Dissertations / Theses: 'Proteiini'

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Pekkala, N. (Niina). "S100B-proteiini lasten kuumekouristuksissa." University of Oulu, 2014. http://urn.fi/URN:NBN:fi:oulu-201412162129.

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S100B-proteiini on gliasoluspesifinen proteiini, jota vapautuu verenkiertoon aivovaurioiden yhteydessä. Kohonneet pitoisuudet korreloivat aivovaurion vaikeusasteen ja lopputuleman kanssa. S100B-proteiini toimii myös merkkiaineena veri—aivoesteen toimintahäiriöille. Lapsilla kohonneet proteiinipitoisuudet on liitetty astrosyyttivaurion markkereiksi jopa lievän aivovamman jälkeen. On mahdollista, että kuumekouristusten yhteydessä seerumin ja likvorin S100B-proteiinipitoisuudet nousevat ollen merkkinä aivoissa käynnissä olevasta patologisesta prosessista ja ennustavat kohtausten uusiutumistodennäköisyyttä. Tässä tutkimuksessa mittasimme seerumin ja likvorin S100B-proteiinipitoisuudet 103 lapselta, jotka olivat sairastaneet ensimmäisen kuumekouristuksensa. 33 lapsipotilasta, joilla oli akuutti kuumeinen infektio ilman kouristuksia, toimivat kontrolleina seerumipitoisuuksien suhteen. Kuumekouristajapotilailla S100B-proteiinipitoisuuksien keskiarvo likvorissa oli 0,21 μg/l ja seerumissa 0,12 μg/l. Kontrollipotilailla vastaava seerumipitoisuuksien keskiarvo oli 0,11 μg/l (ero 0,01 μg/l, 95 %:n luottamusväli -0,02—0.04 μg/l, P = 0,46). Seerumin S100B-proteiinipitoisuus oli riippuvainen potilaiden iästä (r = -0,28, P = 0,008) alle neljävuotiailla lapsilla. Pitoisuus ei kuitenkaan ennustanut kuumekouristuksen vaikeusastetta eikä kohtauksen uusiutumista. Aikaviiveellä kuumekouristuskohtauksen alkamisesta sairaalaan saapumiseen ei ollut korrelaatiota S100B-pitoisuuksiin seerumi- (r = -0,130, P = 0,28) eikä likvorinäytteissä (r = -0,091, P = 0,52). Tutkimustuloksemme tukevat aiempaa käsitystä siitä, että kuumekouristukset ovat vaarattomia kehittyville aivoille.

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Garma, L. D. (Leonardo D. ). "Structural bioinformatics tools for the comparison and classification of protein interactions." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526216065.

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Abstract Most proteins carry out their functions through interactions with other molecules. Thus, proteins taking part in similar interactions are likely to carry out related functions. One way to determine whether two proteins do take part in similar interactions is by quantifying the likeness of their structures. This work focuses on the development of methods for the comparison of protein-protein and protein-ligand interactions, as well as their application to structure-based classification schemes. A method based on the MultiMer-align (or MM-align) program was developed and used to compare all known dimeric protein complexes. The results of the comparison demonstrates that the method improves over MM-align in a significant number of cases. The data was employed to classify the complexes, resulting in 1,761 different protein-protein interaction types. Through a statistical model, the number of existing protein-protein interaction types in nature was estimated at around 4,000. The model allowed the establishment of a relationship between the number of quaternary families (sequence-based groups of protein-protein complexes) and quaternary folds (structure-based groups). The interactions between proteins and small organic ligands were studied using sequence-independent methodologies. A new method was introduced to test three similarity metrics. The best of these metrics was subsequently employed, together with five other existing methodologies, to conduct an all-to-all comparison of all the known protein-FAD (Flavin-Adenine Dinucleotide) complexes. The results demonstrates that the new methodology captures the best the similarities between complexes in terms of protein-ligand contacts. Based on the all-to-all comparison, the protein-FAD complexes were subsequently separated into 237 groups. In the majority of cases, the classification divided the complexes according to their annotated function. Using a graph-based description of the FAD-binding sites, each group could be further characterized and uniquely described. The study demonstrates that the newly developed methods are superior to the existing ones. The results indicate that both the known protein-protein and the protein-FAD interactions can be classified into a reduced number of types and that in general terms these classifications are consistent with the proteins' functions
Tiivistelmä Suurin osa proteiinien toiminnasta tapahtuu vuorovaikutuksessa muiden molekyylien kanssa. Proteiinit, jotka osallistuvat samanlaisiin vuorovaikutuksiin todennäköisesti toimivat samalla tavalla. Kahden proteiinin todennäköisyys esiintyä samanlaisissa vuorovaikutustilanteissa voidaan määrittää tutkimalla niiden rakenteellista samankaltaisuutta. Tämä väitöskirjatyö käsittelee proteiini-proteiini- ja proteiini-ligandi -vuorovaikutusten vertailuun käytettyjen menetelmien kehitystä, ja niiden soveltamista rakenteeseen perustuvissa luokittelujärjestelmissä. Tunnettuja dimeerisiä proteiinikomplekseja tutkittiin uudella MultiMer-align-ohjelmaan (MM-align) perustuvalla menetelmällä. Vertailun tulokset osoittavat, että uusi menetelmä suoriutui MM-alignia paremmin merkittävässä osassa tapauksista. Tuloksia käytettiin myös kompleksien luokitteluun, jonka tuloksena oli 1761 erilaista proteiinien välistä vuorovaikutustyyppiä. Luonnossa esiintyvien proteiinien välisten vuorovaikutusten määrän arvioitiin tilastollisen mallin avulla olevan noin 4000. Tilastollisen mallin avulla saatiin vertailtua sekä sekvenssin (”quaternary families”) sekä rakenteen (”quaternary folds”) mukaan ryhmiteltyjen proteiinikompleksien määriä. Proteiinien ja pienien orgaanisten ligandien välisiä vuorovaikutuksia tutkittiin sekvenssistä riippumattomilla menetelmillä. Uudella menetelmällä testattiin kolmea eri samankaltaisuutta mittaavaa metriikkaa. Näistä parasta käytettiin viiden muun tunnetun menetelmän kanssa vertailemaan kaikkia tunnettuja proteiini-FAD (Flavin-Adenine-Dinucleotide, flaviiniadeniinidinukleotidi) -komplekseja. Proteiini-ligandikontaktien osalta uusi menetelmä kuvasi kompleksien samankaltaisuutta muita menetelmiä paremmin. Vertailun tuloksia hyödyntäen proteiini-FAD-kompleksit luokiteltiin edelleen 237 ryhmään. Suurimmassa osassa tapauksista luokittelujärjestelmä oli onnistunut jakamaan kompleksit ryhmiin niiden toiminnallisuuden mukaisesti. Ryhmät voitiin määritellä yksikäsitteisesti kuvaamalla FAD:n sitoutumispaikka graafisesti. Väitöskirjatyö osoittaa, että siinä kehitetyt menetelmät ovat parempia kuin aikaisemmin käytetyt menetelmät. Tulokset osoittavat, että sekä proteiinien väliset että proteiini-FAD -vuorovaikutukset voidaan luokitella rajattuun määrään vuorovaikutustyyppejä ja yleisesti luokittelu on yhtenevä proteiinien toiminnan suhteen

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Petrov, P. (Petar). "Leukocyte protein Trojan, as a candidate for apoptotic regulatory role." Doctoral thesis, Oulun yliopisto, 2015. http://urn.fi/urn:isbn:9789526210346.

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Abstract Trojan is a novel leukocyte-specific protein cloned from chicken (Gallus gallus) embryonic thymocytes. The molecule is a type I transmembrane protein with an extracellular CCP domain followed by two FN3 domains. Its cytoplasmic tail is predicted to possess a MAPK docking and a PKA phosphorylation site. Trojan displays differential expression on developing thymocyte subpopulations. It is high on CD4 and CD8 double negative, and CD4 or CD8 single positive cells, but diminishes from the surface of selection-undergoing CD4 and CD8 double positive cells. This expression pattern is similar to that of anti-apoptotic molecules such as IL-7Rα and BCL-2. We hypothesised an involvement of Trojan in the regulation of apoptosis, possibly as an anti-apoptotic receptor. Our in vitro studies with a T cell line showed that upon apoptosis induction, Trojan expression rises dramatically on the surface of surviving cells and gradually decreases towards its normal levels as cells recover. When sorted based on their Trojan levels, cells with high expression appear less susceptible to apoptotic induction than those bearing no Trojan on their surface. Cells that overexpress Trojan from a cDNA plasmid show elevated steady state intracellular calcium, suggesting the molecule is able to transmit cytoplasmic signals. In addition, computational analyses pointed towards an involvement of MAPK and a possible regulatory mechanism by PKA. Trojan belongs to a novel gene family that includes two other members in the chicken. One is a receptor-type tyrosine phosphatase named Mystran, and the other – a transmembrane protein with an ITAM, named Thracian. We discovered the family in other avian species and found related genes in reptiles and coalecanth fish. We observed dynamic adaptation of their extracellular regions possibly in concert with ligand-binding, association with other surface molecules or as a response to pathogen challenges. This was coupled to largely unchanged cytoplasmic tails, suggesting a conserved signalling mechanism. The presented study shows that a novel avian leukocyte protein called Trojan possibly has an anti-apoptotic role. It belongs to a gene family that was subjected to evolutionary selection, likely linked to the molecular function of the proteins
Tiivistelmä Trojan on uusi kanan (Gallus gallus) alkioiden kateenkorvan kypsyvistä T soluista tunnistettu molekyyli. Se on tyypin I solukalvoproteiini, jolla on solun ulkopuolinen CCP-domeeni ja kaksi FN3-domeenia. Trojanin solun sisäisessä osassa on rakenteen perusteella MAPK:n sitoutumisalue sekä PKA-fosforylaatiopaikka. Trojania ilmennetään T-solujen kehityksen aikana runsaasti CD4 ja CD8 kaksoisnegatiivisissa ja CD4 tai CD8 yksöispositiivisissa soluissa, mutta ilmentyminen on vähäinen valintaa läpikäyvissä CD4 ja CD8 kaksoispositiivisissa soluissa. Tunnetut apoptoosia eli ohjelmoitua solukuolemaa estävät molekyylit, kuten IL-7Rα ja BCL-2, noudattavat samankaltaista ilmentymistä kypsyvien T solujen pinnalla. Hypoteesimme on, että Trojanilla on rooli apoptoosin säätelyssä, mahdollisesti solukuolemaa estävänä reseptorina. In vitro apoptoosikokeet osoittivat, että aluksi Trojanin ilmentyminen lisääntyy huomattavasti soluissa, jotka välttävät apoptoottisen kuoleman, ja normalisoituu sitten muutaman solujakautumisen jälkeen. Trojania vähän ilmentävät solut ovat alttiimpia ohjelmoidulle solukuolemalle, kuin sitä paljon ilmentävät solut. Solujen sisäinen kalsiumtaso on kohonnut soluilla, jotka yliekspressoivat Trojania cDNA plasmidista. Tämä viittaa siihen, että Trojan voi toimia sytoplasman signaalinvälityksessä. Lisäksi tietokoneperusteiset ennusteet viittaavat siihen, että MAPK ja PKA voivat liittyä Trojan-signalointiin. Tutkimuksessa tunnistettiin Trojan-geeniperhe. Perheeseen kuuluu Trojanin lisäksi kaksi muuta geeniä: reseptorityyppinen tyrosiinifosfataasi Mystran ja ITAM-domeenin sisältävä solukalvon proteiini Trachian. Geeniperhe löydettiin muistakin lintulajeista, sekä niitä läheisesti muistuttavat geenit matelijoilta ja varsieväkalalta. Havaitsimme Trojan-perheen proteiineissa dynaamista sopeutumista, joka voi olla seurausta ligandien sitoutumisesta, vuorovaikutuksesta muiden pintaproteiinien kanssa tai vasteesta patogeenihaasteeseen. Proteiinien solunsisäiset alueet olivat sen sijaan suurilta osin muuttumattomia, joten ne voivat toimia solusignaloinnissa. Väitöstutkimuksessa kuvataan uusi valkosolujen proteiini Trojan, joka toiminnallisesti saattaa estää ohjelmoitua solukuolemaa. Trojan kuuluu geeniperheeseen, johon on kohdistunut sen toimintaan liittyvää valintaa

