HIV-1 has evolved with a great deal of functional complexity contained within a very small genome by encoding small, but critical viral proteins within larger viral genes and dividing the replication cycle into early and late phases to differentially produce all proteins leading to efficient replication and virion release. Early replication is restricted by the host spliceosome that processes HIV-1 vRNA transcripts so only the small intragenomic proteins are produced, one of which is Rev (Regulator of Virion Expression). Rev in turn governs the transition from early to late replication by interacting with a highly structured region of vRNA termed the Rev Response Element (RRE). The binding of Rev to the RRE is believed to cause a change in the vRNA tertiary structure and inhibition of splicing of the vRNA. Once, a Rev:RRE complex is formed, a nuclear export signal within Rev facilitates the export of partially spliced and unspliced vRNA to the cytoplasm. During late replication the partially spliced and unspliced vRNA is translated to polyproteins and is packaged into a budding virion where the viral aspartyl protease (HIV-1 PR) autocatalytically excises itself from the larger polyprotein and processes the remaining polyproteins to release all viral structural and functional proteins to form a mature and infectious virion. Since the vRNA salvaged by Rev is translated to the polyproteins containing HIV-1 PR, the inhibition of Rev function will reduce the amount of HIV-1 PR available and thereby reduce the amount of HIV-1 PR therapeutics required to elicit a clinical effect. Therfore a combination approach to HIV-1 treatment using suitably developed therapeutics that inhibit Rev and HIV-1 PR function represents an attractive synergistic approach to treating HIV-1 infection in vivo. The work of this thesis was divided into two parts, the first part was concerned with HIV-1 PR structural biology and addressing problems encountered with inhibitor design. A bicyclic peptide (based on inhibitors of analogous structure) was co-crystallised with active HIV-1 PR to develop an enzyme-product (E-P) complex and with a catalytically inactive mutant HIV-1 PR to provide an analogy to the enzyme-substrate (E-S) complex. Both structures of the E-P and E-S complexes were solved to 1.6Å resolution and were compared to a hydroxyethylamine isostere enzyme-inhibitor complex (E-I), highlighting the similarity of binding mode for all ligands. The inhibitor in the E-I complex was translated towards the S1 - S3 pockets of the substrate binding cleft relative to the substrate in the E-S complex due to the increased length of the hydroxylethylamine isostere compared to the peptide backbone, although the inhibitor "puckered" the isostere linkage and maintains a binding mode similar to the substrate with very little overall differences in the position of the ligands and surrounding protein. The similarity of the E-S, E-I and E-P complexes was attributed to the macrocyclic ligands ordering the surrounding protein environment, especially the protein -strand "flap" structures that form a roof over the ligands in the active site but were not found to close more tightly in any of the trapped catalytic states. The new structures allowed refinement of details of the mechanism of peptide hydrolysis. The mechanism relies on the optimal nucleophilic attack of a water molecule on the scissile amide bond with concerted acid-base catalysis of the active site aspartyl residues intitiated by D125. The alignment and intrinsic position of the N-terminus of the bicyclic substrate was interpreted as being critical to facilitate efficient electron transfer with the bicyclic substrate. An N-terminal cyclic inhibitor, similar to the N-terminal portion of the bicyclic substrate, was used to address a major problem in HIV-1 PR drug design termed "cooperativity," where the sequential optimisation of an inhibitor (or substrate) to individual pockets of the substrate binding cleft, can negatively impact on adjacent and downfield subsites and thereby alter the binding mode of the "optimised" inhibitor. The