Cette thèse développe, dans le cadre de la biophysique, des modèles théoriques centrés sur les interactions entre les bio-filaments, de longs polymères présents dans les cellules biologiques et les membranes biologiques, qui protègent les cellules de leur environnement. La thèse est divisée en trois parties, traitant différents systèmes. Dans un premier temps, un modèle admettant plusieurs états de courbure préférée des bio-filaments est développé. Ce type de filaments est forcé à former un anneau et leur interaction avec des membranes tubulaires qu'ils enlacent est discutée. Deuxièmement, les déformations de membranes biologiques modèles sous l'action de filaments appliquant des couples sont calculées, dans le régime linéaire. Finalement, la motilité de la bactérie Spiroplasma est abordée. Les résultats préliminaires d'un modèle élastique sont donnés. / This work focuses on the development of theoretical models in the framework of biophysics. In particular, it deals with the interactions between bio-filaments (long polymer chains found in biological cells) and biological membranes which protect cells from their environment. It is divided in three main parts, where different systems are studied. Firstly, a model going beyond the Worm-Like Chain model is developed to take into account different preferred states of curvature of the constituents of the bio-polymer chains. This kind of filaments are forced to close into a ring and their interactions with tubular membranes they entwine are discussed. Secondly, the deformations induced to biological membranes by torque-applying bio-filaments are discussed in the linear regime. Finally, the motility of the bacteria Spiroplasma. Preliminary results on an elastic model describing the cell motility are given.

Sabe-se que em sistemas biológicos, as funções de proteínas e de hormônios estão relacionadas com suas conformações espaciais e que suas estruturas e funções são freqüentemente influenciadas pela interação com os lipídeos das membranas plasmáticas e/ou intracelulares. Devido à importância das interações entre as proteínas e hormônios com as membranas, vários estudos têm sido realizados empregando modelos que simulam as membranas, pois as biológicas são estruturas bastante complexas. Entre esses modelos esta o de micelas reversas que pode ser considerado atualmente como o que melhor reproduz as condições existentes in vivo, pois a água presente nesse sistema e uma ótima representação para a água presente em sistemas biológicos em torno dos receptores de membrana. Visando estudar a interação do hormônio melanócito estimulante (- MSH) e do peptídeo sintético melanotrópico análogo (MSH1) com um modelo de membrana, na tentativa de compreensão de seu papel biológico, usamos micelas reversas preparadas com o anfifílico bis-(2-etilhexil)sulfosucinato de sódio, abreviado AOT. É sabido que - MSH é importante na regulação da pigmentação da pele, alem de estar relacionado a vários processos fisiológicos e neurológicos. Mais recentemente, foram encontradas evidencias de que ele atua também como neurotransmissor ou neuromodulador na aprendizagem, memória e capacidade de concentração. Clinicamente, os peptídeos melanotrópicos podem eventualmente ser utilizados no tratamento de alterações pigmentares e na detecção e erradicação de melanomas. Realizamos medidas de ressonância paramagnética eletrônica e de fluorescência de estado estacionário e resolvida no tempo para estudar a dinâmica interna dos peptídeos melanotrópicos na interação com micelas reversas de AOT. Monitoramos a fluorescência do resíduo Triptofano localizado na nona posição da seqüência de aminoácidos dos peptídeos melanotrópicos. A supressão da fluorescência do resíduo triptofano por acrilamida (que fica no meio micelar) também foi medida para auxiliar na tentativa de localizar a posição do fluoróforo nas micelas reversas. Dos espectros de EPR obtidos com o marcador de spin 5-SASL observamos que, com o aumento do tamanho das micelas reversas pelo aumento da quantidade de água, a região das cabeças polares tende a ficar flexível enquanto que, em oposição, aumenta a rigidez, a polaridade ordem da região das cadeias. Os resultados obtidos para o acréscimo de solução tampão fosfato e para soluções contendo Trp, LTL, -MSH e MSH1 são similares mostrando que essa técnica fornece informações sobre as micelas, independente da interação das mesmas com os peptídeos. Dos resultados obtidos com a fluorescência para o grau de anisotropia, tempo de vida e comprimento de onda de máxima emissão observamos que os fluoróforos utilizados (Trp, LTL, -MSHe MSH1) experimentam uma região menos polar e mais rígida do que a água. Vimos também que com o aumento da quantidade de água nas micelas reversas os peptídeos e o aminoácido tendem a assumir determinadas localizações na interface, sendo que o Triptofano fica no meio mais hidratado que não é a agua bulk. Os espectros de decaimentos associados mostram a ocorrência de conformações com diferentes graus de exposição do Triptofano ao ambiente aquoso. Assim, pudemos perceber que o Trp é o mais exposto à água tendendo a localizar-se na região de água estruturada. O LTL fica ancorado na região da interface e os peptídeos melanotrópicos inserem-se na região das cadeias hidrocarbônicas, sendo que o -MSH insere-se mais profundamente. Observamos também dos espectros de decaimentos associados diferenças das distribuições conformacionais para os hormônios melanotrópicos, especialmente para as micelas reversas maiores que simulam a situação biológica, o que pode estar relacionado com as diferentes atividades bio1ógicas dos mesmos. / The biological function of proteins and hormones is related to their conformations and both structure and function are frequently dependent on the interactions with lipids of plasmatic and intracelular membranes. Due to the complexity of biological membranes, many studies