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Löppönen, P. (Pekka). "Preceding medication, inflammation, and hematoma evacuation predict outcome of intracerebral hemorrhage:a population based study." Doctoral thesis, Oulun yliopisto, 2016. http://urn.fi/urn:isbn:9789526211282.

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Abstract Primary intracerebral hemorrhage (pICH) is a severe, suddenly occurring disease involving high mortality and poor functional outcome. In the absence of curative treatment patient management is mainly supportive with the emphasis on preventing hematoma enlargement and complications. Better understanding of the factors predicting outcome are needed to define effective treatments. An unselected population-based registry study of 982 pICH patients admitted to Oulu University Hospital during the years 1993 to 2008 was conducted The study revealed that concomitant use of warfarin and serotonin-modulating antidepressants at the time of pICH increases the case fatality rate compared to patients with warfarin alone. An elevated C-reactive protein value on admission was an independent predictor of unfavorable outcome after pICH. This association was not explained by pre-existing heart disease, diabetes, severity of the bleeding, or infections. Patients undergoing surgical hematoma evacuation were observed to have improved 3-month survival compared to conservatively treated patients. Improved survival was noticed especially in patients with ≤70 years of age with ≥30ml supratentorial ICHs. Hematoma evacuation did not improve functional outcome. Earlier ischemic stroke was found to be an independent predictor of recurrent pICH. Diabetes seemed to increase and treated hypertension decrease the risk for fatal recurrence. Aspirin or serotonin-modulating antidepressants did not seem to increase the risk of recurrence
Tiivistelmä Primääri aivoverenvuoto (pICH) on vakava, yhtäkkisesti alkava sairaus, johon liittyy korkea kuolleisuus ja vaikea vammautuminen. Parantavan hoidon puuttuessa on hoito lähinnä elintoimintoja tukevaa vuodon laajenemisen ja komplikaatioiden estämistä. Ennusteeseen vaikuttavien tekijöiden parempi tunteminen on ehto tehokkaiden hoitojen löytämiseksi. Väitöskirjatutkimustani varten kerättiin Oulun yliopistollisen sairaalan alueelta vuosien 1993-2008 aikana 982 aivoverenvuotoon sairastuneen potilaan väestöpohjainen aineisto. Tutkimus osoitti, että varfariinin ja selektiivisen serotoniinin takaisinoton estäjän (SSRI) yhteiskäyttö aivoverenvuodon aikana lisäsi kuolevuutta pelkkään varfariiniin nähden. Alkuvaiheen koholla oleva C-reaktiivinen proteiini oli itsenäinen aivoverenvuodon jälkeistä vammautuneisuutta ennustava tekijä. Yhteys ei selittynyt olemassa olevalla sydänsairaudella, diabeteksella, aivoverenvuodon vaikeudella tai infektioilla. Kirurginen aivoverenvuodon poistoleikkaus paransi kolmen kuukauden ennustetta verrattuna potilaisiin ilman leikkausta. Erityisesti leikkaus auttoi alle 70-vuotiaita potilaita, joilla oli yli 30 millilitran kokoinen pinnallisempi vuoto. Leikkaus ei parantanut fyysistä kuntoutumista. Aiempi sairastettu aivoinfarkti oli itsenäinen aivoverenvuodon uusiutumista ennustava tekijä. Diabetes saattaa lisätä ja hoidossa oleva verenpainetauti laskea riskiä tappavaan uusintavuotoon. Aspiriinin tai SSRI:n käyttö eivät lisänneet uusintavuodon riskiä

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Müller, Lukáš. "Analýza proteomu piva pomocí hmotnostní spektrometrie." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2009. http://www.nusl.cz/ntk/nusl-216454.

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The aim of presented diploma thesis was to characterize recent knowledge in the field of beer proteomics. The main part of this work was focused on modern instrumental methods of protein analysis, especially on protein identification by mass spectrometry. In experimental part proteins from selected beer samples were isolated, purified and separated by 2-D electrophoresis. The identification was performed by MALDI MS/MS and LC-MS/MS. Identified proteins were divided into 6 groups - serpines and protein Z, trypsine/-amylase inhibitors, yeast proteins, LTP protein, hordeins and other proteins. Proteomic analysis provided identification of proteins important for final analytical and sensory characteristics of the beer - for final beer quality and taste

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Liukkonen, T. (Timo). "Low-grade inflammation in depression, anxiety and sleep disturbances." Doctoral thesis, Oulun yliopisto, 2011. http://urn.fi/urn:isbn:9789514296475.

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Abstract Depression, anxiety and sleep disorders have been reported to be associated with low level of inflammation, i.e., low-grade inflammation, but mainly in males. The evidence has mainly been based on laboratory or clinical studies with small sample sizes or epidemiological studies with elderly subpopulations. In this study the association of low-grade inflammation with depression, anxiety, and sleep disturbances was investigated using the Northern Finland 1966 Birth Cohort (NFBC 1966). In women, the effect of hormonal factors, menopause and the use of oral contraceptives/hormone replacement therapy on the association between low-grade inflammation and depression was also studied by using the Pieksämäki Study data. In 31-year follow-up of NFBC 1966 (N=6007), the depressive and anxiety symptoms were assessed by Hopkins Symptom Checklist-25 (HSCL-25) and sleep disorders by 15-D questionnaires, while the marker of low-grade inflammation, plasma concentration of high sensitivity C-reactive protein (hs-CRP), was measured. In the Pieksämäki study a representative sample of inhabitants in the town of Pieksämäki were invited to clinical examination. Depressive symptoms were obtained by Beck’s Depression Inventory-21, and hs-CRP was measured (512 women). The results of this study revealed that at epidemiological level, elevated hs CRP levels of ≥1.0 mg/L increased the probability of current depressive symptoms of single depressive episode in the two highest subgroups (i.e., HSCL-25 mean scores ≥1.75 and ≥2.01) 1.4- and 1.7- fold in males, respectively. In addition, anxiety symptoms (HSCL-25 anxiety scale mean score ≥1.75) increased independently the probability of elevated hs-CRP levels (>3.0 mg/L) in males over 2-fold. Risk ratio of 1.3 was found for males with moderate to severe sleep disturbances and elevated hs-CRP levels (≥1.0 mg/L). Regarding females, a positive correlation between elevated hs-CRP levels and depressive symptoms was found only among peri- and postmenopausal women not using exogenous hormones. The results suggest that low-grade inflammation is associated not only with depression but also with anxiety and sleep disturbances in young adult men. In women, hormonal factors may have an effect on the association between low-grade inflammation and depression. Further investigations are called for to confirm these findings and furthermore, to determine the possible role of low-grade inflammation in the pathophysiology of these disorders
Tiivistelmä Depressio, ahdistuneisuushäiriöt ja unihäiriöt on yhdistetty elimistön matala-asteiseen tulehdustilaan, joskin pääasiallisesti vain miehillä. Tulosten yleistettävyyttä ovat rajoittaneet tutkimusten pienet otoskoot tai painottuminen iäkkäisiin väestöaineistoihin. Tässä tutkimuksessa selvitettiin matala-asteisen tulehduksen yhteyttä depressioon, ahdistuneisuuteen ja unihäiriöihin Pohjois-Suomen syntymäkohortti 1966 -aineistossa. Lisäksi Pieksämäki-tutkimuksen aineistossa selvitettiin naisilla menopaussin ja ehkäisyvalmisteiden/vaihdevuosihormonikorvaushoidon vaikutusta depression ja matala-asteisen tulehduksen väliseen yhteyteen. Pohjois-Suomen syntymäkohortti 1966 -tutkimuksen 31-vuotisseurannassa kartoitettiin 6007 henkilöltä masennus- ja ahdistuneisuusoireita Hopkins Symptom Checklist-25 -arviointiasteikolla (HSCL-25) ja unihäiriöitä 15-D-kyselyllä. Lisäksi mitattiin matala-asteisen tulehduksen mittarina käytetyn herkän C-reaktiivisen proteiinin (CRP) pitoisuus. Pieksämäki-tutkimuksessa edustava otos Pieksämäen asukkaista kutsuttiin kliiniseen tutkimukseen ja depressiivisiä oireita kartoitettiin Beckin 21-osioisella arviointiasteikolla ja mitattiin herkkä CRP (512 naista). Nuorilla aikuisilla miehillä, joiden herkkä CRP oli kohonnut (≥1.0 mg/l), todettiin 1.7-kertainen masennusoireiden riski, kun katkaisupisteenä käytettiin HSCL-25-kyselyn masennuskeskiarvopistettä ≥2.01. Ahdistuneisuusoireet (HSCL-25-kyselyn ahdistuneisuuskeskiarvopisteet ≥1.75) lisäsivät kohonneen herkän CRP:n riskiä (>3.0 mg/l) yli kaksinkertaiseksi miehillä. Keskivaikeasta tai vaikeasta unihäiriöstä kärsivillä todettiin 1.3-kertainen kohonneen herkän CRP:n (≥1.0 mg/l) riski. Naisilla positiivinen yhteys masennuksen ja kohonneen herkän CRP:n välillä todettiin vain peri- ja postmenopausaalisilla naisilla, jotka eivät käyttäneet hormonikorvaushoitoa tai suun kautta otettavia ehkäisyvalmisteita. Tutkimustulokset viittaavat matala-asteisen tulehduksen liittyvän depressioon, ahdistukseen ja unihäiriöön nuorilla aikuisilla miehillä. Naisilla hormonaaliset seikat mahdollisesti vaikuttavat depression ja matala-asteisen tulehduksen väliseen yhteyteen. Tulevaisuuden tutkimushaasteena on selvittää matala-asteisen inflammaation mahdollinen merkitys depression, ahdistuneisuuden ja unihäiriöiden patofysiologiassa

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Gill, Katrina Louise. "Protein-protein interactions in membrane proteins." Thesis, University of Newcastle Upon Tyne, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400016.

