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Experimental data of analytical ultracentrifugation (AUC) experiments is defined by sedimentation and diffusion transport of molecules in solution. While the sedimentation properties define the position of the measured sedimentation boundaries, information on the diffusion is included in the broadening. Both effects are then analysed with well-established finite element solutions of Lamm’s equation The results from this multidimensional analysis provide e.g. molecular mass or size distributions or information on core-shell structures [1,2].

L’utilisation de nanoparticules (NPs) dans divers domaines industriels est de plus en plus fréquente ce qui génère leur propagation dans l’environnement. Selon leur persistance, mobilité, bioaccumulation et toxicité, des risques inconnus pour la santé et pour des écosystèmes peuvent en résulter. En effet, la caractérisation et la quantification sont des défis analytiques très complexes en raison de la nature dynamique (petite taille, grande réactivité et instabilité) des nanomatériaux. L'objectif de cette étude est donc de caractériser par ultracentrifugation analytique (AUC) des nanoparticules polymériques (Allosperse® dites allosphères) qui sont destinées à des fins agricoles. Pour y parvenir, différentes NPs métalliques (argent, quantum dot), oxydes métalliques (dioxyde de titane, oxyde de zinc) et NPs de polystyrène ont d’abord été mesurés par AUC à l’aide des différents systèmes de détection (absorbance, fluorescence et interférence). Dans le cas des allosphères, un grand nombre d'essais préliminaires ont été réalisés afin d'optimiser la vitesse d'ultracentrifugation, le temps d'ultracentrifugation, le nombre de numérisations et la concentration de l'échantillon. Un protocole optimisé a été utilisé pour la détermination du diamètre hydrodynamique (dh) des NPs. Les différentes analyses qui ont été réalisées dans cette étude révèlent que l’AUC permet de déterminer la taille de très petites NPs. Par ailleurs, une étude du comportement de ces allosphères pour des pH entre 4-8, des forces ioniques de 0 à 500 mM, en présence ou absence de matière organique naturelle a été entreprise. Les travaux ont montré que le dH était d’environ 7,0 nm avec de petites augmentations à faible pH, ou à très grande force ionique ou dureté. Ces résultats indiquent la grande stabilité physique et chimique des allosphères qui auront, ainsi, une grande mobilité dans les sols. La diffusion de lumière dynamique et la spectroscopie de corrélation de fluorescence ont été utilisées afin de valider les résultats obtenus par l’AUC. / The use of nanoparticles (NPs) in numerous industrial fields is becoming more common, which increases their propagation in the environment. Their generally unknown persistence, mobility, bioaccumulation and toxicity all contribute to increased risks to human health and to ecosystems. Unfortunately, their characterization and quantification are complex analytical challenges due in large part to their dynamic nature (small size, high reactivity and instability). The objective of this study was to characterize polymeric nanoparticles (Allosperse®), which are intended for the dispersion of the nanopesticides using analytical ultracentrifugation (AUC). To achieve this goal, the sizes of various metallic nanoparticles (nAg, QD), metallic oxides (nTiO2, nZnO) and polystyrene nanoparticles (nPS) were first determined by AUC using different detectors (absorbance, fluorescence and interference). In the case of polymeric nanoparticles, a number of preliminary tests were carried out in order to optimize the speed and duration of the ultracentrifugation, the number of scans and the concentration of the NPs for the determination of their hydrodynamic diameter (dh). The analysis indicated that the AUC was able to measure the sizes of the smallest nanoparticles. In addition, evaluations of the behavior of these nanoparticles between pH 4-8, ionic strengths from 0 to 500 mM, in the presence and absence of natural organic matter (NOM) showed that they had a dh of about 7.0 nm with small increases at low pH or for large ionic strengths or hardness. These results strongly demonstrated a high physical and chemical stability of allosphères, which implied that they would have a high mobility in soils. Dynamic light scattering (DLS) and fluorescence correlation spectroscopy (FCS) were used to validate the results obtained by the AUC.

