Dissertations / Theses on the topic 'Protein oligomers'
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Andrade, Helena. "DNA Oligomers - From Protein Binding to Probabilistic Modelling." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-218709.
Full textRushworth, Joanne Valerie Humphrey. "The cellular prion protein as a receptor for amyloid-beta oligomers." Thesis, University of Leeds, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.581951.
Full textMa, Xin. "Ion Mobility Mass Spectrometry of DNA/SgrAI Nuclease Oligomers." Thesis, The University of Arizona, 2012. http://hdl.handle.net/10150/247282.
Full textLimbocker, Ryan Alexander. "Mitigating protein aggregation to reduce the toxicity inherent to Parkinson's and Alzheimer's diseases." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284937.
Full textPhan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer." Scholarly Commons, 2013. https://scholarlycommons.pacific.edu/uop_etds/859.
Full textXu, Xiaojun [Verfasser], and A. S. [Akademischer Betreuer] Ulrich. "Protein-protein interactions in oligomers studied by solid-state NMR in biomembranes / Xiaojun Xu. Betreuer: A. S. Ulrich." Karlsruhe : KIT-Bibliothek, 2016. http://d-nb.info/1108453198/34.
Full textPhan, Jamie. "Investigating protein folding by the de novo design of an α-helix oligomer : a thesis." Scholarly Commons, 2001. https://scholarlycommons.pacific.edu/uop_etds/859.
Full textZych, Andrew John. "Conformational characterization of abiotic secondary structure based on aromatic stacking /." Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3008484.
Full textDe, Giorgi Marcella. "Design and synthesis of novel thienylpyridyl oligomers as alpha helix mimetics with protein-protein interaction disrupting activity and possible biological applications." Caen, 2012. http://www.theses.fr/2012CAEN4076.
Full textProtein-protein interactions (PPIs) are attractive targets for drug discovery. Indeed, most of cellular processes are composed or influenced by PPIs and their misregulation can result in numerous disease states. Even if proteins surfaces are generally large, some key elements are responsible of the interaction and the recognition (hot spots). The most common secondary structure in natural proteins is an alpha helix. Small molecules seem to be attractive candidates for stabilizing or disrupting protein-protein interactions based on alpha helices. We are particularly interested in Bcl-2 family proteins which are central regulators of apoptosis. They are overexpressed in many cancers and contribute to tumour initiation, progression and resistance to therapy. The aim of our study is to design small molecules able to interact with anti-apoptotic members and restore the intrinsic apoptosis mechanism. These foldamers would mimic only the key elements of a protein surface and potentially lead to small molecules having almost the full activity of a protein domain. For this, we synthesized a library of thienylpyridyl oligomers. Most of these compounds underwent molecular modeling studies based on radiocrystallography in order to evaluate the ability to mimic an alpha helix and the spatial orientation of different substituents. Moreover, biological tests have been done to evaluate the ability to induce apoptosis in cancer cells
Fluharty, Brian Richard. "Identification of novel cellular prion protein-based compounds to block the toxicity of amyloid-beta oligomers." Thesis, Boston University, 2013. https://hdl.handle.net/2144/12955.
Full textAlzheimer's disease (AD) is characterized by progressive dementia and accumulation of a cleavage product of the amyloid precursor protein, amyloid-β (Aβ) peptide, in the brain. Several lines of evidence suggest that soluble, oligomeric intermediates of Aβ are primarily responsible for synaptic dysfunction and the cognitive deficit observed in AD. The cellular prion protein (PrP^c), a cell surface glycoprotein involved in transmissible spongiform encephalopathies, was previously identified as a high affinity receptor for Aβ oligomers. It has been suggested that binding of Aβ oligomers to PrP^c transduces the synaptotoxic events seen in AD. The two reported binding sites of Aβ oligomers are located on the unstructured N-terminal tail of PrP^c. We show here that the soluble physiological cleavage fragment of PrP^c, N1, was necessary and sufficient for binding Aβ oligomers. This binding interaction was influenced by positively charged residues in the two binding sites and is dependent on the length ofthe sequence between them. Importantly, the addition of synthetic N1 peptide suppressed Aβ oligomer toxicity in cultured murine hippocampal neurons and in a mouse model of Aβ-induced memory dysfunction. Collectively, these data suggest that N1, or small peptides derived from it, could be potent inhibitors of Aβ oligomer toxicity by targeting Aβ oligomers and represent an entirely new class of therapeutic agents for AD. To directly target PrP^c as a toxicity receptor, in silica screening and molecular dynamics were used to generate small molecule ligands. We screened these ligands using biochemical and biophysical assays to identify high affinity ligands for PrP^c that block the binding of Aβ oligomers. We found one compound, called DS26 that bound to PrP^c with sub-micromolar affinity. Further, DS26 inhibited Aβ-dependent suppression of long-term potentiation in mouse hippocampal slices. Interestingly, we show that DS26 operated by an unexpected allosteric mechanism in which ligand binding to a site in the structured C-terminal half of PrP^c induced an intramolecular interaction with the N-terminal tail, thereby preventing Aβ binding. Together, these data demonstrate that pharmacologically targeting PrP^c can suppress Aβ toxicity. Additionally, this study clarifies previous conflicting studies regarding the role of PrP^c in AD.
Andrade, Helena [Verfasser], Yixin [Akademischer Betreuer] [Gutachter] Zhang, and Carsten [Gutachter] Werner. "DNA Oligomers - From Protein Binding to Probabilistic Modelling / Helena Andrade ; Gutachter: Yixin Zhang, Carsten Werner ; Betreuer: Yixin Zhang." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://d-nb.info/112585099X/34.
Full textAzevedo, Teixeira de Andrade Maria Helena [Verfasser], Yixin [Akademischer Betreuer] Zhang, and Carsten [Gutachter] Werner. "DNA Oligomers - From Protein Binding to Probabilistic Modelling / Helena Andrade ; Gutachter: Yixin Zhang, Carsten Werner ; Betreuer: Yixin Zhang." Dresden : Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2017. http://d-nb.info/112585099X/34.
Full textHolmquist, Melody L. "Using native mass spectrometry to study the role of homo-oligomeric proteins in gene regulation by using TRAP as a model protein system." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1595571760595304.
Full textItkin, Anna. "Multidisniplinary study of Alzheimer's disease-related peptides : from amyloid precursor protein (APP) to amyloid β-oligomers and γ-secretase modulators." Thesis, Strasbourg, 2012. http://www.theses.fr/2012STRAF051/document.
Full textA histopathological characteristic of Alzheimer’s disease (AD) is the presence of amyloid plaques formed by amyloid β(A) peptides of 40 and 42 residues-long, which are the cleavage products of APP by proteases. To understand the role of structural changes in the TM domain of APP, APP_TM4K peptides were studied in the lipid bilayer using ATR-FTIR and ssNMR. While the overall secondary structure of the APP_TM4K peptide is helical, conformational and orientational heterogeneity was observed for the y- and for the -cleavage sites, which may have implications for the cleavage mechanism and therefore the production of Aβ. Starting from its monomeric form, Aβ peptides aggregate into fibrils and / or oligomers, the latter being the most neurotoxic. We found that in the presence of Ca2 +, Aβ (1-40) preferably forms oligomers, whereas in the absence of a2 + Aβ (1-40) aggregates into fibrils. In samples without Ca2 +, ATR-FTIR shows conversion from antiparallel β sheet conformation of oligomers into parallel β sheets, characteristic of fibrils. These results led us to conclude that Ca2 +stimulates the formation of oligomers of Aβ (1-40), that have been implicated in the pathogenesis of AD. Position and precise orientation of two new drugs powerful modulators of γ-secretase benzyl-carprofen and carprofen sulfonyl in the lipid bilayer were obtained from neutron scattering and ssNMR experiments. These results indicate that carprofen-derivatives can directly interact with APP. Such interaction would interfere with proper APP-dimer formation, which is necessary for the sequential cleavage by β -secretase, diminishing or greatly reducing Aβ42 production
Kabulski, Jarod L. "Development of Au-immobilized P450 platform for exploring the effect of oligomer formation on P450-mediated metabolism for In vitro to In vivo drug metabolism predictions." Morgantown, W. Va. : [West Virginia University Libraries], 2010. http://hdl.handle.net/10450/10892.