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Hon, Jiří. "Vyhledávání příbuzných proteinů s modifikovanou funkcí." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2015. http://www.nusl.cz/ntk/nusl-234914.

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Protein engineering is a young dynamic discipline with great amount of potential practical applications. However, its success is primarily based on perfect knowledge and usage of all existing information about protein function and structure. To achieve that, protein engineering is supported by plenty of bioinformatic tools and analysis. The goal of this project is to create a new tool for protein engineering that would enable researchers to identificate related proteins with modified function in still growing biological databases. The tool is designed as an automated workflow of existing bioinformatic analyses that leads to identification of proteins with the same type of enzymatic function, but with slightly modified properties - primarily in terms of selectivity, reaction speed and stability.

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Smetana, Juliana Helena Costa. "Caracterização das proteinas TIPRL e alfa4, reguladores de fosfatases 2A." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/317177.

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Orientador: Nilson Ivo Tonin Zanchin
Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
Made available in DSpace on 2018-08-13T09:08:00Z (GMT). No. of bitstreams: 1 Smetana_JulianaHelenaCosta_D.pdf: 8660811 bytes, checksum: cb33e97d4c49fdce1e29094a2f6089cc (MD5) Previous issue date: 2009
Resumo: As células respondem constantemente a uma enorme variedade de estímulos, que são interpretados e integrados por meio de redes de sinalização, dando origem a uma resposta biológica. Defeitos nesses circuitos são a causa de diversas doenças, incluindo muitos, se não todos os tipos de câncer. As fosfatases, enzimas que removem grupamentos fosfato dos substratos de quinases, dependem principalmente de subunidades regulatórias para definir sua especificidade. As fosfatases do tipo 2A constituem a subfamília PPP, que é formada por PP2A, PP4 e PP6. PP2A é a principal fosfatase solúvel de fosfosserina e fosfotreonina em células animais e é encontrada predominantemente como uma holoenzima formada por uma subunidade catalítica (C), uma subunidade regulatória (B, B', B'' ou B''') e uma de ancoragem (PR65/A). Em levedura, as fosfatases 2A desempenham um importante papel na via da quinase TOR, o que ocorre por meio da proteína essencial Tap42. A proteína Tip41 foi identificada como um parceiro de interação de Tap42 e regulador da via da quinase TOR em levedura. A homóloga de Tap42 em mamíferos, chamada de a4, está envolvida na regulação de diversos processos celulares, como diferenciação, desenvolvimento, migração celular e apoptose, por meio de seu papel conservado de regulador de fosfatases 2A. A homóloga em mamíferos de Tip41, chamada TIPRL, é uma proteína ainda pouco caracterizada. Este trabalho teve como objetivo analisar a função das proteínas a4 e TIPRL humanas e esclarecer seu papel na regulação de fosfatases 2A. A caracterização estrutural de a4 e Tap42, usando dados de SAXS, dicroísmo circular e proteólise limitada, mostrou que essas proteínas apresentam um domínio N-terminal compacto formado por a-hélices e um domínio C-terminal desestruturado. Em uma triagem de interações com a proteína TIPRL humana, identificamos as fosfatases PP2Ac, PP4c e PP6c como seus parceiros de interação, assim como os fatores de transcrição MafB e TAF10. Ao contrário do esperado a partir do modelo de levedura, a4 e TIPRL não interagem diretamente, mas formam um complexo ternário com PP2Ac. Uma triagem de substratos de fosfatases 2A regulador por TIPRL identificou os fatores de splicing SF2/ASF e SF2p32. Nossos resultados sugerem um modelo estrutural para a regulação das fosfatases 2A por a4 e mostram que TIPRL é um novo regulador comum dessas fosfatases com funções na regulação da expressão gênica.
Abstract: Cells respond constantly to a variety of stimuli, which are interpreted and integrated through signaling networks, giving rise to biological responses. Defects in this circuitry are a cause of many diseases, including cancer. Protein phosphatases are enzymes which remove phosphate groups from kinase substrates, relying mainly on regulatory subunits for their substrate specificity. Type 2A phosphatases belong to the PPP subfamily, which is formed by PP2A, PP4 and PP6. PP2A is the major soluble serine/threonine phosphatase in animal cells and is found predominantly as a heterotrimer composed of a catalytic (C), a regulatory (B, B', B'' or B''') and a scaffold (PR65/A) subunit. Type 2A phosphatases play a major role in the yeast TOR signaling pathway through their interaction with the essential protein Tap42. Tip41 was identified as a Tap42 interacting protein and regulator of the TOR pathway. a4, the mammalian orthologue of Tap42, regulates many cellular processes such as differentiation, development, cell migration and apoptosis as a conserved type 2A phosphatase regulator. TIPRL, the mammalian orthologue of Tip41, is still poorly characterized. The objective of the present work was to analyse the function of a4 and TIPRL and improve the understanding of their role as type 2A phosphatase regulators. The structural characterization of a4 using SAXS analyses, circular dichroism and limited proteolysis, showed that these proteins are formed by an a-helical N-terminal domain and an unfolded C-terminal domain. A screen for TIPRL interacting proteins identified PP2Ac, PP4c and PP6c and also the transcription factors MafB and TAF10. Unlike their yeast conterparts, a4 and TIPRL do not interact directly, but rather form a ternary complex with PP2A. A search for type 2A phosphatase substrates regulated by TIPRL identified the splicing factor SF2/ASF and its regulatory protein SF2p32. Our results suggest a structural model for the regulation of type 2A phosphatases by a4 and show that TIPRL is a novel common regulator of these phosphatases which functions in regulation of gene expression.
Doutorado
Genetica Animal e Evolução
Doutor em Genetica e Biologia Molecular

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Santaniemi, M. (Merja). "Genetic and epidemiological studies on the role of adiponectin and PTP1B in the metabolic syndrome." Doctoral thesis, University of Oulu, 2010. http://urn.fi/urn:isbn:9789514261855.

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Abstract The metabolic syndrome is a cluster of components predisposing to type 2 diabetes and cardiovascular disease. Abdominal obesity and insulin resistance seem to be central in the metabolic syndrome, although no unifying pathophysiological mechanism is available. The aim of this thesis was to determine out how the variation in PTP1B and adiponectin gene as well as variations in the plasma adiponectin concentration contribute to the risk of obesity related diseases. PTP1B is a negative regulator of insulin signalling and therefore considered a candidate gene for type 2 diabetes. In the first study, it was found that three PTP1B polymorphisms studied have not strong impact on type 2 diabetes. However, one SNP may be slightly protective against type 2 diabetes, since it was more frequent in the healthy group compared to group of patients with type 2 diabetes. Another SNP was associated with body mass index (BMI). The combination of certain alleles of PTP1B and LEPR (leptin receptor) genes was also associated to BMI. Adiponectin is an adipocytokine expressed in adipose tissue. It has insulin sensitizing effects in liver and muscle and it has also beneficial effects on cardiovascular health. In the second study, the contribution of adiponectin genotypes with obesity-related phenotypes was studied. In Caucasians, the carriers of rare allele of Tyr111His polymorphism were more insulin resistant and at a higher risk of developing type 2 diabetes. In African-Americans, other polymorphisms were associated with BMI and lipids. Thus, the effects of polymorphisms on obesity related phenotypes seemed to be different between ethnic groups. Plasma adiponectin levels were measured from different study groups. In the third study, it was found out that low plasma adiponectin levels associated with different components of the metabolic syndrome and there was a trend towards reductions in adiponectin with an increasing number of components. Fourth study indicated that baseline low adiponectin level associated with a more than 2-fold risk for developing impaired glucose tolerance or type 2 diabetes in the follow-up study of normoglycemic middle-aged Finnish subjects. In the fifth study, plasma adiponectin levels were measured from postmenopausal women receiving estrogen replacement therapy. We observed a reduction in adiponectin levels in women having peroral estradiol which could be part of the "early harm" profile on cardiovascular risk factors of the peroral estrogen replacement therapy detected in clinical trials. These studies further strengthen the role of plasma adiponectin in the obesity related diseases and bring new information of polymorphisms in the adiponectin and PTP1B genes in different populations
Tiivistelmä Metabolinen oireyhtymä on kertymä tekijöitä, jotka altistavat tyypin 2 diabetekselle ja sydän- ja verisuonitaudeille. Keskivartalolihavuus ja insuliiniresistenssi, eli insuliinin heikentynyt teho, vaikuttavat olevan keskeisiä metabolisessa oireyhtymässä. Kuitenkaan taustalla olevaa syntymekanismia ei täysin tunneta. Väitöskirjatyön tavoitteena oli tutkia PTP1B- ja adiponektiinigeenin muuntelun sekä plasman adiponektiinitason yhteyttä metaboliseen oireyhtymään, sen osatekijöihin ja seurauksiin. PTP1B on insuliinin toimintaa soluissa estävä molekyyli. Ensimmäisessä tutkimuksessa havaittiin että kolme tutkittua PTP1B-geenin nukleotidimuutosta eivät ole vahvasti yhteydessä tyypin 2 diabetekseen. Eräs nukleotidimuutos saattaisi olla lievästi suojaava tyypin 2 diabetesta vastaan, sillä se oli yleisempi terveillä kuin tyypin 2 diabetesta sairastavilla. PTP1B:n ja leptiinireseptorigeenin eräiden alleelien yhdistelmä oli yhteydessä painoindeksiin. Adiponektiini on rasvakudoksen erittämä hormoni, jolla on suotuisia, insuliinin vaikutusta edesauttavia vaikutuksia elimistössä sekä edullisia vaikutuksia verenkiertoelimistössä. Toisessa työssä havaittiin että Amerikan valkoihoisilla, joilla oli eräs harvinainen adiponektiinigeenin alleeli (Tyr111His), oli heikompi insuliinin teho kuin henkilöillä joilla ei ollut kyseistä muutosta. Tämä alleeli oli yleisempi suomalaisilla tyypin 2 diabetesta sairastavilla kuin terveillä, mikä saattaa tarkoittaa että se liittyy suurentuneeseen riskiin tyypin 2 diabetekselle. Afroamerikkalaisilla taas toiset nukleotidimuutokset olivat yhteydessä lihavuuteen ja plasman rasva-arvoihin. Adiponektiinin pitoisuutta plasmassa mitattiin erilaisissa aineistoissa. Kolmannessa tutkimuksessa havaittiin, että matala pitoisuus oli yhteydessä metabolisen oireyhtymän eri osatekijöihin ja pitoisuus oli sitä matalampi, mitä enemmän osatekijöitä henkilöllä on. Neljännessä tutkimuksessa havaittiin että matala plasman adiponektiinipitoisuus oli yhteydessä suurentuneeseen riskiin saada huonontunut glukoosin sietokyky tai tyypin 2 diabetes tulevaisuudessa. Viidennessä tutkimuksessa adiponektiinitaso määritettiin naisilta jotka olivat ohittaneet vaihdevuodet ja saivat estrogeenikorvaushoitoa. Havaittiin että plasman adiponektiinitaso laski niillä naisilla, jotka saivat korvaushoitoa suun kautta. Tämä saattaisi osittain selittää suun kautta annettavan estrogeenikorvaushoidon epäedullista vaikutusta sydän ja -verisuonitautien riskitekijöihin. Tutkimus vahvistaa edelleen adiponektiinin merkitystä lihavuuteen liittyvissä sairauksissa ja tuo uutta tietoa adiponektiini- ja PTP1B-geenien muuntelun merkityksestä eri väestöissä