about these interactions employ model membranes. The reverse micelle is a good model, for it offers an adequate representation of the structured water that is present in biological systems around the membrane receptors. We report here studies of the interaction of -melanocyte stimulating hormone (-MSH) and one synthetic analogue (MSH1) with reverse micelles prepared from the amphyphylic sodium bis-(2-ethylhexyl)sulfosuccinate (AOT) in isooctane. The -MSH is important in the regulation of skin pigmentation and is also involved with other physiological process. It was recently found evidences of its action as a neurotransmitter or neuromodulator in learning, memory and attention. It is claimed that potent analogues of melanotropin hormones could be used in the therapy of pigmentary disorders and detection and treatment of melanome. Electron paramagnetic resonance (EPR), steady state fluorescence and time-resolved fluorescence were employed to study the internal dynamics of the melanotropins in interaction with reverse micelles of AOT. We monitored the fluorescence of the residue tryptophan located in the 9 position of the aminoacids sequence of -MSH and MSH-l. The tripeptide Lysil-tryptophyl-Lysine (LTL) and the isolated aminoacid tryptophan were also investigated as simpler molecules interacting with the reverse micelles. It was also measured the fluorescence quenching by acrylamide, to obtain more information about the peptide location in reverse micelles. We monitored the EPR spectra of the spin label 5-doxyl stearate acid (5-SASL) at increasing values of Wo hat is the ratio between the number of water molecules and the number of AOT molecules. The region of the polar head gains flexibility when the size of the reverse micelles increases (due to increase in water content) and, opposite to this, the region of the hydrophobic tail becomes more rigid, showing higher order and polarity. Similar effects were observed upon addition of solutions containing either tryptophan, or LTL, or -MSH and MSH-1, indicating that the EPR measurements gave information about the changes in the micelles promoted by water molecules, independent of the interactions with the peptides. Monitoration of fluorescence parameters like spectral position of emission band, anisotropy and lifetime demonstrated that the environment around the fluorophore, in all compounds, is less polar and more rigid than bulk water. Those parameters reflect the location of the compounds in the heterogeneous isooctane/AOT/water medium and are sensitive to the changes induced in the micelles by the increasing the amount of water. However, in large micelles having wo above 10, the modifications detected by fluorescence re small and the addition of water no more affects the location of the fluorophores. Quenching measurements gave additional support to the data indicating that the different compounds occupy different positions in the large reverse micelles, but in any case they are in the interface region, without dispersing into the bulk water. Decay associated spectra allowed the identification of conformations with various degree of exposition to polar and non polar media. The conformation related to the long lifetime is more exposed to water while that associated to the intermediate lifetime is preferentially stabilised in non polar media. The native hormone -MSH in the large micelles shows predominance of the conformation sensing a non polar environment, with similar results presented by the analogue MSH-1. Those melanotropins are in the region of the hydrocarbon chain, with slightly deep location for the native hormone. The tripeptide LTL is anchored in the interface region, probably stabilised by electrostatic interaction between the charged groups in the peptide and the negative charge in AOT. Finally, the tryptophan is most exposed to water, probably interacting with structural water near to the interface.

Molecular modeling has come a long way during the past decades and in the current thesis modeling of biological membranes is the focus. The main method of choice has been classical Molecular Dynamics simulations and for this technique a model Hamiltonian, or force field (FF), has been developed for lipids to be used for biological membranes. Further, ways of more accurately simulate the interactions between solutes and membranes have been investigated. A FF coined Slipids was developed and validated against a range of experimental data (Papers I-III). Several structural properties such as area per lipid, scattering form factors and NMR order parameters obtained from the simulations are in good agreement with available experimental data. Further, the compatibility of Slipids with amino acid FFs was proven. This, together with the wide range of lipids that can be studied, makes Slipids an ideal candidate for large-scale studies of biologically relevant systems. A solute's electron distribution is changed as it is transferred from water to a bilayer, a phenomena that cannot be fully captured with fixed-charge FFs.  In Paper IV we propose a scheme of implicitly including these effects with fixed-charge FFs in order to more realistically model water-membrane partitioning. The results are in good agreement with experiments in terms of free energies and further the differences between using this scheme and the more traditional approach were highlighted. The free energy landscape (FEL) of solutes embedded in a model membrane is explored in Paper V. This was done using biased sampling methods with a reaction coordinate that included intramolecular degrees of freedom (DoF). These DoFs were identified in different bulk liquids and then used in studies with bilayers. The FELs describe the conformational changes necessary for the system to follow the lowest free energy path. Besides this, the pitfalls of using a one-dimensional reaction coordinate are highlighted.

