Thèse numérisée par la Division de la gestion de documents et des archives de l'Université de Montréal.

L’exposition aux aérosols microbiologiques présents dans les environnements clos est susceptible de provoquer, chez les occupants, diverses pathologies telles que des infections, des toxi-infections et des allergies. Pour s’en prémunir, diverses stratégies passant notamment par l’emploi de dispositifs épurateurs d’air, ont été développées et commercialisées par les industriels de la ventilation et du traitement de l’air. Cependant, à ce jour, aucune méthodologie d’évaluation y compris normative ne permet d’évaluer la pertinence de ces stratégies. Ce travail de recherche se propose, d’une part, d’appréhender le devenir des aérosols microbiologiques au sein des espaces clos : de la source à l’individu exposé, en explorant le rôle de la ventilation dans ce transport et, d’autre part, d’explorer le gain apporté par les nouvelles technologies de traitement microbiologique de l’air sur l’exposition des occupants. Pour ce dernier point de l’étude, une démarche globale d’évaluation en 3 volets a été adoptée avec l’étude de l’efficacité du ou des principes d’épuration mis en oeuvre, la détermination du rendement intrinsèque en condition dynamique de ces systèmes et l’évaluation du gain apporté par ces derniers sur l’exposition des occupants. Les travaux menés avec les dispositifs épurateurs (filtration et photocatalyse) ont montré que les efficacités intrinsèques des systèmes ne permettent pas de préjuger de leur gain vis-à-vis du niveau de l’exposition des individus lorsqu’ils sont mis en oeuvre en environnement intérieur. Les résultats obtenus ont également mis en évidence que la prise en compte des flux aérauliques et du transport des particules induit par la ventilation et le dispositif épurateur est indispensable à la définition d’une stratégie cohérente de traitement d’air / Exposure to bioaerosols in indoor environments is associated with a wide range of adverse effects on health including infectious diseases, acute toxic effects and allergies. In order to guard against this phenomenon, the ventilation and air treatment industry has developed and marketed many air control strategies. However, at present, there is no methodology adapted to the evaluation of the relevance of these strategies. The aim of this research work was to characterize, in a first time, the progress of microbiological aerosol from the original source, to their eventual inhalation by person exposed, considering their dissemination through the indoor environments. Secondly, the work consisted of determining the efficiency of air cleaner devices applied to control indoor air quality. For this point, a global approach of evaluation in 3 steps was adopted, consisting of studying the efficiency of the epuration principle implemented, determining the intrinsic performance of the systems in dynamic conditions and their impact on the exposure level of the exposed persons. The tests carried out with air cleaner devices (filtration and photocatalysis) have shown that the intrinsic performance wasn’t able to estimate the beneficial impact of these systems on the exposure level of people when there were applied in indoor environments. So the intrinsic performance of devices is not the single impact factor, the airflow promoted by the device is also a factor to consider. Moreover, the characterization of indoor airflows and airborne particles transport is essential to define a coherent strategy of air treatment

Le VIH-1 est l'agent infectieux qui cause le SIDA. De nombreuses thérapies existent pour combattre le SIDA mais aucune ne permet son éradication et des résistances apparaissent. Le développement de nouvelles thérapies est donc nécessaire. Les anticorps simple-domaine (sdAb) de lamas présentent les propriétés idéales pour le développement de molécules neutralisantes. Des lamas ont donc été immunisés avec Vpr et les formes native, ou induite par un miniCD4, du trimère de gp140 (partie extracellulaire de l'enveloppe (Env)). Des banques de sdAbs ont ensuite été construites et des sélections par phage display et par double hybride ont été réalisées. Trois sdAbs se liant au site de liaison du co- récepteur de l'Env et un sdAb se liant au site de liaison du CD4 ont ainsi été sélectionnés. Ces sites sont conservés mais difficile d'accès pour des immunoglobulines conventionnelles. Ces sdAbs ont ensuite été caractérisés par ELISA, SPR et cytométrie de flux pour leur capacité de liaison à différentes Env, et en « single round assay » pour leur capacité de neutralisation d'un large spectre (LS) de pseudovirus. Des protéines multidomaines (plusieurs sdAbs reliés par un linker) ont ensuite été construites et testées pour leur neutralisation. Plusieurs