Les vésicules sont des bicouches fermées de molécules tensioactives, remplies de liquide, à l'intérieur d'un autre liquide. Leur taille peut être comprise entre dix et 100 microns : elles sont alors dites géantes. Nous nous intéressons à la dynamique de deux de ces objets dans un cisaillement simple, c'est à dire l'écoulement d'un liquide situé entre deux plaques planes se translatant l'une par rapport à l'autre à vitesse et distance constante. Nous commençons par une étude asymptotique, pour des vésicules quasi-sphériques en interaction lointaine. Nous utilisons ensuite un code de calcul basé sur la méthode des éléments de frontière pour étudier le cas de vésicules moins sphériques et plus proches, et comparons les résultats obtenus avec des expériences. Nous présentons enfin comment cette étude peut être utilisée pour prédire certaines propriétés de diffusion d'une suspension de vésicules, dans le régime semi-dilué, où seul le détail des interactions à deux corps est considéré. / Vesicles are closed bilayers of tensioactive molecules, filled with liquid, inside another liquid. Their size can be between 10 and 100 microns : in this case, they are called giant vesicles. We study the dynamic of two of these objects in a simple shear flow, which is the one of a liquid sheared between two walls translating with respect to each other at a constant speed and distance. We begin by an asymptotic study, for quasispherical vesicles in the far field interacting regime. We then use a numerical code based on the boundary element method to study the case of less spherical and closer vesicles, and compare our results with experiments. We finish by presenting how this study can be used to predict some diffusing properties of a sheared suspension of vesicles, in the semidilute regime, where only the details of two body interactions are considered.

Les vésicules sont gouttes de rayon de quelques dizaines de micromètres, limitées par une membrane lipidique imperméable d'environ 4 nm d'épaisseur, et immergées dans un fluide visqueux externe. Les propriétés spécifiques de la membrane de la vésicule rendent le système très déformable et très contraint dans le même temps. Les vésicules représentent également un modèle simplifié intéressant pour les globules rouges, car ils partagent aussi certains comportements mécaniques similaires.Ce manuscrit s’intéresse à la modélisation d'une vésicule soumise à des contraintes externes d'origine hydrodynamique, dans le régime Stokes et dans des domaines confinés. À partir d'un modèle BEM déjà existant pour des fluides infinis, des méthodes numériques originales sont développés pour faire face au calcul des interactions entre la membrane de la vésicule et les frontières solides. Une attention particulière est accordée à la situation d'une vésicule qui sédimente vers un mur horizontal et une vésicule soumise à un écoulement de Poiseuille dans un capillaire étroit. / Vesicles are drops of radius of a few tens micrometers, bounded by an impermeable lipid membrane of approximately 4 nm thickness, and embedded in an external viscous fluid. The specific properties of the vesicle membrane make the system very deformable and very constrained at the same time. Vesicles represent also an interesting simplified model for red blood cells, since they also share some similar mechanical behaviours.This manuscript deals with the modeling of a vesicle subjected to external stresses of hydrodynamical origin, in the Stokes regime and in confined domains. Starting from an existing BEM model for free space flows, original numerical methods are developed to deal with the computation of interactions between the vesicle membrane and solid boundaries. A particular attention is paid to the situation of a vesicle sedimenting towards a planar wall and a vesicle submitted to a Poiseuille flow in a narrow capillary.