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Mattila, R. (Riikka). "The roles of virulence factors Us3 and γ₁34.5 during different phases of HSV-1 life cycle." Doctoral thesis, Oulun yliopisto, 2015. http://urn.fi/urn:isbn:9789526210469.

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Abstract Herpes simplex virus type 1 (HSV-1) is a common pathogen with an age-standardized seroprevalence of 52% in Finland. The most common manifestation of HSV-1 infection is labial herpes, but recently HSV-1 has emerged as the most common cause of primary genital herpes in Finnish women. HSV-1 can also lead to severe conditions such as encephalitis. After the primary lytic HSV-1 infection at the epithelia, the progeny viruses infect the innervating sensory neurons. The neuronal infection may lead to a quiescent infection form, called latency. Periodically, the virus may reactivate, which can lead to recurrent infection at the epithelia. During different phases of the viral life cycle the host cells try to restrict the infection. This study set out to investigate the roles of two HSV-1 proteins, γ134.5 and Us3 during different phases of the HSV-1 life cycle. The aim of the first study was to investigate how the deletion of Us3 affected host responses, especially Toll-like Receptor (TLR) signaling, in monocytic U937 cells. TLR3 expression was increased during Us3 deletion virus infections. This also led to increased activation of IRF-3 and increased expression of type I interferons (IFN) and an interferon stimulated protein. This study shows that TLR3 is involved in controlling the HSV-1 infection and that Us3 regulates IRF-3 activation. The second study focused on the role of the γ134.5 protein in HSV-1 latency. Embryonic mouse dorsal root ganglion (DRG) cultures were used as a cell culture model for HSV-1 latency and reactivation. In this model γ134.5 deletion viruses did not reactivate as efficiently as wild-type viruses, even though they replicated well and established latency in the neurons. Stress granules are part of the host response. In the third study, the roles of the innate immunity effectors HSV-1 Us3 and human Z-DNA binding protein 1 (ZBP1) in stress granule formation (SG) were studied. Wild-type HSV-1 efficiently prevented the formation of SGs. The overexpression of ZBP1 resulted in accumulation of smaller but more abundant SGs during oxidative stress. Overexpression of Us3 did not significantly affect the size or number of SGs, but during Us3 deletion virus infection, SG proteins localized to cis-Golgi. This work shows that HSV-1 uses Us3 to evade and modulate host responses and that the γ134.5 protein is required for reactivation in mouse DRG cultures
Tiivistelmä Herpes simplex virus tyyppi 1 (HSV-1) on yleinen taudinaiheuttaja, jonka ikävakioitu seroprevalenssi Suomessa on 52 %. HSV-1 tunnetaan yleisimmin huuliherpeksen aiheuttajana, mutta myös kasvava osuus genitaaliherpeksistä on HSV-1:n aiheuttamia. HSV-1 voi johtaa myös vakaviin ilmentymiin, kuten aivotulehdukseen. Epiteelisolujen infektion tuottamia viruksia siirtyy aluetta hermottaviin tuntohermosoluihin, mikä voi johtaa piilevään infektiomuotoon eli latenssiin. Latentti virus voi ajoittain reaktivoitua, mistä voi seurata uusintainfektio. Isäntäsolu pyrkii rajoittamaan infektiota sen eri vaiheissa. Tämän tutkimuksen tarkoituksena oli selvittää kahden HSV-1:n virulenssiproteiinin, γ134.5:n ja Us3:n, merkitystä HSV-1:n elinkierrossa. Osatyössä I tutkittiin, miten Us3:n poisto vaikuttaa luontaisen immuniteetin vasteisiin, keskittyen etenkin Tollin kaltaisten reseptorien (TLR) signaalivälitykseen U937-monosyyttisoluissa. Us3-poistogeenisillä viruksilla suoritetuissa infektioissa TLR3:n ilmentyminen lisääntyi merkittävästi. Tämä johti myös lisääntyneeseen IRF-3-aktivaatioon sekä tyypin I interferonien ja interferonistimuloituvan proteiinin lisääntyneeseen ilmentymiseen. Tämä osoittaa, että TLR3 osallistuu HSV-1-viruksen tunnistukseen ja että Us3 säätelee IRF-3:n aktivaatiota. Osatyössä II keskityttiin γ134.5-proteiinin merkitykseen HSV-1:n latenssissa. Hiirialkioiden takajuuren hermoganglioita käytettiin soluviljelymallina HSV-1:n latenssin ja reaktivaation tutkimisessa. Tässä mallissa γ134.5-poistogeeniset virukset kasvoivat hyvin ja asettuivat latenteiksi, mutta eivät silti reaktivoituneet kuten luonnonkannan virukset. Stressijyväset ovat osa luontaista immuniteettia. Osatyössä III määritettiin HSV-1:n Us3-proteiinin ja ihmisen Z-DNA:han sitoutuvan proteiini 1:n (ZBP1) merkitystä stressijyvästen muodostumisessa. Luonnonkannan virus kykeni tehokkaasti estämään jyvästen muodostumisen. ZBP1:n yli-ilmentäminen oksidatiivisen stressin aikana johti suureen määrään pienikokoisia stressijyväsiä. Us3:n yli-ilmentäminen ei vaikuttanut stressijyväsiin, kun taas Us3-poistogeenisellä viruksella suoritetuissa infektioissa stressijyväsproteiinit paikantuivat Golgin laitteeseen. Tämä tutkimus osoittaa, että HSV-1 käyttää Us3-proteiinia luontaisten immuunivasteiden muunteluun ja että γ134.5-proteiini on välttämätön reaktivaatiossa hiiren hermoganglioissa

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Stylianou, Julianna. "Protein-protein interaction of HSV-1 tegument proteins." Thesis, Imperial College London, 2013. http://hdl.handle.net/10044/1/24663.

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Herpes simplex virus type 1 virions contain a proteinaceous layer between the nucleocapsid and the virus envelope termed the tegument. The mechanism underlying tegumentation remains largely undefined for all herpesviruses, as does the role of many tegument proteins in virus replication. The networks of protein interactions involved in virus assembly have been largely explored and although large-scale studies have been carried out using yeast two hybrid analyses of herpesvirus protein interactions, few of the identified networks have been validated in infected cells. Here, the molecular interactions that occur between the major tegument proteins VP22, VP16 and VP13/14 and a range of glycoproteins and tegument proteins were defined in detail. Two alternative studies were performed from infected cells, however one based on the purification of GFP-tagged proteins and their protein partners proved more successful. These studies validated previous findings and also identified VP13/14, UL21, UL16 and vhs as novel binding partners of VP22, and VP22, UL21, UL16 and vhs as novel binding partners of VP13/14. Thus, these results have led to the identification of two discrete tegument protein complexes in the infected cell: VP22-VP16-VP13/14-vhs and VP22-VP13/14-UL21-UL16. To investigate the nature of the VP22-VP16-VP13/14-vhs complex in more detail, a number of techniques were used and showed that VP22 and VP13/14 both bind directly to the C-terminus of VP16, but were unable to interact with each other. As anticipated from other studies on transfected cell extracts, vhs was shown to be incorporated into this complex by virtue of its direct binding to VP16 during infection, and did not have the capacity to interact directly with VP22. This work has established a defined network of protein-protein interactions encompassing over one third of tegument proteins, and will improve our understanding of the wider protein interaction networks that lead to the assembly of the herpesvirus tegument.

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Jämsä, J. (Joel). "Flow cytometric analysis of leukocyte surface molecule expression in critical illness:comparison between septic and non-septic patients." Doctoral thesis, Oulun yliopisto, 2017. http://urn.fi/urn:isbn:9789526215778.