de ces molécules, neutralisant un LS de virus, pourraient être utilisées dans des microbicides. La stabilité caractéristique des sdAbs, même en absence de formation de pont disulfure, par exemple dans un environnement réducteur tel que le cytoplasme, est primordiale dans le développement d'anticorps intracellulaires (intrabodies). / HIV-1 is the infectious agent of AIDS. Numerous therapies exist to fight AIDS, but they are not able to eradicate it, and resistances appear. So, new therapy development is necessary. Single-domain antibodies (sdAb) of llamas have ideal properties to develop neutralizing molecules. So, llamas have been immunized with Vpr and with free or miniCD4 induced trimeric gp140 (extracellular part of the envelope (Env)). SdAb libraries have been built and selections were done by phage display and yeast two hybrid. Three sdAbs targeting the co-receptor binding site of the Env and one sdAb targeting the CD4 binding site have been selected. These sites are conserved but inaccessible by conventional immunoglobulins. These sdAbs have been characterized by ELISA, SPR and FACS for their ability to bind different Env and by single-round assay for their neutralization ability. Multimeric proteins (linked sdAbs) have been built and tested for their neutralization ability. Several of these molecules are able to neutralize a broad spectrum of pseudoviruses. They can be used in microbicides. The characteristic stability of these sdAbs, even without disulfide bound formation, ie into reducing environment, as the cytoplasm, is primordial for intracellular antibody (intrabody) development. One sdAb anti-Vpr has been selected using the Sos Recruitment System (SRS), an yeast two-hybrid system allowing detection of cytoplasmic protein-protein interactions. This sdAb is able to alter the localization of its antigen into eukaryotic cells. It is a proof of concept ot the use of SRS in the selection of intracellularly functional sdAbs.

O conceito de heterogeneidade vascular é bem aceito pela comunidade cientifica, desempenhando papel essencial em processos fisiológicos e patológicos. Uma vez que os vasos sanguíneos são importantes na organogênese, diferenciação e morfogênese de tecidos e órgãos, torna-se interessante desvendar a diversidade vascular cerebral, identificando novos marcadores moleculares para este órgão tão importante. Utilizando tecnologia combinatorial de phage display in vivo, identificamos um novo motivo peptídico, na qual os aminoácidos FenilalaninaArginina-Triptofano (Phe-Arg-Trp; FRW) predominam. Este motivo peptídico é um ligante seletivo para vasos sanguíneos cerebrais e não se acumula em outros órgãos, incluíndo tecidos como intestinos e gônadas, que também apresentam barreiras endoteliais especificas. No entanto, mais surpreendente foi a observação de que o motivo FRW não se liga aos vasos sanguíneos da retina, o que implica em uma diferença até então desconhecida entre duas barreiras: a barreira hematoencefálica e a barreira hematoretiniana. Combinando phage display in vivo e microscopia eletrônica de transmissão, observamos a presença de partículas de fago ligadas à vasculatura cerebral em um nível supramolecular: aglomerados de fagos filamentosos expressando o motivo FRW foram visualizados ligados às regiões de contato entre as células endoteliais. Por fim, a utilização do peptídeo CFFWKFRWMC permite imageamento in vivo, demonstrando que novas ferramentas para estudar e visualizar o cérebro podem surgir deste motivo. / The concept of vascular heterogeneity is well accepted by the scientific community, playing an essential role in physiological and pathological processes. Since blood vessels are important in organogenesis, differentiation, and morphogenesis of tissues and organs, it becomes interesting to unveil the cerebral vascular diversity, identifying new molecular markers for such important organ. Using in vivo phage display, we show that a new peptide motif that emerged from our combinatorial screening of the vasculature binds selectively to blood vessels in the brain in vivo but not to vessels in other organs. Peptides containing a conserved motif in which amino acids Phenylalanine-Arginine-Tryptophan (Phe-Arg-Trp; FRW) predominate could be visualized by transmission electron microscopy bound to the junctions between endothelial in all areas of the brain, including the optic nerve but not in other barrier containing tissues, such as intestines and testis. Remarkably, peptides containing the motif do not bind to vessels in the retina, implying an important molecular difference between these two vascular barriers. Furthermore, the peptide allows for in vivo imaging, demonstrating that new tools for studying and imaging the brain are likely to emerge from this motif.