Orientador: Delphim da Graça Macoris / Banca: Ana Maria de Guzzi Plepis / Banca: Luis Cláudio Lopes Correia da Silva / Banca: José Wanderley Cattelan / Banca: Antonio Carlos Alessi / Resumo: Neste trabalho, objetivou-se, a obtenção de biomembranas a partir de centros tendinosos diafragmáticos de eqüinos submetidos a soluções alcalinas por diferentes períodos de tempo. As amostras foram tratadas durante 24, 48, 72, 120 e 144 horas em solução alcalina, liofilizadas e analisadas quanto à flexibilidade, viabilidade para sutura e homogeneidade. Em seguida, as amostras obtidas e o material in natura foram caracterizados por calorimetria exploratória diferencial, microscopia eletrônica de varredura e ensaio de degradação enzimática pela colagenase. As membranas tratadas por 72 horas em solução alcalina se mostraram mais homogêneas e flexíveis em relação às membranas tratadas por tempos menores e mais resistentes à sutura em relação às tratadas por tempos maiores em solução alcalina. A calorimetria exploratória diferencial demonstrou que não houve desnaturação do colágeno após o tratamento alcalino. Concluiu-se que o tratamento por 72 horas é o mais indicado para a implantação cirúrgica na parede abdominal de eqüinos. / Abstract: The objective of this work was to obtaining biomembranes from equines tendineous diaphragmatic centers submitted to alkaline solutions at different times. The samples were treated during 24, 48, 72, 120 and 144 hours in alkaline solution and analyzed the flexibility, viability for suture and homogeneity. After that, the samples and the material in natura were characterized by diferential scanning calorimetry, scan ning electronic microscopy and biological stability in vitro hydrolysis of collagen by colagenase. The 72 hours alkaline treatment showed be intermediary in relation to flexibility, suture resistance and homogeneity. diferential scanning calorimetry demonstrated that the alkaline treatment did not have denaturated the collagen. It 23 was concluded that the treatment for 72 hours is the most indicated for the surgical implantation. / Doutor

Made available in DSpace on 2014-06-11T19:31:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-01-16Bitstream added on 2014-06-13T20:21:58Z : No. of bitstreams: 1 vulcani_vas_dr_jabo.pdf: 1018347 bytes, checksum: 9774f91bfa84c854291e7dacae87b4e9 (MD5) / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Neste trabalho, objetivou-se, a obtenção de biomembranas a partir de centros tendinosos diafragmáticos de eqüinos submetidos a soluções alcalinas por diferentes períodos de tempo. As amostras foram tratadas durante 24, 48, 72, 120 e 144 horas em solução alcalina, liofilizadas e analisadas quanto à flexibilidade, viabilidade para sutura e homogeneidade. Em seguida, as amostras obtidas e o material in natura foram caracterizados por calorimetria exploratória diferencial, microscopia eletrônica de varredura e ensaio de degradação enzimática pela colagenase. As membranas tratadas por 72 horas em solução alcalina se mostraram mais homogêneas e flexíveis em relação às membranas tratadas por tempos menores e mais resistentes à sutura em relação às tratadas por tempos maiores em solução alcalina. A calorimetria exploratória diferencial demonstrou que não houve desnaturação do colágeno após o tratamento alcalino. Concluiu-se que o tratamento por 72 horas é o mais indicado para a implantação cirúrgica na parede abdominal de eqüinos. / The objective of this work was to obtaining biomembranes from equines tendineous diaphragmatic centers submitted to alkaline solutions at different times. The samples were treated during 24, 48, 72, 120 and 144 hours in alkaline solution and analyzed the flexibility, viability for suture and homogeneity. After that, the samples and the material in natura were characterized by diferential scanning calorimetry, scan ning electronic microscopy and biological stability in vitro hydrolysis of collagen by colagenase. The 72 hours alkaline treatment showed be intermediary in relation to flexibility, suture resistance and homogeneity. diferential scanning calorimetry demonstrated that the alkaline treatment did not have denaturated the collagen. It 23 was concluded that the treatment for 72 hours is the most indicated for the surgical implantation.