A hemoglobina extracelular gigante do anelídeo Glossoscolex paulistus (HbGp) é homológa à hemoglobina da Lumbricus terrestris (HbLt). Baseado nos estudos de MALDI-TOF-MS foi determinada a massa molecular (MM) das subunidades da HbGp. Entretanto, ainda não era possível propor o valor exato da MM para a HbGp íntegra, pois a estequiometria deste oligômero ainda não era totalmente clara. Este trabalho objetiva avaliar a massa molecular do oligômero em dois estados de oxidação: oxi- e cianometa-HbGp, bem como avaliar a estabilidade desta proteína, ou seja, a dissociação e desnaturação em função do pH em meio ácido. O estudo por ultracentrifugação analítica permitiu uma avaliação independente da massa molecular da HbGp. Valores de MM de 3600 ± 100 e 3700 ± 100 kDa foram obtidos para a oxi- e cianometa-HbGp, respectivamente. Estes valores está de acordo com a massa esperada, assumindo a estequiometria proposta por Vinogradov para a HbLt. Os dados de ultracentrifugação para as amostras do monômero d puro mostraram um coeficiente de sedimentação de 1,95 ± 0,04 S para ambos os valores de pH 7,0 e 10,0. Além disso, as distribuições c (s) do monômero d puro indicaram que uma pequena contribuição (5%) de dímero de monômeros, d2, com valores de s020,w de 3,2 S estava presente em solução. Para a oxi-HbGp íntegra no pH 10,0 nenhuma contribuição em 58 - 59 S foi observada, sugerindo completa dissociação oligomérica. As distribuições c (s) mostraram dois picos adicionais em relação ao monômero puro: um pico em 4,2 - 4,4 S, que está associado ao trímero, abc; e um segundo pico em 5,8 - 6,0 S, que poderia ser associado ao tetrâmero, abcd. A adição de β-mercaptoetanol leva ao desaparecimento do pico em 4,2 S, consistente com a redução das pontes dissulfeto do trímero abc e produção dos monômeros a, b e c. Cerca de 19 % da forma cianometa-HbGp íntegra coexiste em equilíbrio com as subunidades dissociadas. Finalmente, estudos em meio ácido mostravam que na faixa de pH 5,0 - 7,0 as três formas de oxidação de HbGp apresentaram alta estabilidade oligomérica. Abaixo de pH 5,0 os dados de fluorescência mostrava que a estabilidade diminui na sequência cianometa > oxi > meta. Assim a estabilidade das formas oxi-, meta- e cianometa-HbGp foi avaliada, ficando evidenciada a maior estabilidade da forma cianometa-HbGp. / The giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) is homologous to Lumbricus terrestris (HbLt). Based on MALDI-TOF-MS the molecular masses (MM) of HbGp subunits were determined. However, the exact value of the MM for the HbGp oligomer is not known. This study has as a main goal to evaluate the molecular weight of the oligomer in two oxidation states: oxy- and cyanomet-HbGp. Also the stability of the protein dissociation and denaturation as a function of pH was monitored. The present analytical ultracentrifugation study allowed us to assess the molecular mass of the whole oligomer giving valores of MM of 3600 ± 100 and 3700 ± 100 kDa for the oxy- and cyanomet-HbGp, respectively. These values are in agreement with the expected mass based on Vinogradov model for HbLt. Data were obtained of so20, w for the pure monomer d as 1.95 ± 0.04 S for both pH values 7.0 and 10.0. C(s) distributions for pure monomer indicated that a small contribution of dimer of monomers (5%), d2, was also present with so20, w of 3.2 S in solution. For the whole oxy- HbGp at pH 10.0 no contribution at 58 - 59 S was observed, suggesting complete oligomeric dissociation. C(s) distribution showed two additional peaks as compared to pure monomer: a peak at 4.2 - 4.5 S, probably due to the trimer, abc; a second peak at 5.8 - 6.0 S, that could be associated to the tetramer, abcd. Addition of beta-mercaptoethanol leads to the disappearance of the peak at 4.2 S, consistent with the reduction of the trimer abc disulfide bridges and production of monomers a, b and c. It may be noted that about 19% of cyanomet-HbGp, undissociated, coexist in equilibrium with the isolated subunits. Finally, studies in acidic pH values show that in the pH range 5.0-7.0 the oligomeric stability for the three oxidation forms of HbGp is quite high. Below pH 5.0, fluorescence emission data suggest that the stability is reduced in the following order: cyanomet > oxy > met-HbGp. Thus the stability of the oxy-, meta- and cyanomet-HbGp forms was evaluated evidenced making it clear the higher stability of the cyanomet-HbGp.