O tratamento atual indicado para casos de envenenamentos por peçonhas é a administração intravenosa de antivenenos, produzidos através da hiperimunização de animais. Entretanto, os antivenenos disponíveis podem, algumas vezes, não proteger os pacientes e causar reações de hipersensibilidade. Fosfolipases A2 (PLA2), L-aminoácido oxidases (LAAO), metalo e serinoproteases são os principais componentes de peçonhas ofídicas e contribuem para a neurotoxicidade, hemorragia, hemólise, miotoxicidade, cardiotoxicidade e formação de edemas. Foram empregados ensaios para avaliar as atividades das enzimas presentes na peçonha de serpentes da espécie Lachesis muta rhombeata e aquele para atividade de protease foi otimizado. A tecnologia de Phage display foi empregada para a seleção de fagos-anticorpos capazes de reconhecer a peçonha bruta. Os fagos foram amplificados em Escherichia coli TG1 e usados para infectar E. coli HB2151, a qual produz fragmentos de anticorpos humanos solúveis. Estes foram purificados e utilizados em testes de inibição de alguns dos componentes tóxicos da peçonha. Os testes de atividade para PLA2, protease e Laminoácido oxidase foram padronizados com sucesso e as 3 proteínas mostraram elevada atividade enzimática. Após otimização, a quantidade de peçonha necessária para o ensaio de protease foi reduzida em 25 vezes. A massa molecular de PLA2 foi estimada em 17 kDa e as massas moleculares de proteases foram estimadas em 40, 35 e 24 kDa, através de zimogramas. O método de bio panning foi eficiente para a seleção de fagos-anticorpos contra a peçonha bruta. Diversos fragmentos de anticorpos foram purificados e incubados com a peçonha bruta para testar suas capacidades de neutralização sobre cada enzima. Cinco clones demonstraram-se hábeis em inibir a PLA2 através da inibição da hemólise. O clone 4E inibiu 100% da hemólise durante as duas horas de ensaio quando pré-incubado na proporção 2:1 (scFv:peçonha). Os clones 2C e 4E inibiram 100% durante uma hora quando pré-incubados na proporção 1:1 e os clones 2F e 9F inibiram a hemólise parcialmente. Outros testes serão conduzidos para a seleção de clones capazes de neutralizar as demais enzimas, os quais, juntamente com os clones já selecionados, serão analisados através de ensaios in vivo. Espera-se que eles possam contribuir para a construção de um novo antiveneno capaz de superar algumas das dificuldades associadas às técnicas de imunoterapia convencionais / The current treatment for animal envenoming is the intravenous administration of antivenoms, produced by animal hyperimmunization. Unfortunately, available antivenoms sometimes do not protect patients and may cause hypersensitivity reactions. Phospholipases A2 (PLA2), L-amino acid oxidases, metallo and serine proteases are considered the most important snake venom components and contribute to neurotoxicity, hemorrhage, hemolysis, myotoxicity, edematogeny and cardiotoxicity. Assays for evaluating the enzymes present in Lachesis muta rhombeata venom were developed and the protease one was optimized. Phage display technology was used to select phage antibodies able to recognize the crude venom. Phages were amplified in Escherichia coli TG1 and used to infect E. coli HB2151, which produces human antibody fragments. Inhibition tests aiming the neutralization of some toxic components of the venom were performed using purified antibody fragments. Activity assays for evaluating PLA2, protease and L-aminoacid oxidase were successfully performed and all enzymes showed high activity levels. The molecular mass of PLA2 was estimated in 17 kDa and the molecular mass of proteases were estimated in 40, 35 and 24 kDa, by zymography. After optimizing the conditions for proteolytic assay, it was possible to use 25 times less venom than it was necessary at first. The bio panning method was efficient for selecting specific phage antibodies against the crude venom. Several clones were selected to infect HB2151 and to produce soluble antibody fragments, which were purified and incubated with the venom to test their inhibition capacity over each enzyme. Five clones demonstrated ability to neutralize PLA2 by inhibiting hemolysis. The clone 4E could inhibit 100% of hemolysis for over 2 hours when preincubated at the ratio 2:1 (scFv:venom). Clones 2C and 4E could inhibit 100% for 1 hour when preincubated at the ratio 1:1 and clones 2F e 9F could inhibit partially. Other tests will be performed to select clones able to neutralize other enzymes and, together with the clones already selected, will be evaluated by in vivo experiments. It is expected that they may contribute to the construction of a potential new antivenom able to overcome some of the problems associated with conventional immunotherapy