technique referred to here as "templating" uses the N-terminal cycle to lock the binding mode into a known conformation, probing the S1' and S2' pockets. The structure activity relationship suggested that by viewing the S1' - S3' pockets as a single trough, bulky aromatic groups attached to an N-alkyl sulfonamide could be directed along the line of the trough without adverse interactions with the tops of the S1' and S3' pockets, providing very potent inhibitors. It was also found that specificity and potency of an inhibitor can be maintained with smaller functionalities that carry their bulk low and close to the inhibitor backbone in the S2' pocket, making the P2 functionalities more substrate-like. The second part of the thesis was concerned with establishing suitable surface plasmon resonance assays for testing potential inhibitors of Rev function. Recombinant Rev and its minimal RNA aptamer target (stem loop II of the RRE termed RBE3), were expressed, purified, and used to develop BIAcore-based assays and test potential inhibitors of their interaction. The system was applied to screening of aminoglycoside antibiotics and other small molecules in a competitive assay, and also to quantitative assay of Neomycin and moderate sized analytes: Rev and three peptidic analogues of the high-affinity binding site of Rev - the native peptide, succinylated form of the peptide and a form incorporating a novel helix-inducing cap. The peptide and protein assay was undertaken to test the proposition that helix induction of the high-affinity binding site of Rev can increase affinity for the biologically important RNA target and thereby form the basis of a new class of inhibitors. The screen of small molecule antagonists found that Neomycin was the best inhibitor of the Rev:RBE3 interaction and that efficacy of other aminoglycosides was due to the neamine-base structure presenting charge to bind to the RNA and blocking interaction with Rev. The quantitative assay was optimised to reduce non-specific interactions of Rev protein to allow reliable studies of the analytes with RBE3 by the sytematic testing of buffers and modifiers. It was found that mutliple analytes bound to the RBE3 aptamer and a comparison of the KD values found that the native and capped peptides had similar affinity for RBE3 RNA (native slightly greater at 21 ± 7nM cf capped 41 ± 10nM) that was greater than the Rev protein (101 ± 19nM), however the succinylated peptide exhibited stronger binding with a KD ≤8nM and Neomycin had the lowest affinity (KD 13 ± 3M). The similarity of the native and capped peptides may be due to the high concentration of salt in the assay buffers and was necessary for the stability of the Rev protein, but is sufficient to influence secondary structure of the peptides. Therefore, it could not be stated that the helix-inducing cap increased the affinity of the native peptide for the biologically important therapeutic target. The work conducted in this thesis firmly establishes foundations for the continued development of inhibitors against both Rev and HIV-1 PR that play key roles in the HIV-1 replication strategy. It is envisaged this work could lead to a novel synergistic therapeutic approach to treating HIV-1 infection.

No description available.

Ces dernières années, les matériaux à transition de spin (TS) ont suscité un intérêt marqué en raison de leurs applications potentielles, notamment en tant que capteurs ou dispositifs électroniques; typiquement, ces complexes présentent - via un stimulus externe (ex. : température, rayonnement) - une transition de spin réversible "Haut Spin (HS)  Bas Spin (BS)". Dans ce contexte, le travail présenté a porté sur la conception et les études magnétostructuralesde monocristaux de nouveaux systèmes FeII à TS à base de ligands 4-R-1,2,4-triazole comprenant un espaceur alkyl, en combinaison avec soit (i) des entités tétracyanométallates inorganiques ([M(CN)4]2-, M = NiII, PtII, PdII) ou (ii) des cyanocarbanions organiques spécifiques ((tcnsR')-: anions 1,1,3,3-tétracyano-2 thioalkylpropénide) - et ce afin de comprendre