Orientadores: Mirna Lucia Gigante, Rafael Jimenez-Flores / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-09-11T21:12:34Z (GMT). No. of bitstreams: 1 Costa_MarceladeRezende_D.pdf: 1269005 bytes, checksum: be9b972dd7766eba5cc6917dd666c5f0 (MD5) Previous issue date: 2008 / Resumo: O leitelho de soro é um subproduto do processamento de manteiga a partir do creme de soro. Esse subproduto lácteo contém fragmentos da membrana do glóbulo de gordura do leite (MGGL), material rico em componentes com funções nutricionais e efeitos benéficos à saúde, destacando-se os fosfolipídeos. O objetivo desse trabalho foi obter um ingrediente lácteo enriquecido em fosfolipídeos da MGGL a partir do leitelho de soro utilizando a associação de duas tecnologias de fracionamento: ultrafiltração e extração com fluido supercritico (EFS). O leitelho de soro foi submetido à ultrafiltração e a cinco diafiltrações a 25 °C e o retentado obtido foi seco em spray-dryer, obtendo-se o leitelho de soro em pó (LSP), o qual foi submetido a três ciclos de extração a 50 °C com dióxido de carb ono supercrítico. As matériasprimas, produtos finais e uma amostra comercial de leitelho tradicional em pó (LTP) foram analisados quanto a sua composição centesimal, teor de fosfolipídeos, perfis lipídico e protéico. Os leitelhos de soro em pó, submetidos ou não à EFS, e o LTP foram avaliados quanto ao tamanho de partículas e suas propriedades funcionais (solubilidade protéica e capacidade emulsificante) em pH 5 e 7. A filtração em membrana reduziu em 74 e 96% os teores de lactose e cinzas no retentado e aumentou os de proteínas, lipídeos e fosfolipídeos em 91, 190 e 300%, respectivamente. A EFS reduziu em 55,4% o teor de lipídeos, removendo exclusivamente lipídeos apolares, com isso aumentou em 71% o teor de fosfolipídeos no leitelho de soro em pó, resultando em um produto com 73% de proteínas, 21% de lipídeos, 3% de lactose, 3% de cinzas e 12% de fosfolipídeos, em base seca. As propriedades funcionais dos leitelhos de soro em pó, submetidos à extração supercrítica (LSP-EFS) ou não (LSP), foram pouco ou não afetadas pelo pH, enquanto o abaixamento de pH prejudicou as características do LTP, devido ao alto teor de caseínas nesse tipo de pó em relação aos de leitelhos de soro. Os pós em soluções (5% de proteína) apresentaram de 69 a 84% de suas partículas, em % volumétrica, entre 10 e 100 µm. A solução de LTP em pH 5 foi a que apresentou a maior quantidade de partículas acima de 100 µm. LSP e LSP-EFS apresentaram solubilidades protéicas em torno de 86 e 84%, respectivamente, independente do pH. O LTP teve a solubilidade reduzida de 86 para 73% quando o pH foi reduzido de 7 para 5. Em pH 7, as emulsões (20% óleo de canola, 1% proteína) de LSP e de LSPEFS apresentaram melhor estabilidade (IC de 0,2 e 0,4%, respectivamente) do a emulsão de LTP (IC de 3,0%). Em pH 5, a emulsão de LSP-EFS foi a que mostrou melhor estabilidade, apresentando um IC de 7%, valor cerca de 82% menor do que os das emulsões de LSP e LTP. Os leitelhos de soro em pó obtidos podem ser considerados ingredientes com características promissoras, associando propriedades tecnológicas, especialmente para uso em alimentos de baixo pH, e conteúdo de compostos potencialmente benéficos à saúde, principalmente após o tratamento com extração supercrítica / Abstract: OBTENTION OF DAIRY INGREDIENT ENRICHED IN POLAR LIPIDS FROM WHEY BUTTERMILK. Whey buttermilk is a by-product from the whey cream processing into butter. This dairy by-product contains milk fat globule membrane (MFGM) fragments, a material rich in components with nutritional functions and beneficial health effects, especially phospholipids. The objective of this research was obtaining a dairy ingredient enriched in MFGM phospholipids from whey buttermilk using the association of two fractionation technologies: ultrafiltration and supercritical fluid extraction (SFE). Whey buttermilk was submitted to ultrafiltration and five diafiltrations at 25 °C. The retentate was spray-dried and later s ubmitted to three cycles of extraction at 50 °C with supercritical