Full textTitle from document title page. Document formatted into pages; contains xiv, 180 p. : ill. (some col.). Includes abstract. Includes bibliographical references.
APETRI, MARIA MIHAELA. "BIOPHYSICAL STUDIES OF THE ALPHA-SYNUCLEIN PROTEIN ASSOCIATED WITH PARKINSON’S DISEASE AND OTHER SYNUCLEINOPATHIES." Case Western Reserve University School of Graduate Studies / OhioLINK, 2006. http://rave.ohiolink.edu/etdc/view?acc_num=case1133387293.
Full textTolin, Serena. "Interaction between alpha-lactalbumin and lipids: conformational features and effects on protein aggregation." Doctoral thesis, Università degli studi di Padova, 2008. http://hdl.handle.net/11577/3425937.
Full textL’argomento di questa Tesi di Dottorato riguarda in generale aspetti del problema del folding e unfolding proteico, in linea con la tematica di ricerca condotta nel laboratorio di Chimica delle Proteine al CRIBI, dove le attività sono state per la maggior parte svolte. Il meccanismo di acquisizione della struttura tridimensionale di una proteina (folding) è un evento biologico importante. In generale, è un processo multi-stadio che coinvolge la formazione di intermedi, che sono stati parzialmente strutturati contenenti alcune caratteristiche strutturali della proteina nativa, ma non le interazioni finali tra le catene laterali che permettono alla proteina di esercitare la sua funzione specifica. Il fallimento nell’acquisizione del corretto folding (misfolding) può causare aggregazione proteica. Infatti, proteine parzialmente strutturate possono facilmente auto-assemblarsi in aggregati regolari insolubili (fibrille amiloidi), associati a gravi malattie, le cosiddette amiloidosi (Chiti & Dobson, 2006). In particolare, il mio progetto di Dottorato è focalizzato sull’?-lattalbumina (?-LA), una metallo-proteina del latte, ampiamente utilizzata come modello di studio del folding proteico. Nell’ultimo decennio, questa proteina ha suscitato un nuovo interesse per la scoperta di una variante che, oltre al ruolo fisiologico nella lattazione, è in grado di indurre apoptosi nelle cellule tumorali (Svensson et al., 1999). L’attività citotossica risiede nella formazione di un complesso con un acido grasso del latte, l’acido oleico (OA), denominato HAMLET (Human Alpha-lactalbumin Made LEthal to Tumor cells) (Svensson et al., 2000). Gli eventi cellulari causati da HAMLET sono stati estesamente studiati (Kohler et al., 2001; Duringer et al., 2003). Al contrario, il meccanismo e la natura dell’interazione tra ?-LA e OA e le proprietà fisico-chimiche del complesso non sono ancora completamente chiariti. Infatti, nonostante l’effettiva associazione dell’OA con la proteina in soluzione (Polverino de Laureto et al., 2002), si ritiene che il complesso così ottenuto possieda attività antitumorale minore dell’HAMLET, preparato secondo una procedura cromatografica (Svensson et al., 2000). Altre questioni dibattute riguardano la stechiometria proteina/acido grasso e lo stato monomerico/oligomerico dell’?-LA nel complesso. Inoltre, manca un’indagine sistematica dell’effetto della proteina sul comportamento di fase dell’OA. Lo scopo di questa Tesi di Dottorato è lo studio della capacità di legare OA ed esprimere attività citotossica di tre derivati proteolitici di ?-LA bovina, ottenuti per proteolisi limitata con pepsina a pH acido. L’uso di un approccio di proteolytic dissection di una proteina è stato largamente impiegato per studiare il folding di molte proteine (Wetlaufer, 1981; Gegg et al., 1997; Llinás & Marqusee, 1998). La caratterizzazione di frammenti proteici, contenenti elementi strutturali specifici della proteina intera (?-elica, ?-sheet) e in grado di assumere struttura in modo autonomo, è stata usata con successo per chiarire caratteristiche strutturali di ?-LA (Polverino de Laureto et al., 1999; 2001). Infatti, frammenti corrispondenti a domini strutturali in proteine multi-dominio hanno mostrato in alcuni casi la capacità di acquisire in soluzione una conformazione simile a quella nativa (Fontana et al., 2004). I frammenti di ?-LA studiati sono: la specie 1–40/53–123, priva di parte del dominio ? della?proteina nativa; 1–40/104–123, formato dal frammento N-terminale 1-40 legato covalentemente al frammento C-terminale 104-123 mediante due ponti disolfuro e contenente tre delle quattro ?-eliche di ?-LA; 53-103, contenente l’elica C e il sito di legame al calcio (Polverino de Laureto et al., 1999; 2001). Le differenze conformazionali dei tre frammenti sono state utilizzate come razionale per studiare la loro efficacia di legame all’OA, e per approfondire quindi il meccanismo di questo legame. Questo studio ha anche rilevanza fisiologica: la pepsina è un enzima dello stomaco e quindi queste specie potrebbero essere generate in vivo, nelle stesse condizioni di pH acido in cui si è ipotizzata la formazione del complesso HAMLET, contribuendo così all’attività apoptotica del complesso formato dalla proteina intera. I complessi dei tre frammenti con OA sono stati preparati prima seguendo la procedura cromatografica descritta per l’HAMLET, poi per diretto miscelamento in soluzione dei due componenti. Le proprietà conformazionali dei complessi sono state caratterizzate mediante dicroismo circolare, mostrando che i complessi preparati attraverso entrambe le procedure presentano conformazioni simili e acquisizione di ?-elica. Inoltre, è stato valutato l’effetto del calcio sulla conformazione dei complessi mediante dicroismo circolare. La spettroscopia di fluorescenza è stata utilizzata per analizzare il coinvolgimento dei residui di Trp nell’interazione con OA. Inoltre, è stata studiata la capacità dei complessi di indurre morte cellulare per apoptosi, in linea con l’attività citotossica mostrata dall’HAMLET. Per analizzare lo stato fisico dell’OA coinvolto nell’interazione con l’?-LA, il comportamento di aggregazione di OA è stato studiato con diverse tecniche, quali microscopia elettronica a trasmissione (TEM), titolazione con un colorante fluorescente e analisi turbidimetriche, ed è stato osservato un effetto di solubilizzazione dell’OA. Questi risultati hanno permesso di preparare un articolo che sarà presto spedito ad una rivista internazionale e che è allegato alla Tesi. Nella seconda parte del Dottorato, la ricerca è stata focalizzata sulla tendenza di ?-LA e dei suoi tre frammenti proteolitici ad aggregare. ?-LA è in grado di formare fibrille amiloidi in vitro, sebbene non sia associata a patologie. Fibrille di ?-LA si producono quando la struttura della proteina è parzialmente destabilizzata, ad esempio a pH acido, per riduzione di tre ponti disolfuro a pH neutro (Goers et al., 2002), o per taglio proteolitico (Polverino de Laureto et al., 2005). I lipidi possono agire come efficaci catalizzatori della fibrillogenesi, creando un ambiente in cui le molecole proteiche adottano una conformazione e un’orientazione che promuove il loro assemblaggio in strutture fibrillari (Thirumalai et al., 2003; Stefani, 2004; Sparr et al., 2004; Zhao et al., 2004). In particolare, poiché è noto che le interazioni proteina-acido grasso modulano il processo di fibrillogenesi (Kim & Takahashi 2006), i processi di aggregazione di ?-LA e dei suoi frammenti sono stati studiati per capire se e come l’OA possa influenzare la formazione di fibrille. In primo luogo, l’aggregazione è stata seguita a pH 2.0, in parallelo con il già noto comportamento fibrillogenico di ?