in fine l'origine physico-chimique de la forte coopérativité dans ces matériaux remarquables, mais aussi de rationaliser le contrôle et l’optimisation des propriétés de TS. Dans un premier temps, un nouveau sel de polymère 1D [Fe(bntrz)3][Pt(CN)4].H2O (1) - présentant une TS abrupte et une résilience exceptionnelle lors de cycles répétés de commutation - a été synthétisé; les études structurales fines - réalisées sur monocristaux - des états HS et BS ont clairement révélé l'impact des interactions à longue distance sur les propriétés de la TS dans ce système. Ensuite, la substitution de l'anion « rigide » tétracyanométallate ([Pt(CN)4]2-) par l'entité plus « flexible » (tcnset)- nous a conduit au premier exemple de complexe neutre trinucléaire à base de triazole [Fe3(bntrz)6(tcnset)6] (2) présentant une TS complète en une seule étape au-dessus de la température ambiante. La variation systématique du substituant R' de l'anion fonctionnalisé(tcnsR')- a permis l’obtention de deux nouveaux systèmes à TS, à savoir le complexe trinucléaire neutre [Fe3 (bntrz)6(tcnspr)6] (3) et le dérivé 1D [Fe3(bntrz)8(tcnsme)4].(tcnsme)2,4H2O (4), avec des caractéristiques structurales et des comportements de TS distincts. Enfin, dans le but d'évaluer précisément l'impact de différents substituants en 4ème position sur le ligand 1,2,4-triazole, deux nouveaux matériaux 3D basés sur le triazole 2-(3-(4H-l,2,4-triazol-4-yl)propyl)isoindoline-1,3-dione (phtptrz) - i.e. {Fe3(μ2-phtptrz)6[μ2-Pt(CN)4]3}.C2H5OH,5.5H2O (5) et {Fe(phtptrz)[Pt(CN)4].H2O} (6) - ont été synthétisés et caractérisés; une TS en deux étapes est observée pour le composé 5, tandis que le dérivé 6 exprime un comportement paramagnétique caractéristique de l’état de spin S = 2. / In recent years, the spin-crossover (SCO) materials have attracted much interest because of their potential applications such as sensors or electronic displays; these complexes typically exhibit - via an external disturbance (e.g. temperature, radiation) - a reversible “High Spin (HS) Low Spin (LS)” spin transition. In this context, the present work has focused on the design and the magneto-structural investigations of single crystals of novel FeII SCO systems based on 4-R-1,2,4-triazole ligands including an alkyl spacer - with either (i) inorganic tetracyanometallates ([M(CN)4]2-, M = NiII, PtII, PdII) or (ii) specific organic cyanocarbanions ((tcnsR’)-: 1,1,3,3-tetracyano-2-thioalkylpropenide anions) - in order to ultimately understand the physicochemical origin of the strong cooperativity in such striking materials, but also to rationalize the tuning of the SCO properties. At first, a new 1D polymer [Fe(bntrz)3][Pt(CN)4].H2O (1) salt - exhibiting an abrupt spin transition and an exceptional resilience upon repeated switching - has been synthesized; the accurate single crystal investigations of both HS and LS states of the latter clearly revealed the impact of the longrange interactions on SCO properties in this system. Then, the substitution of the ‘rigid’ [Pt(CN)4]2- tetracyanometallate anion by the more ‘flexible’ (tcnset)- entity lead us to the first example of triazole-based SCO FeII trinuclear neutral complex [Fe3(bntrz)6(tcnset)6] (2) exhibiting a complete one-step spin transition above room temperature. The systematic variation of the R’ substituent from the functionalized (tcnsR’)- anion resulted in two new FeII SCO systems, i.e. the neutral trinuclear complex [Fe3(bntrz)6(tcnspr)6] (3) and the 1D [Fe3(bntrz)8(tcnsme)4](tcnsme)2.4H2O (4) derivative, with distinct structural characteristics and SCO behaviours. Finally, with the purpose to further evaluate the impact of different substituents at the 4th position onto 1,2,4-triazole ligand, two new 3D materials based on the functionalised triazole 2-(3-(4H-1,2,4-triazol-4-yl)propyl)isoindoline-1,3-dione (phtptrz) - {Fe3(μ2-phtptrz)6[μ2-Pt(CN)4]3}.C2H5OH,5.5H2O (5) and {Fe(phtptrz)[Pt(CN)4].H2O} (6) - have been synthesized and characterized; a two-step SCO behaviour is observed only in 5, while 6 shows a characteristic paramagnetic behavior.

No description available.

