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[{"key": "dc.contributor.advisor", "value": "Permi, Perttu", "language": null, "element": "contributor", "qualifier": "advisor", "schema": "dc"}, {"key": "dc.contributor.author", "value": "Kauppinen, Linda", "language": null, "element": "contributor", "qualifier": "author", "schema": "dc"}, {"key": "dc.date.accessioned", "value": "2018-03-26T17:04:04Z", "language": null, "element": "date", "qualifier": "accessioned", "schema": "dc"}, {"key": "dc.date.available", "value": "2018-03-26T17:04:04Z", "language": null, "element": "date", "qualifier": "available", "schema": "dc"}, {"key": "dc.date.issued", "value": "2018", "language": null, "element": "date", "qualifier": "issued", "schema": "dc"}, {"key": "dc.identifier.other", "value": "oai:jykdok.linneanet.fi:1862979", "language": null, "element": "identifier", "qualifier": "other", "schema": "dc"}, {"key": "dc.identifier.uri", "value": "https://jyx.jyu.fi/handle/123456789/57428", "language": null, "element": "identifier", "qualifier": "uri", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Src-homologi 3 (SH3) domeenit ovat solun signaalireiteill\u00e4 toimivia v\u00e4ltt\u00e4m\u00e4tt\u00f6mi\u00e4, ei-katalyyttisi\u00e4 domeeneja. Kuten monilla muilla aitotumaisten solujen proteiineilla tai domeeneilla, my\u00f6s SH3-domeeneilla on homologinen SH3b-domeeni bakteerisoluissa. Rakenteellisesti n\u00e4m\u00e4 kaksi ovat samanlaisia muodostaen viiden beetas\u00e4ikeen rungon, jota t\u00e4ydent\u00e4v\u00e4t erilaiset silmukkarakenteet. N\u00e4ill\u00e4 silmukkarakenteilla on merkityst\u00e4 mm. domeenien toimintaan ja koska ne ovat yleisesti ottaen erilaisia SH3- ja SH3b-domeenien v\u00e4lill\u00e4, domeenien on oletettu olevan toiminnaltaan erilaisia. SH3-domeenit ovatkin hyvin tutkittuja ja niiden toimintaperiaatteet tiedet\u00e4\u00e4n, mutta niiden bakteerihomologit ovat viel\u00e4 suhteellisen tuntemattomia. Er\u00e4s t\u00e4llainen on solusein\u00e4n peptidoglykaania (PG) pilkkovan proteiinin, lysostafiinin, solusein\u00e4\u00e4n kohdistuva domeeni, jolla on SH3b-laskos. Lysostafiini on Staphylococcus simulansin biovaarin staphylolyticuksen eritt\u00e4m\u00e4 proteiini, joka kyseisen domeenin avulla kohdistetaan l\u00e4hisukuisen Staphylococcus aureus -bakteerin solusein\u00e4lle. Solusein\u00e4ll\u00e4 lysostafiini hajottaa PG:t\u00e4 ollen siten antimikrobinen, mutta t\u00e4t\u00e4 ominaisuutta ei viel\u00e4k\u00e4\u00e4n tunneta tai hy\u00f6dynnet\u00e4 t\u00e4ysin. T\u00e4ss\u00e4 ty\u00f6ss\u00e4 lysostafiinin solusein\u00e4\u00e4n kohdistuvan domeenin rakennetta ja toimintaa tutkittiin ydinmagneettisen resonanssin avulla. Sekvenssikohtaisen kemiallisten siirtymien assignoimiseksi sek\u00e4 dynamiikan ja sitoutumisominaisuuksien m\u00e4\u00e4ritt\u00e4miseksi mitattiin useita spektrej\u00e4. Tuloksena saatiin 94,3 % p\u00e4\u00e4ketjun amidiryhmist\u00e4 sek\u00e4 85,2 % sivuketjujen 1H- ja 13C-siirtymist\u00e4 assignoitua. Relaksaatiomittausten ja dynamiikka-analyysin perusteella domeenin havaittiin olevan ligandin sitoutumiskohta mukaan lukien suhteellisen j\u00e4ykk\u00e4. Ainoastaan \u03b23-s\u00e4ie osoittautui muuta rakennetta joustavammaksi. Mielenkiintoista on se, ett\u00e4 t\u00e4m\u00e4 s\u00e4ie on osa suurta silmukkaa, jonka rakenteelliset erot SH3- ja SH3b-domeenien v\u00e4lill\u00e4 aiheuttavat osaltaan n\u00e4iden toiminnallisen eroavaisuuden. Solusein\u00e4\u00e4n kohdistuvan domeenin tiedet\u00e4\u00e4n sitoutuvan PG:n pentaglysiinisiltoihin. Ligandin sitoutumiskohtaa tutkittiin tarkemmin PG:t\u00e4 j\u00e4ljittelev\u00e4ll\u00e4 peptidill\u00e4, L-Ala-D-Glu-L-Lys-D-Ala-GGGGG-L-Ala-D-Glu-D-Lys-D-Ala. Tulokset vahvistavat aiemmin m\u00e4\u00e4ritetyn sitoutumiskohdan sijainnin sek\u00e4 tukevat hypoteesia, jonka mukaan pentaglysiinin ymp\u00e4rill\u00e4 olevat aminohapot PG:ss\u00e4 osallistuisivat vuorovaikutukseen.