-LA intera. In secondo luogo, l’aggregazione è stata studiata a pH 7.4, poiché in questa condizione fisiologica nella prima parte della Tesi sono stati studiati i cambiamenti conformazionali indotti dall’OA sulla struttura dei frammenti e la loro attività citotossica. La formazione di fibrille è stata seguita mediante saggi di fluorescenza con la tioflavina T (ThT), dicroismo circolare e TEM. Tutti e tre i frammenti sono in grado di produrre fibrille amiloidi a pH 2.0, analogamente all’?-LA. Ai valori di concentrazione proteica e rapporto proteina/lipide utilizzati, OA sembra accelerare la velocità di formazione di fibrille di ?-LA e dei frammenti a pH 2.0. A pH 7.4, ?-LA non forma fibrille amiloidi sia in assenza sia in presenza di OA. Anche i tre frammenti non sono stati in grado di formare fibrille a pH neutro, mentre in presenza di OA hanno mostrato un cambiamento conformazionale verso una struttura ?-sheet, hanno legato ThT e formato aggregati con la tipica morfologia amiloide. Durante il Dottorato, ho inoltre collaborato ad un progetto in corso nel laboratorio al CRIBI, relativo alla caratterizzazione di specie oligomeriche nel processo di aggregazione del lisozima umano, che appartiene alla cosiddetta “superfamiglia lisozima/lattalbumina”. Oligomeri solubili di lisozima sono stati prodotti a pH acido e alta temperatura, e quindi analizzati con varie tecniche, quali legame a molecole fluorescenti, spettroscopia infrarosso in trasformata di Fourier (FTIR) e proteolisi limitata. Gli oligomeri presentano superfici idrofobiche esposte al solvente, e gli spettri FTIR sono indicativi di specie altamente destrutturate. Inoltre, gli aggregati oligomerici di lisozima si sono rivelati più suscettibili alla proteolisi rispetto sia alla proteina monomerica sia alle fibrille mature, indicando la mancanza di una struttura organizzata. Questo studio ha dimostrato che gli oligomeri solubili di lisozima sono specie strutturalmente flessibili presenti a bassa concentrazione durante le fasi iniziali dell’aggregazione. I risultati di questo studio sono stati accettati per la pubblicazione in una rivista internazionale e il manoscritto in press è allegato alla Tesi. Durante il terzo anno di Dottorato, ho trascorso un periodo di sei mesi all’Università di Cambridge (UK), presso il Cambridge Centre for Proteomics, sotto la supervisione della Dr.ssa Kathryn Lilley. L’obiettivo di questo periodo è stato di apprendere metodologie di proteomica per l’identificazione di proteine su larga scala, ottimizzando le mie conoscenze di spettrometria di massa. Ho collaborato ad un progetto in corso nel laboratorio, incentrato su un metodo di purificazione di affinità in parallelo accoppiata a spettrometria di massa per identificare complessi proteici in embrioni di Drosophila melanogaster (Veraksa et al., 2005). Proteine con tre tags sono state generate (Spradling et al., 1999) e isolate da vari tessuti embrionali. La purificazione di affinità usando due tags in parallelo ha permesso di isolare complessi proteici nativi intatti. L’alta sensibilità e l’alta accuratezza di massa dello strumento ibrido LTQ-Orbitrap ha assicurato la massima copertura di componenti di complessi poco abbondanti, generando dati ad alta confidenza con basse false discovery rates. È stato utilizzato il software ProteinCenter™ (Proxeon) per la visualizzazione e l’analisi statistica dei set di dati. I risultati sono stati confrontati con dati presenti in database pubblici, confermandone la validità e aumentando l’autenticità delle interazioni individuate. Sono state inoltre mappate nuove interazioni proteiche non riportate in precedenza. Questi set di dati in vivo aggiungono alta confidenza al proteoma e ‘interattoma’ di D. melanogaster attualmente incompleto. In questa Tesi sono riportati in dettaglio i risultati di cinque proteine di diverse dimensioni e localizzazione cellulare, per presentare la procedura e l’efficienza della metodologia. In sintesi, questa Tesi di Dottorato è composta da una parte principale che riguarda la caratterizzazione dell’interazione tra ?-LA e acido oleico e gli effetti sull’aggregazione proteica, e una parte minore relativa all’analisi di spettrometria di massa di complessi proteici in Drosophila, oltre alla pubblicazione sulle specie oligomeriche studiate nel processo di aggregazione del lisozima.
Shafiq, Mohsin [Verfasser], Saima [Akademischer Betreuer] Zafar, Thomas [Gutachter] Meyer, and Michael [Gutachter] Hoppert. "Characterization of high-density prion protein oligomers in rapid progressive and sporadic Alzheimer’s disease / Mohsin Shafiq ; Gutachter: Thomas Meyer, Michael Hoppert ; Betreuer: Saima Zafar." Göttingen : Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2019. http://d-nb.info/1203372191/34.
Full textSarroukh, Rabia. "Etude de la structure et de la toxicité des oligomères du peptide amyloïde-beta: implication dans la maladie d'Alzheimer." Doctoral thesis, Universite Libre de Bruxelles, 2011. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209874.
Full textNotre étude structurale minutieuse du processus d’agrégation du peptide Aβ démontre la formation d’agrégats dont le degré d’assemblage augmente au cours du temps. Nous avons montré que les agrégats identifiés comme étant des oligomères adoptent une structure en feuillets β antiparallèles. Tandis que l’interconversion de la structure β d’antiparallèle à parallèle conduit à la formation de fibrilles. Sur base de l’interprétation des spectres infrarouges analysés par corrélation à 2 dimensions, nous suggérons que ce changement de conformation est rendu possible grâce aux modifications des liens hydrogènes. En effet, les liens hydrogènes intramoléculaires qui stabilisent la structure antiparallèle des brins β disparaissent en faveur de liens intermoléculaires conduisant à la formation de feuillets β parallèles. De plus, ce changement de conformation requière la rotation des brins β le long de leur axe respectif.
Notre travail a pu mettre en avant le rôle central des oligomères dans la pathologie d’une part par leur rôle d’intermédiaires transitoires nécessaires et obligatoires à la formation des fibrilles mais également par la relation étroite qui existe entre leur structure en feuillets β antiparallèles et leur toxicité cellulaire. La modulation et/ou suppression de cette conformation est requise spécifiquement pour réguler leur toxicité et empêcher le processus de mauvais reploiement du peptide conduisant au développement de la maladie.
Enfin, nous avons également apporté de nouvelles informations concernant l’implication des membranes biologiques dans le mécanisme de toxicité des oligomères. Nos résultats démontrent que l’interaction du peptide avec un modèle de la membrane biologique ne conduit pas à la déstabilisation de cette dernière. L’hypothèse suggérant la formation de pores et/ou de canaux ioniques comme mécanisme de cytotoxicité est de facto réfutée par notre travail. Néanmoins, nous suggérons que l’interaction du peptide avec les lipides modifie le processus d’agrégation décrit dans la première partie de notre travail. Elle accélère l’étape de nucléation permettant la formation rapide d’oligomères à la surface de la membrane et accentuant ainsi leur probabilité d’interaction avec les protéines membranaires neuronales telles que les récepteurs de neurotransmetteurs./
Aggregation of amyloid-β peptides (Aβ1-40 and Aβ1-42) leads to formation of heterogeneous
toxic species, oligomers and fibrils, implicated in Alzheimer’s disease. As oligomers were
identified as the most cytotoxic entities, our research did focus on their implications in
pathology and the Aβ aggregation process which are currently not fully understood.