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Abstract Sepsis is a common problem in the intensive care unit (ICU) still having a high mortality and causing high costs to health care system. Currently, there is no marker to distinguish sepsis from other causes of systemic inflammation. Leukocyte surface molecules have been proposed as markers of sepsis. The most promising markers have been neutrophil CD64 and CD11b on monocytes and neutrophils and HLA-DR on monocytes. In this thesis, leukocyte surface molecules were investigated using quantitative flow cytometry in critically ill patients with sepsis, non-septic ICU controls, and healthy volunteers. The surface molecules of interest were neutrophil CD11b and CD64, monocyte CD11b, CD14, CD40, CD64, CD80, HLA-DR, and lymphocyte CD69. First, a special emphasize was indicated in methodological aspects of the quantitative flow cytometry. Then, the surface molecule kinetics was investigated in different types of critically ill patients. Finally, the diagnostic performance of the molecules was determined and compared to that of traditionally used sepsis markers. Furthermore, an example of multiple marker analysis was introduced as a diagnostic tool. The optimal circumstances for leukocyte surface molecule analysis were +4°C temperature throughout the collection and preparation of the samples using tubes containing acid citrate dextrose (ACD) as an anticoagulant, followed by flow cytometry within 6 hours from sampling. Monocyte CD11b and CD40, neutrophil CD11b and CD64, and CD69 on CD4+ T cells and natural killer (NK) cells separated sepsis from non-septic ICU controls and healthy volunteers, neutrophil CD64, having the best area under curve. Procalcitonin (PCT) was second best marker. Monocyte CD40 and NK CD69 may predict positive blood culture detection, whereas CD11b may predict early mortality. In multiple marker analysis, combination of positive neutrophil CD64, C-reactive protein (CRP) and PCT increased post-test probability for sepsis. In conclusion, pre-analytical and analytical factors have effects on results of leukocyte surface molecule analysis. Leukocyte surface molecules may improve sepsis diagnostics in ICU setting. Neutrophil CD64 was the most promising marker. Combination of CD64, CRP and PCT increased the detection of sepsis in ICU
Tiivistelmä Sepsis on yleinen tehohoidon ongelma, johon liittyy korkea kuolleisuus ja suuret hoidolliset kustannukset. Toistaiseksi ei ole laboratoriomerkkiainetta, joka erottaisi sepsistä sairastavat muista kriittisesti sairaista, joilla on yleistynyt tulehdusvaste. Valkosolujen pintamolekyylien käyttöä sepsiksen laboratoriomerkkiaineena on tutkittu. Lupaavimmat näistä molekyyleistä ovat olleet neutrofiilien CD64, monosyyttien ja neutrofiilien CD11b ja monosyyttien HLA-DR. Tässä väitöskirjassa tutkittiin valkosolujen pintamolekyylejä kriittisesti sairailla sepsistä sairastavilla potilailla, niillä tehohoitopotilailla, joilla ei ollut sepsistä, ja terveillä vapaaehtoisilla virtaussytometriaa käyttäen. Mielenkiinnon kohteina olivat neutrofiilien CD11b ja CD64, monosyyttien CD11b, CD14, CD40, CD64, CD80 ja HLA-DR, sekä lymfosyyttien CD69. Ensimmäiseksi tutkittiin kvantitatiivista virtaussytometriaa menetelmänä. Sen jälkeen pintamolekyylien kinetiikkaa tutkittiin eri potilasryhmillä. Lopuksi määritettiin pintamolekyylien diagnostinen tehokkuus ja sitä verrattiin perinteisempiin sepsiksen diagnostiikassa käytettyihin laboratoriomerkkiaineisiin. Lisäksi selvitettiin usean merkkiaineen mallin diagnostista osuvuutta. Parhaat olosuhteet virtaussytometrialle olivat: +4 °C:n lämpötila näytteenoton ja -käsittelyn aikana, näytteiden ottaminen putkiin, joissa on antikoagulanttina hapan sitraatti-dekstroosi (ACD) ja näytteiden analysointi kuuden tunnin kuluessa näytteenotosta. Monosyyttien CD11b ja CD40, neutrofiilien CD11b ja CD64 sekä CD4+ T-solujen ja NK-solujen CD69 erottivat sepsistä sairastavat tehohoitoverrokeista ja terveistä. Neutrofiilien CD64:llä oli paras erottelukyky. Prokalsitoniini (PCT) oli toiseksi paras merkkiaine. Monosyyttien CD40 ja NK-solujen CD69 voivat parantaa positiivisen veriviljelylöydöksen havaitsemista, kun taas CD11b voi ennustaa varhaista potilaan menehtymistä. Usean merkkiaineen mallissa neutrofiilien CD64 paransi C-reaktiivisen proteiinin (CRP) ja PCT:n tehoa sepsiksen diagnostiikassa. Loppupäätelmänä on, että valkosolujen pintamolekyylien analysointivaiheen eri muuttujilla on vaikutusta virtaussytometriatuloksiin. Valkosolujen pintamolekyylien käyttö voi parantaa sepsiksen diagnostiikkaa teho-osastolla. Neutrofiilien CD64 oli lupaavin merkkiaine. Neutrofiilien CD64:n, CRP:n ja PCT:n yhdistelmä paransi sepsiksen diagnostiikkaa teho-osastolla

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Tse, Muk-hei. "Investigations on recombinant Arabidopsis acyl-coenzyme A binding protein 1." View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36427664.

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Hubačová, Klára. "Výroba a charakterizace proteinových koncentrátů z pšeničných otrub." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2020. http://www.nusl.cz/ntk/nusl-433519.

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The diploma thesis deals with usage of wheat bran as a source of high-quality proteins. Every year mill industry produces large amounts of by-products. These by-products are constituted by wheat bran. There is a big effort to use these type of materials within a circular economy. Wheat bran contains about 14–18 % proteins which appears to be a good component for valorisation. It is possible to extract proteins from bran according to their behaviour in the range of pH. Proteins are soluble in alkaline pH and can be precipitated around their isoelectric point. The final treatment of precipitated proteins is lyophilisation. The next step is characterisation of the product. There are a few parameters to analyse: purity of the isolate, amino acid profile, composition of minerals, water contain etc. Interest in nutrition is on the rise not only by professional sportsman. This isolated product could serve as a potential protein supplement.

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Aikio, M. (Mari). "Novel roles for basement membrane collagens:isoform-specific functions of collagen XVIII in adipogenesis, fat deposition and eye development, and effects of the collagen IV-derived matricryptin arresten on oral carcinoma growth and invasion." Doctoral thesis, Oulun yliopisto, 2013. http://urn.fi/urn:isbn:9789526203188.

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Abstract Collagen XVIII is an evolutionarily conserved, ubiquitously-expressed basement membrane (BM) proteoglycan produced in three isoforms, the individual roles of which are largely unknown. The physiological in vivo roles of these collagen XVIII isoforms are studied here using novel genetically modified mouse strains deficient in either the short or the medium/long isoforms of the molecule. In addition, the effects of keratin-14-driven overexpression of the thrombospondin-1 (Tsp-1) –like domain, which is common to all three collagen XVIII isoforms, are studied. The findings underline the importance of the short collagen XVIII isoform in the eye, as its absence was sufficient to cause the aberrant vascularisation of the retina previously reported in mice lacking all isoforms of collagen XVIII. In addition, an excess of the collagen XVIII Tsp-1 domain led to serious eye abnormalities, possibly by interfering with the functions of the full-length collagen XVIII produced in mice. Collagen XVIII was also shown to contribute to adipogenesis in an isoform-specific manner, in that a lack of the medium/long isoforms of collagen XVIII led to impaired adipocyte maturation and the subsequent reduction in the adipocyte number induced liver steatosis and hypertriglyceridaemia. Hence this work establishes a new extracellular matrix ECM-directed mechanism contributing to control over the multistep adipogenesis programme and points to the functional consequences of its impairment for ectopic fat deposition. The enzymatic remodelling of ECM components results in molecules with novel biological activities. Arresten is a collagen IV(α1)-derived fragment with anti-angiogenic properties which was originally described as not having any direct anti-tumour effects on cancer cells themselves. The present data revealed novel inhibitory roles for arresten in oral squamous carcinoma cell proliferation, survival, motility and invasion. Since arresten is a potent inhibitor of angiogenesis, the data generated here further underline the possibility for using it as a therapeutic agent in cases of cancer
Tiivistelmä Kollageeni XVIII on tyvikalvojen proteoglykaani ja yksi harvoista evoluutiossa konservoituneista kollageeneista. Se esiintyy elimistössä kolmena isomuotona, joiden biologiset tehtävät ovat vielä jokseenkin epäselviä. Tässä tutkimuksessa selvitettiin kollageeni XVIII:n isomuotojen fysiologista merkitystä hyödyntäen uusia hiirilinjoja, joilta kollageeni XVIII:n lyhyt tai kaksi pisintä varianttia oli geneettisesti inaktivoitu. Poistogeenisten hiirimallien rinnalle tehtiin kaikille varianteille yhteistä trombospondiini-1 (Tsp-1)-domeinia yli-ilmentävä hiirilinja. Tämän väitöskirjatutkimuksen avulla saatiin uutta tietoa kollageeni XVIII:n ja etenkin sen lyhimmän variantin tärkeästä roolista silmässä. Aikaisemmat tutkimukset ovat osoittaneet kollageeni XVIII:n puutteen häiritsevän silmän verkkokalvon verisuonituksen normaalia kehittymistä. Tässä työssä havaittiin, että pelkästään lyhyen isomuodon puute riitti altistamaan hiiret muutoksille verkkokalvon suonituksessa. Tsp-1-osan ylimäärän havaittiin lisäksi alistavan hiiret muutoksille silmän rakenteessa, mahdollisesti häiritsemällä silmässä jo olemassa olevan kollageeni XVIII:n toimintaa. Tässä työssä havaittiin myös uusi yhteys kollageeni XVIII:n ja rasvasolujen kypsymisen välillä. Verrokkihiiriin verrattuna muodostuvan rasvakudoksen havaittiin jäävän merkittävästi vähäisemmäksi poistogeenisillä hiirillä, joilta kollageeni XVIII:n pitkät isomuodot olivat geneettisesti inaktivoitu. Heikentynyt rasvakudoksen muodostuminen lisäsi triglyseridien kertymistä hiiren verenkiertoon ja maksaan. Tutkimustulos on merkittävä avaus soluväliaineen merkityksestä rasva-aineenvaihdunnalle ja kannustaa lisätutkimuksilla selvittämään, onko kollageeni XVIII:lla yhteys myös ihmisen metaboliseen oireyhtymään. Soluväliaineen komponenttien entsymaattinen muokkaus tuottaa usein molekyylejä, joilla on uusia isäntämolekyyleistä poikkeavia ominaisuuksia. Tässä työssä tutkittiin yhden tällaisen molekyylin, tyvikalvokollageenin IV hajoamistuotteen, arrestenin, suoria vaikutuksia syöpäsoluille. Arrestenin tiedettiin entuudestaan estävän syöpäkasvainten verisuonten uudismuodostusta koe-eläimillä. Työssä osoitettiin, että arresten vaikutti endoteelisolujen lisäksi myös itse syöpäsoluihin estäen niiden lisääntymistä ja vähentäen niiden elinkykyä ja liikkuvuutta, mikä tekee arrestenista entistä houkuttelevamman ehdokasmolekyylin lääkekehitystyöhön

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Jedličková, Lenka. "Charakterizace sladkých proteinů thaumatinů kapalinovou chromatografií a hmotnostní spektrometrií." Master's thesis, Vysoké učení technické v Brně. Fakulta chemická, 2008. http://www.nusl.cz/ntk/nusl-216209.

