\u00e4\u00e4n kyennyt palautumaan takaisin lepotilaan kuten villityyppi.\r\n\r\nHiljattain on ehdotettu, ett\u00e4 fytokromeissa isomerisaation lis\u00e4ksi varauksensiirtotila (elektroninsiirto yhdistettyn\u00e4 protoninsiirtoon) on t\u00e4rke\u00e4ss\u00e4 roolissa biliverdiinin virittyneen tilan dynamiikassa. T\u00e4m\u00e4 varauksensiirtotila voidaan n\u00e4hd\u00e4 aikaerotteisessa spektroskopiassa positiivisena signaalina l\u00e4hi-infrapuna-alueella. N\u00e4iden mittausten mukaan H260 on mukana varauksensiirtotilan muodostuksessa, mik\u00e4 osoitettiin nyt ensimm\u00e4isen kerran. T\u00e4m\u00e4n lis\u00e4ksi H260A ja H260S variantit eiv\u00e4t saavuttaneet ensimm\u00e4ist\u00e4 suhteellisen vakaata valoaktivaatioreitin tuotetta. N\u00e4ist\u00e4 tuloksista huolimatta fluoresenssin kvanttisaanto ei yll\u00e4tt\u00e4en kasvanut yhdell\u00e4k\u00e4\u00e4n variantilla. T\u00e4m\u00e4 osoittaa, ett\u00e4 fytokromien viritystilan vaimenemisreitit ovat oletettua monimutkaisempia ja H260 ei vaikuta sen fluoresoiviin ominaisuuksiin. T\u00e4ss\u00e4 ty\u00f6ss\u00e4 tehdyt havainnot auttavat uusien fluoresoivien merkkiaineiden kehityksess\u00e4 ja antavat uutta tietoa H260:n merkityksest\u00e4 fytokromin valoktivaatioprosessissa.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Phytochromes are red and far-red light sensitive proteins found in bacteria, algae and plants. They work as photoreceptors in cell signaling. Red and far-red light convert phytochromes back and forth between the active and resting states. The photoactivation mechanism from the resting state to the active state contains several steps but is initiated by the isomerization of a covalently bound chromophore. In bacterial phytochromes, the chromophore is usually biliverdin. The near-infrared fluorescence properties of phytochromes offer potential to tissue imaging, although, typically the fluorescence quantum yield of phytochromes is poor. This can be increased by diminishing the photoactivation pathway that leads the excited protein to the stable photoproduct. In this way, pathways that lead to de-excitation and protein fluorescence are favored. In order to improve the fluorescence properties, the excited state properties need to be known.\r\n\r\nIn this study, the photoactivation mechanism of a chromophore-binding domain from Deinococcus radiodurans phytochrome was explored. The effects of polar and nonpolar substitutions of the residue H260, which is a conserved amino acid in close proximity to the biliverdin chromophore, were compared. Ser, Ala and Leu mutations were made to disturb the hydrogen bond network between H260 and biliverdin vicinity. All these H260 variants were produced and they all bind covalently biliverdin. The photoactivation of the variants was studied by steady-state and time-resolved spectroscopies. The absorption spectra of the H260A and H260S variants resemble the spectrum of the wild type in the resting state. The absorption spectrum of the H260L variant differs from the wild type spectrum, which suggests that a nonpolar Leu residue changes the binding pocket considerably. The photoconversion potential for all H260 variants was also tested. After illumination with red light, the photoproduct of all H260 variants differed from the wild type and none of them was able to revert to the resting state with far-red illumination as the wild type does.\r\n\r\nRecently, it has been suggested that in addition to isomerization, a charge-transfer state (electron transfer coupled to proton transfer) of biliverdin plays an important role in the excited state dynamics of biliverdin in phytochromes. This shows up as a positive transient signal at the near-infrared spectral region. According to the time-resolved absorption measurements, it was shown for the first time that H260 is one of the central amino acids needed in the formation of the charge-transfer state. In addition, H260A and H260S variants did not reach the first relatively stable photoproduct in the photoactivation pathway. Surprisingly, despite these observations, the fluorescence quantum yields of the variants were not increased. This indicates that the de-excitation pathways of phytochromes are more complicated than excepted and H260 does not affect the fluorescence properties. Findings in this study will help in developing new fluorescent markers and give new information about the role of H260 in the photoactivation process of a phytochrome.