A temperatura é o fator ambiental mais importante que afeta a atividade de animais ectotérmicos, como peixes. Ajustes compensatórios à temperatura ocorrem em diferentes cursos temporais, que variam de menos de um minuto a mais de um mês, e as membranas são os primeiros alvos afetados pelas mudanças de temperatura, com resposta imediata dos componentes lipídicos a este desafio. Este trabalho teve como objetivo estimar a capacidade alostática (na estrutura e funções de membrana) no contexto das variáveis climáticas relevantes e caracterizar o âmbito e os mecanismos de mudança, incluindo os mecanismos que concedem tolerância a mudanças de temperatura agudas e crônicas. Juvenis de Steindachneridion parahybae uma espécie de peixe nativa ameaçada de extinção, foram progressivamente resfriados de 30° C a 24, 17 e 12 ° C, nas quais foram mantidas por até 5 dias no tratamento agudo e por até 30 dias no tratamento crônico. Os tecidos hepático, encefálico e branquial foram amostrados, com análises subsequentes das principais frações fosfolipídicas (fosfatidilcolina (FC) e fosfatidiletanolamina (FE) e análises posicionais de cada fração), atividade da Na+/ K+-ATPase e histomorfologia branquial. Os animais mantidos na temperatura mais baixa mostraram uma elevada taxa de mortalidade, provavelmente devido à proximidade desta temperatura ao limite térmico inferior para esta espécie. A atividade da Na+/ K+-ATPase se mostrou aumentada nas temperaturas mais baixas, corroborando o aumento das lesões morfológicas branquiais e massa de fígado para estas temperaturas. Em geral o perfil de ácidos graxos de FC mantiveram-se mais estáveis do que o observado para FE. O teste agudo aparentemente afetou consideravelmente C20-22n3 (FC hepática e sn-1 ; FE encefálica e hepática), enquanto que no teste crônico, C20-22n6 foi o grupamento mais afetado (FC e FE hepático em sn-2 e sn-1). O ensaio agudo mostrou um padrão de manutenção da estrutura de membrana cerebral, com uma diminuição de C20-22n3 hepática e aumento destes ácidos graxos no encéfalo durante o tratamento. Em ambos os tecidos e frações analisados foi possível detectar evidências significativas de reestruturação da membrana, mostrando que o Surubim do Paraíba foi capaz de proporcionar ajustes compensatórios em respostas de aclimatação. / Temperature is the most important environmental factor affecting the activity of ectothermic animals such as fish. Compensatory adjustments to temperature occur with time courses ranging from less than a minute to more than a month, and membranes are the first targets affected by change of temperature, and their lipid components respond immediately to this challenge. This project aimed to estimate the allostatic capacity (in membrane structure and function) in the context of relevant climate variables, and to characterize the scope and the defense mechanisms available, including those yielding tolerance to acute and chronic temperature shifts. Steindachneridion parahybae juveniles, an endangered native fish species, were progressively cooled from 30°C to 24, 17 and 12°C, in which they were maintained for up to 5 days in the acute trial and for up 30 days in the chronic trial. Brain, liver and branchial tissues were sampled, with subsequent analyses of the main phospholipids fractions (phosphatidylcholine (PC) and phosphatidylethanolamine (PE), and the positional analyses of each fraction), Na+/K+-ATPase activity and histomorphology of gills. The animals maintained atlower temperature showed a high rate of mortality, probably because this temperature is near the lower thermal limit for this species. The activity of Na+ K+ATPase increased at lower temperatures, the same pattern observed for morphological injuries in gills and increased liver mass. Generally the fatty acid profiles of PC remained more stable than those in PE. The acute test apparently had affected considerably C20-22n3 (liver PC and sn-1 PC; PE in brain and liver), while for the chronic test, C20-22n6 was more affected (PC and PE liver on sn-2 and sn-1). The acute trial showed a pattern of maintenance of brain membrane structure, with a decrease of PE-associated C20-22n3 in the liver and an increase of these fatty acids in brain during the test. In both tissues and fractions analyzed it was possible to detect significant evidences of membrane restructuring, showing that the Surubim do Paraiba was able to provide compensatory adjustments in acclimation responses

The focus of this dissertation is to understand the physicochemical factors that affect the spatiotemporal control of phosphoinositide signaling events. Despite their low abundance in cellular membranes ( ~ 1% of total lipids) phosphoinositides are assuming major roles in the spatiotemporal regulation of cellular signaling, therefore making this group of lipids an attractive area of study, especially for identifying drug targets. The main phosphoinositide studied in this dissertation is phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2], which regulates various intracellular signaling pathways, notably the PI3K/AKT pathway. The PI3K/AKT pathway plays a critical role in regulating diverse cellular functions including metabolism, growth, proliferation, and survival. Thus, dysregulation of the PI3K/AKT pathway is implicated in a number of human diseases including cancer, diabetes, cardiovascular disease and neurological diseases. PI(4,5)P2 regulates phosphoinositide signaling in the PI3K/AKT pathway through interaction of its highly anionic headgroup with polybasic proteins. The highly specific manner that allows hundreds of structurally diverse proteins to interact with lipid species found in such low supply may require the local formation of PI(4,5)P2 clusters (domains). Although a significant amount of evidence has accumulated over the past decade that supports the notion of PI(4,5)P2-rich clusters, our understanding regarding the structural determinants required for cluster formation remains limited. Studies have shown that PI(4,5)P2 clustering is induced by cellular cations interacting with PI(4,5)P2 via electrostatic interactions, suggesting that non-clustering/clustering transitions are particularly sensitive to ionic conditions. However, why some ions are more effectively cluster PI(4,5)P2 than others remains to be understood. For our first research aim, we investigated the effects of divalent (Ca2+) and monovalent cations (Na+, K+ ) on PI(4,5)P2 clustering to understand the ionic environment required for electrostatic PI(4,5)P2 cluster formation. We used monolayers at the air/water interface (Langmuir films) to monitor PI(4,5)P2 molecular packing in the