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Nguyen, Giang Huong. "A functional analysis of the human LPA₁G protein coupled receptor." Thesis, Available online, Georgia Institute of Technology, 2004:, 2004. http://etd.gatech.edu/theses/available/etd-06072004-131304/unrestricted/nguyen%5Fgiang%5Fh%5F200405%5Fms.pdf.

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Koscky, Paier Carlos Roberto 1983. "Padronização da expressão heterologa e de modelo de ensaio de atividade para a proteina quinase humana S6K." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/314787.

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Orientador: Nilson Ivo Tonin Zanchin
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: A quinase de 70 kDa da proteína ribossomal S6, isoforma 1 (S6K1), é uma fosfoproteína implicada na regulação de genes relacionados ao controle da tradução em mamíferos e possui uma forma nuclear (a1) e uma citoplasmática (a2). A fosforilação do seu principal alvo, a proteína RPS6, tem sido comumente associada ao recrutamento seletivo dos 5'-TOP (5' tract of oligopyrimidine) mRNAs pela maquinaria de tradução, embora haja estudos contrariando esta hipótese. Devido às funções de seus demais alvos, S6K1 tem sido implicada na sobrevivência celular e em diversos outros processos, como crescimento, câncer e resistência à insulina. S6K1 é ativada por um mecanismo que envolve fosforilação seqüencial através da ativação das vias mTORC1 (complexo 1 do alvo da rapamicina em mamíferos) e PI3K (fosfoinositol-3 quinase). Como uma quinase da família AGC, S6K1 deve ser fosforilada por mTORC1 no resíduo Thr389 do domínio hidrofóbico e, em seguida, por PDPK1 (proteína quinase 1 dependente de fosfoinositol) no resíduo Thr229 da alça T do domínio catalítico. Estes eventos ocorrem somente após a fosforilação em diversos sítios do domínio auto-inibitório carboxiterminal, por mTORC1. O objetivo deste trabalho foi desenvolver um ensaio modelo para análise da função da S6K1 in vitro e utilizá-lo como ferramenta na elucidação do papel de proteínas adaptadoras da via de mTOR em interações com a S6K1. Para isso foi necessário produzir as proteínas recombinantes para ensaios de interação e para realização de um ensaio de atividade para a S6K1. Foram testados vários sistemas de expressão para Escherichia coli para produção das construções GST-S6K1a1-His6, GST-S6K1a2-His6 e GST-S6K1a2T389E?CT (forma a2 de S6K1 com a substituição T389E e o carboxiterminal truncado), GST-PDPK1 e GST-CDPDPK1 (domínio catalítico de PDPK1 fusionado a GST). A expressão das formas truncadas de S6K1 e PDPK1 foi mais eficiente em E. coli. Embora o rendimento tenha ficado muito aquém do esperado, foi suficiente para os ensaios de interação in vitro. Também foi feita a expressão em E. coli da região C-terminal da proteína RPS6, que é o substrato da S6K1, em fusão com a proteína D do fago ?. Posteriormente, foram montados sistemas de expressão das construções His6-S6K1a2T389E?CT e His6-CDPDPK1 em células de inseto, a partir de vetor de baculovírus. Constatou-se que essas construções são expressas na forma de fosfoproteínas em células de inseto. Ensaios de GST pull-down com GST-S6K1a2-His6 e GST-S6K1a2T389E?CT contra as duas isoformas da subunidade catalítica da PP2AC, His6-PP2ACa(maior) e His6-PP2ACa(menor), revelaram que His6-PP2ACa(maior) não interage com GST-S6K1a2-His6, embora interaja fortemente com GST-S6K1a2T389E?CT. Já a construção His6-PP2ACa(menor) interage fracamente com as construções GST-S6K1a2-His6 e GST-S6K1a2T389E?CT. Tomados em conjunto, os resultados sugerem que a presença do C-terminal não fosforilado de S6K1a2 impede a interação com PP2ACa(maior). PP2ACa(menor) comporta-se de forma completamente diferente da isoforma maior, pois a interação entre PP2ACa(menor) e S6K1a2 parece ser independente do carboxiterminal da quinase, visto que as quantidades de S6K1a2T389E?CT e de S6K1a2 inteira que interagem com PP2ACa(menor) são semelhantes. Esses resultados necessitam ainda serem confirmados in vivo. Outros experimentos de GST pull-down confirmaram que as construções de S6K1 não interagem com a4, embora interajam com TIPRL1. Se confirmado in vivo, esse resultado compõe um novo quadro na regulação coordenada entre mTOR1 e PP2A, do qual TIPRL1 parece participar. As construções genéticas e os sistemas de expressão gerados neste trabalho possibilitaram a obtenção dos reagentes necessários para analisar o mecanismo de regulação da quinase S6K1, mediado por proteínas regulatórias. Permitem também desenvolver uma série de experimentos, como busca de inibidores específicos para a S6K1, que dependem da reconstituição de ensaios de atividade in vitro com a S6K1 ativada. Contudo, o ensaio de atividade realizado não apresentou resultados satisfatórios e precisa ser desenvolvido.
Abstract: The 70kDa ribosomal S6 protein kinase 1 (S6K1) is a phosphoprotein involved in the regulation of genes related to translational control in mammals. S6K1 shows distinct nuclear (a1) and cytoplasmic (a2) forms. Phosphorylation of the S6K1 best characterized target, the protein of the small ribosomal subunit (RPS6), has been generally associated to the selective recruitment of the 5'-TOP mRNAs (5' tract of oligopyrimidine) by the translational machinery, although there is still some controversy on this issue. Due to the function of its targets, S6K1 has been implicated in several cellular processes including cell growth, cancer and insulin resistance. S6K1 is activated by a mechanism of sequential phosphorylation following activation of the mTORC1 (mammalian target of rapamycin complex 1) and PI3K (phosphoinositide-3-kinase) pathways. As a kinase of the AGC family, S6K1 activation requires mTORC1 phosphorylation of residue Thr389 of the hydrophobic domain followed by PDPK1 (phosphoinositide dependent protein kinase 1) phosphorylation of residue Thr229 at the T loop of the catalytic domain. These take place only after phosphorylation by mTORC1 of several residues of the autoinhibitory C-terminal domain. The objective of this work was to develop an assay to analyze the function of S6K1 in vitro and use it as a tool in the discovering of the functions of regulators proteins of the mTOR cascade in interactions with S6K1. For these purposes, expression systems were constructed to produce the various recombinant proteins to be used in the interaction and activity assays. Several genetic constructions were tested in Escherichia coli for the production of GST-S6K1a1-His6, GST-S6K1a2-His6 and GST-S6K1a2T389E?CT (a2 form of S6K1 with the T389E substitution and truncated carboxiterminus), GST-PDPK1 and GST-CDPDPK1 (GST fusion protein of the catalytic domain of PDPK1). The truncated forms were expressed more efficiently in E. coli. Although the yield in E. coli was lower than expected, it was sufficient to perform interaction assays. The C-terminal domain of RPS6, a substrate for S6K1, was successfully expressed in E. coli as a fusion protein with the phage ? protein D. Subsequently, expression systems for production of His6-S6K1a2T389E?CT and His6-CDPDPK1 in insect cells were constructed using baculovirus vectors. It was found that these constructs are expressed in the form of phosphoproteins in insect cells. GST pull-down assays using GST-S6K1a2-His6 e GST-S6K1a2T389E?CT to test interaction with the PP2AC isoforms His6-PP2ACa(major) and His6-PP2ACa(minor) revealed that His6-PP2ACa(major) does not interact with GST-S6K1a2-His6, although it interacts strongly with GST-S6K1a2T389E?CT. On the other hand, His6-PP2ACa(minor) interacts weakly with both GST- S6K1a2-His6 and GST-S6K1a2T389E?CT. This finding suggests that the unphosphorylated C-terminal of S6K1a2 inhibits interaction with PP2ACa(major). His6-PP2ACa(minor) behaves differently form His6-PP2ACa(major). Its interaction with S6K1a2 seems to be independent of the C-terminal since the amounts of S6K1a2T389E?CT and S6K1a2 that interact with His6-PP2ACa(minor) are similar. Future work in vivo is required to confirm these results. GST pull-down assays confirmed that a4 does not interact with the constructions of S6K1, while TIPRL1 interacts with them. If confirmed in vivo, these results provides a new perspective for the coordinated regulation between mTOR1 and PP2A, which apparently involves also TIPRL1. The genetic constructions and expression systems established in this work allow the production of the reagents required to study the mechanism of S6K1 regulation mediated by adaptor proteins. They will also allow the development of experiments such as screening for specific S6K1 inhibitors, which depend on reconstitution of S6K1 activity assays using activated S6K1. Nevertheless, the activity assay performed did not yield satisfactory outcomes and must be improved.
Mestrado
Bioquimica
Mestre em Biologia Funcional e Molecular

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Nauli, Sehat. "Folding kinetics and redesign of Peptostreptococcal protein L and G /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/9237.

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Li, Wei. "Protein-protein interaction specificity of immunity proteins for DNase colicins." Thesis, University of East Anglia, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.302033.

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Pateman, Cassandra Sophie Catherine. "RGS proteins and G protein signalling." Thesis, University of Warwick, 2002. http://wrap.warwick.ac.uk/2367/.