A hemoglobina extracelular gigante do anelídeo Glossoscolex paulistus (HbGp) é homológa à hemoglobina da Lumbricus terrestris (HbLt). Baseado nos estudos de MALDI-TOF-MS foi determinada a massa molecular (MM) das subunidades da HbGp. Entretanto, ainda não era possível propor o valor exato da MM para a HbGp íntegra, pois a estequiometria deste oligômero ainda não era totalmente clara. Este trabalho objetiva avaliar a massa molecular do oligômero em dois estados de oxidação: oxi- e cianometa-HbGp, bem como avaliar a estabilidade desta proteína, ou seja, a dissociação e desnaturação em função do pH em meio ácido. O estudo por ultracentrifugação analítica permitiu uma avaliação independente da massa molecular da HbGp. Valores de MM de 3600 ± 100 e 3700 ± 100 kDa foram obtidos para a oxi- e cianometa-HbGp, respectivamente. Estes valores está de acordo com a massa esperada, assumindo a estequiometria proposta por Vinogradov para a HbLt. Os dados de ultracentrifugação para as amostras do monômero d puro mostraram um coeficiente de sedimentação de 1,95 ± 0,04 S para ambos os valores de pH 7,0 e 10,0. Além disso, as distribuições c (s) do monômero d puro indicaram que uma pequena contribuição (5%) de dímero de monômeros, d2, com valores de s020,w de 3,2 S estava presente em solução. Para a oxi-HbGp íntegra no pH 10,0 nenhuma contribuição em 58 - 59 S foi observada, sugerindo completa dissociação oligomérica. As distribuições c (s) mostraram dois picos adicionais em relação ao monômero puro: um pico em 4,2 - 4,4 S, que está associado ao trímero, abc; e um segundo pico em 5,8 - 6,0 S, que poderia ser associado ao tetrâmero, abcd. A adição de β-mercaptoetanol leva ao desaparecimento do pico em 4,2 S, consistente com a redução das pontes dissulfeto do trímero abc e produção dos monômeros a, b e c. Cerca de 19 % da forma cianometa-HbGp íntegra coexiste em equilíbrio com as subunidades dissociadas. Finalmente, estudos em meio ácido mostravam que na faixa de pH 5,0 - 7,0 as três formas de oxidação de HbGp apresentaram alta estabilidade oligomérica. Abaixo de pH 5,0 os dados de fluorescência mostrava que a estabilidade diminui na sequência cianometa > oxi > meta. Assim a estabilidade das formas oxi-, meta- e cianometa-HbGp foi avaliada, ficando evidenciada a maior estabilidade da forma cianometa-HbGp. / The giant extracellular hemoglobin of Glossoscolex paulistus (HbGp) is homologous to Lumbricus terrestris (HbLt). Based on MALDI-TOF-MS the molecular masses (MM) of HbGp subunits were determined. However, the exact value of the MM for the HbGp oligomer is not known. This study has as a main goal to evaluate the molecular weight of the oligomer in two oxidation states: oxy- and cyanomet-HbGp. Also the stability of the protein dissociation and denaturation as a function of pH was monitored. The present analytical ultracentrifugation study allowed us to assess the molecular mass of the whole oligomer giving valores of MM of 3600 ± 100 and 3700 ± 100 kDa for the oxy- and cyanomet-HbGp, respectively. These values are in agreement with the expected mass based on Vinogradov model for HbLt. Data were obtained of so20, w for the pure monomer d as 1.95 ± 0.04 S for both pH values 7.0 and 10.0. C(s) distributions for pure monomer indicated that a small contribution of dimer of monomers (5%), d2, was also present with so20, w of 3.2 S in solution. For the whole oxy- HbGp at pH 10.0 no contribution at 58 - 59 S was observed, suggesting complete oligomeric dissociation. C(s) distribution showed two additional peaks as compared to pure monomer: a peak at 4.2 - 4.5 S, probably due to the trimer, abc; a second peak at 5.8 - 6.0 S, that could be associated to the tetramer, abcd. Addition of beta-mercaptoethanol leads to the disappearance of the peak at 