Using ATR-FTIR spectroscopy, we demonstrated that Aβ oligomers adopt an antiparallel β-
sheet structure. β-sheet interconversion from antiparallel to parallel seems to be an important
step in the Aβ oligomers-to-fibrils transformation. Furthermore, 2-D correlation analysis of
infrared spectra recorded during aggregation showed that Aβ isoforms undergo different β-
sheet reorganizations explaining their distinct aggregation kinetics. Aβ1-40 misfolding seems
to be related to a greater extent of secondary structure changes (increase of β-sheet structure
while α-helices and random coil structures content decrease). On the contrary, the same
analysis for Aβ1-42 suggests that a possible β-strand ‘rotation’ triggering inter-H bonding
formation and stabilizing fibrils may probably explain the antiparallel to parallel β-sheet
conversion.
We also provided evidence that cytotoxicity is strongly related to the oligomeric antiparallel
β-sheet structure of Aβ. The concomitant absence of antiparallel β-sheet structure due to
incubation with whey protein-derived peptide hydrolysate strongly suggests that cytotoxicity
and β-sheets organization are related.
Formation of β-barrel spanning the lipid membrane has been proposed to explain this Aβ
structure-toxicity relationship. In the last part of our work, we demonstrated that the
interaction of Aβ1-42 with anionic lipid membranes creates and/or stabilizes specific-size
oligomers. These oligomers, especially the dodecamer, are known to be the most toxic.
Nevertheless, we could not show that these specific oligomers are implicated in membrane
destabilization. Further works are needed to separate and study the individual properties of
each oligomer.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Pemberton, Samantha. "Molecular chaperones in the assembly of α-Synuclein and Parkinson’s Disease." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA114840/document.
Full textThe formation and deposition of α-Synuclein fibrils in the human brain is at the origin of Parkinson’s disease. The objective of my thesis was to document the role of two molecular chaperones on the assembly of α-Syn into fibrils: Hsc70, a constitutively expressed human heat shock protein, and Ssa1p, its yeast equivalent. The aim was to expand the catalogue of known effects of molecular chaperones on the PD implicated protein, which could have therapeutic significance. We showed that Hsc70 inhibits the assembly of α-Syn into fibrils, by binding with high affinity to the soluble form of α-Syn. We documented that Hsc70 binds preferentially to α-Syn fibrils and that this binding has a cytoprotective effect, as it renders the fibrils less toxic to cultured mammalian cells. Similarly to Hsc70, Ssa1p inhibits the assembly of α-Syn into fibrils, and has a higher affinity for fibrils than for the soluble form of α-Syn. On the other hand, binding of Ssa1p to α-Syn fibrils does not have a cytoprotective effect, almost certainly due to differences in the amino acid sequences of the peptide binding sites of the two molecular chaperones, which mean that Ssa1p has a lower affinity than Hsc70 for α-Syn fibrils. We stabilized the complex between Ssa1p and α-Syn using chemical cross-linkers, to then map the interaction site between the two proteins. This is indispensable if a “mini” Ssa1p, comprised of only what is necessary and sufficient of Ssa1p, is to be used as a therapeutic agent to decrease the toxicity of α-Syn fibrils. A therapeutic agent based on exogenous protein Ssa1p is less likely to trigger an autoimmune response than for example the endogenous protein Hsc70
Boehringer, Régis. "Synthèse chimique de protéines pour l'étude structurale et fonctionnelle de fibres amyloïdes." Thesis, Strasbourg, 2018. http://www.theses.fr/2018STRAF001/document.
Full textAmyloid fibrils are associated with many human disorders including Alzheimer’s or Parkinson’s diseases. The formation of insoluble plaques is the result of protein misfolding and aggregation due to abnormal conformational isomerization of the involved protein. The structural and biological studies of amyloids are highly complex. In this thesis, we report on the development of different synthetic methodologies for the preparation of distinct amyloid fibril polymorphs as homogeneous samples for structural and biological studies. We also synthesized covalently-tethered oligomers composed of nine copies of an amyloidogenic peptide segment, where we were able to control the self-assembly of the structure by insertion of N-methylated amino-acids and to obtain monomeric oligomers mimicking a cross section of an amyloid fibril. We also report on the chiral recognition of L-peptides and L-proteins towards corresponding D-enantiomers during amyloid formation. Moreover, we studied various N-methylated peptide analogues to suppress amyloid growth. Overall, the results obtained in this thesis pave the way towards rational design of peptide-based inhibitors and diagnostics against amyloid propagation
Vecchi, Giulia. "Proteomics studies of protein homeostasis and aggregation in ageing and neurodegeneration." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/273348.
Full textSahlin, Charlotte. "Pathogenic Mechanisms of the Arctic Alzheimer Mutation." Doctoral thesis, Uppsala University, Department of Public Health and Caring Sciences, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7582.
Full textAlzheimer’s disease (AD) is a progressive neurodegenerative disorder, neuropathologically characterized by neurofibrillay tangles and deposition of amyloid-β (Aβ) peptides. Several mutations in the gene for amyloid precursor protein (APP) cause familial AD and affect APP processing leading to increased levels of Aβ42. However, the Arctic Alzheimer mutation (APP E693G) reduces Aβ levels. Instead, the increased tendency of Arctic Aβ peptides to form Aβ protofibrils is thought to contribute to the pathogenesis.
In this thesis, the pathogenic mechanisms of the Arctic mutation were further investigated, specifically addressing if and how the mutation affects APP processing. Evidence of a shift towards β-secretase cleavage of Arctic APP was demonstrated. Arctic APP did not appear to be an inferior substrate for α-secretase, but the availability of Arctic APP for α-secretase cleavage was reduced, with diminished levels of cell surface APP in Arctic cells. Interestingly, administration of the fatty acid docosahexaenoic acid (DHA) stimulated α-secretase cleavage and partly reversed the effects of the Arctic mutation on APP processing.
In contrast to previous findings, the Arctic mutation generated enhanced total Aβ levels suggesting increased Aβ production. Importantly, this thesis illustrates and explains why measures of both Arctic and wild type Aβ levels are highly dependent upon the Aβ assay used, with enzyme-linked immunosorbent assay (ELISA) and Western blot generating different results. It was shown that these differences were due to inefficient detection of Aβ oligomers by ELISA leading to an underestimation of total Aβ levels.
In conclusion, the Arctic APP mutation leads to AD by multiple mechanisms. It facilitates protofibril formation, but it also alters trafficking and processing of APP which leads to increased steady state levels of total Aβ, in particular at intracellular locations. Importantly, these studies highlight mechanisms, other than enhanced production of Aβ peptide monomers, which could be implicated in sporadic AD.
Ouadah, Nesrine. "Caractérisation de chlorhydrates d’aluminium et étude de leurs interactions avec des protéines par électrophorèse capillaire." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTS007.
Full textAluminum chlorohydrates (ACH) are used by the cosmetics industry as antiperspirant active ingredients to limit sweating. Their mechanism of action, is still poorly understood. The development of new characterization tools to improve the understanding of their antiperspirant action at the molecular level is therefore crucial, to ultimately optimize their use, or even to replace them with other active compounds. The purposed of this work, was to characterize by a new analytical approach the oligomers contained in ACH and to study their interactions with model proteins. In a first part, a method was developed by capillary electrophoresis zone (CZE) for the separation, characterization and quantitative analysis of ACH oligomers (in particular Al13 and Al30). The choice of counter-ion, ionic strength and capillary coating was crucial for the success of the separation, the stability of the species during the electrophoretic process and the repeatability / reproducibility of the separation. The optimization of the separation conditions has made it possible to the separation of other oligomeric and colloidal species of aluminum, and to set up an on-line coupling of CZE to Taylor dispersion. analysis (TDA). Capillary isotachophoresis (ITP) was also explored for ACH analysis at high concentrations, close to those used in antiperspirant formulations. It was shown that it is possible to analyze samples up to 40 g / L in ACH. Finally, interactions of ACH with model proteins (BSA and lysozyme) were studied by capillary affinity electrophoresis (ACE) to shed more light on the phenomena of complexation leading to the obstruction of the sweat duct. The electrolyte used in ACE consists solely of ligands (ACH), at relatively high concentrations (up to 50 g / L), in order to mimic the conditions of application. From an analytical point of view, the challenge of this work was to correct the electrophoretic mobilities of the proteins from the experimental parameters varying with the concentration ACH (Joule heating, viscosity, state of charge of the protein as a function of the pH, ionic strength). It was possible to quantitatively demonstrate differences in the interactions between ACH and the two studied model proteins (BSA and lysozyme)
Tao, Peng. "Computational studies to understand molecular regulation of the TRPC6 calcium channel, the mechanism of purine biosynthesis, and the folding of azobenzene oligomers." Columbus, Ohio : Ohio State University, 2007. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1166718985.