\nVuorovaikutuksen dissosiaatiovakioksi m\u00e4\u00e4ritettiin ~3 mM. Ty\u00f6n tuloksena saatiin arvokasta tietoa lysostafiinin solusein\u00e4\u00e4n kohdistavan domeenin rakenteellisista ominaisuuksista ja sen sitoutumisesta PG:iin, ja tuloksia voidaan hy\u00f6dynt\u00e4\u00e4 my\u00f6hemmiss\u00e4 tutkimuksissa.", "language": "fi", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.abstract", "value": "Src homology 3 (SH3) domains are essential, small non-catalytic domains involved in intracellular signaling processes in eukaryotic cells. As many other eukaryotic proteins or domains, these also have their prokaryotic homologues, designated as SH3b domains. Structurally similar to each other, they adopt a conserved core of five \u03b2-strands surrounded by more variable loop structures. These loops, having a huge impact on ligand binding properties, generally differ between these domains for which functionally they are distinct. Although SH3 domains are well characterized, their prokaryotic homologues are still somewhat uncharted. One such is a cell wall-targeting (CWT) domain of peptidoglycan (PG)-cleaving protein, lysostaphin. Secreted by Staphylococcus simulans biovar staphylolyticus, lysostaphin is targeted via its SH3b-folded CWT domain to the cell wall of its close relative, Staphylococcus aureus. Once there, lysostaphin acts as a bacteriocin and degrades the PG, thus, displaying antimicrobial potential that, however, is still incompletely exploited. Here, functional and structural properties of the lysostaphin-CWT domain are studied with nuclear magnetic resonance (NMR) spectroscopy. Several multidimensional NMR spectra were recorded in order to assign backbone and side chain resonances and to define protein dynamics and binding properties of the CWT domain. As a result, 94.3 % of backbone and 85.2 % of side chain resonances of the CWT domain have been assigned. Protein dynamics described by relaxation measurements and model-free analysis imply that the CWT domain is relatively rigid. A binding groove for its ligand, a pentaglycine bridge in the PG, shows no exception to this. The only relatively mobile part is the \u03b23-strand which is interestingly a part of the loop structure causing main functional differences between SH3 and SH3b domains. The binding groove was further studied with a PG-mimicking peptide L-Ala-D-Glu-L-Lys-D-Ala-GGGGG-L-Ala-D-Glu-D-Lys-D-Ala. Results are in accordance with previous results obtained with pentaglycine (KGGGGG or GGGGGK) and further indicate that additional residues surrounding the pentaglycine truly enhanced the binding. Dissociation constant for the PG-mimicking peptide was determined to be ~3 mM. Results obtained here bring out novel information about structural properties and functional characteristics of the CWT domain, and they can be exploited in subsequent studies.", "language": "en", "element": "description", "qualifier": "abstract", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Submitted using Plone Publishing form by Linda Kauppinen (lilamaka) on 2018-03-26 17:04:03.406332. 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 2018-03-26T17:04:04Z\nNo. of bitstreams: 2\nURN:NBN:fi:jyu-201803261848.pdf: 2765655 bytes, checksum: f1c1f7d89f6f943b1cb108fdcb901d62 (MD5)\nlicense.html: 1193 bytes, checksum: d0a74024f0d13a5eed985b679fc44f99 (MD5)", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.description.provenance", "value": "Made available in DSpace on 2018-03-26T17:04:04Z (GMT). No. of bitstreams: 2\nURN:NBN:fi:jyu-201803261848.pdf: 2765655 bytes, checksum: f1c1f7d89f6f943b1cb108fdcb901d62 (MD5)\nlicense.html: 1193 bytes, checksum: d0a74024f0d13a5eed985b679fc44f99 (MD5)\n Previous issue date: 2018", "language": "en", "element": "description", "qualifier": "provenance", "schema": "dc"}, {"key": "dc.format.extent", "value": "1 verkkoaineisto (74 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": "SH3b", "language": null, "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "lysostaphin", "language": null, "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.subject.other", "value": "nuclear magnetic resonance", "language": null, "element": "subject", "qualifier": "other", "schema": "dc"}, {"key": "dc.title", "value": "Structural and functional characterization of the cell wall-targeting domain of lysostaphin with NMR spectroscopy", "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-201803261848", "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": "2018-03-26T17:04:04Z", "language": null, "element": "date", "qualifier": "updated", "schema": "dc"}, {"key": "yvv.contractresearch.funding", "value": "0", "language": null, "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.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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