4.2 S, consistent with the reduction of the trimer abc disulfide bridges and production of monomers a, b and c. It may be noted that about 19% of cyanomet-HbGp, undissociated, coexist in equilibrium with the isolated subunits. Finally, studies in acidic pH values show that in the pH range 5.0-7.0 the oligomeric stability for the three oxidation forms of HbGp is quite high. Below pH 5.0, fluorescence emission data suggest that the stability is reduced in the following order: cyanomet > oxy > met-HbGp. Thus the stability of the oxy-, meta- and cyanomet-HbGp forms was evaluated evidenced making it clear the higher stability of the cyanomet-HbGp.

Ephrin type-B receptor 2 (EphB2) is a receptor tyrosine kinase which phosphorylates proteins and thereby regulates cell migration, vascular development, axon guidance synaptic plasticity, and formation of borders between tissues. It has been seen overexpressed in several cancers, which make it an interesting protein to study. In this thesis EphB2 kinase domain (KD) and juxtamembrane segment with kinase domain (JMS-KD) have been expressed, purified and studied using analytical ultracentrifugation to evaluate the oligomerisation of the KD and how the double mutation S677/680A affects this. A program for data analysis have been written and used for analysis of the acquired data. The values of the dissociation constant were 2.94±1.04 mM for KD wild type and 3.46±2.26 mM for JMS-KD wild type have been calculated. Due to varied problems with the measurements no data was acquired on the double mutant, and not enough data was gained to draw any conclusions. Additional experiments will be needed to understand the oligomerisation of this intriguing protein.

Adaptor proteins, like Tollip and Tom1, facilitate cellular cargo sorting through their ubiquitin-binding domains. Tollip and Tom1 bind to each other through their TBD and GAT domains, respectively, whereas Tollip interacts with phosphatidylinositol-3-phosphate (PtdIns(3)P)-containing endosomal membranes. Tom1 and Tollip interaction and association with endosomes is proposed to be involved in the lysosomal degradation of polyubiquitinated cargo. Through cellular, biochemical, and biophysical techniques, we have further characterized the association of Tom1 with Tollip. Mutations in the binding interface of the Tom1 GAT and Tollip TBD complex leads to a subcellular mis-localization of both proteins, indicating that Tom1 may serve to direct Tollip to specific cellular pathways. It was determined that Tom1 inhibits the binding of Tollip to PtdIns(3)P and inhibition was reversed when mutations in the binding interface of the Tom1 GAT and Tollip TBD were present. Furthermore, it was established that, upon the binding of Tollip TBD to Tom1 GAT, ubiquitin is inhibited from binding to Tom1 GAT. It was also demonstrated that Tom1 GAT, but not Tollip TBD, can weakly bind to PtdIns(3)P. Consequently, we propose that association of Tom1 may serve to direct Tollip for involvement in specific cell signaling pathways. Gaining insight into the function of Tom1 and Tollip may lead to their use as therapeutic targets for increasing the efficiency of cargo trafficking and also for patients recovering from various cardiac injuries. / Master of Science