Full textDesbene, Cédric. "Implication de la phospholipase A2 cytoplamique dans la pathogénèse de la maladie d'Alzheimer." Thesis, Université de Lorraine, 2012. http://www.theses.fr/2012LORR0235/document.
Full textSoluble beta-amyloid (A-beta) oligomers putatively play a critical role in the early synapse loss and cognitive impairment observed in Alzheimer's disease. We previously demonstrated that A-beta oligomers activate cytosolic phospholipase A2 (cPLA2) which specifically releases arachidonic acid from membrane phospholipids. By using a single A-beta oligomers intra cerebro ventricular injection, we observed that cPLA2 gene suppression prevents both the alterations of cognitive abilities and the reduction of hippocampal synaptic markers levels which are observed in wild type mice. We further demonstrated that the A-beta oligomers-induced sphingomyelinase activation is suppressed and that the phosphorylation of Akt/PKB is preserved in neuronal cells isolated from KO mice. Interestingly, expression of the A-beta precursor protein (APP) is reduced in hippocampus homogenates and neuronal cells from KO mice, but the relationship with the resistance of these mice to the A-beta oligomers toxicity requires further investigation. These results therefore show that cPLA2 plays a key role in the A-beta oligomers-associated neurodegenerative effects, and as such represents a potential therapeutic target for the treatment of Alzheimer's disease
Serra, Vidal Bernat. "Study of the aggregation process of the amyloid beta-protein associated to Alzheimer's disease. Examination of pharmaceutically important small molecules." Doctoral thesis, Universitat de Barcelona, 2014. http://hdl.handle.net/10803/283133.
Full textL’agregació de la proteïna beta-amiloide (βA) està associada amb la malaltia d’Alzheimer (MA). Tanmateix, l’heterogeneïtat del procés d’agregació fa molt difícil la caracterització de les diferents espècies conformant el procés, dificultant, per tant, la identificació de trets comuns explicant la neurotoxicitat d’aquests agregats. Els experiments de bescanvi protó/protó deuteri amb marcatge de pols analitzats per espectrometria de masses (PL-HDX-ESI-MS, de l’anglès Pulse-labelling hydrogen deuterium exchange electrospray mass spectrometry) possibiliten la detecció, caracterització i quantificació de les espècies formades durant l’agregació. Vam aplicar aquesta metodologia a l’estudi de l’agregació de tres variants de βA: la βA40, la variant que es produeix més abundantment, βA42, la variant més associada amb la neurotoxicitat de la MA, i el mutant E22Δ-βA42, que primer es va descriure que només formava oligòmers però posteriorment es va constatar que també formava fibril•les. La detecció de diferents espècies implica que hi ha agregats diversos poblant l’agregació de βA i que es dónen reordenaments estructurals. També vam dur a terme experiments paral•lels de toxicitat en cultius primaris neuronals i així vam trobar que les espècies intermèdies protofibril•lars correlacionaven en gran mesura amb la neurotoxcitat observada. Havent determinat el nombre i les característiques dels agregats en l’agregació de βA, vam decidir d’estudiar l’efecte d’una biblioteca de 20 compostos en l’agregació de la proteïna βA42. Vam fer una primer criba utilitzant l’assaig de retenció en filtre (ARF) i vam seleccionar 5 molècules per a un estudi més detallat utilitzant el PL-HDX-ESI-MS. Utilitzant aquesta metodologia, doncs, vam poder determinar que la diamida del dial•liltartrat i l’entacapona acceleraven la cinètica de formació de fibril•les i la 2,2’-dihidroxibenzofenona inhibia l’agregació de βA42 estabilitzant un oligòmer. El pèptid inrD inhibia la fibril•lació de βA42 en l’escala de temps usada en els nostres experiments, mentre que el gal•lat d’epigal•locatequina modificava covalentment els agregats de βA42. Com a conclusió, hem demostrat que els experiments de PL-HDX-ESI-MS permeten la detecció, caracterització i quantificació de les espècies poblant l’agregació de βA a més de donar informació valuosa en el mecanisme d’acció de compostos interaccionant amb l’agregació de βA.
Placek, Brandon Jeremy. "Stability and folding of the H2A/H2B dimer effect of N-terminal tail removal and incorporation of the histone variant H2A.Z /." Online access for everyone, 2004. http://www.dissertations.wsu.edu/Dissertations/Summer2004/b%5Fplacek%5F072804.pdf.
Full textPemberton, Samantha. "Molecular chaperones in the assembly of α-Synuclein and Parkinson's Disease." Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00762970.
Full textDickinson, Sally Clare. "Cartilage oligomeric matrix protein and cartilage degradation." Thesis, University of Sheffield, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323419.
Full textItkin, Anna. "Etude pluridisciplinaire de peptides liés à la maladie d'Alzheimer: de la protéine précurseur de l'amyloïde (APP) aux oligomères de beta-amyloïde et aux inhibiteurs de gamma-sécrétase." Doctoral thesis, Universite Libre de Bruxelles, 2012. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/209705.
Full textLes propriétés conformationnelles du segment transmembranaire (TM) de l’APP peuvent affecter sa protéolyse par la γ-sécrétase. Ces propriétés ne sont pas encore clairement établies. Afin de comprendre le rôle des variations structurelles du TM dans le traitement de l'APP, des détails structurels des peptides APP_TM4K, chimiquement synthétisés, ont été étudiés dans la bicouche lipidique en utilisant la réflexion totale atténuée par spectroscopie infrarouge à transformée de Fourier (ATR-FTIR) et la résonance magnétique nucléaire à l’état solide (ssNMR). Tandis que la structure secondaire globale du peptide APP_TM4K est hélicoidale, une hétérogénéité conformationnelle et orientée a été observée pour le site de clivage γ et, dans une plus faible mesure, pour le site de clivage ζ. Ces variabilités conformationnelles autour des sites de clivage γ et ζ peuvent avoir des implications importantes dans le mécanisme de clivage et donc dans la production d’Aβ. Il a été aussi démontré que la dernière glycine dans le motif de dimérisation GxxxG est transmembranaire. Ceci peut impliquer que la dimérisation via ce motif pourrait servir d’ancrage et conférer une orientation transmembranaire stable au segment transmembranaire de l’APP.