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The work within this thesis is concerned with the creation of a temperature-sensitive Schizosaccharomyces pombe marker protein, and the regulation of the pheromone communication system of Sz. pombe reporter strains by RGS proteins. There are a limited number of marker proteins available for use in the genetic manipulation of Sz. pombe, and the generation of a temperature-sensitive Ura4p was envisaged to expand the scope of carrying out sequential gene disruptions in the fission yeast. PCR-based mutagenesis was used to introduce mutations in the ura4 cassette, and a leucine to proline mutation identified at residue 261 in the ura4 open reading frame conferred a temperature-sensitive requirement for uracil. To demonstrate the use of the Ura4sp marker in gene disruption, the Sz. pombe irpl gene was disrupted with the ura4u cassette, and subsequently, the prkl gene was disrupted with the wild-type ura4 cassette. RGS proteins are a recently discovered family of proteins that negatively regulate G protein-coupled signalling pathways. This thesis describes the ability of mammalian RGS proteins to regulate the pheromone communication system of Sz. pombe reporter strains. Human RGS 1 and human RGS4 displayed the greatest ability to negatively regulate the Sz. pombe pheromone signalling pathway when expressed from multicopy expression vectors. Human RGS2, human RGS3, human RGS9-2 and murine RGS2 displayed lesser, varying abilities. Expression of human RGS 1 from single copy reduced signalling at low pheromone concentrations. Expression of human RGS4 from single copy was incapable of reducing pheromone-independent and pheromone-dependent signalling. This thesis also describes the search for gain-of-function RGS proteins. Two potential gain-of-function szRgslp mutants were previously identified, and these mutants were recreated. The two mutations identified (histidine to arginine at szRgslp residue 171 and valine to isoleucine at szRgslp residue 305) conferred gain-of-function szRgslp phenotypes in an sxa2:: ura4 reporter strain. Hydroxylamine treatment of the human RGS4 open reading frame resulted in the identification of a potential gain-of-function RGS4 mutant. The lysine to arginine mutation at huRGS4p residue 20 conferred a gain-of-function huRGS4p phenotype in an sxa2:: ura4 reporter strain.

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Xu, Ping. "Sensing and analyzing unfolded protein response during heterologous protein production :." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 205 p, 2008. http://proquest.umi.com/pqdweb?did=1555621341&sid=2&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Diaz, Manisha Regina. "Use of bionanotechnology to decipher the patterns of assemblage and interactions of multi-protein complexes." Bowling Green, Ohio : Bowling Green State University, 2009. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=bgsu1250955267.

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Dressel, Frank. "Sequenz, Energie, Struktur - Untersuchungen zur Beziehung zwischen Primär- und Tertiärstruktur in globulären und Membran-Proteinen." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1222781322751-68621.

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Proteine spielen auf der zellulären Ebene eines Organismus eine fundamentale Rolle. Sie sind quasi die „Maschinen“ der Zelle. Ihre Bedeutung wird nicht zuletzt in ihrem Namen deutlich, welcher 1838 erstmals von J. Berzelius verwendet wurde und „das Erste“, „das Wichtigste“ bedeutet. Proteine sind aus Aminosäuren aufgebaute Moleküle. Unter physiologischen Bedingungen besitzen sie eine definierte dreidimensionale Gestalt, welche für ihre biologische Funktion bestimmend ist. Es wird heutzutage davon ausgegangen, dass diese dreidimensionale, stabile Struktur von Proteinen eindeutig durch die Abfolge der einzelnen Aminosäuren, der Sequenz, bestimmt ist. Diese Abfolge ist für jedes Protein in der Desoxyribonukleinsäure (DNS) gespeichert. Es ist allerdings eines der größten ungelösten Probleme der letzten Jahrzehnte, wie die Beziehung zwischen Sequenz und 3D-Struktur tatsächlich aussieht. Die Beantwortung dieser Fragestellung erfordert interdisziplinäre Ansätze aus Biologie, Informatik und Physik. In dieser Arbeit werden mit Hilfe von Methoden der theoretischen (Bio-) Physik einige der damit verbundenen Aspekte untersucht. Das Hauptaugenmerk liegt dabei auf Wechselwirkungen der einzelnen Aminosäuren eines Proteins untereinander, wofür in dieser Arbeit ein entsprechendes Energiemodell entwickelt wurde. Es werden Grundzustände sowie Energielandschaften untersucht und mit experimentellen Daten verglichen. Die Stärke der Wechselwirkung einzelner Aminosäuren erlaubt zusätzlich Aussagen über die Stabilität von Proteinen bezüglich mechanischer Kräfte. Die vorliegende Arbeit unterteilt sich wie folgt: Kapitel 2 dient der Einleitung und stellt Proteine und ihre Funktionen dar. Kapitel 3 stellt die Modellierung der Proteinstrukturen in zwei verschiedenen Modellen vor, welche in dieser Arbeit entwickelt wurden, um 3D-Strukturen von Proteinen zu beschreiben. Anschließend wird in Kapitel 4 ein Algorithmus zum Auffinden des exakten Energieminimums dargestellt. Kapitel 5 beschäftigt sich mit der Frage, wie eine geeignete diskrete Energiefunktion aus experimentellen Daten gewonnen werden kann. In Kapitel 6 werden erste Ergebnisse dieses Modells dargestellt. Der Frage, ob der experimentell bestimmte Zustand dem energetischen Grundzustand eines Proteins entspricht, wird in Kapitel 7 nachgegangen. Die beiden Kapitel 8 und 9 zeigen die Anwendung des Modells an zwei Proteinen, dem Tryptophan cage protein als dem kleinsten, stabilen Protein und Kinesin, einem Motorprotein, für welches 2007 aufschlussreiche Experimente zur mechanischen Stabilität durchgeführt wurden. Kapitel 10 bis 12 widmen sich Membranproteinen. Dabei beschäftigt sich Kapitel 10 mit der Vorhersage von stabilen Bereichen (sog. Entfaltungsbarrieren) unter externer Krafteinwirkung. Zu Beginn wird eine kurze Einleitung zu Membranproteinen gegeben. Im folgenden Kapitel 11 wird die Entfaltung mit Hilfe des Modells und Monte-Carlo-Techniken simuliert. Mit dem an Membranproteine angepassten Wechselwirkungsmodell ist es möglich, den Einfluss von Mutationen auch ohne explizite strukturelle Informationen vorherzusagen. Dieses Thema wird in Kapitel 12 diskutiert. Die Beziehung zwischen Primär- und Tertiärstruktur eines Proteins wird in Kapitel 13 behandelt. Es wird ein Ansatz skizziert, welcher in der Lage ist, Strukturbeziehungen zwischen Proteinen zu detektieren, die mit herkömmlichen Methoden der Bioinformatik nicht gefunden werden können. Die letzten beiden Kapitel schließlich geben eine Zusammenfassung bzw. einen Ausblick auf künftige Entwicklungen und Anwendungen des Modells.

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Flöck, Dagmar. "Protein-protein docking and Brownian dynamics simulation of electron transfer proteins." [S.l. : s.n.], 2003. http://deposit.ddb.de/cgi-bin/dokserv?idn=969418736.

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Marri, Lucia <1977&gt. "CP12: Intrinsically Unstructured Proteins regulating photosynthetic enzymes through protein-protein interactions." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/423/.

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Wei, Heng. "Split PH domain identification & redundancy analyses in the classification of PDZ domains /." View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BICH%202006%20WEI.

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Baas, Tracey Lynn. "The design, synthesis, and characterization of template assembled synthetic proteins /." Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/11561.

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Ndabambi, Nonkululeko. "Recombinant expression of the pRb- and p53-interacting domains from the human RBBP6 protein for in vitro binding studies." Thesis, University of the Western Cape, 2004. http://etd.uwc.ac.za/index.php?module=etd&amp.

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The aim of this thesis was to produce DNA expression constructs and use them to investigate the feasibility of recombinantly expression proteins for future interaction studies between human RBBP6 and p53 and pRb proteins.

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Baisden, Joseph M. "AFAP-110 is a cSrc activator." Morgantown, W. Va. : [West Virginia University Libraries], 2003. http://etd.wvu.edu/templates/showETD.cfm?recnum=2766.

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Thesis (Ph. D.)--West Virginia University, 2003.
Title from document title page. Document formatted into pages; contains v, 149 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

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Filipponi, Luisa. "New micropatterning techniques for the spatial addressable immobilization of proteins." Australian Digital Thesis Program, 2006. http://adt.lib.swin.edu.au/public/adt-VSWT20060905.113858/index.html.

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Thesis (PhD) - Swinburne University of Technology, Industrial Research Institute Swinburne - 2006.
A thesis submitted in fulfilment of the requirements for the degree of Doctor of Philosophy, Industrial Research Institute Swinburne, Swinburne University of Technology - 2006. Typescript. Includes bibliographical references (p. 184-197).

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Louie, Brenton E. "Modeling uncertainty in data integration for improving protein function assignment /." Thesis, Connect to this title online; UW restricted, 2008. http://hdl.handle.net/1773/7154.

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Lam, Wai Kwan. "Investigation of interaction between solube adenylyl cyclase and p34SEI-1 /." View abstract or full-text, 2010. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202010%20LAM.

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Smits, Callum, and n/a. "Structures of the pro-survival protein A1 in complex with BH3-domain peptides." University of Otago. Department of Biochemistry, 2007. http://adt.otago.ac.nz./public/adt-NZDU20071218.131743.