A doença de Chagas, causada pelo parasita protozoário Trypanosoma cruzi, afeta milhões de pessoas, a maioria delas vivendo na América latina. Apesar dos avanços da medicina e da biotecnologia, ainda existem poucas opções de tratamento para indivíduos com a doença. Assim, é importante compreendermos os detalhes moleculares da infecção parasitária, para que novas alternativas terapêuticas e de diagnóstico possam ser desenvolvidas para esses pacientes. Neste trabalho estudamos esta doença em duas frentes, uma do ponto de vista do parasita, e a outra, da resposta do hospedeiro. Utilizando bioinformática, identifcamos um peptídeo conservado (denominado TS9) presente nas proteínas de superfície gp85/transsialidases do parasita. Este peptídeo é capaz de promover adesão celular e, na sua forma sintética, inibe a entrada do T. cruzi na célula hospedeira. Análise da estrutura proteica revelou que o peptídeo TS9 encontra-se num domínio do tipo laminina-G, lado-a-lado com o peptídeo FLY, outro peptídeo conservado desta grande família, previamente descrito pelo nosso grupo. Juntos, eles formam um sítio de adesão a citoqueratinas e proteínas de flamento intermediário. Na segunda parte, investigamos os antígenos e epítopos reconhecidos pelas imunoglobulinas de pacientes portadores da doença nas suas diferentes formas clínicas: assintomática e cardiomiopatias, leve ou grave. Criamos uma biblioteca de phage display contendo, virtualmente, todos os fragmentos proteicos existentes no T. cruzi, que foi varrida contra imunoglobulinas para a construção de um mapa da resposta humoral dos pacientes com a doença de Chagas. Nossos resultados mostram que a resposta dos pacientes é complexa, e mais de dois mil epítopos foram mapeados. Muitos deles, como os antígenos B13, SAPA e FRA já foram previamente descritos, validando nosso método. Porém, um grande número de novos epítopos, inclusive contra proteína descritas como hipotéticas ou sem função conhecida, também foram encontrados. Seus papéis na infecção e resposta imune da doença merecem, portanto, atenção. Em resumo, as abordagens e técnicas utilizadas nesta tese são inovadoras, e permitiram a identifcação de peptídeos e moléculas que poderão ser úteis para o desenvolvimento de novos métodos diagnósticos e terapêuticos para a doença de Chagas. / Chagas disease, caused by the protozoan parasite Trypanosoma cruzi, afects millions of people, most of them living in Latin America. Despite advances in medicine and biotechnology, there are still few treatment options for individuals with the disease. Thus, it is important to understand the molecular details of the parasitic infection, so that new therapeutic and diagnostic alternatives can be developed for these patients. In this work, we study this disease in two fronts, one from the point of view of the parasite, and the other, of the response of the host. Using bioinformatics, we identifed a conserved peptide (called TS9) present in the surface proteins gp85 / trans-sialidases of the parasite. This peptide is capable of promoting cell adhesion and, in its synthetic form, inhibits the entry of T. cruzi into the host cell. Analysis of the protein structure revealed that the TS9 peptide is in a laminin-G-like domain, side-by-side with the peptide FLY, another conserved peptide of this large family, previously described by our group. Together, they form an adhesion site to cytokeratins and intermediate flament proteins. In the second part, we investigated the antigens and epitopes recognized by the immunoglobulins of patients with the disease in their diferent clinical forms: asymptomatic and cardiomyopathies, mild or severe. We created a phage display library containing virtually all existing protein fragments in T. cruzi. This library was screened against immunoglobulins for the construction of a humoral response map of patients with Chagas disease. Our results show that the response of the patients is complex, and more than 2,000 epitopes have been mapped. Many of them, such as the B13, SAPA and FRA antigens have been previously described, validating our method. However, a large number of new epitopes, including many against proteins described as hypothetical or with no known function, were also found. Their roles in infection and immune response of the disease deserve, therefore, attention. In summary, the approaches and techniques used in this thesis are innovative and have allowed the identifcation of new peptides and molecules that may be useful for the development of new diagnostic and therapeutic methods for Chagas disease.