Le peptide amyloïde β est directement lié à la maladie d’Alzheimer. Partant de sa forme monomérique, l’Aβ s'agrège pour produire en final des fibrilles et aussi de manière transitoire toute une gamme d'oligomères, ces derniers étant la plupart neurotoxiques. Une dérégulation de l’homéostasie du Ca2+ dans le cerveau vieillissant et dans des troubles neurodégénératifs joue un rôle crucial dans de nombreux processus et contribue au dysfonctionnement et à la mort cellulaire. Nous avons postulé que le calcium peut permettre ou accélérer l'accumulation d'Aβ. Le modèle d'accumulation d'Aβ (1-40) et celui d'Aβ (1-40) E22G, un peptide amyloïde portant la mutation arctique qui cause une apparition prématurée de la maladie, ont été comparé. Nous avons constaté qu'en présence de Ca2+, l’Aβ (1-40) forme de préférence des oligomères semblables à ceux formés par l’Aβ (1-40) E22G avec ou sans Ca2+, tandis qu'en absence de Ca2+ l'Aβ (1-40) s’agrège sous forme de fibrilles. Les ressemblances morphologiques entre oligomères ont été confirmées par microscopie de force atomique. La distribution des oligomères et des fibrilles dans des échantillons différents a été détectée par électrophorèse sur gel suivie d’une analyse par Western blot, dont les résultats ont été confirmés par des expériences de fluorescence à la thioflavine T. Dans les échantillons sans Ca2+, l’ATR-FTIR révèle la conversion des oligomères en feuillets β antiparallèles en la conformation caractéristique des fibrilles en feuillets β parallèles. En général, ces résultats nous ont ameré à conclure que les ions calcium stimulent la formation d'oligomères d'Aβ (1-40), qui sont impliqués dans la pathogénèse d'AD.
Malgré les progrès énormes obtenus dans la compréhension de la maladie (AD), il reste un défi majeur, celui du développement de médicaments nouveaux et efficaces. Afin d’obtenir des éclaircissements sur le mécanisme d'action de deux nouveaux puissants modulateurs de la γ-sécrétase - le benzyl-carprofen et le sulfonyl-carprofen dans la bicouche lipidique, la technique de RMN à l’état solide a été employée. Précédemment, les dérivés du carprofen ont été localisés dans des membranes de lipides par des expériences de diffusion (scattering) des neutrons. Les contraintes déterminées à partir des expériences de ssNMR ont permis d’affiner leurs positions et d’obtenir une orientation précise dans la double couche lipidique. Ces résultats combinés indiquent que le mécanisme probable de modulation du clivage par la γ-sécrétase est une interaction directe des carprofènes avec le domaine TM de l’APP. Une telle interaction, empêcherait à la formation de dimères d'APP, dimérisation nécessaire au clivage séquentiel par la γ-sécrétase, diminuant ou réduisant ainsi énormément la production d’Aβ, tout particulièrement d’Aβ42.
Les résultats de ce travail apporte de nouvelles informations sur les processus clés impliqués dans l'AD; Production de l'Aβ à partir de l'APP, formation des oligomères d'Aβ et mécanisme d'action potentiel de molécules thérapeutiques. Nous pensons que ces résultats pourront permettre une meilleure compréhension de la maladie et pourront aider dans la conception de nouveaux médicaments contre cette maladie.
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and the most common form of dementia. There is no cure and the disease is fatal. One of the characteristic histopathological markers of AD is the presence of proteinaceous deposits, amyloid plaques, in the brain. These plaques are formed by the amyloid β-peptides (Aβ) 40- and 42-residue-long, which are protease cleavage products of the amyloid precursor protein (APP). Elucidation of some of the key processes in the cause and the development of AD is crucial for the development of new and efficient treatments.
Conformational properties of the transmembrane (TM) segment of APP may affect its proteolytic processing by γ-secretase. These properties have not been definitely established. In addressing the role of structural variations of the TM sequence in APP processing, structural details of the chemically synthesized APP_TM4K peptides within the membrane bilayers were studied using Attenuated total reflection Fourier transform spectroscopy (ATR-FTIR) and solid-state nuclear magnetic resonance (ssNMR) techniques. While the overall secondary structure of the APP_TM4K peptide is an α-helix, conformational and orientational heterogeneity was observed for the γ-cleavage site and, to a smaller extent, for the ζ-cleavage site. Evidence for the conformational variability around γ- and ζ-cleavage sites may have important implications for the cleavage mechanism and hence for the Aβ production. It was also found that the last glycine within the sequence of GxxxG motifs is in the transmembrane orientation, implying that dimerization via these motifs may act as an anchor, confining the TM dimer to the stable transmembrane orientation.
Amyloid β-peptide is directly linked to AD. Starting from its monomeric form, Aβ aggregates into fibrils and / or oligomers, the latter being the most neurotoxic. Dysregulation of Ca2+ homeostasis in aging brains and in neurodegenerative disorders plays a crucial role in numerous processes and contributes to cell dysfunction and death. Here we postulated that calcium may enable or accelerate the aggregation of Aβ. The aggregation pattern of Aβ(1-40) and of Aβ(1-40)E22G, an amyloid peptide carrying the Arctic mutation that causes early onset of the disease, were compared. We found that in the presence of Ca2+, Aβ(1-40) preferentially formed oligomers similar to those formed by Aβ(1-40)E22G with or without added Ca2+, whereas in the absence of added Ca2+ the Aβ(1-40) aggregated to form fibrils. Morphological similarities of the oligomers were confirmed by contact mode atomic force microscopy (AFM) imaging. The distribution of oligomeric and fibrillar species in different samples was detected by gel electrophoresis and Western blot analysis, the results which were further supported by thioflavin T fluorescence experiments. In the samples without Ca2+, Fourier transform infrared spectroscopy revealed conversion of oligomers from an anti-parallel β-sheet to the parallel β-sheet conformation characteristic of fibrils. Overall, these results led us to conclude that calcium ions stimulate the formation of oligomers of Aβ(1-40), that have been implicated in the pathogenesis of AD.
Despite the tremendous progress in understanding AD, there remains the challenge of the development of new and efficient drugs. In order to shed light onto the mechanism of action of two new potent γ-secretase modulators -- benzyl-carprofen and sulfonyl-carprofen within lipid bilayers, ssNMR technique was employed. Using neutron scattering experiments it was previously found that sulfonyl-carprofen and benzyl-carprofen partition into the headgroup region of the lipid bilayer. The orientational constraints derived from the ssNMR experiments refined their position into precise orientation. Combined, these results indicate that carprofen-derivatives can directly interact with the region of APP that mediates dimerization. Such interaction, would interfere with proper APP-dimer formation, which is necessary for the sequential cleavage by γ-secretase, diminishing or greatly reducing Aβ42 production.
Results obtained during this work shed new light onto some of the key processes in AD: Aβ production from APP, formation of Aβ oligomers and insights into the mechanism of action of potential therapeutics. We believe that these results will promote a better understanding of the disease and will help in future drug design.
Doctorat en Sciences
info:eu-repo/semantics/nonPublished
Thevenin, Damien. "Roles of transmembrane domains in the folding and assembly of the adenosine A2A receptor." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 170 p, 2007. http://proquest.umi.com/pqdweb?did=1260822171&sid=2&Fmt=2&clientId=8331&RQT=309&VName=PQD.
Full textMoraes, Fábio Rogério de 1984. "Revelando as características do nano-ambiente das interfaces entre proteinas." [s.n.], 2012. http://repositorio.unicamp.br/jspui/handle/REPOSIP/316805.
