In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.

No description available.

In the last few decades, an increasing number of physicists specialized in soft matter, including polymers, have turned their attention to biologically relevant materials. The properties of various molecules and fibres, such as DNA, RNA, proteins, and filaments of all sorts, are studied to better understand their behaviours and functions. Self-assembled biological membranes, or lipid bilayers, are also the focus of much attention as many life processes depend on these. Small lipid bilayers vesicles dubbed liposomes are also frequently used in the pharmaceutical and cosmetic industries. In this thesis, work is presented on both the elastic properties of polymers and the response of lipid bilayer vesicles to extrusion in narrow-channels. These two areas of research may seem disconnected but they both concern deformed soft materials. The thesis contains four articles: the first presenting a fundamental study of the entropic elasticity of circular chains; the second, a simple universal description of the effect of sequence on the elasticity of linear polymers such as DNA; the third, a model of the symmetric thermophoretic stretch of a nano-confined polymer; the fourth, a model that predicts the final sizes of vesicles obtained by pressure extrusion. These articles are preceded by an extensive introduction that covers all of the essential concepts and theories necessary to understand the work that has been done.

Vesicles are simple structures, but display complex, non-linear dynamics in fluid flow. I investigate the deformation of nanometer-sized vesicles, both fully-inflated and those with excess area, as they travel in tightly confined capillaries. By varying both channel size and flow strength, I simulate vesicles as they transition from steady-state to unstable shapes, and then rupture in strong flow fields. By employing a molecular dynamics model of the vesicle, fluid, and capillary system one is able to rupture the lipid bilayer of these vesicles. This is unique in that most other numerical methods for modelling vesicles are unable to show rupture. The rupture of fully-inflated vesicles is applicable to drug delivery in which the release of the encapsulated medicine needs to be controlled. The deformation and rupture of vesicles with excess area could be applicable to red blood cells which have similar rheological properties.

No description available.

No / Chemical means of manipulating the distribution of lipids across biological membranes is of considerable interest for many biomedical applications as a characteristic lipid distribution is vital for numerous cellular functions. Here we employ atomic-scale molecular simulations to shed light on the ability of certain amphiphilic compounds to promote lipid translocation (flip-flops) across membranes. We show that chemically induced lipid flip-flops are most likely pore-mediated: the actual flip-flop event is a very fast process (time scales of tens of nanoseconds) once a transient water defect has been induced by the amphiphilic chemical (dimethylsulfoxide in this instance). Our findings are consistent with available experimental observations and further emphasize the importance of transient membrane defects for chemical control of lipid distribution across cell membranes

No / To gain a better understanding of how ethanol affects biological membranes, we have performed a series of atomic-scale molecular dynamics simulations of phospholipid membranes in aqueous solution with ethanol, whose concentration was varied from 2.5 to 30 mol % (lipid-free basis). At concentrations below the threshold value of ~12 mol % (30.5 v/v %) ethanol induces expansion of the membrane, accompanied by a drop in the membrane thickness as well as disordering and enhanced interdigitation of lipid acyl chains. These changes become more pronounced with increase in ethanol concentration, but the bilayer structure of the membrane is maintained. Above the threshold concentration the appearance of multiple transient defects in the lipid/water interface eventually gives rise to desorption and assembly of some of the lipids into non-bilayer structures within the membrane interior. These structures, being small and irregular, resemble inverted micelles and have a long-lived character. Furthermore, formation of the non-bilayer structures is accompanied by mixing of lipids that belong to the opposite membrane leaflets, thereby leading to irreversible changes in the membrane structure. Remarkably, this observation of the formation of non-bilayer structures within the membrane interior, being in good agreement with experimental data, is found to be robust with respect to both the simulation conditions (the system size and the presence of salt) and the type of lipids (phosphatidylcholine and phosphatidylethanolamine). We discuss the significance of these non-bilayer structures in relation with the well-known ability of ethanol to promote membrane hemifusion as well as with the possible role of the micelle-like structures as a delivery system for polar solutes and ions. The ethanol-induced "damage" to the bilayer structure also suggests that strong alcoholic beverages (~40 v/v %) might be potentially hazardous to the epithelial tissues of the human body (such as lips, mouth, throat, gullet, and stomach) that come in direct contact with high-concentrations of ethanol.

Carbohydrate molecules are essential parts of living cells. They are used as energy storage and signal substances, and they can be found incorporated in the cell membranes as attachments to glycoproteins and glycolipids, but also as free molecules. In this thesis the effect of carbohydrate molecules on phospholipid model membranes have been investigated by the means of Molecular Dynamics (MD) computer simulations. The most abundant glycolipid in nature is the non-bilayer forming monogalactosyldiacylglycerol (MGDG). It is known to be important for the membrane stacking typical for the thylakoid membranes in plants, and has also been found essential for processes related to photosynthesis. In Paper I, MD simulations were used to characterize structural and dynamical changes in a lipid bilayer when MGDG is present. The simulations were validated by direct comparisons between dipolar couplings calculated from the MD trajectories, and those determined from NMR experiments on similar systems. We could show that most structural changes of the bilayer were a consequence of lipid packing and the molecular shape of MGDG. In certain plants and organisms, the enrichment of small sugars such as sucrose and trehalose close to the membrane interfaces, are known to be one of the strategies to survive freezing and dehydration. The cryoprotecting abilities of these sugar molecules are long known, but the mechanisms at the molecular level are still debated. In Papers II–IV, the interactions of trehalose with a lipid bilayer were investigated. Calculations of structural and dynamical properties, together with free energy calculations, were used to characterize the effect of trehalose on bilayer properties. We could show that the binding of trehalose to the lipid bilayer follows a simple two state binding model, in agreement with recent experimental investigations, and confirm some of the proposed hypotheses for membrane–sugar interactions. The simulations were validated by dipolar couplings from our NMR investigations of TRH in a dilute liquid crystal (bicelles). Furthermore, the assumption about molecular structure being equal in the ordered and isotropic phases was tested and verified. This assumption is central for the interpretation of experimentally determined dipolar couplings in weakly ordered systems. In addition, a coarse grain model was used to tackle some of the problems with slow dynamics that were encountered for trehalose in interaction with the bilayer. It was found that further developments of the interaction models are needed to properly describe the membrane–sugar interactions. Lastly, from investigations of trehalose curvature sensing, we concluded that it preferably interacts in bilayer regions with high negative curvature. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 4: Manuscript.</p>

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

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.