Diese Dissertation konzentriert sich auf die Untersuchung multivalenter Wechselwirkungen zwischen Hämagglutinin (HA) sowie Neuraminidase (NA) zweier Stämme des Influenzavirus (H1N1 und H3N2) und dem zellulären Liganden Sialinsäure (SA) unter Verwendung von Rasterkraftmikroskopie und Einzelmolekülkraftspektroskopie (SMFS). Bindungskräfte sowie Dissoziations- und Assoziationskinetiken, zusammen mit den intermolekularen Potentiallandschaften wurden, nach bestem Wissen erstmalig, auf Einzelmolekülebene mittels SMFS quantifiziert. Zu diesem Zweck wurden mono- und multivalente SA-Liganden (SAPEGLA und dPGSA) eingesetzt. Abweichungen der experimentellen Kraftspektren vom klassischen Kramers-Bell-Evans-Modell vorhergesagten Verhalten wurden durch das Friddle-Noy-De Yoreo-Model berücksichtigt. NA beider Virusstämme zeigte trotz ähnlicher Bindungskräfte eine stabilere Bindung mit SA als HA und dissoziierte 3 – 7 mal langsamer. Es wird vermutet, dass die höhere Stabilität die geringere Oberflächendichte von NA auf der Virushülle im Vergleich zu HA ausgleicht. Die Bindungskräfte eines SAPEGLA-Clusters nehmen mit der Anzahl der Bindungen und die Dissoziationskinetik folgt dem theoretisch vorhergesagten Trend. Die Dissoziationsrate von NA ist etwa 6-mal höher ist als ihre katalytische Rate, weshalb Mehrfachbindungen zur Spaltung von SA erforderlich sind. Die Dissoziationsrate von N1 in der gleichen Größenordnung wie die von H3 und es wird vermutet, dass derartige Ähnlichkeiten die Übertragbarkeit des Virus begünstigen. Darüber hinaus wird gezeigt, dass die thermische Stabilität von HA-dPGSA höher ist als von HA-SAPEGLA und im Bereich von 3 - 4 Einzelbindungen liegt, was für NA-dPGSA nicht beobachtet werden konnte. Daher bindet dPGSA spezifisch und kooperativ multivalent an HA. Kompetitive Bindungstests zeigen, dass SMFS zum Screening von antiviralen Inhibitoren verwendet werden und Zugang zu deren Design auf Einzelmolekülebene liefern könnte. / This thesis focuses on studying multivalent interactions between influenza virus hemagglutinin (HA) as well as neuraminidase (NA) of two viral strains (H1N1 and H3N2) and the cellular ligand sialic acid (SA) by using scanning force microscopy and single molecule force spectroscopy (SMFS). Unbinding forces as well as dissociation and association kinetics together with the free energy landscapes were, to the best knowledge for the first time, individually quantified on the single molecule level using SMFS. To this extent, designed synthetic monovalent (SAPEGLA) and multivalent (dPGSA) SA displaying ligands were employed. Surprisingly, the experimental force spectra did not show the log-linear trend predicted by the classical Kramers-Bell-Evans model, but rather follow the more recent Friddle-Noy-De Yoreo model. NA of both viral strains forms a more stable bond with SA than HA, and dissociates 3 to 7 times slower. It is reasoned that the higher stability compensates for the lesser amount of NA compared to HA that is typically found on the viral envelope. The unbinding forces of the cluster of SAPEGLA increased gradually with the number of bonds in the cluster and the dissociation kinetics follow the theoretically predicted trend. The dissociation rate of NA was found to be about 6 times higher than its catalytic rate, indicating that multiple bonds are needed for cleavage of SA. The dissociation rate of N1 is on the same order as that of H3, suggesting that these similarities between the two strains favor transmissibility. The thermal stability of the HA-dPGSA bond is higher than the HA-SAPEGLA reaching that of three to four single bonds, proving specificity and cooperativity. Such an enhancement could not be observed for the binding of NA. This thesis also shows that SMFS could be used as a tool to screen antiviral inhibitors in competitive binding assays, which may contribute insight into the design of antiviral inhibitors on the single molecule level.

L’autoassemblage de diverses biomolécules pour former des complexes moléculaires est à la base de la machinerie cellulaire et des processus biologiques qui s’y rattachent. Il est typiquement considéré qu’un assemblage de plusieurs protéines offre des avantages régulatifs comparativement à une structure protéique similaire construite avec une ou un nombre inférieur de composantes. Ces assemblages offrent, par exemple, la possibilité de contrôler l’activité d’un complexe grâce à la dépendance directe de l’assemblage sur la concentration de ces composantes. De plus, la coopérativité d’interaction entre ces diverses composantes ouvre la voie vers l’obtention de nouveaux mécanismes de régulation. Toutefois, les avantages et les inconvénients directement reliés au nombre de composantes impliquées dans un assemblage