presence of each cation. Our results indicated that Ca2+ individually and Ca2+ along with K+ had a greater effects on PI(4,5)P2 cluster formation than Na+ and K+, individually and combined. We hypothesize that the cations shield the negatively charged headgroups, allowing adjacent PI(4,5)P2 molecules to interact via H- bonding networks. The analysis of the electrostatic environment required for stable PI(4,5)P2 clustering will help us understand important aspects of PI(4,5)P2 mediated signaling events, such as the temporal control of protein binding to PI(4,5)P2 clusters to enhance their function. Another important spatiotemporal modulator that affects the local concentration of PI(4,5)P2 clusters is cholesterol, a steroid present in large quantities (30-40 mole%) in the plasma membrane. Cholesterol has been shown to induce the formation of liquid-ordered domains when interacting with an otherwise gel phase forming lipid, however, the interaction of cholesterol with an inner leaflet lipid species that favors more of a disordered environment to form clusters is poorly understood. We hypothesize that cations along with cholesterol work synergistically to induce PI(4,5)P2 clustering. Thus, our second research aim was to investigate the role of cholesterol on PI(4,5)P2 clustering by monitoring the molecular packing of PI(4,5)P2 in the presence of both cholesterol and cations. This aim was investigated similarly to the first aim with Langmuir trough monolayer film experiments. Our results showed that cholesterol in the presence of Ca2+ had an additive effect leading to the strongest condensation of the monolayer (increase in PI(4,5)P2 packing). Our hypothesis is that Ca2+ significantly reduces the negative electron density of the phosphate groups, allowing the cholesterol hydroxyl group to interact with PI(4,5)P2 headgroup through hydrogen-bond formation. To confirm our hypothesis, we collaborated with a computational group at the NIH that performed all-atom molecular dynamics (MD) simulations that closely agreed with our experimental data. Thus we were able to determine that the cholesterol hydroxyl group directly interacts via hydrogen-bonding with the phosphodiester group as well as the PI(4,5)P2 hydroxyl groups in the 2- and 6-position. The insight into the structural positioning of cholesterol moving closer to the PI(4,5)P2 headgroup region suggests this unique interaction is important for PI(4,5)P2 cluster formation. Other anionic lipid species are suspected to interact with PI(4,5)P2 and strengthen PI(4,5)P2 clustering. We were particularly interested in the interaction of PI(4,5)P2 with phosphatidylinositol (PI) and phosphatidylserine (PS) because both are abundant in the plasma membrane, ~6-10% and ~10-20% respectively, and both electrostatically bind to peripheral proteins. Therefore, the third research aim analyzed the capacity of PI and PS to form stable clusters with PI(4,5)P2. We hypothesize that a mixed PI/PI(4,5)P2 or PS/PI(4,5)P2 domains are ideal for protein binding, since in combination PI or PS with PI(4,5)P2 would provide the necessary negative electrostatic environment, while PI(4,5)P2 would provide the high specificity and additional electrostatics for protein binding. Langmuir trough monolayer films were used to investigate the stabilization of PI/PI(4,5)P2 and PS/PI(4,5)P2 monolayers in the presence of Ca2+. Our results showed a condensation of the monolayer for both PI/PI(4,5)P2 and PS/PI(4,5)P2 with an increase in Ca2+concentrations, which suggests that Ca2+ shields the highly negatively charged phosphomonoester groups of PI(4,5)P2 allowing PI and PS to participate in PI(4,5)P2’s hydrogen-bond network. Interestingly, both PI and PS equally stabilized PI(4,5)P2 cluster formation, therefore it is highly likely that these lipids interact in vivo to form large stable electrostatic domains required for protein binding. The first three aims provided us with information about the physiological relevant environments required for PI(4,5)P2 cluster formation, while the last aim was geared towards understanding the temporal control of protein association with phosphoinositides in the plasma membrane. Specifically, we analyzed the plasma membrane association of PTEN-L, a translation variant protein of PTEN, that has the ability to exit and enter back into cells, unlike classical PTEN. The ability of PTEN-L to facilitate entry across the anionic and hydrophobic layers of the plasma membrane (in the case of direct transport of PTEN-L across the membrane) or into phospholipid transport vesicles (in the case of vesicular transport of PTEN-L across cells) is likely due to the addition of the 173 N-terminal amino acids, the alternative translated region (ATR-domain). Thus, our fourth research aim focused on the biophysical role of the ATR-domain to associate with inner leaflet plasma membrane lipids. Using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy to monitor secondary structural changes of the ATR-domain upon lipid binding, it was revealed that both PS and PI(4,5)P2 induced conformational change towards a slight increase in β-sheet content in an otherwise unstructured domain suggesting these lipids are required for ATR-domain interaction with the PM. Further studies revealed that the ATR-domain affects the integrity of PS lipid vesicles, further indicating the presence of PS is required to drive ATR-domain across the membrane. This aim provides information on ATR-domain lipid binding preferences aiding in our understanding of the biological and functional role of PTEN-L as a deliverable tumor suppressor protein. The overall goal of the research in this dissertation is to understand factors that fine-tune PI(4,5)P2 cluster formation in space and time. Our first three research aims were designed to understand the synergistic effects of spatiotemporal modulators (cations, cholesterol, and anionic lipids) on local concentration of PI(4,5)P2 clusters. Our results indicate that Ca2+, cholesterol, and the presence of anionic lipids PI and PS all induce stable domains, thus it is highly likely this is part of the biological environment required in vivo for cationic proteins to bind. The last aim, the association of the ATR-domain with phospholipids in the plasma membrane, provided evidence that PS is likely required to drive the ATR-domain across the plasma membrane. This dissertation unifies nearly two decades worth of research by shedding light on synergistic modulators of PI(4,5)P2 cluster formation (Figure 1). Thus, this work has potentially far reaching consequences for understanding temporal control of the spatially resolved protein activity.