carbon dioxi de. Raw materials, final products and a commercial traditional buttermilk powder sample (BMP) were analyzed for gross composition, lipid and protein profiles, and phospholipids content. Whey buttermilk powders, before and after the SFE, and the BMP had particle size and some functional properties (protein solubility and emulsifying capacity) evaluated in pH 5 and 7. Membrane filtration reduced in 74 and 96% lactose and ash contents in the retentate and increased proteins, lipids and phospholipids in 91, 190 and 300%, respectively. SFE reduced in 55.4% the lipids content, removing exclusively non-polar lipids, while increased in 71% the phospholipids content in whey buttermilk powder, resulting in a product with 73% of proteins, 21% of lipids, 3% of lactose, 3% of ash and 12% of phospholipids, in dry matter basis. Functional properties of the whey buttermilk powders, treated (WBP-SFE) or not through SFE (WBP), were little or not affected by pH, while dropping the pH impaired the BMP features, due the high casein content in this type of powder in relation to the ones from whey buttermilk. The powders in solutions (5% protein) presented from 69 to 84% of the particles, in volume%, between 10 and 100 µm. The BMP solution in pH 5 was the one with the biggest amount of particles above 100 µm. WBP and WBP-SFE showed protein solubilities around 86 and 84%, respectively, independent of pH. BMP had the solubility reduced from 86 to 73% when pH was reduced from 7 to 5. In pH 7, the emulsions (20% canola oil, 1% protein) of the WBP and the WBP showed better stability (CI of 0.2 and 0.4%, respectively) than the BMP emulsion (CI of 3.0%). When in pH 5, WBP-SFE emulsion had the best stability, presenting CI of 7%, value about 82% smaller than the ones of WBP and BMP emulsions. Whey buttermilk powders obtained in this work can be considered ingredients with promising features, combining technological properties, especially for use in low pH foods, and content of components with potential health benefits, mainly after the supercritical extraction treatment / Doutorado / Doutor em Tecnologia de Alimentos

Résumé confidentiel / Résumé confidentiel

Le globule rouge a une grande faculté à se déformer, notamment lorsqu?il traverse des capillaires dont le diamètre peut être inférieur au sien. Cette résistance au cisaillement est attribuée à sa membrane particulière. Celle-ci est constituée d?une bicouche lipidique sur laquelle est fixé un réseau bidimensionnelle de protéines : le squelette. Ce squelette est principalement constitué de longs filaments de spectrine (~200 nm) reliés entre eux et à la bicouche lipidique par des complexes de jonction. Dans la première partie de ce travail, nous avons mesuré le module de cisaillement µ de la membrane (bicouche lipidique + squelette) à l?aide de deux pinces optiques. Deux billes de silice attachées à la membrane sont utilisées pour lui appliquer des forces connues. Le module de cisaillement est déduit de la déformation mesurée en fonction de la contrainte appliquée. Nous avons trouvé µ = 2.5 +/- 0.4 µN/m, valeur du même ordre de grandeur, mais inférieure, à celles obtenues par d?autres techniques. Dans une seconde partie, nous mesurons les modules d?extension KC et de cisaillement µC du squelette seul. Un globule rouge avec trois billes un piégé, et une solution de détergent est injectée afin de dissoudre la bicouche lipidique. Le squelette reste attaché aux billes et il est ensuite déformé en déplaçant les billes les unes par rapport aux autres. Les modules élastiques sont déduits de la mesure des contraintes et des déformations. Nous trouvons KC = 4.8 +/- 2.7 µN/m et µC = 2.4 +/- 0.7 µN/m dans une solution d?osmolarité égale à 25 mOsm/kg. De ces mesures, nous pouvons déduire la longueur de persistance de la spectrine, ici 5 nm. Ces valeurs sont en bon accord avec des prédictions théoriques et numériques réalisées sur des réseaux bidimensionnels de ressorts. L?influence de la force ionique et du vieillissement du squelette après l?extraction sont étudiés dans la dernière partie.