ne sont pas totalement bien compris puisque les protéines ont évolué et ont divergé suivant des millions d’années d’évolution. L’objectif principal de cette thèse est d’abord de créer un modèle moléculaire simplifié permettant de mieux comprendre les avantages coopératifs des autoassemblages biologiques pour ensuite s’en inspirer afin de mettre au point de nouveaux mécanismes moléculaires permettant d’optimiser la plage dynamique d’interrupteurs moléculaires autoassemblés. En même temps, il sera possible de mettre en lumière certains avantages évolutifs qui ont poussé les protéines à acquérir plus de composantes moléculaires. Tout d’abord, la création d’assemblages moléculaires fut effectuée en fragmentant une structure unimoléculaire en plusieurs fragments qui pourront, grâce à leurs interactions, reformer la structure originale. Grâce à une nanostructure simple d’ADN, c.-à-d. une jonction à trois branches, il fut possible d’étudier directement l’impact du nombre de composantes sur la fonctionnalité et la régulation d’assemblages multimériques. Il fut observé, malgré l’association plus lente d’un assemblage de trois composantes, que ce même assemblage s’associe de manière plus coopérative tout en permettant la création de nouveaux mécanismes de régulation (p. ex. plage dynamique étendue, auto-inhibition et minuterie moléculaire). Ce système simplifié d’ADN a donc permis de conclure que la fragmentation d’une nanostructure en plusieurs composantes est une méthode simple permettant d’optimiser un nanosystème artificiel ou naturel. Ensuite, une autre méthode de création d’assemblages moléculaires fut étudiée. Celle-ci consiste à fusionner des domaines interagissant par le biais d’un espaceur. Dans une telle stratégie, l’espaceur est appelé à jouer un rôle important dans les propriétés de l’assemblage. Ainsi, en utilisant le même modèle d’ADN à trois composantes, il fut en effet observé que les propriétés de l’espaceur (p. ex. sa longueur, sa composition ou sa nature chimique) affectent grandement les propriétés d’assemblage d’un système à trois composantes (p. ex. sa stabilité, son niveau de coopérativité ou sa plage dynamique d’assemblage). En effectuant une étude thermodynamique approfondie sur divers assemblages trimériques d’ADN, il fut découvert qu’un espaceur optimal stabilise l’association des diverses composantes en créant une structure plus compacte où les espaceurs se cachent au coeur de la jonction. Il fut aussi démontré qu’en optimisant l’espaceur, il est possible de programmer précisément la plage dynamique d’un assemblage moléculaire à trois composantes. Finalement, ces découvertes sur les avantages d’un assemblage à trois composantes ont permis la création d’une nouvelle stratégie afin d’optimiser la plage dynamique d’interrupteurs moléculaires. À l’inverse des activateurs allostériques classiques qui altèrent la force d’interaction d’un ligand, c.-à-d. le KD, en modifiant la conformation de l’interrupteur, un activateur multivalent permet de programmer précisément la plage dynamique de l’interrupteur en exploitant une nouvelle surface d’interaction grâce à la formation d’un assemblage à trois composantes. Cette nouvelle stratégie d’optimisation des interrupteurs moléculaires fut validée grâce à une tige-boucle d’ADN servant comme balise moléculaire. Cette preuve de concept permet de démontrer la viabilité des assemblages moléculaires pour conceptualiser de nouvelles nanotechnologies avec une plage dynamique optimisée. Il est donc possible d’imaginer que les assemblages moléculaires auront un impact immédiat dans divers domaines de la nanotechnologie comme en diagnostic médical, en délivrance contrôlée de médicaments ou en imagerie moléculaire. / The self-assembly of various biomolecules to form molecular complexes is at the basis of the cellular machinery and their related biological processes. It is typically thought that an assembly of several proteins provides regulatory advantages compared to a similar protein built with one or fewer molecular components. These molecular assemblies offer, for example, the possibility to control their activity through the direct dependency of the assembly on the concentration of its components. Moreover, the cooperativity of interaction between their multiple components opens the door to acquiring novel regulation mechanisms. However, the advantages and disadvantages directly related to the number of components involved in an assembly are not totally understood since proteins have evolved and diverged over millions of years of evolution. The main objective of this thesis is to first create a simplified molecular model that will enable to better understand the cooperative advantages of biological self-assemblies. Then, inspired by these