O vírus sincicial respiratório humano (VSRH) é o agente viral mais freqüentemente relacionado a doenças do trato respiratório inferior em crianças abaixo de um ano de idade. Analíse da varibilidade antigênica e gênica mostraram que o VSRH pode ser divido em dois grupos: A e B. O vírus é um membro do gênero Pneumovirus pertencente a família Paramyxoviridea, e possui três principais proteínas que são: glicoproteina F (fusão), glicoproteina G (adesão), glicoproteina SH (pequena proteína hidrofóbica). A proteína F é responsável pela fusão da célula ao vírus, enquanto a proteína G tem papel fundamental na replicação do vírus, porém a função da proteína SH, ainda não está bem definida, estudos recentes mostram-na como responsável por inibir a sinalização do fator de necrose tumoral alfa (TNF-a). Neste estudo foram colhidas amostras de 965 crianças, entre os anos de 2004 e 2005, dentre as quais 424 foram positivas. 117 amostras foram seqüenciadas a proteína SH e G e comparadas com amostras que circularam mundialmente. A analíse filogenética mostrou uma baixa variabilidade entre os genótipos estudados tanto do grupo A quanto do B. / The human respiratory syncytial virus (HRSV) is the major cause of lawer respiratory tract infections in infantis, young children and elderly. Analysis of the antigenic and genetic variability has shown that there are two groups of the virus HRSV, A and B. The virus (HRSV) is a member of the genus pneumovirus in the paramyxoviridae family. The virus encodes three membrane-bound glicoproteins, namely the fusion (F) attachment (G) and small hydrophobic (SH) proteins. The F mediates fusion of the virus and cell membranes and the G proteins is involved in virus attachment. The biological properties of the F and G glicoproteins and role that they play during virus replication relatively well understood, however the functional significance of the SH protein during replication remains unclear, although recent study shown that it can inhibit TNF-alpha. In this study, HRSV strains were isolated from nasopharyngeal aspirates collected from 965 children between 2004 and 2005, yielding 424 positive samples. We sequenced the small hydrophobic protein (SH) gene and protein (G) of 117 samples and compared them with other viruses identified worldwide. The phylogenetic analysis showed a low genetic variably among the isolates but allowed us to classify the viruses into different genotypes for the A and B HRSV strains.

Domain swapping is a wide spread phenomenon which involves the association between two or more protein subunits such that intra-molecular interactions between domains in each subunit are replaced by equivalent inter-molecular interactions between the same domains in different subunits. This thesis is devoted to the analysis of the factors that drive proteins to undergo such association modes. The specific system analyzed is the monomer to swapped dimer formation of the B1 domain of the immunoglobulin G binding protein (GB1). The formation of this dimer was shown to be fostered by 4 amino acid substitutions (L5V, F30V, Y33F, A34F) (Byeon et al. 2003). In this work, computational protein design and molecular dynamics simulations, both with detailed atomic models, were used to gain insight into how these 4 mutations may promote the domain swapping reaction.<p>The stability of the wt and quadruple mutant GB1 monomers was assessed using the software DESIGNER, a fully automatic procedure that selects amino acid sequences likely to stabilize a given backbone structure (Wernisch et al. 2000). Results suggest that 3 of the mutations (L5V, F30V, A34F) have a destabilizing effect. The first mutation (L5V) forms destabilizing interactions with surrounding residues, while the second (F30V) is engaged in unfavorable interactions with the protein backbone, consequently causing local strain. Although the A34F substitution itself is found to contribute favorably to the stability of the monomer, this is achieved only at the expense of forcing the wild type W43 into a highly strained conformation concomitant with the formation of unfavorable interactions with both W43 and V54.<p>Finally, we also provide evidence that A34F mutation stabilizes the swapped dimer structure. Although we were unable to perform detailed protein design calculations on the dimer, due to the lower accuracy of the model, inspection of its 3D structure reveals that the 34F side chains pack against one another in the core of the swapped structure, thereby forming extensive non-native interactions that have no counterparts in the individual monomers. Their replacement by the much smaller Ala residue is suggested to be significantly destabilizing by creating a large internal cavity, a phenomenon, well known to be destabilizing in other proteins. Our analysis hence proposes that the A34F mutation plays a dual role, that of destabilizing the GB1 monomer structure while stabilizing the swapped dimer conformation.<p>In addition to the above study, molecular dynamics simulations of the wild type and modeled quadruple mutant GB1 structures were carried out at room and elevated temperatures (450 K) in order to sample the conformational landscape of the protein near its native monomeric state, and to characterize the deformations that occur during early unfolding. This part of the study was aimed at investigating the influence of the amino acid sequence on the conformational properties of the GB1 monomer and the possible link between these properties and the swapping process. Analysis of the room temperature simulations indicates that the mutant GB1 monomer fluctuates more than its wild type counter part. In addition, we find that the C-terminal beta-hairpin is pushed away from the remainder of the structure, in agreement with the fact that this hairpin is the structural element that is exchanged upon domain swapping. The simulations at 450 K reveal that the mutant protein unfolds more readily than the wt, in agreement with its decreased stability. Also, among the regions that unfold early is the alpha-helix C-terminus, where 2 out of the 4 mutations reside. NMR experiments by our collaborators have shown this region to display increased flexibility in the monomeric state of the quadruple mutant.