A digoxina é um dos medicamentos indicados para o tratamento de falência cardíaca. Possui janela terapêutica estreita, sendo responsável por casos de intoxicação. O único antídoto disponível para a desintoxicação é o anticorpo policlonal DigiFab®, no formato Fab. O seu uso é eficaz, porém de custo elevado. Clones bacterianos produtores de fragmento Fab monoclonal anti-digoxina foram obtidos previamente pelo nosso grupo, pela técnica de phage display. Neste trabalho as variantes Fab dos 4 clones foram expressas em E.coli para estabelecer o método para a purificação. Com a obtenção dos fragmentos Fab purificados, foi caracterizada a sua afinidade ao antígeno e especificidade, em ensaios de inibição por digoxina, digitoxina, digoxigenina e ouabaina. Os parâmetros cinéticos da ligação dos fragmentos Fab dos 4 clones e do DigiFab® foram avaliados por SPR. Nas condições experimentais, não foram verificadas diferenças significativas entre os produtos dos 4 clones e o comercial, demonstrando o potencial dos fragmentos Fab monoclonais obtidos como antídoto à digoxina. / Digoxin is a medication indicated for heart failure treatment. Its therapeutic window is narrow, being responsible for intoxication cases. The only antidote available for the detoxification is a polyclonal antibody - DigiFab® in Fab format. Its use is effective, but costly. Bacterial clones producing anti-digoxin monoclonal Fab fragments were previously obtained by our group using phage display technology. In this work the Fab variants of the 4 clones were expressed in E.coli to establish the purification method. The purified fragments were characterized regarding the affinity to the antigen and the specificity through inhibition assays with digoxin, digitoxin, digoxigenin and ouabain. The binding kinetic parameters of Fab fragments of the 4 clones and the commercial product to Dig-BSA conjugate were assessed by SPR. Under the experimental conditions no significant differences were observed among the 4 clones and the commercial product, demonstrating the potential of monoclonal Fab fragments as an antidote to digoxin.

Les travaux décrits dans ce mémoire ont pour objectif d’une part le développementd’une nouvelle famille de protéines artificielles et d’autre part la création de nouveaux sitesde fixation spécifiques dans ces protéines. L’objectif général était de développer une approchegénérale permettant d’obtenir rapidement des protéines reconnaissant toute macromoléculecible choisie. On peut voir ces protéines artificielles spécifiques comme des sortes d’anticorpsartificiels pour leur spécificité et leur affinité mais dont les propriétés physiques : stabilité,solubilité, efficacité d’expression, insensibilité à l’agrégation sont nettement plus favorablesque celles des anticorps et de leur dérivés.Le premier chapitre, présente la conception et la construction d’une bibliothèque deprotéines artificielles dite de première génération où les protéines sont formées par larépétition d’un motif idéalisé à partir d’une famille de motifs naturels appelés HEAT repeats.Toutes les protéines de la bibliothèque, dénommées αRep, sont conçues pour avoir la mêmearchitecture générale mais diffèrent les unes des autres par le nombre de motifs et par laséquence dans certaines positions rendues variables au sein de chaque motif. Cette banquenous a permis de valider l’architecture αRep choisie : Les protéines s’expriment sous formesoluble, sont très stables et adoptent la structure secondaire et tertiaire attendue quel que soitla séquence des positions hypervariables. Le second chapitre présente alors les approchessuivies pour l’amélioration de la qualité et de la diversité de la bibliothèque et a conduit à laconstruction d’une bibliothèque d’αRep de deuxième génération. Cette dernière bibliothèque(2 .1) repose sur le même schéma général mais contient une diversité ayant été optimiséelors de la conception puis améliorée expérimentalement par une