<div>Large protein molecules are abundant in biological cells but are very difficult to study in physiological conditions due to molecular disorder. For large proteins, most structural information is obtained in crystalline states which can be achieved in certain conditions at very low temperature. X-ray and neutron crystallography methods can then be used for determination of crystalline structures at atomic level. However, in solution at room or physiological temperatures such highly resolved descriptions cannot be obtained except in very few cases. Scattering methods that can be used to study this type of structures at room temperature include small-angle x-ray and neutron scattering. These methods are used here to study two distinct proteins that are both classified as glycoproteins, which are a large class of proteins with diverse biological functions. In this study, two specific plasma glycoproteins were used: Fibrinogen (340 kDa) and Alpha 1-Antitrypsin or A1AT (52 kDa). These proteins have been chosen based on the fact that they have a propensity to form very large molecular aggregates due to their tendency to polymerize. One goal of this project is to show that for such complex structures, a combination of scattering methods that include SAXS, SANS, and DLS can address important structural and interaction questions despite the fact that atomic resolution cannot be obtained as in crystallography. A1AT protein has been shown to have protective roles of lung cells against emphysema, while fibrinogen is a major factor in the blood clotting process. A systematic approach to study these proteins interactions with lipid membranes and other proteins, using contrast-matching small-angle neutron scattering (SANS), small angle x-ray scattering (SAXS) and dynamic light scattering (DLS), is presented here. A series of structural reference points for each protein in solution were determined by performing measurements under osmotic stress controlled by the addition of polyethylene glycol-1,500 MW (PEG 1500) in the samples. Osmotic pressure changes the free energy of the molecular mixture and has consequences on the structure and the interaction of molecular aggregates. In particular, the measured radius of gyration (Rg) for A1AT shows a sharp structural transition when the concentration of PEG 1500 is between 33 wt\% and 36 wt\%. Similarly, a significant structural change was observed for fibrinogen when the concentration of PEG 1500 was above 40 wt\%. This analysis is applied to a study of A1AT interacting with lipid membranes and to a study of fibrinogen polymerization in the presence of the enzyme thrombin, which catalyzes the formation of blood clots. The experimental approach presented here and the applications to specific questions show that an appropriate combination of scattering methods can produce useful information on the behavior and the interactions of large protein systems in physiological conditions despite the lower resolution compared to crystallography.</div>

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Noble metal nanoparticles have attracted the attentions of many researchers because of unique plasmonic properties since their discovery and successful preparation. Nanocluster formed by the assembly of noble metal nanoparticles can exhibit plasmonic characteristics beyond those of individual nanoparticles, which can be tuned, to a large extent, by adjusting the size, shape, chemical composition, and arrangement of individual nanoparticles. Usually nanocluster with special ordered structures is called as superstructure, which can be designed for different purposes through various methods. Colloidal assembly as a cost-efficient approach can be widely used for fabrication of plasmonic superstructure in solution media. As an introduction of background, the developments of plasmonic nanoparticles and nanoclusters have been discussed in the aspects of their LSPR properties, surface modification for colloidal assembly, and sensing applications. Both colorimetry and SERS detection based on plasmonic assemblies have been presented as effective sensing methods, which are also the motivations for the main experiments in this thesis. As a proof-of-motivation, the different kinds of thiol-terminated PEG assisted hybrid gold nanoparticles have been applied for the protein colorimetric detections based on the specific interaction between heparin and proteins with different surface affinities. In addition, PEG-assisted core/satellite superstructures with various polymer thickness as SERS platform have been demonstrated for trace sensing of specific target molecules in solution. Especially, the method to differentiate between the radiative and non-radiative contributions of plasmonic superstructure has been proposed using diffuse reflectance spectroscopy, which provides a favorable selection and design of best candidates for specific application scenarios. Finally, the concept of NIR-II SERS using biological transparency window has been introduced including the fundamental requirements, which proposed a future experiment to fabricate suitable superstructures for potential biomedical applications with high penetration depth at low laser powers. Generally speaking, the central focus of this thesis is the effect of polymer modification on the structures and properties of plasmonic superstructure and its sensing application. The main research efforts are divided into three parts: (I) investigate the topological effect of polymer structure parameters on plasmonic properties for colorimetric analytics; (II) investigate the impact of interparticle spacing within the assemblies and polymer dimensions on the SERS activity; (III) investigate the plasmonic properties tailoring of superstructures as well as the contribution of scattering (radiative) and absorption (non-radiative), i.e. light-to-heat conversion, within the ensemble optical response.