<p>Our atomic scale investigation has thus provided insights into how sequence modifications can foster domain swapping of GB1. Our findings indicate that the role of the amino acid substitutions is to decrease the stability of individual monomers while at the same time increase the stability of the swapped dimer, through the formation of non-native interactions. Both roles cooperate to foster swapping. / Doctorat en sciences, Spécialisation biologie moléculaire / info:eu-repo/semantics/nonPublished

Understanding the function of membrane proteins is crucial to elucidate the molecular mechanisms by which transmembrane signaling based physiological processes,i. e., the interactions of extracellular ligands with membrane-bound receptors, are regulated. In this work, synthetic transmembrane segments derived from the visual photoreceptor rhodopsin, the full length system rhodopsin and mutants of opsin are used to study physical processes that underlie the function of this prototypical class-A G-protein coupled Receptor. The dependency of membrane protein hydration and protein-lipid interactions on side chain charge neutralization is addressed by fluorescence spectroscopy on synthetic transmembrane segments in detergent and lipidic environment constituting transmembrane segments of rhodopsin in the membrane. Results from spectroscopic studies allow us to construct a structural and thermodynamical model of coupled protonation of the conserved ERY motif in transmembrane helix 3 of rhodopsin and of helix restructuring in the micro-domain formed at the protein/lipid water phase boundary. Furthermore, synthesized peptides and full length systems were studied by time resolved FTIR-Fluorescence Cross Correlation Hydration Modulation, a technique specifically developed for the purpose of this study, to achieve a full prospect of time-resolved hydration effects on lipidic and proteinogenic groups, as well as their interactions. Multi-spectral experiments and time-dependent analyses based on 2D correlation where established to analyze large data sets obtained from time-resolved FTIR difference spectra and simultaneous static fluorescence recordings. The data reveal that lipids play a mediating role in transmitting hydration to the subsequent membrane protein response followed by water penetration into the receptor structure or into the sub-headgroup region in single membrane-spanning peptides carrying the conserved proton uptake site (monitored by the fluorescence emission of hydrophobic buried tryptophan). Our results support the assumption of the critical role of the lipid/water interface in membrane protein function and they prove in particular the important influence of electrostatics, i. e., side chain charges at the phase boundary, and hydration on that function. / Für die Aufklärung der molekularen Wirkungsweise von physiologischen, auf Signaltransduktion, d. h. dem Zusammenspiel von extrazellulären Reizen und membrangebundenen Rezeptoren, beruhenden Prozessen ist das Verständnis der Funktion von Membranproteinen unerlässlich. In dieser Arbeit werden von Rhodopsin abgleitete, synthetische transmembrane Segmentpeptide, Opsin-Mutanten und der vollständige Photorezeptor Rhodopsin untersucht, um die physikalischen Prozesse zu beleuchten, die der Funktionen dieses prototypischen Klasse-A G-Protein gekoppelten Rezeptors zugrunde liegen. Die Abhängigkeit der Membranprotein-Hydratation und der Lipid-Protein-Wechselwirkung von der Ladung einer Aminosäuren-Seitenkette wird erforscht. Hierzu werden synthetische, transmembrane Segmentpeptide in Lipid und Detergenz, als Modell transmembraner Segmente von Rhodopsin in der Membran mittels Fluoreszenzspektroskopie untersucht. Aus den erhaltenen Ergebnissen wird ein thermodynamisches und strukturelles Modell hergeleitet, welches die Kopplung der Protonierung des hochkonservierten ERY-Motivs in Transmembranhelix 3 von Rhodopsin an die Restrukturierung der Helix in der Mikroumgebung der Lipid-Wasser-Phasengrenze erklärt. Des Weiteren werden sowohl die Segementpeptide als auch die vollständigen Systeme Opsin und Rhodopsin mittels zeitaufgelöster FTIR-Fluoreszenz-Kreuzkorrelations-Hydratations-Modulation untersucht. Diese Technik wurde eigens zur Aufklärung von zeitabhängigen Hydratationseffekten auf Lipide und Proteine oder Peptide entwickelt. Dabei werden zeitaufgelöste FTIR Differenz-Spektren und gleichzeitig statische Fluoreszenzsignale aufgenommen und diese zeitabhängigen multispektralen Datensätze mittels 2D Korrelation analysiert. Die Auswertung der Experimente enthüllt einen sequentiellen Hydratationsprozess. Dieser beginnt mit der Bildung von Wasserstoffbrückenbindungen an der Carbonylgruppe des Lipids, gefolgt von Strukturänderungen der Transmembranproteine und abgeschlossen durch das Eindringen von Wasser in das Proteininnere. Letzteres wird nachgewiesen durch die Fluoreszenz von Tryptophan im hydrophoben Peptid- oder Proteininneren. Die Ergebnisse dieser Arbeit unterstreichen die Annahme, dass Lipid-Protein-Wechselwirkungen eine entscheidende Rolle in der Funktion von Membranproteinen spielen und das insbesondere Elektrostatik, in Form von Ladungen an der Phasengrenze, und die Hydratisierung einen kritischen Einfluss auf diese Funktion haben.