The focus of this dissertation is to understand the physicochemical factors that affect the spatiotemporal control of phosphoinositide signaling events. Despite their low abundance in cellular membranes ( ~ 1% of total lipids) phosphoinositides are assuming major roles in the spatiotemporal regulation of cellular signaling, therefore making this group of lipids an attractive area of study, especially for identifying drug targets. The main phosphoinositide studied in this dissertation is phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2], which regulates various intracellular signaling pathways, notably the PI3K/AKT pathway. The PI3K/AKT pathway plays a critical role in regulating diverse cellular functions including metabolism, growth, proliferation, and survival. Thus, dysregulation of the PI3K/AKT pathway is implicated in a number of human diseases including cancer, diabetes, cardiovascular disease and neurological diseases. PI(4,5)P2 regulates phosphoinositide signaling in the PI3K/AKT pathway through interaction of its highly anionic headgroup with polybasic proteins. The highly specific manner that allows hundreds of structurally diverse proteins to interact with lipid species found in such low supply may require the local formation of PI(4,5)P2 clusters (domains). Although a significant amount of evidence has accumulated over the past decade that supports the notion of PI(4,5)P2-rich clusters, our understanding regarding the structural determinants required for cluster formation remains limited. Studies have shown that PI(4,5)P2 clustering is induced by cellular cations interacting with PI(4,5)P2 via electrostatic interactions, suggesting that non-clustering/clustering transitions are particularly sensitive to ionic conditions. However, why some ions are more effectively cluster PI(4,5)P2 than others remains to be understood. For our first research aim, we investigated the effects of divalent (Ca2+) and monovalent cations (Na+, K+ ) on PI(4,5)P2 clustering to understand the ionic environment required for electrostatic PI(4,5)P2 cluster formation. We used monolayers at the air/water interface (Langmuir films) to monitor PI(4,5)P2 molecular packing in the presence of each cation. Our results indicated that Ca2+ individually and Ca2+ along with K+ had a greater effects on PI(4,5)P2 cluster formation than Na+ and K+, individually and combined. We hypothesize that the cations shield the negatively charged headgroups, allowing adjacent PI(4,5)P2 molecules to interact via H- bonding networks. The analysis of the electrostatic environment required for stable PI(4,5)P2 clustering will help us understand important aspects of PI(4,5)P2 mediated signaling events, such as the temporal control of protein binding to PI(4,5)P2 clusters to enhance their function. Another important spatiotemporal modulator that affects the local concentration of PI(4,5)P2 clusters is cholesterol, a steroid present in large quantities (30-40 mole%) in the plasma membrane. Cholesterol has been shown to induce the formation of liquid-ordered domains when interacting with an otherwise gel phase forming lipid, however, the interaction of cholesterol with an inner leaflet lipid species that favors more of a disordered environment to form clusters is poorly understood. We hypothesize that cations along with cholesterol work synergistically to induce PI(4,5)P2 clustering. Thus, our second research aim was to investigate the role of cholesterol on PI(4,5)P2 clustering by monitoring the molecular packing of PI(4,5)P2 in the presence of both cholesterol and cations. This aim was investigated similarly to the first aim with Langmuir trough monolayer film experiments. Our results showed that cholesterol in the presence of Ca2+ had an additive effect leading to the strongest condensation of the monolayer (increase in PI(4,5)P2 packing). Our hypothesis is that Ca2+ significantly reduces the negative electron density of the phosphate groups, allowing the cholesterol hydroxyl group to interact with PI(4,5)P2 headgroup through hydrogen-bond formation. To confirm our hypothesis, we collaborated with a computational group at the NIH that performed all-atom molecular dynamics (MD) simulations that closely agreed with our experimental data. Thus we were able to determine that the cholesterol hydroxyl group directly interacts via hydrogen-bonding with the phosphodiester group as well as the PI(4,5)P2 hydroxyl groups in the 2- and 6-position. The insight into the structural positioning of cholesterol moving closer to the PI(4,5)P2 headgroup region suggests this unique interaction is important for PI(4,5)P2 cluster formation. Other anionic lipid species are suspected to interact with PI(4,5)P2 and strengthen PI(4,5)P2 clustering. We were particularly interested in the interaction of PI(4,5)P2 with phosphatidylinositol (PI) and phosphatidylserine (PS) because both are abundant in the plasma membrane, ~6-10% and ~10-20% respectively, and both electrostatically bind to peripheral proteins. Therefore, the third research aim analyzed the capacity of PI and PS to form stable clusters with PI(4,5)P2. We hypothesize that a mixed PI/PI(4,5)P2 or PS/PI(4,5)P2 domains are ideal for protein binding, since in combination PI or PS with PI(4,5)P2 would provide the necessary negative electrostatic environment, while PI(4,5)P2 would provide the high specificity and additional electrostatics for protein binding. Langmuir trough monolayer films were used to investigate the stabilization of PI/PI(4,5)P2 and PS/PI(4,5)P2 monolayers in the presence of Ca2+. Our results showed a condensation of the monolayer for both PI/PI(4,5)P2 and PS/PI(4,5)P2 with an increase in Ca2+concentrations, which suggests that Ca2+ shields the highly negatively charged phosphomonoester groups of PI(4,5)P2 allowing PI and PS to participate in PI(4,5)P2’s hydrogen-bond network. Interestingly, both PI and PS equally stabilized PI(4,5)P2 cluster formation, therefore it is highly likely that these lipids interact in vivo to form large stable electrostatic domains required for protein binding. The first three aims provided us with information about the physiological relevant environments required for PI(4,5)P2 cluster formation, while the last aim was geared towards understanding the temporal control of protein association with phosphoinositides in the plasma membrane. Specifically, we analyzed the plasma membrane association of PTEN-L, a translation variant protein of PTEN, that has the ability to exit and enter back into cells, unlike classical