Il existe, aujourd'hui, de nombreuses et efficaces méthodes de caractérisation structurale tridimensionnelle de composés biologiques en phase condensée (RMN, diffraction des rayons X ou dichroïsme circulaire). Depuis une dizaine d'années, ce champ d'études s'est étendu à la phase gazeuse. Ce travail s'inscrit dans ce contexte et concerne le rôle structurant de Na+ sur les acides aminés Gly et Pro et sur des oligo-peptides de Gly et Ala, en combinant approches théoriques et expérimentales de spectroscopie infrarouge d'ions gazeux par dissociation multiphotonique (IRMPD) couplée à la spectrométrie de masse. Les spectres IRMPD expérimentaux des complexes sodiés d'acide aminé, nous ont permis d'identifier la présence exclusive de la forme zwitterionique dans le cas de Pro-Na+ et la présence de la forme non-zwitterionique dans le cas de Gly-Na+, conformément aux résultats de chimie quantique. Ainsi nous avons fourni la première démonstration directe de la présence d'un zwitterion d'acide aminé en phase gazeuse. Il s'agissait des premiers spectres infrarouge d'ions biologiques en phase gazeuse. L'étude théorique des complexes Glyn-Na+ et Alan-Na+ a montré que, pour n<=5, les conformères de plus basse énergie maximisent l'interaction électrostatique du métal avec les n groupements carbonyles, avec ou sans l'amine terminale. Ce comportement a été confirmé d'une part, par des expériences de spectroscopie IRMPD pour n=2,3 et d'autre part, par la détermination des énergies de liaison de ces complexes par la méthode cinétique de Cooks (n=2-4). Pour l'étude théorique de Glyn-Na+, 5<=n<=10, nous avons couplé des recherches conformationnelles Monte-Carlo basées sur des calculs de champ de forces AMBER, à des optimisations par calculs de type ri-BLYP utilisant l'approximation "résolution de l'identité". Cette approche a permis d'explorer en détail des sur! faces de potentiel très complexes. On peut distinguer deux classes limites de conformères, celle où le peptide est globulaire et celle où il adopte une conformation en hélice alpha ou 310. Nous avons montré que les structures les plus basses en énergie présentent le plus souvent une complexation tétradentate avec une forte auto-solvatation. Ces structures sont toutes globulaires pour n<10. Dans le cas de Gly10-Na+, le conformère le plus bas en énergie a une structure globulaire autour du sodium et un domaine de cinq résidus en hélice 310.

Fluctuations in protein structure are vital to function. This contrasts the dominating structure-function paradigm, which connects the well-defined three-dimensional protein structure to its function. However, catalysis is observed in disordered enzymes, which lack a defined structure. Disordered proteins are involved in molecular recognition events as well. The aim of this Thesis is to describe the structural changes occuring in protein structure and to investigate the mechanism of molecular recognition. Protein architecture is classified in a hierarchical manner, that is, it is categorized into primary, secondary, and tertiary levels. One of the major questions in biology today is how proteins fold into a defined three-dimensional structure. Some protein folding models, like the framework model, suggest that the secondary structure, like α-helices, is formed before the tertiary structure. This Thesis raises two questions: First, are structural fluctuations that occur in the protein related to the folding of the protein structure? Second, is the hierarchic classification of the protein architecture useful to describe said structural fluctuations? Kinetic studies of protein folding show that important dynamical processes of the folding occur on the microsecond timescale, which is why time-resolved fluorescence spectroscopy was chosen as the principal method for studying structural fluctuations in the peptides. Time-resolved fluorescence spectroscopy offers a number of experimental advantages and is useful for characterizing typical structural elements of the peptides on the sub-microsecond timescale. By observing the fluorescence lifetime distribution of the fluorescent probe, which is a part of the hydrophobic core of a four-helix bundle, it is shown that the hydrophobic core changes hydration state, from a completely dehydrated to a partly hydrated hydrophobic core. These fluctuations are related to the tertiary structure of the four-helix bundle and constitute structural transitions between the completely folded four-helix bundle and the molten globule version. Equilibrium unfolding of the four-helix bundle, using chemical denaturants or increased temperature, shows that the tertiary structure unfolds before the secondary structure, via the molten globule state, which suggests a hierarchic folding mechanism of the four-helix bundle. Fluctuations of a 12 amino acid long helical segment, without tertiary structure, involve a conformational search of different helical organizations of the backbone. Binding and recognition of a helix-loop-helix to carbonic anhydrase occurs through a partly folded intermediate before the final tertiary and bimolecular structure is formed between the two biomolecules. This confirms the latest established theory of recognition that the binding and the folding processes are coupled for the binding molecules.