Extracellular vesicles (EV) originate from various cell types and reflect the contents of the originating cells. EVs are ubiquitous in nearly all body fluids, including blood plasma, and exhibit significant potential as biomarkers in disease diagnostics. However, isolating EVs from blood plasma remains challenging due to the lack of a standardised method. This study aimed to compare and optimize a density gradient ultracentrifugation workflow (DUC) against size exclusion chromatography-cation exchange chromatography (SEC-CEC) and evaluate SEC versus SEC-CEC. Common contaminants during isolation include lipoproteins (LP); previous studies have shown that lowering the pH of blood plasma can precipitate LP, enhancing isolation efficiency. Acidified blood plasma was compared with neutral plasma for EV isolation using all above mentioned methods. To assess the ability of the isolation methods to purify contaminants while retaining maximal EV yield, samples were analysed using multiple techniques, including particle quantity, free proteins, LP-associated apolipoprotein B, purity index (μg protein/particle), and EV-associated surface markers. The results indicate potential for DUC, but further optimization is necessary to improve the method and its isolation of EV. SEC-CEC emerged as an effective method, reducing contaminants by 71% (SEC) to 99% (SEC-CEC), increasing purity by 80%, and yielding positive signals from EV markers (SEC-CEC). The effect of acidification was ambiguous, it reduced apolipoprotein-B levels in plasma pre-isolation. However, post- isolation, neutral plasma exhibited significantly lower contaminations, albeit at the expense of total particle content and risking EV loss. The study underscored several advantages of SEC-CEC but indicated that acidification did not optimise isolation efficiency.

Orientador: Carlos Henrique Inácio Ramos / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-18T21:37:15Z (GMT). No. of bitstreams: 1 Gava_LisandraMarques_D.pdf: 9573403 bytes, checksum: 4d69a29d08ffc20e4544b876f131fb0d (MD5) Previous issue date: 2011 / Resumo: A função biológica das proteínas está relacionada à sua estrutura tridimensional adquirida pelo processo de enovelamento protéico. Neste contexto, proteínas denominadas, genericamente, de chaperonas moleculares exercem papel fundamental atuando no auxílio do enovelamento correto, no reenovelamento e na dissociação de agregados protéicos. A Hsp90 é uma das chaperonas moleculares mais importantes, é essencial para a viabilidade celular em eucariotos e está normalmente associada a proteínas atuantes no ciclo e sinalização celular, o que torna essa chaperona um alvo bastante interessante para abordagens terapêuticas de diversas doenças. A Hsp90 pode ser modulada por co-chaperonas diversas. Nesse trabalho foram caracterizadas as proteínas CHsp90 (domínio C-terminal da Hsp90 humana), e as co-chaperonas Hop e Tom70, além da interação entre C-Hsp90 e Tom70. Foram aplicadas técnicas de dicroísmo circular e emissão de fluorescência do triptofano; seguidas pela caracterização por ultracentrifugação analítica, gel filtração analítica, espalhamento dinâmico de luz, cromatografia de gel filtração acoplada a espalhamento de luz em multi-ângulos (SEC-MALS) e gel nativo. Para os ensaios de interação foram aplicadas técnicas de pull-down, SEC-MALS e calorimetria de titulação isotérmica. As proteínas foram produzidas puras e enoveladas, com estado oligomérico determinado como dímero para C-Hsp90 e monômero para Hop e Tom70, sendo que essas também foram encontradas como espécies diméricas. A estequiometria de interação entre a C-Hsp90 e Tom70 foi determinada em 1 monômero da Tom70 para 1 dímero da C-Hsp90, com KD de 360 ± 30 nM, ?Happ = -2,6 ± 0,1 kcal/mol e ?S = 21 ± 1 cal/mol.K, sugerindo que a interação é dirigida por entalpia e entropia. Os resultados obtidos nesse trabalho contribuem para uma melhor compreensão do sistema Hsp90, que está envolvido em diversos processos celulares essenciais e patológicos, como doenças neurodegenerativas, processos inflamatórios, infecções e câncer / Abstract: The biological function of proteins is related to its three dimensional structure acquired via protein folding process. In this context, the molecular chaperones play a key role acting