PTEN. The ability of PTEN-L to facilitate entry across the anionic and hydrophobic layers of the plasma membrane (in the case of direct transport of PTEN-L across the membrane) or into phospholipid transport vesicles (in the case of vesicular transport of PTEN-L across cells) is likely due to the addition of the 173 N-terminal amino acids, the alternative translated region (ATR-domain). Thus, our fourth research aim focused on the biophysical role of the ATR-domain to associate with inner leaflet plasma membrane lipids. Using attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy to monitor secondary structural changes of the ATR-domain upon lipid binding, it was revealed that both PS and PI(4,5)P2 induced conformational change towards a slight increase in β-sheet content in an otherwise unstructured domain suggesting these lipids are required for ATR-domain interaction with the PM. Further studies revealed that the ATR-domain affects the integrity of PS lipid vesicles, further indicating the presence of PS is required to drive ATR-domain across the membrane. This aim provides information on ATR-domain lipid binding preferences aiding in our understanding of the biological and functional role of PTEN-L as a deliverable tumor suppressor protein. The overall goal of the research in this dissertation is to understand factors that fine-tune PI(4,5)P2 cluster formation in space and time. Our first three research aims were designed to understand the synergistic effects of spatiotemporal modulators (cations, cholesterol, and anionic lipids) on local concentration of PI(4,5)P2 clusters. Our results indicate that Ca2+, cholesterol, and the presence of anionic lipids PI and PS all induce stable domains, thus it is highly likely this is part of the biological environment required in vivo for cationic proteins to bind. The last aim, the association of the ATR-domain with phospholipids in the plasma membrane, provided evidence that PS is likely required to drive the ATR-domain across the plasma membrane. This dissertation unifies nearly two decades worth of research by shedding light on synergistic modulators of PI(4,5)P2 cluster formation (Figure 1). Thus, this work has potentially far reaching consequences for understanding temporal control of the spatially resolved protein activity.

Drug delivery technology is currently advancing faster than at any time in biotechnology history. The challenge of drug delivery is to achieve a controlled release of therapeutic agents over an extended period. Controlled release potentially offers significant advantages over conventional dosage forms, by eliminating both under- and overdosing while maintaining a desired range of drug concentrations. An existing drug regimen for induced calving produces a declining blood profile that does not mimic the naturally occurring, gradually increasing, cortisol blood level around parturition effectively, causing animal health issues. Likewise, while the existing progesterone controlled release systems for oestrous control successfully synchronise oestrus, it is however, associated with reduced fertility and as such other drugs have to be administered to improve the fertility during oestrus. Therefore, there is a need for a drug delivery system that is capable of delivering multiple drugs at various times and patterns. This research aimed to investigate, characterize, identify steroids with high absorption rates through vaginal mucosa and evaluate the potential of an electronic drug delivery system for the delivery of steroids for either the control of the bovine oestrous cycle or induced calving. In order to identify steroids with high absorption rates across the vaginal mucosa, an in vitro permeation method was developed to screen selected steroids for their ability to permeate artificial and biological membranes. The steroids were pre-formulated to enhance their solubility and permeation through these membranes. Analytical UV and HPLC assays to characterise the pure and formulated steroidal compounds were also developed and validated. An assessment of an intravaginal Electronically Modulated Intravaginal Device (EMID) for the control of the bovine oestrous cycle or induced calving was carried out. Five different release assessment methods were investigated and critically evaluated in order to identify the most appropriate release assessment method for the EMID. These were: 1) the Drug Dissolution Test, 2) a weight loss method, 3) the dispensed weight method, 4) the determination of piston travel distance method, and 5) the rod expulsion from the EMID method. The methods investigated were critically evaluated in terms of ease of use and automation, reproducibility and cost/time savings. Optimisation of various components and construction materials of the EMID were also investigated. Animal trials were carried out using the original EMID (manufactured from polypropylene polymer) and modified inserts (manufactured from high density polyethylene polymer) to determine their retention rate in the animals. Accelerated stability testing of progesterone in suspension, oestradiol-17 tablets, cloprostenol as a powder blend and the driving mechanism of the EMID were examined. The flux of the steroids was evaluated through poly-&-caprolactone and excised cow mucosa membranes using side-by-side permeation cells. Results indicated that progesterone followed by dexamethasone acetate and dexamethasone valerate showed higher permeability values through vaginal mucosa compared to dexamethasone or its other analogues. The weight loss method of the EMID proved to be an easy and appropriate method to measure the release rate from the EMID. A high density polyethylene polymer was identified as the most ideal body material for the insert compared to polypropylene body. Also double O-ring silicone, Elastollan WYO 1388-5 and solid silicone pistons were found to be amongst the best pistons tested and all performed well compared to other piston materials. There was a low retention rate with either the original EMID or the modified inserts. Further modification of retention wings of the EMID did not improve the retention rate, but a good blood profile response was obtained from cows treated with the complete EMID containing formulated progesterone. The formulations and driving mechanism were found to be stable under the tested conditions. Therefore, the EMID has potential for commercial application of induced calving or oestrous control per vaginum administration, reliant on improvement of its retention mechanism.