procédure dite deFiltration/shuffling. Cette bibliothèque très diverse (1.7*109 clones indépendants) a été alorsexploitée pour y rechercher, par des méthodes d’exposition sur phages, de nouvelles αRepreconnaissant des protéines cibles préalablement choisies. L’ensemble des résultats montretrès clairement que des αRep reconnaissant spécifiquement, avec une affinité élevée, desprotéines cibles choisies arbitrairement peuvent être effectivement obtenues. Les structurestridimensionnelles de plusieurs complexes formés entre les αRep et leur cible a été résoluepermet de comprendre la nature et l’organisation précise de ces capacités de reconnaissancemoléculaire nouvellement créées. / The main objective of this work was to design, produce and characterize a new familyof artificial proteins and to introduce new tailored specific binding sites within this structuralframework. Our general goal was to develop method allowing to rapidly generate newprotein binding specifically to any predefined target macromolecule. Binders based onartificial proteins can be viewed as antibody-like molecules but due to their different structurehave more favorable physical properties (expression, solubility, folding efficiency, stability)than antibodies and derivatives.The design and experimental assembly of a first generation artificial protein library isdescribed in part I. Proteins of this library are made by a repetition of a motif idealized from afamily of natural protein repeats (HEAT repeat). These artificial proteins, named αRep, havethe same general fold but the number of the repeated motif vary from protein to protein.Furthermore, a set of positions of each motif is highly variable within the library. Proteinisolated from this first generation library are well expressed, soluble, extremely stable andwere shown to have the designed secondary and tertiary structure.The methods used to improve the diversity and the experimental quality of the protein libraryare described in the second part of this thesis and have allowed us to create a secondgeneration αRep library. This library is based on the same general scheme but its diversitywas optimized by an improved design and experimental procedures known as filtration/shuffling.This highly diverse second generation library (1.7*109 independent clones) was usedto select variants with tailored binding specificities using phage display method. The resultsclearly show that news αReps binding tightly and specifically a range of arbitrarily definedprotein targets can be efficiently selected. The tertiary structure of complexes between αRepand their cognate target molecule were solved and allow to analyze the nature and detailedorganization of this newly engineered molecular recognition capacities.

Kohlenhydrate stellen aufgrund der strukturellen Vielfalt und ihrer oft exponierten Lage auf Zelloberflächen wichtige Erkennungsstrukturen dar. Die Wechselwirkungen von Proteinen mit diesen Kohlenhydraten vermitteln einen spezifischen Informationsaustausch. Protein-Kohlenhydrat-Interaktionen und ihre Triebkräfte sind bislang nur teilweise verstanden, da nur wenig strukturelle Daten von Proteinen im Komplex mit vorwiegend kleinen Kohlenhydraten erhältlich sind. Mit der vorliegenden Promotionsarbeit soll ein Beitrag zum Verständnis von Protein-Kohlenhydrat-Wechselwirkungen durch Analysen struktureller Thermodynamik geleistet werden, um zukünftig Vorhersagen mit zuverlässigen Algorithmen zu erlauben. Als Modellsystem zur Erkennung komplexer Kohlenhydrate diente dabei das Tailspike Protein (TSP) aus dem Bakteriophagen HK620. Dieser Phage erkennt spezifisch seinen E. coli-Wirt anhand der Oberflächenzucker, der sogenannten O-Antigene. Dabei binden die TSP des Phagen das O-Antigen des Lipopolysaccharids (LPS) und weisen zudem eine hydrolytische Aktivität gegenüber dem Polysaccharid (PS) auf. Anhand von isolierten Oligosacchariden des Antigens (Typ O18A1) wurde die Bindung an HK620TSP und