new understandings, novel molecular mechanisms will be developed to enable the optimization of the dynamic range of self-assembled molecular switches. Meanwhile, it will be possible to highlight some advantages that have pushed proteins to acquire more molecular components. The creation of molecular assemblies was demonstrated by fragmenting a nanostructure into multiple fragments which, through their intermolecular interactions, reassemble into the original structure. Using a simple DNA-based nanostructure, i.e., a three-way junction, it was possible to directly study the impact of the number of components on the functionality and regulation of multimeric assemblies. It was found that despite the slower assembly rate of a three-component assembly, this same assembly undergoes a more cooperative assembly enabling the creation of new regulatory mechanisms (e.g., extended dynamic range, self-inhibition and molecular timers). This simplified DNA-based system has therefore made it possible to conclude that fragmenting a nanostructure into multiple components is a simple method to optimize an artificial or a natural nanosystem. Next, another method to create molecular assemblies was studied. This method consists in fusing interacting domains through a linker. In this strategy, the linker will play an important role in dictating the properties of the assembly. Therefore, by using the same three-component DNA-based model, it has been observed that the chemical properties of the linker (e.g., its length, its composition, or its chemical nature) considerably affect the assembly properties of a three-component system (e.g., its stability, its level of cooperativity, or its dynamic range). Through an exhaustive thermodynamic study on various trimeric DNA-based assemblies, it was determined that the optimal linker stabilizes the association of all components by creating a more compact assembly where the linkers are buried within the core of the junction. It was also demonstrated that the optimization of the linkers allows to precisely program the dynamic range of the assembly. Finally, these discoveries on the advantages of a three-component assembly have enabled the creation of a new design strategy to optimize the dynamic range of molecular switches. In contrast to the classic allosteric activator which alters the affinity of a ligand (i.e., the KD) by changing the conformation of the switch, a multivalent activator enables to precisely program the dynamic range of a switch by exploiting a new interacting interface through the formation of a three-component assembly. This new strategy to optimize molecular switches was validated using a DNA-based molecular beacon. This proof of concept demonstrates the viability of molecular assemblies to design novel nanotechnologies with optimized dynamic range. It is possible to imagine that these molecular assemblies could have a direct impact on multiple fields of nanotechnology including medical diagnostics, controlled drug delivery and molecular imaging.

Aus den frühen Bindungsstudien des globalen Regulators AbrB mit der ausgedehnten phyC-Promotorregion von Bacillus amyloliquefaciens FZB45 konnte ein mehrstufiger kooperativer Bindungsprozess abgeleitet werden. Dabei verlangt die AbrB-vermittelte Repression von phyC nach Integrität zweier großer Bindungsstellen, ABS1 und ABS2, die 162 bp voneinander entfernt liegen. In der vorliegenden Arbeit wurden die ersten Echtzeitkinetiken zur DNA-AbrB-Interaktion mittels der Oberflächenplasmonresonanz (SPR) gemessen und analysiert. AbrB zeigte hohe Affinitäten zu den 40 bp langen Oligonukleotiden, die den beiden Bindungsstellen entstammen. Dabei verursachten alle Oligonukleotide der ABS2 und nur eine kurze Region innerhalb der ABS1 bei der Bindung von AbrB Konformationsänderungen im Protein und in der DNA (CD - Zirkulardichroismusspektroskopie) und wiesen eine Kooperativität von 2 / In previous binding studies it could be demonstrated that a global regulator AbrB and the extensive phyC promoter region of Bacillus amyloliquefaciens FZB45 interact in a complex manner. AbrB binding is a multistep cooperative process. The integrity of both binding sites, ABS1 and ABS2, which are separated by 162 bp, is crucial for the AbrB-mediated repression of phyC. This work presents the first real-time binding kinetics of the AbrB-DNA interaction using surface plasmon resonance (SPR). AbrB exhibited high affinities to all analyzed 40-bp oligonucleotides that were derived from the ABSs of phyC. All parts of the ABS2, but only a small region within ABS1, were bound cooperatively to AbrB with a stoichiometry of 2 DNA to 1 AbrB tetramer and with 2