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Protein:protein interactions are central to the regulation of the intrinsic programmed cell death (apoptosis) pathway. Opposing members of the Bcl-2 family of proteins, which have distinct sequence features, interact with each other on the outer mitochondrial membrane to regulate apoptosis. Pro-survival proteins such as Bcl-2, Bcl-x[L], Bcl-w, Mcl-1 and A1 protect cells from apoptosis and contain up to four regions of homology to Bcl-2 (Bcl-2 homology domains 1 - 4, BH1-4). Pro-apoptotic BH3-only proteins such as Bim, Puma, Noxa, Bad, Bmf, and Bid promote apoptosis by interacting with and inactivating pro-survival proteins, and contain just the BH3-domain. The pro-apoptotic proteins Bax and Bak are essential for apoptosis and contain three regions of homology to Bcl-2 (the BH1-, BH2- and BH3-domains). In this study, two different sets of interactions involving pro-survival proteins were investigated. Initially, the pro-apoptotic protein Bnip3 was examined to determine if it was a mitochondrial anchor for the pro-survival protein Bcl-w. Secondly, to characterise the interactions between a pro-survival protein and different BH3-domains, structures were solved of the pro-survival protein A1 in complex with four different BH3-domains. In the structure of Bcl-w, the hydrophobic C-terminus is bound to its own BH3-domain binding groove. This location of the C-terminus is consistent with the observation that Bcl-w is only loosely associated with the outer mitochondrial membrane in healthy cells. Upon interaction of Bcl-w with a BH3-domain, Bcl-w becomes tightly associated with the mitochondrial membrane, presumably due to displacement of the C-terminal residues by the BH3-only protein. In healthy cells it has been suggested that Bcl-w is associated with the membrane due to an interaction with an unidentified membrane protein, which preliminary experiments suggested may be Bnip3. Protein interaction experiments performed in vitro and in vivo did not reveal an interaction between Bnip3 and Bcl-w. It was originally thought that each pro-apoptotic BH3-only protein could interact with all pro-survival proteins. However, it has recently become clear that there is selectivity within the pathway suggesting functional groupings. Bim and Puma behave as originally predicted and can interact with all pro-survival proteins and are potent killers. In contrast, Noxa and Bad interact with distinct subsets of pro-survival proteins. Noxa only binds Mcl-1 and A1, while Bad binds Bcl-2, Bcl-x[L] and Bcl-w. As a result, either Noxa or Bad acting alone is a weak killer, but together they are potent. Other BH3-only proteins bind tightly to some pro-survival proteins and weakly to others. The diversity that exists between BH3-domain sequences precludes sequence-based identification of the determinants of specificity. In this study, crystal structures of A1:Puma BH3-domain, A1:Bmf BH3-domain, A1:Bak BH3-domain and A1:Bid BH3-domain complexes have been solved. Differences identified between these structures explain some of the variation in affinities observed in pro-survival protein:BH3-domain complexes. These observations, in combination with published data, suggest that BH3-domains bind weakly when the optimal interactions with conserved residues cannot be formed. Additionally, differences were observed in the A1:Bak BH3-domain structure that may be functionally important for the regulation of Bak.

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Wang, Chu. "Improved conformational sampling for protein-protein docking /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9194.

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Björkholm, Patrik. "Protein Interactions from the Molecular to the Domain Level." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-101795.

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The basic unit of life is the cell, from single-cell bacteria to the largest creatures on the planet. All cells have DNA, which contains the blueprint for proteins. This information is transported in the form of messenger RNA from the genome to ribosomes where proteins are produced. Proteins are the main functional constituents of the cell, they usually have one or several functions and are the main actors in almost all essential biological processes. Proteins are what make the cell alive. Proteins are found as solitary units or as part of large complexes. Proteins can be found in all parts of the cell, the most common place being the cytoplasm, a central space in all cells. They are also commonly found integrated into or attached to various membranes. Membranes define the cell architecture. Proteins integrated into the membrane have a wide number of responsibilities: they are the gatekeepers of the cell, they secrete cellular waste products, and many of them are receptors and enzymes. The main focus of this thesis is the study of protein interactions, from the molecular level up to the protein domain level. In paper I use reoccurring local protein structures to try and predict what sections of a protein interacts with another part using only sequence information. In papers II and III we use a randomization approach on a membrane protein motif that we know interacts with a sphingomyelin lipid to find other candidate proteins that interact with sphingolipids. These are then experimentally verified as sphingolipid-binding. In the last paper, paper IV, we look at how protein domain interaction networks overlap and can be evaluated.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 3: Manuscript.

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Wong, Chung Kai. "The DIX domain protein Ccd1 inhibits JNK activation by axin and dishevelled through distinct mechanisms /." View abstract or full-text, 2004. http://library.ust.hk/cgi/db/thesis.pl?BICH%202004%20WONG.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2004.
Includes bibliographical references (leaves 60-68). Also available in electronic version. Access restricted to campus users.

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Sarkar, Mohosin M. "Engineering Proteins with GFP: Study of Protein-Protein Interactions In vivo, Protein Expression and Solubility." The Ohio State University, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=osu1261418776.

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Henderson, Julius Nathan. "Crystallographic and spectroscopic studies of photoswitching in fluorescent proteins /." view abstract or download file of text, 2007. http://proquest.umi.com/pqdweb?did=1417810431&sid=5&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2007.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 143-151). Also available for download via the World Wide Web; free to University of Oregon users.

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Lira, Nayara Patricia Vieira de 1988. "Expressão, purificação e ensaio de atividade dos domínios DUF442 e ETHE1 da proteína Blh de Xylella fastidiosa e Agrobacterium tumefaciens." [s.n.], 2014. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316593.

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Orientador: Celso Eduardo Benedetti
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Xylella fastidiosa e Agrobacterium tumefaciens são bactérias fitopatogênicas que infectam, respectivamente, o interior do xilema e de tecidos vasculares de raiz, ambientes cuja tensão de oxigênio é relativamente baixa. Uma vez que Xylella e Agrobacterium são bactérias estritamente aeróbicas, elas apresentam o operon bigR, responsável pela detoxificação do sulfeto de hidrogênio ou gás sulfídrico, um potente inibidor do citocromo c oxidase e respiração aeróbica. O operon bigR codifica cinco proteínas denominadas Blh (Beta-lactamase-like hydrolase), BigR (biofilm growth-associated repressor), um repressor transcricional e regulador do operon, e MP1-3, proteínas que compõem um transportador de membrana. Em trabalho anterior, foi demonstrado que mutantes de Agrobacterium deficientes na produção de Blh acumulavam gás sulfídrico, enquanto mutantes no repressor BigR secretavam mais sulfito, indicando que a proteína Blh convertia gás sulfídrico em sulfito e que este, que também é tóxico, seria exportado pelo complexo MP1-3. Além disso, dados de modelagem molecular indicaram que Blh poderia desempenhar funções de sulfotransferase e dioxigenase de enxofre, uma vez que apresenta os domínios DUF442 (rodanase) e ETHE1 (dioxigenase). A fim de testar tais hipóteses, este trabalho teve como principais objetivos a caracterização enzimática dos domínios DUF442 e ETHE1 da Blh de Xylella e Agrobacterium, como também confirmar interações proteína-proteína entre os componentes do operon bigR. Ensaios de atividade enzimática usando-se proteínas recombinantes purificadas confirmaram a função de dioxigenase de enxofre e de rodanase dos domínios ETHE1 e DUF442, respectivamente. Além disso, verificou-se que ambos os domínios produzem sulfito como produto final da reação, embora atuando em substratos diferentes. Ainda, ensaios de duplo híbrido de levedura mostraram haver inúmeras interações entre as proteínas do operon bigR, mas não entre os dois domínios DUF442 e ETHE1 de Blh que, de acordo com os ensaios enzimáticos, atuam de forma independente.
Abstract: Xylella fastidiosa and Agrobacterium tumefaciens are phytopathogenic bacteria that infect, respectively, the xylem vessels and root vascular tissues, where the oxygen tension is relatively lower. Since Xylella and Agrobacterium are strict aerobic organisms, they use the bigR operon for the detoxification of hydrogen sulfide, a potent inhibitor of cytochrome c oxidase and aerobic respiration. The bigR operon encodes five proteins designated Blh (Beta-lactamase-like hydrolase), BigR (biofilm growth-associated repressor), a transcriptional repressor that regulates the operon, and MP1-3, proteins that act as a membrane transporter. In a previous work, it was shown that Agrobacterium mutants deficient in Blh production accumulated hydrogen sulfide, whereas BigR-deficient mutants secreted sulfite at higher levels than the wild type bacteria, indicating that Blh converted hydrogen sulfide into sulfite, which would be exported by the MP1-3 complex. In addition, molecular modeling indicated that Blh could function as a sulfur transferase and sulfur dioxigenase, since it carries a DUF442 (rhodanese) and ETHE1 (dioxygenase) domains. To test such hypothesis, this work aimed to demonstrate the enzymatic activities of the DUF442 and ETHE1 domains of Blh from Xylella and Agrobacterium, as well as to confirm protein-protein interactions between components of the bigR operon. Enzyme activity assays using the purified proteins confirmed the sulfur dioxygenase and rhodanese activities of the ETHE1 and DUF442 domains, respectively. In addition, it was found that both domains produce sulfite as a final product, although having different substrates. Furthermore, yeast two-hybrid assays showed that many of the bigR operon proteins interact with each other, suggesting the formation of a protein complex. However, no physical interactions were detected between DUF442 and ETHE1 domains, which, according to the enzyme activity assays, act independently.
Mestrado
Microbiologia
Mestra em Genética e Biologia Molecular

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42

Joachimiak, Lukasz A. "In silico evolution of protein-protein interactions : from altered specificities to de novo complexes /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/9211.

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Chivian, Dylan Casey. "Application of information from homologous proteins for the prediction of protein structure /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9264.

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Wang, Hua. "Control of protein-surface, protein-protein, and cell-matrix interactions for biomaterials as tissue engineering scaffolds /." Thesis, Connect to this title online; UW restricted, 2005. http://hdl.handle.net/1773/9894.

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Cherezova, Lidia Nikolayevna. "Determining the effects of phosphorylation on AFAP-110 function." Morgantown, W. Va. : [West Virginia University Libraries], 2002. http://etd.wvu.edu/templates/showETD.cfm?recnum=2492.

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Thesis (M.S.)--West Virginia University, 2002.
Title from document title page. Document formatted into pages; contains v, 105 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

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Tse, Muk-hei, and 謝牧熙. "Investigations on recombinant Arabidopsis acyl-coenzyme A binding protein 1." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36427664.

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Crane, Jennine Marie. "Characterization of two modes of interaction between the chaperone SecB and its binding partners." Free to MU Campus, others may purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3144410.

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Measey, Thomas J. Schweitzer-Stenner Reinhard. "Unfolded, misfolded, and self-organized short alanine-rich peptides : implications for fundamental science, human disease, and biotechnology /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3317.

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Prigge, Justin Robert. "Identification and characterization of novel protein-protein interactions with the basal transcription factor, TATA-binding protein." Diss., Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/prigge/PriggeJ0506.pdf.

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Kwan, Ann H. Y. "Protein design based on a PHD scaffold." Connect to full text, 2004. http://setis.library.usyd.edu.au/adt/public_html/adt-NU/public/adt-NU20041202.102526/index.html.

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Thesis (Ph. D.)--School of Molecular and Microbial Biosciences, Faculty of Science, University of Sydney, 2004.
Chapter headings on separately inserted unnumbered cream coloured leaves. Bibliography: leaves 122-135.

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Dissertations / Theses on the topic 'Proteiini'

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