Full textTese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia
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Resumo: Dentro do ambiente celular, há uma variedade de moléculas e a interação entre si regulam praticamente todos os processos necessários e essenciais para a manutenção da vida. Interações entre proteínas estão envolvidas no controle de vários processos intra e intercelulares, como regulação metabólica e da expressão gênica, reconhecimento antígeno-anticorpo etc. que definem as características biológicas do funcionamento da vida entre os diversos organismos. Ao conhecer a interface de interação de uma proteína chave para desenvolvimento de casos patológicos, é possível desenhar drogas com alta especificidade com o sítio de ligação. Para avançar nessa frente, o conhecimento da estrutura proteica é fundamental, porém não suficiente. É necessário conhecermos o sítio de ligação alvo para cada parceiro de interação. Este estudo visa entender as características do nano-ambiente das interfaces proteicas - área através da qual as macromoléculas se comunicam e exercem sua funcionalidade. Propomos utilizar uma abordagem de estudo das características físico-químicas e estruturais dos resíduos formadores de interfaces de complexos conhecidos e com estrutura quaternária resolvida experimentalmente, utilizando um conjunto de dados sem redundância sequencial, extraindo os parâmetros/descritores que descrevem de forma objetiva as diferentes classes de complexos, revelando as características principais sobre interações proteína-proteína. A finalidade deste trabalho é de conhecer os detalhes que definem uma área como interface e aplicá-lo em uma ferramenta preditiva para todas as proteínas com arranjo estrutural conhecido e/ou modelado. Propomos de forma pioneira, o uso de classificadores específicos para cada tipo de aminoácido e independente do uso de descritores sobre conservação de aminoácidos. Resultados obtidos com classificador linear e por ensemble de redes neurais destacam a nossa abordagem, desenhada e aplicada nesta tese, como uma com os melhores indicadores de desempenho na predição precisa dos resíduos de aminoácido na interface entre as abordagens descritas recentemente na literatura. Ainda, enquanto os outros métodos dependem de descritores sobre conservação de aminoácidos, é mostrado aqui que nenhum ganho de desempenho é obtido com a incorporação de tais descritores em nosso modelo classificador. Esse resultado indica que o uso de descritores puramente físico-químicos e estruturais é suficiente para explicar o grau de conservação dos aminoácidos
Abstract: Inside cells, there is a variety of molecules and their interactions regulate virtually all necessary and essential processes to the maintenance of life. Interactions among proteins are involved in the control of several processes within and out of the cell, such as, metabolic and gene expression regulation, anti-body and antigen recognition, etc. that defines biological characteristics of life among many organisms. If the protein interface amino acids of a key protein related to a given pathologic phenomenon are known, it is possible to rationally design drugs with high specificity for a specific binding site. To gain insight in this field, the knowledge of the protein three-dimensional structure is mandatory, but not sufficient. It is also necessary to know the interface between the target protein and its partners. This study focuses in understanding the characteristics of the area through which the macromolecules communicate to each other and exercise their function. Here, it is proposed an approach to study the physicochemical and structural characteristics of the interface forming residues with known quaternary structure (experimentally solved). It was selected a sequence non-redundant dataset and by extracting parameters/descriptors, that objectively describe different complex classes, it was possible to unravel the basic characteristics of protein-protein binding. The goal of this study is to unravel the details that outline a specific area as interface and apply it in a form of a predictive tool for all proteins with known atomic structure. It is proposed by the first time, the use of amino acid specific classifiers regarding amino acid type and free of amino acid conservation attributes. The results obtained here by employing linear and ensemble of neural network classifiers show that, based on purely physicochemical and structural descriptors, it is possible to get precise predictions about interface forming residues in protein-protein assemblies. Comparatively, the method described here retains better performance indicators than the ones recently described in the literature. In addition, we showed that, for our method, adding "conservation" attributes does not induce any performance gain, which is a major difference if compared to other described methods. This result indicates the purely physicochemical and structural descriptors are sufficient to explain how conserved amino acids are
Doutorado
Bioinformatica
Doutor em Genetica e Biologia Molecular
Ryazanov, Sergey. "Oligomer modulator anle138b and related compounds in neurodegeneration and beyond." Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2020. http://hdl.handle.net/21.11130/00-1735-0000-0005-1519-8.
Full textKelly, Sharon Mary. "Studies on the unfolding and refolding of oligomeric proteins." Thesis, University of Stirling, 1994. http://hdl.handle.net/1893/21548.
Full textDietzen, Matthias Michael [Verfasser], and Thomas [Akademischer Betreuer] Lengauer. "Modeling protein interactions in protein binding sites and oligomeric protein complexes / Matthias Michael Dietzen. Betreuer: Thomas Lengauer." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2014. http://d-nb.info/1063330718/34.
Full textDietzen, Matthias Michael Verfasser], and Thomas [Akademischer Betreuer] [Lengauer. "Modeling protein interactions in protein binding sites and oligomeric protein complexes / Matthias Michael Dietzen. Betreuer: Thomas Lengauer." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2014. http://nbn-resolving.de/urn:nbn:de:bsz:291-scidok-59402.
Full textLloyd, Janice A. "The Human Rad52 Protein: a Correlation of Protein Function with Oligomeric state: a Dissertation." eScholarship@UMMS, 2002. https://escholarship.umassmed.edu/gsbs_diss/248.
Full textKies, Ursula. "Faltung oligomerer Proteine im endoplasmatischen Retikulum und in vitro." [S.l.] : [s.n.], 2001. http://deposit.ddb.de/cgi-bin/dokserv?idn=963683357.
Full textMičetić, Ivan. "SAXS study of the quaternary structure of oligomeric proteins." Doctoral thesis, Università degli studi di Padova, 2005. http://hdl.handle.net/11577/3426519.
Full textLa diffusione a piccoli angoli di raggi X (SAXS) è una tecnica molto efficace nello studio della struttura quaternaria delle proteine in soluzione. Anche se l'acquisizione di tali misure è relativamente facile dal punto di vista sperimentale, la loro interpretazione non è immediata. In letteratura sono descritti diversi programmi con i quali si possono ottenere modelli strutturali direttamente dalle curve SAXS, anche a risoluzione relativamente elevata. Per contro nessun programma tiene conto di alcune caratteristiche note delle proteine oggetto di questo lavoro (emocianine), quali per esempio la presenza delle simmetrie Dn e la struttura delle subunità strutturali che le costituiscono. Questa tesi riguarda lo sviluppo di un metodo di determinazione della struttura quaternaria delle proteine oligomeriche a partire da curve SAXS di molecole intere e modelli semplificati di subunità strutturali. I modelli delle subunità strutturali sono costruiti partendo da informazioni derivanti da tecniche biochimiche, microscopia elettronica o strutture ad alta risoluzione. Questi modelli, composti da sfere a raggio diverso, sono stati usati per ricostruire la struttura delle molecole oligomeriche, fittando i dati su curve SAXS tramite programmi realizzati ad hoc. Tali programmi possono essere utilizzati per modellare qualsiasi proteina con caratteristiche di simmetria simili. Il metodo è stato verificato sulle emocianine di artropodi dove è riuscito a ricostruire in maniera soddisfacente la struttura quaternaria delle molecole intere. A questo punto, l'analisi è stata estesa anche sulle emocianine di molluschi, proteine con struttura molto più complessa. In questo caso, si è riusciti ad ottenere, in maniera soddisfacente, solamente le posizioni delle subunità strutturali che compongono la proteina intera, mentre non era possibile determinarne il corretto orientamento nello spazio. Questo risultato sarebbe da attribuire alla forma pressoché sferica dei monomeri strutturali usati nei fit. La generazione di monomeri ad una risoluzione più elevata è prevista dal metodo ma comporterebbe un tempo di calcolo maggiore.
Hoch, Johanna M. "SERUM CARTILAGE OLIGOMERIC MATRIX PROTEIN: A BIOMARKER FOR ACUTE ARTICULAR CARTILAGE DAMAGE." UKnowledge, 2012. http://uknowledge.uky.edu/rehabsci_etds/3.
Full textChamberlain, Dean. "Expression and structural studies of multidomain proteins and complexes." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.314366.
Full textSorensen, Christina M. "ESI-MS and MALDI-TOF-MS for the characterization and analysis of metallo-oligomers and proteins." Laramie, Wyo. : University of Wyoming, 2005. http://proquest.umi.com/pqdweb?did=1031044031&sid=4&Fmt=2&clientId=18949&RQT=309&VName=PQD.
Full textDunne, Emma Louise. "Regulatory domains of GABAâ†A receptors." Thesis, University College London (University of London), 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325661.
Full textAli, Mayssam H. (Mayssam Hani) 1976. "The design and structural characterization of oligomeric beta beta alpha mini-proteins." Thesis, Massachusetts Institute of Technology, 2004. http://hdl.handle.net/1721.1/17737.