O problema do folding de proteínas tem sido investigado intensamente há mais de sessenta anos. Entretanto ainda não é encontrado na literatura um modelo que seja capaz de explicar plenamente qual é o mecanismo responsável pelo processo de folding. Neste contexto, a presente tese de doutorado é uma proposta minimalista para investigar o papel de um código estereoquímico, que é centrado no efeito hidrofóbico e nos vínculos estéricos dos aminoácidos (o modelo estereoquímico), no processo em pauta. Esse modelo quando combinado com um método para incluir a flutuação térmica local no sistema cadeia protéica-solvente, possibilita a investigação de um dos aspectos mais extraordinários do problema, a saber, a rapidez do processo de folding, considerado aqui por meio da correlação entre a complexidade da estrutura nativa (alvo) e a taxa de folding. Esse método é motivado por argumentos físico-químicos e biológicos, e é fundamentado na Mecânica Estatística Não Extensiva, via o uso do peso de Tsallis em simulações Monte Carlo (MC). O tempo característico de folding (obtido daquelas simulações e utilizado aqui como um parâmetro analítico do problema), cobre várias ordens de grandeza para cadeias com o mesmo tamanho. Dois conjuntos principais de simulações foram considerados com a finalidade de análise: (i) alguns alvos foram especialmente selecionados e submetidos a simulações MC a várias temperaturas T do reservatório térmico (o meio solvente); e (ii) um total de duzentos alvos com topologias diversas foram submetidos a simulações à mesma temperatura T = 1 (unidades arbitrárias). Com essas simulações foi possível verificar comparativamente o efeito dos dois pesos estatísticos, o de Boltzmann e o de Tsallis, sobre a cinética do processo de folding, e assim revelar comportamentos intrigantes, porém consistentes com o fenômeno focado, como a robustez do processo de folding e , este último emergindo como uma grandeza que depende da complexidade da estrutura nativa. Para estruturas distintas, cobre quatro ordens de grandeza. Os resultados da investigação da correlação entre e parâmetros globais destinados a avaliar a complexidade da topologia da estrutura nativa, como a ordem de contato e a cooperatividade estrutural, corroboram com a noção de que a rapidez do processo de folding é determinada fundamentalmente pela complexidade da topologia da estrutura nativa. / The protein folding problem has been investigated for more than sixty years. However is not yet found in literature a model that is able to fully explain the mechanism behind the folding process. In this context, the present doctoral thesis is a speculative and minimalist proposal to investigate the role of a stereochemical code -grounded in the hydrophobic effect and steric constraints of amino acids (the stereochemical model), in the discussed process. This model, when combined with a method to include local thermal fluctuations in the protein chain-solvent system, enables the investigation of one of the most extraordinary aspects of the problem, namely, the fastness of the folding process, which is studied here by means of the correlation between the complexity of the native structure (target) and the folding process rate. This method is motivated by physical chemistry and biological arguments, and is based on the Nonextensive Statistical Mechanics, by the use of the Tsallis weight in Monte Carlo simulations (MC), where the entropic index q is adjusted at each new conformation of the protein chain. For chains with the same length, the characteristic folding time (estimated from those simulations and used here as an analytical parameter of the problem) span several order of magnitude. Two main sets of simulations were performed for analysis purposes. First, some targets were specially selected and submitted to MC simulations with several temperatures of the thermal reservoir (the solvent), and then a total of two hundred targets with diverse topologies were submitted to simulations with the same reservoir temperature T = 1 (arbitrary units). With such set of simulations, we could compare the effect of two statistical weights, namely the Boltzmann and the Tsallis weight, on the kinetics of the folding process. Intriguing but consistent behavior with respect to the folding phenomenon was reveled, such as the robustness of the process, and about the characteristic folding time , which emerges as an amount that depends on the complexity of the native structure. For distinct structures, covers four orders of magnitude. Our results about the correlation between and global parameters to assess the complexity of the topology of the native structure, such as contact order and structural cooperativity, support the notion that the fastness of the folding process is essentially determined by the complexity of the topology of native structure.