Dans les pays industrialisés, une alimentation riche en lipides et en sucres et le manque d'exercice sont responsables d'une épidémie d'obésité, d'insulino-résistance (IR) et de stéatose hépatique non-alcoolique (NAFLD). L'alimentation apporte différents types de lipides, et non seulement la quantité mais également la qualité des lipides alimentaires module le métabolisme lipidique et joue un rôle important dans le développement de ces pathologies. La nature des acides gras (AG) ingérés peut également influencer la composition des membranes biologiques, et ainsi leurs fonctions comme la fluidité membranaire, la signalisation cellulaire, la translocation des protéines vers la membrane ou à travers la membrane, et des activités enzymatiques variées. Le fonctionnement de la cellule toute entière dépend donc de la composition membranaire en lipides. Par ailleurs, certains microconstituants alimentaires, tels les polyphénols, pourraient moduler le métabolisme lipidique, prévenant ainsi la NAFLD et l'IR.L'objectif de ce travail de thèse est d'explorer, en même temps, l'impact potentiellement protecteur des polyphénols lors d'une surcharge en graisses et en saccharose d'un côté et l'effet de différents profils lipidiques nutritionnels d'un autre sur la composition en acides gras et les taux des différents lipides complexes (triglycérides (TG) tissulaires et phospholipides (PL) membranaires) et sur le métabolisme lipidique en s'intéressant au tissu tout entier et à la mitochondrie en particulier ; puisque de plus en plus d'arguments expérimentaux et cliniques suggèrent qu'un déficit de la chaîne respiratoire mitochondriale joue un rôle physiopathologique important dans la NAFLD et l'IR. Ainsi, ce travail de thèse nous a permis de montrer qu'une supplémentation en polyphénols à dose nutritionnelle modulerait différemment le métabolisme lipidique au niveau des tissus, (1) en activant l'oxydation des AG et prévenant l'accumulation des TG intra-hépatiques et la stéatose au niveau du foie ; et (2) en modulant la composition membranaire en AG des cellules musculaires ainsi que l'expression de certains transporteurs prévenant ainsi l'accumulation cytosolique des lipides et améliorant le transport du glucose ce qui préviendrait une IR au niveau du muscle. De plus, nous avons pu montrer que la qualité et la quantité des AG apportés par l'alimentation affecteraient de façon significative la composition en acide gras de l'ensemble des PL membranaires de la mitochondrie du foie, particulièrement le cardiolipide; altérant ainsi la fonction de la mitochondrie et le métabolisme lipidique au niveau du foie, ce qui pourrait jouer un rôle dans le développement de la NAFLD. / High fat and high sugar diets and lack of physical activity are believed to contribute to the increasing rates of obesity in wealthy societies. This trend is associated with a parallel increase in the prevalence of insulin resistance (IR) and non-alcoholic fatty liver disease (NAFLD). Diets contains different types of lipids, and not only the quantity but also the quality of dietary lipids modulates lipid metabolism and are involved in these nutritional associated pathologies. Moreover, the quality of dietary lipids influences the biological membrane composition and thus their functions. So, membrane fluidity, cellular signalisation pathways, protein translocation into and across the membrane and many enzymatic activities, which are crucial for cell functions, are influenced by membrane lipid composition. However, some dietary nutrients as polyphenols may also modulate lipid metabolism and thus prevent against hepatic steatosis and/or IR. In that aim, this work was designed to determine, firstly, the preventive effect of polyphenols in rats fed a high fat high sucrose diet and, secondly, the impact of the quantity and the quality of dietary lipids, on triglycerides (TG) and membranes phospholipids (PL) content and/or fatty acid composition and on lipid metabolism in the whole tissue and particularly in mitochondria. Indeed, mitochondria are both a major site for fat metabolism and the main source of reactive oxygen species in hepatocytes and they are postulated to play a central role in the pathogenesis of NAFLD and IR. Our results showed clearly that polyphenols modulate differently lipid metabolism in tissues. In liver, polyphenols prevent lipid accumulation and hepatic steatosis by activating fatty acid oxidation. In skeletal muscle, polyphenols regulate membrane fatty acids composition and fatty acid and glucose transporters expression, thus preventing lipid accumulation and enhancing glucose transport. These modifications may prevent IR in skeletal muscle. In addition, dietary fatty acids quantity and quality influenced significantly fatty acids composition of membrane phospholipids from liver mitochondria, particularly cardiolipin; and thus altered mitochondria functions and liver lipid metabolism which could play a role in the NAFLD pathogenesis.