Caractériser la fonction des protéines est crucial pour notre compréhension des mécanismes moléculaires de la vie, des maladies, et aussi pour inspirer de nouvelles applications en bionanotechnologie. Pour y arriver, il est nécessaire de caractériser la structure et la dynamique de chaque état occupé par la protéine durant sa fonction. La caractérisation expérimentale des états transitoires des protéines représente encore un défi majeur parce que les techniques à haute résolution structurelle, telles que la spectroscopie RMN et la cristallographie aux rayons X, peuvent difficilement être appliquées à l’étude des états de courte durée. De plus, les techniques à haute résolution temporelle, telles que la spectroscopie de fluorescence, nécessitent généralement une chimie complexe pour introduire des fluorophores à des endroits spécifiques dans la protéine. Dans cette thèse nous introduisons l’utilisation des nanoantennes fluorescentes en tant que nouvelle stratégie pour détecter et signaler les changements de conformation des protéines via des interactions non covalentes entre des fluorophores spécifiques et la surface de la protéine. En utilisant des expériences et des simulations moléculaires, nous démontrons que des fluorophores chimiquement divers peuvent se lier et être utilisés pour sonder différentes régions d’une enzyme modèle, la phosphatase alcaline (PA). Ces nanoantennes peuvent être fixées directement aux protéines ou utilisées à l'aide du système de fixation simple et modulaire, le complexe biotine-streptavidine (SA), qui permet un criblage rapide et efficace de la nanoantenne optimale tant dans sa composition que sa longueur. Dans le cas de la PA, nous montrons que nos nanoantennes permettent la détection et la caractérisation des conformations distinctes incluant les changements conformationnels nanoscopiques produisant durant la catalyse du substrat. Nous démontrons également que les signaux fluorescents émis par la nanoantenne peuvent également permettre de caractériser la cinétique enzymatique d’une protéine en une seule expérience tout en incluant la détermination des paramètres « Michaelis-Menten » de ses substrats et inhibiteurs. Nous avons également exploré l'universalité de la stratégie ces nanoantennes fluorescentes en utilisant une autre protéine modèle, la Protéine G et son interaction avec les anticorps, et avons démontré son utilité pour mettre au point un essai permettant de détecter les anticorps. Ces nanoantennes simples et faciles à utiliser peuvent être appliquées pour détecter et analyser les changements conformationnels de toutes tailles et nos résultats suggèrent qu'elles pourraient être utilisées pour caractériser n’importe quel type de fonction. / The characterisation of protein function is crucial to understanding the molecular mechanisms of life and disease, and inspires new applications in bionanotechnology. To do so, it is necessary to characterise the structure and dynamics of each state that proteins adopt during their function. Experimental study of protein transient states, however, remains a major challenge because high-structural-resolution techniques, including NMR spectroscopy and X-ray crystallography, can often not be directly applied to study short-lived protein states. On the other hand, high-temporal-resolution techniques, such as fluorescence spectroscopy, typically require complicated site-specific labelling chemistry. This thesis introduces the use of fluorescent nanoantennas as a new strategy for sensing and reporting on protein conformational changes through noncovalent dye-protein interactions driven by a high local concentration. Using experiments and molecular simulations, we first demonstrate that chemically diverse dyes can bind and be used to probe different regions of a model enzyme, intestinal alkaline phosphatase (AP). These nanoantennas can be attached directly to proteins or employed using the simple and modular biotin-streptavidin (SA) attachment system, which enables rapid and efficient screening for high sensitivity by tuning their length and composition. We show that these nanoantennas enable the detection and characterisation of distinct conformational changes of AP, including nanoscale conformational changes that occur during substrate catalysis. We also show that the fluorescent signal emitted by the nanoantenna enables complete characterisation of enzyme kinetics in one experiment, including determination of Michaelis-Menten parameters of substrates and inhibitors of AP. We then explored the universality of the nanoantenna strategy by using a different model protein system. Protein G was shown to interact with antibodies, using a rapid screening strategy for antibody detection. These effective and easy-to-use nanoantennas could potentially be employed to monitor various conformational changes, and our results offer potential for characterising various protein functions.