Full textVita.
Includes bibliographical references.
Oligomeric mini-proteins, short peptides with protein-like features, constitute valuable minimal models for the study of oligomeric proteins. Oligomerization is a common feature of cellular proteins that may confer structural and functional advantages. Oligomerization is proposed to have arisen by several evolutionary pathways. The structural characterization of peptide 1, a stable oligomeric mini-protein previously developed in the Imperiali group, was undertaken by X-ray crystallography, as knowledge of the structure would enable the rational design of subsequent generations of BBA oligomers varying in packing and stoichiometry. The structure of peptide 1 could not be solved by direct methods, by molecular replacement with search models derived from the monomeric precursor, or by the introduction of heavy atoms. Two selenomethionine mutants having solution-phase properties comparable to the native were identified. The structures of these two peptides were independently solved via MAD phasing experiments, and the refined structures employed as search models for a molecular replacement solution of 1. The structures of the three peptides are homologous, and constitute the first reported structures of a mixed act/ oligomeric mini-protein. The X-ray crystal structures reveal that the oligomeric BBA motif has a domain-swapped architecture that supports a protein-like and water-exclusive core. The structures elucidate the unique role of unnatural amino acids in conferring native secondary structure in a short peptide sequence (21 residues per monomer).
(cont.) Furthermore, the crystal structures reveal that the stoichiometry of the oligomer is tetrameric, rather than trimeric, as originally proposed. A tetrameric solution-phase stoichiometry for this mini-protein family was confirmed by rigorous analytical ultracentrifugation experiments. Heterooligomeric BBA peptides have been designed and characterized in collaboration with Christina M. Taylor and Professor Amy E. Keating of the MIT Biology Department. Acidic and basic residues were substituted along the inter-monomer interface and specific steric interactions were designed in order to disfavor homoassociation and favor heteroassociation. Heterotetramers comparable to peptide 1 in terms of structure and stoichiometry, and approaching the native homotetramer in terms of stability, have been characterized by a variety of biophysical techniques.
by Mayssam H. Ali.
Ph.D.
Puig, Gomà-Camps Eduard. "Structural characterization of amyloid beta oligomers with functional links associated to Alzheimer's disease." Doctoral thesis, Universitat de Barcelona, 2019. http://hdl.handle.net/10803/667258.
Full textLa malaltia d'Alzheimer (AD) és la forma més comuna de demència. Va ser descrita per primera vegada el 1906 per Alois Alzheimer. Més endavant, al 1984, George Glenner i Colin Masters van aïllar el pèptid amiloide-beta (Aβ) d'un cervell humà i el van associar a la malaltia. Des de llavors, la hipòtesi amiloide ha estat un tema bastant controvertit discutit entre la comunitat científica. Una possible explicació és l’alta complexitat del sistema a causa de la varietat de formes d’agregació que Aβ pot adoptar. Per tant, entendre els vincles entre l'agregació de proteïnes i la neurotoxicitat, i especialment l'obtenció de les estructures 3D dels agregats responsables de la neurotoxicitat, és clau per dissenyar estratègies diagnòstiques i terapèutiques efectives. Malauradament, aquest tema continua sent un dels problemes pendents més importants. El grup de la Dra. Carulla ha estat treballant en la hipòtesi que l'Aβ interactua amb la membrana cel·lular que condueix a una deshomeostasi iònica. Per estudiar aquest escenari, el grup ha canviat el paradigma i ha tractat Aβ com a proteïna de membrana i aplicant tècniques biofísiques ben establertes per a caracteritzar proteïnes de membrana per tal d’estudiar Aβ. D'aquesta manera, el grup ha demostrat que Aβ és capaç de formar un tipus d'oligòmers en presència de micel·les de detergent que adopten una estructura molt específica i definida amb capacitat de formar porus a través de membranes lipídiques. Es refereixen a aquest tipus d’oligòmers com a oligòmers formadors de porus barril β (βPFO). A la present tesi doctoral, presentem l’estudi realitzat per identificar mitjançant diferents tècniques biofísiques, l'estructura 3D de βPFO. Hem utilitzat detergents per estudiar el procés d’oligomerització en un entorn mimètic de membrana. Les micel·les en comparació amb altres entorns biomimètics basats en lípids, permeten l'aplicació d’estratègies d'espectrometria de masses (MS) i de ressonància magnètica nuclear (RMN) ben establertes, proporcionant així informació estructural d'alta resolució. Atès que l’acumulació de diferents quantitats d’Aβ a la membrana és un escenari plausible en el context de la malaltia, hem utilitzat diferents relacions de micel·les Aβ a detergents ([Aβ]: [M]) per estudiar el paper d’aquesta variable en l’oligomerització. procés d'Aβ.
Halabelian, L. C. "DECIPHERING THE AGGREGATION MECHANISMS IN HUMAN B2-MICROGLOBULIN." Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/243399.
Full textJansen, Katja. "Dimere und Oligomere des Prion-Proteins als Modell für den Umwandlungsmechanismus von der zellulären Isoform des Prion-Proteins in die pathogene Form." [S.l. : s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=966041461.
Full textSolé, i. Codina Laura. "Role of KCN E4 on the voltage gated potassium channel Kv1.3 = Paper de KCNE4 en el canal de potassi dependent de voltage Kv1.3." Doctoral thesis, Universitat de Barcelona, 2013. http://hdl.handle.net/10803/129685.
Full textEls canals de potassi dependents de voltatge (Kv) juguen un paper molt important tant en cèl•lules excitables com no excitables. La possibilitat de formar hetero-oligomers i la d’associació amb subunitats reguladores són uns dels mecanismes que existeixen per tal de proveir de diferents mecanismes per a respondre de manera diferent enfront a canvis en el potencial de membrana. La composició del canalosoma modula tant la seva expressió a superfície com l’activitat d’aquests. Aquesta tesi es centra en l’estudi de l’efecte del la família de les subunitats reguladores KCNE sobre diferents Kv. Primerament s’estudià l’efecte que causaven en el tràfic del canal Kv7.1 (canal model per a l’estudi dels KCNEs) i posteriorment s’amplià l’estudi a un altre membre de la mateixa família, Kv7.5. A continuació s’estudià un canal d’elevada importància per a l’activació i proliferació leucocitària: Kv1.3, centrant-nos sobretot en l’efecte causat per un dels KCNEs: KCNE4. Aquesta subunitat no només inhibeix dràsticament el corrent del canal Kv1.3, sinó que a més a més, modifica el seu tràfic i localització. Aquests canvis són deguts a una interacció directa entre ambdues proteïnes. A continuació s’estudià en detall el complex Kv1.3-KCNE4. Mitjançant la combinació d’experiments d’electrofisiologia i monitorització de fluorescència de molècules individuals en la membrana, es va poder establir l’estequiometria d’aquest complex. Posteriorment, mitjançant l’anàlisi de diverses proteïnes quimèriques i mutants, tant del canal com de la subunitat reguladora, es van cercar els determinants moleculars implicats en l’associació entre ambdues proteïnes. S’han pogut determinar els motius claus en KCNE4 i Kv1.3 implicats en la formació del complex, però no en la modulació del canal. Finalment, degut a la importància de Kv1.3 en el sistema immunitari, s’han analitzat els nivells d’expressió dels KCNEs en diferents línies leucocitàries. S’ha observat que aquestes subunitats pateixen una regulació diferencial en funció de la manera d’activació i al llarg de la proliferació del leucòcits, suggerint un possible paper en la regulació precisa de la resposta immunològica.
Henriksson, Peltola Petri. "Molecular Studies of Three Coliphage Repressor Proteins P2 C, P2 Hy dis C and Wphi C : Kinetics, Oligomeric States and Structural Studies /." Stockholm : Department of genetics, microbiology and toxicology, Stockholm university, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-6879.
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