Proteinadsorption ist in vielen biotechnologischen Anwendungen ubiquitär und ein zentrales Forschungsfeld in der Physik der weichen Materie. Das Verstehen der treibenden Kräfte hinter der Proteinadsorption würde zu einer besseren Kontrolle des Adsorptionsprozesses führen und die Entwicklung von Biosystemen mit beispielloser Funktionalität ermöglichen. In der vorliegenden Arbeit wird die Proteinadsorption an weichen polymerartigen Biomaterialien sowie deren physikalische Wechselwirkungen unter Verwendung von zwei unterschiedlichen neu entwickelten Ansätzen theoretisch untersucht. Im ersten Teil wird ein neues mehrkomponentiges kooperatives Bindungsmodell entwickelt, um die Gleichgewichts-Adsorption von Proteinen auf Mikrogelen zu beschreiben. Es war somit möglich, die wahre treibende Kraft der Proteinadsorption zu identifizieren, die hauptsächlich elektrostatischen Ursprungs ist. Eine Errungenschaft des kooperativen Bindungsmodells ist die Vorhersage der kompetitiven Proteinadsorption und -desorption auf das Mikrogel, die auf thermodynamischen Parametern der Adsorption von Proteinen einzelner Sorten basiert. Vergleiche zwischen Experimenten mit binären Proteinmischungen und theoretischen Berechnungen zeigten sehr gute Übereinstimmungen. Der zweite Teil fokussiert auf Protein-Wechselwirkungen mit Polyelektrolyten, um Adsorptionsprozesse auf mikroskopischer Ebene zu erklären. Dafür wurden geladene fleckige Partikel konstruiert und als Proteinmodelle verwendet, während ein einfaches Kugel-Feder-Modell für das Polyelektrolyt und Polyelektrolytbürste benutzt wurde. Ein zentraler Aspekt war die Bestimmung der freien Energie, das Potential der mittleren Kraft (PMF), für die Komplexbildung der beiden Bestandteile mit Vergleichen zur Modellentwicklungen. Die Simulationsergebnisse legen ein komplexes Wechselspiel von elektrostatischen Kräften und Ionenfreisetzungsmechanismen dar, die für die starken attraktiven Wechselwirkungen in den PMFs verantwortlich sind. / Protein adsorption is ubiquitous in many biotechnological applications and has become a central research field in soft matter. Understanding the driving forces behind protein adsorption would allow a better control of the adsorption process and the development of biosystems with unprecedented functionality. In this thesis, protein adsorption onto soft polymeric biomaterials and their physical interactions is studied theoretically by using two different and newly developed approaches. In the first part, a novel multi-component cooperative binding model is developed to describe the equilibrium adsorption of proteins onto microgels. It was thus possible to correctly identify the true driving force behind the protein adsorption which was found to be mainly of electrostatic origin. A key achievement by the cooperative binding model is the prediction of competitive protein adsorption and desorption onto the microgel that is based on thermodynamic parameters related to single-type protein adsorption without any variable parameters. Comparisons between experimental data of binary protein mixtures and theoretical calculations have shown excellent agreements. The second part is focused on protein interactions with polyelectrolyte materials to elucidate adsorption processes on a microscopic level. For this purpose, charged patchy particles are constructed and used as protein models while a simple bead-spring model is employed for the polyelectrolyte and polyelectrolyte brush. A central aspect was the determination of the associated free energy, the potential of mean force (PMF), on the complex formation between the two constituents with comparisons to theoretical model developments. The simulation results evidenced a complex interplay of electrostatic forces and ion release mechanisms to be responsible for the strong attractive interactions observed in the PMFs.

L’any 2002 tres grups de recerca, entre ells el nostre grup, van demostrar teòricament que la interacció entre anions i anells aromàtics electrodeficients, anomenada interacció anió–, era favorable. Des de llavors s’ha dut a terme un intens estudi de la seva naturalesa física fins la total comprensió. Aquesta tesi es basa amb l’estudi de la interacció anió– des de tres punts de vista. Primerament, la investigació es basa en el disseny teòric de motius estructurals per donar lloc a un receptor on la interacció anió– siga molt favorable, per posteriorment avaluar la força de la interacció experimentalment en dissolució. A continuació, es va analitzar la interrelació entre un gran nombre de combinacions d’interaccions no covalents. A partir d’aquest estudi es defineixen nous conceptes i es proposen diferents formules per calcular efectes de cooperativitat. Finalment, hem anat un pas més enllà en l’estudi de la interacció analitzant: 1) l’impacte de la interacció anió– a sistemes biològics; 2) la influència de modificacions a l’anió sobre la naturalesa física de la interacció. / In 2002 three research groups, among them our research group, theoretically demonstrated that the interaction between anions and electron-deficient aromatic rings, named anion– interaction, was favourable. Since then, an intense study of its physical nature has been performed to understand it completely. This thesis is based on the study of the anion– interaction from three points of view. Firstly, theoretical design of binding units to build a receptor and to obtain the most favourable binding based on anion– interactions. The binding properties of these receptors have been experimentally assessed in solution. Secondly, we have studied the interplay between a great combination of noncovalent interactions. From this study, new concepts and formula to calculate cooperativity effects have been described. Finally, we have study one step further the anion– interaction analysing: 1) the impact of anion– interaction in biological systems; 2) how the modifications in the anion influence the physical nature of the interaction.