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted using Plone Publishing form by Sami Kurkinen (satakurk) on 2017-03-29 16:23:03.244157. Form: Pro gradu -lomake (https://kirjasto.jyu.fi/julkaisut/julkaisulomakkeet/pro-gradu-lomake). JyX data: [jyx_publishing-allowed (fi) =False]", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted by jyx lomake-julkaisija (jyx-julkaisija.group@korppi.jyu.fi) on 2017-03-29T16:23:03Z\r\nNo. of bitstreams: 2\r\nURN:NBN:fi:jyu-201703291816.pdf: 2806051 bytes, checksum: 6be51c627cc035cbbee97c8ff9382a05 (MD5)\r\nlicense.html: 1315 bytes, checksum: b9406bbb4f0c60db9d1c010e210b363e (MD5)", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2017-03-29T16:23:04Z (GMT). No. of bitstreams: 2\r\nURN:NBN:fi:jyu-201703291816.pdf: 2806051 bytes, checksum: 6be51c627cc035cbbee97c8ff9382a05 (MD5)\r\nlicense.html: 1315 bytes, checksum: b9406bbb4f0c60db9d1c010e210b363e (MD5)\r\n Previous issue date: 2017", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "1 verkkoaineisto (46 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": "eng", "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": "phytochrome", "language": null, "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "Deinococcus radiodurans", "language": null, "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "The importance of biliverdin-pyrrole water-histidine interaction in the photoactivation of Deinococcus radiodurans phytochrome", "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-201703291816", "language": null, "element": "identifier", "qualifier": "urn", "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": "Bio- ja ymp\u00e4rist\u00f6tieteiden laitos", "language": "fi", "element": "contributor", "qualifier": "department", "schema": "dc"}, {"key": "dc.contributor.department", "value": "Department of Biological and Environmental Science", "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": "Solu- ja molekyylibiologia", "language": "fi", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.subject.discipline", "value": "Cell and molecular biology", "language": "en", "element": "subject", "qualifier": "discipline", "schema": "dc"}, {"key": "dc.date.updated", "value": "2017-03-29T16:23:04Z", "language": "", "element": "date", "qualifier": "updated", "schema": "dc"}, {"key": "yvv.contractresearch.funding", "value": "0", "language": "", "element": "contractresearch", "qualifier": "funding", "schema": "yvv"}, {"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": "restrictedAccess", "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": "4013", "language": null, "element": "subject", "qualifier": "oppiainekoodi", "schema": "dc"}, {"key": "dc.subject.yso", "value": "spektroskopia", "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.rights.accessrights", "value": "Aineistoon p\u00e4\u00e4sy\u00e4 on rajoitettu tekij\u00e4noikeussyist\u00e4. Aineisto on luettavissa Jyv\u00e4skyl\u00e4n yliopiston kirjaston arkistoty\u00f6asemalta. Ks. https://kirjasto.jyu.fi/fi/tyoskentelytilat/laitteet-ja-tilat.", "language": "fi", "element": "rights", "qualifier": "accessrights", "schema": "dc"}, {"key": "dc.rights.accessrights", "value": "This material has a restricted access due to copyright reasons. It can be read at the workstation at Jyv\u00e4skyl\u00e4 University Library reserved for the use of archival materials: https://kirjasto.jyu.fi/en/workspaces/facilities.", "language": "en", "element": "rights", "qualifier": "accessrights", "schema": "dc"}, {"key": "dc.type.okm", "value": "G2", "language": null, "element": "type", "qualifier": "okm", "schema": "dc"}]
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