<p>Proteins with highly specific binding properties constitute the basis for many important applications in biotechnology and medicine. Immunoglobulins have so far been the obvious choice but recent advances in protein engineering have provided several novel constructs that indeed challenge antibodies. One class of such binding proteins is based on the 58 residues three-helix bundle Z domain from staphylococcal protein A (SPA). These so-called affibodies are selected from libraries containing Z domain variants with 13 randomised positions at the immunoglobulin Fc-binding surface. This thesis aims to describe the principles for molecular recognition in two protein-protein complexes involving affibody proteins. The first complex is formed by the Z_SPA-1 affibody binding to its own ancestor, the Z domain (Kd ~1 μM). The second complex consists of two affibodies: Z_Taq, originally selected to bind Taq DNA polymerase, and anti-Z_Taq, an anti-idiotypic binder to Z_Taq with a Kd ~0.1 μM. The basis for the study is the determination of the three-dimensional structures using NMR spectroscopy supported by biophysical characterization of the uncomplexed proteins and investigation of binding thermodynamics using isothermal titration calorimetry. The free Z_SPA-1 affibody is a molten globule-like protein with reduced stability compared to the original scaffold. However, upon target binding it folds into a well-defined structure with an interface topology resembling that displayed by the immunoglobulin Fc fragment when bound to the Z domain. At the same time, structural rearrangements occur in the Z domain in a similar way as in the Fc-binding process. The complex interface buries 1632 Ų total surface area and 10 out of 13 varied residues in Z_SPA-1 are directly involved in inter-molecular contacts. Further characterization of the molten globule state of Z_SPA-1 revealed a native-like overall structure with increased dynamics in the randomised regions (helices 1 and 2). These features were reduced when replacing some of the mutated residues with the corresponding wild-type Z domain residues. The nature of the free Z_SPA-1 affects the thermodynamics of the complex formation. The contribution from the unfolding equilibrium of the molten globule was successfully separated from the binding thermodynamics. Further decomposition of the binding entropy suggests that the conformational entropy penalty associated with stabilizing the molten globule state of Z_SPA-1 upon binding seriously reduces the binding affinity. The Z_Taq:anti-Z_Taq complex buries in total 1672 Ų surface area and all varied positions in anti-Z_Taq are directly involved in binding. The main differences between the Z:Z_SPA-1 and the Z_Taq:anti-Z_Taq complexes are the relative subunit orientation and certain specific interactions. However, there are also similarities, such as the hydrophobic interface character and the role of certain key residues, which are also found in the SPA:Fc interaction. Structural rearrangements upon binding are also common features of these complexes. Even though neither Z_Taq nor anti-Z_Taq shows the molten globule behaviour seen for Z_SPA-1, there are indications of dynamic events that might affect the binding affinity. This study provides not only a molecular basis for affibody-target recognition, but also contributions to the understanding of the mechanisms regulating protein stability and protein-protein interactions in general.</p>

Un polypeptide néosynthétisé est capable de trouver rapidement le chemin vers sa structure tri-dimensionnelle finale, en passant par des intermédiaires partiellement structurés. L'acquisition d'information sur le rôle et l'importance de ces intermédiaires est rendue difficile parce qu'ils se forment très rapidement pendant la réaction de repliement et que cette période de temps n'est pas accessible aux appareils de mélange usuels.<br />L'objet de cette thèse était de caractériser les évènements cinétiques initiaux du repliement des protéines, notamment de l'apomyoglobine (apoMb), en utilisant des appareils de mélange ultra-rapide. Un appareil de type stopped-flow équipé d'une micro-cuve a permis de diminuer le temps mort de ce type de mélangeur. Une réaction bimoléculaire (NATA et NBS), à permis d'évaluer le temps mort à 400±10 µs, dans un mode d'utilisation permettant de suivre simultanément le signal de fluorescence et le signal de dichroïsme circulaire dans l'UV lointain. L'apoMb est une protéine particulièrement intéressante pour l'étude des évènements précoces du repliement des protéines. Le stopped-flow ultra rapide, a permis de suivre des cinétiques (k jusqu'à 1500 s-1) et montré que chaque étape précédemment identifiée, conduisant l'apoMb de sa forme dépliée à sa forme native (soit les réactions UIa, IaIb, et IbN), présente les caractéristiques typiques d'une réaction à deux états, hautement coopérative.<br />Nous avons étudié l'effet d'osmolytes sur les cinétiques et sur la stabilité à l'équilibre des formes U, I et N de l'apoMb. Des études cinétiques en présence de sucrose ont permis d'observer le comportement de la réactions UIa. Ces résultats indiquent que le sucrose déstabilise de manière relative la forme U et l'état de transition de la réaction UIa, par rapport à la forme Ia. L'étape limitante ne correspondrait donc pas à une compaction de la chaîne peptidique. Dans les mêmes conditions, l'étude de la transition IbN permet d'observer que l'état de transition présente des caractéristiques proches de Ib. Ces résultats, décrivant l'effet osmophobique sur l'intermédiaire I, ainsi que des résultats préliminaires de l'effet d'encombrement moléculaire sur le repliement du cytochrome C, sont discutés dans ce mémoire.