as auxiliary protein on protein folding, refolding and dissociation of protein aggregates. Hsp90 is one of the most important molecular chaperones, is essential for cell viability in eukaryotes and is usually associated with proteins involved in cell cycling and cell signaling, which makes these chaperone a very interesting targeting for therapeutic approaches for several diseases. The chaperone activity of Hsp90 can be modulated by other proteins, called co-chaperones. In this work, we characterized the protein C-Hsp90 (Cterminal domain of human Hsp90) and the co-chaperones Hop and Tom70, and also the interaction between C-Hsp90 and Tom70. Circular dichroism and fluorescence emission of tryptophan was first applied for initial characterization of the proteins, followed by analytical ultracentrifugation, analytical gel filtration, dynamic light scattering, size exclusion chromatography - multi angle light scattering (SEC-MALS) and native gel. The interaction between C-Hsp90 and Tom70 were measured by techniques like pull-down, SEC-MALS and isothermal titration calorimetry. The proteins were produced pure and soluble and their oligomeric state were determined as dimer for C-Hsp90, and monomer for Hop and Tom70, these two co-chaperones were also found as dimeric species. The stoichiometry of interaction between C-Hsp90 and Tom70 was determined by SEC-MALS and ITC as been 1 dimer of C-Hsp90 to 1 monomer of Tom70, with a KD of 360 ± 30 nM, ?Happ = -2.6 ± 0.1 kcal/mol and ?S = 21 ± 1 cal/mol.K, suggesting that these interaction is driven by both, enthalpy and entropy. The results contribute to a better understanding of the important Hsp90 machinery, which is involved in many essential cellular and pathological processes, such as neurodegenerative diseases, inflammation, infection and cancer / Doutorado / Bioquimica / Doutor em Biologia Funcional e Molecular

The EcoR124INT restriction-modification (R-M) system contains the genes HsdS3, HsdM and HsdR. S3 encodes the N-terminal domain of the wild-type S subunit and has been shown to dimerise in solution (Smith et al., 1998). Following purification of the subunits of the EcoR124INT R-M system, complexes of the methyltransferase S3/M and restriction endonuclease S3/M/R were formed and shown to have activity in vitro, methylating and hydrolysing a symmetrical DNA recognition sequence, respectively. The DNA mimic OCR (overcome classical restriction) protein inhibited the methyltransferase activity in vitro, with maximum inhibition at a 1: 2 molar ratio of (S3/M)2 to an ocr dimer. Dynamic light scattering (DLS), sedimentation equilibrium (SE) and sedimentation velocity (SV) experiments showed S3 to exist as a dimer and S11 (the central conserved domain of S) to exist as a tetramer in solution. M was found to be dimeric in solution, whilst the R protein was monomeric. A complex of S3/M was found to have a stoichiometry (S3/M)2 and a complex of S3/M/R had a stoichiometry of S3/M/R1, even when a 2: 1 molar ratio of R to S3/M, was added. Small angle neutron scattering (SANS) experiments provided values for the radius of gyration (Rg), which for S3 was comparable to that calculated for the recently published crystal structure of the S subunit from Methanococcus jannaschii (Kim et al., 2005). These experiments also showed a decrease in the Dmax in the presence of the 30 bp DNA recognition sequence from 200A to 140A, suggesting a similar conformational change in the positioning of the subunits as has been detected for the wild-type M. EcoR124I and a related type 1 1/2 system AhdI. This change following DNA binding was also observed by SV experiments. Furthermore ab initio modelling from the SANS data has provided a low-resolution structure for the EcoR124INT MTase and its complex with DNA.