Dans cette thèse, des particules de polymère fonctionnalisées en surface avec des groupes poly (éthylène glycol) (PEG) ont été synthétisées pour favoriser leur interaction avec les dérivés cellulosique via liaisons hydrogène intermoléculaires. Deux voies de synthèse ont été proposées pour obtenir ses composites cellulose/latex.La première voie est basée sur l'auto-assemblage induit par polymérisation (PISA) pour former des nanoparticules fonctionnalisées avant leur adsorption sur un substrat cellulosique. La PISA tire profit de la formation de copolymères blocs amphiphiles dans l'eau en combinant la polymérisation en émulsion avec les techniques de polymérisation radicalaire contrôlées (RDRP). Ces dernières sont utilisées pour synthétiser des polymères hydrophiles agissant à la fois comme précurseur pour la polymerization en émulsion d'un monomère hydrophobe, et comme stabilisant des particules de latex obtenues. Deux techniques de RDRP ont été étudiées : les polymérisations RAFT et SET-LRP. Des polymères hydrophiles à base de PEG de faible masse molaire ont été synthétisés en utilisant ses deux techniques qui sont ensuite utilisés pour la polymérisation d'un bloc hydrophobe dans l'eau. Le transfert de l'agent de contrôle au site de la polymérisation était difficile en utilisant la SET-LRP en émulsion, conduisant à la formation de larges particules. En utilisant la RAFT en émulsion, des particules nanométriques ont été obtenues, avec un changement morphologique observé en fonction de la taille du segment hydrophobe, puis adsorbées sur des nanofibrilles de cellulose (CNF).La seconde voie utilise la polymérisation en émulsion classique réalisée en présence de nanocristaux de cellulose (CNC) conduisant à une stabilisation Pickering des particules de polymère. L'interaction cellulose/particule est assurée grâce à l'ajout d’un comonomère à type PEG. Une organisation a été visualisé dans laquelle plusieurs particules de polymère recouvrent chaque CNC / In this thesis, polymer particles surface-functionalized with poly(ethylene glycol) (PEG) groups were synthesized to promote their interaction with cellulose derivatives via intermolecular hydrogen bond. Two synthetic routes were proposed to obtain such cellulose/latex composites.The first route was based on the polymerization-induced self-assembly (PISA) to form functionalized polymer nanoparticles prior to adsorption onto cellulosic substrate. PISA takes advantage of the formation of amphiphilic block copolymers in water by combining emulsion polymerization with reversible-deactivation radical polymerization (RDRP) techniques. The latter were used to synthesize well-controlled hydrophilic polymer chains, acting as both precursor for the emulsion polymerization of a hydrophobic monomer, and stabilizer of the final latex particles. Two RDRP techniques were investigated: reversible addition-fragmentation chain transfer (RAFT), and single electron transfer-living radical polymerization (SET-LRP). Low molar mass PEG-based hydrophilic polymers have been synthesized using both techniques, used for the polymerization of a hydrophobic block in water. The transfer of controlling agent at the locus of the polymerization was challenging for SET-LRP in emulsion conditions leading to surfactant-free large particles. Nanometric latex particles were obtained via RAFT-mediated emulsion polymerization, with morphology change from sphere to fibers observed depending on the size of the hydrophobic segment, which were then able to be adsorbed onto cellulose nanofibrils (CNFs).The second route used conventional emulsion polymerization performed directly in presence of cellulose nanocrystals (CNCs) leading to Pickering-type stabilization of the polymer particles. Cellulose/particle interaction was provided thanks to the addition of PEG-based comonomer. Original organization emerged where CNCs were covered by several polymer particles