Proteins with highly specific binding properties constitute the basis for many important applications in biotechnology and medicine. Immunoglobulins have so far been the obvious choice but recent advances in protein engineering have provided several novel constructs that indeed challenge antibodies. One class of such binding proteins is based on the 58 residues three-helix bundle Z domain from staphylococcal protein A (SPA). These so-called affibodies are selected from libraries containing Z domain variants with 13 randomised positions at the immunoglobulin Fc-binding surface. This thesis aims to describe the principles for molecular recognition in two protein-protein complexes involving affibody proteins. The first complex is formed by the ZSPA-1 affibody binding to its own ancestor, the Z domain (Kd ~1 μM). The second complex consists of two affibodies: ZTaq, originally selected to bind Taq DNA polymerase, and anti-ZTaq, an anti-idiotypic binder to ZTaq with a Kd ~0.1 μM. The basis for the study is the determination of the three-dimensional structures using NMR spectroscopy supported by biophysical characterization of the uncomplexed proteins and investigation of binding thermodynamics using isothermal titration calorimetry. The free ZSPA-1 affibody is a molten globule-like protein with reduced stability compared to the original scaffold. However, upon target binding it folds into a well-defined structure with an interface topology resembling that displayed by the immunoglobulin Fc fragment when bound to the Z domain. At the same time, structural rearrangements occur in the Z domain in a similar way as in the Fc-binding process. The complex interface buries 1632 Å2 total surface area and 10 out of 13 varied residues in ZSPA-1 are directly involved in inter-molecular contacts. Further characterization of the molten globule state of ZSPA-1 revealed a native-like overall structure with increased dynamics in the randomised regions (helices 1 and 2). These features were reduced when replacing some of the mutated residues with the corresponding wild-type Z domain residues. The nature of the free ZSPA-1 affects the thermodynamics of the complex formation. The contribution from the unfolding equilibrium of the molten globule was successfully separated from the binding thermodynamics. Further decomposition of the binding entropy suggests that the conformational entropy penalty associated with stabilizing the molten globule state of ZSPA-1 upon binding seriously reduces the binding affinity. The ZTaq:anti-ZTaq complex buries in total 1672 Å2 surface area and all varied positions in anti-ZTaq are directly involved in binding. The main differences between the Z:ZSPA-1 and the ZTaq:anti-ZTaq complexes are the relative subunit orientation and certain specific interactions. However, there are also similarities, such as the hydrophobic interface character and the role of certain key residues, which are also found in the SPA:Fc interaction. Structural rearrangements upon binding are also common features of these complexes. Even though neither ZTaq nor anti-ZTaq shows the molten globule behaviour seen for ZSPA-1, there are indications of dynamic events that might affect the binding affinity. This study provides not only a molecular basis for affibody-target recognition, but also contributions to the understanding of the mechanisms regulating protein stability and protein-protein interactions in general. / QC 20101025