verschiedener Varianten davon systematisch analysiert. Die Bindung der komplexen Kohlenhydrate durch HK620TSP zeichnet sich durch große Interaktionsflächen aus. Durch einzelne Aminosäureaustausche im aktiven Zentrum wurden Varianten generiert, die eine tausendfach erhöhte Affinität (KD ~ 100 nM) im Vergleich zum Wildtyp-Protein (KD ~ 130 μM) aufweisen. Dabei zeichnet sich das System dadurch aus, dass die Bindung bei Raumtemperatur nicht nur enthalpisch, sondern auch entropisch getrieben wird. Ursache für den günstigen Entropiebeitrag ist die große Anzahl an Wassermolekülen, die bei der Bindung des Hexasaccharids verdrängt werden. Röntgenstrukturanalysen zeigten für alle TSP-Komplexe außer für Variante D339N unabhängig von der Hexasaccharid-Affinität analoge Protein- und Kohlenhydrat-Konformationen. Dabei kann die Bindestelle in zwei Regionen unterteilt werden: Zum einen befindet sich am reduzierenden Ende eine hydrophobe Tasche mit geringen Beiträgen zur Affinitätsgenerierung. Der Zugang zu dieser Tasche kann ohne große Affinitätseinbuße durch einen einzelnen Aminosäureaustausch (D339N) blockiert werden. In der zweiten Region kann durch den Austausch eines Glutamats durch ein Glutamin (E372Q) eine Bindestelle für ein zusätzliches Wassermolekül generiert werden. Die Rotation einiger Aminosäuren bei Kohlenhydratbindung führt zur Desolvatisierung und zur Ausbildung von zusätzlichen Wasserstoffbrücken, wodurch ein starker Affinitätsgewinn erzielt wird. HK620TSP ist nicht nur spezifisch für das O18A1-Antigen, sondern erkennt zudem das um eine Glucose verkürzte Oligosaccharid des Typs O18A und hydrolysiert polymere Strukturen davon. Studien zur Bindung von O18A-Pentasaccharid zeigten, dass sich die Triebkräfte der Bindung im Vergleich zu dem zuvor beschriebenen O18A1-Hexasaccharid verschoben haben. Durch Fehlen der Seitenkettenglucose ist die Bindung im Vergleich zu dem O18A1-Hexasaccharid weniger stark entropisch getrieben (Δ(-TΔS) ~ 10 kJ/mol), während der Enthalpiebeitrag zu der Bindung günstiger ist (ΔΔH ~ -10 kJ/mol). Insgesamt gleichen sich diese Effekte aus, wodurch sehr ähnliche Affinitäten der TSP-Varianten zu O18A1-Hexasaccharid und O18A-Pentasaccharid gemessen wurden. Durch die Bindung der Glucose werden aus einer hydrophoben Tasche vier Wassermoleküle verdrängt, was entropisch stark begünstigt ist. Unter enthalpischen Aspekten ist dies ebenso wie einige Kontakte zwischen der Glucose und einigen Resten in der Tasche eher ungünstig. Die Bindung der Glucose in die hydrophobe Tasche an HK620TSP trägt somit nicht zur Affinitätsgenerierung bei und es bleibt zu vermuten, dass sich das O18A1-Antigen-bindende HK620TSP aus einem O18A-Antigen-bindenden TSP evolutionär herleitet. In dem dritten Teilprojekt der Dissertation wurde der Infektionsmechanismus des Phagen HK620 untersucht. Es konnte gezeigt werden, dass analog zu dem verwandten Phagen P22 die Ejektion der DNA aus HK620 allein durch das Lipopolysaccharid (LPS) des Wirts in vitro induziert werden kann. Die Morphologie und Kettenlänge des LPS sowie die Aktivität von HK620TSP gegenüber dem LPS erwiesen sich dabei als essentiell. So konnte die DNA-Ejektion in vitro auch durch LPS aus Bakterien der Serogruppe O18A induziert werden, welches ebenfalls von dem TSP des Phagen gebunden und hydrolysiert wird. Diese Ergebnisse betonen die Rolle von TSP für die Erkennung der LPS-Rezeptoren als wichtigen Schritt für die Infektion durch die Podoviren HK620 und P22. / Carbohydrates are important for recognition events because of their diverse structure and their exposition on cell surfaces. Interactions between proteins and carbohydrates mediate a specific exchange of information crucial for manifold biological functions. The energetics of protein-carbohydrate-interactions are not very well understood so far due to the lack of structural data of proteins in complex with extensive oligosaccharides consisting of more than two building blocks. This dissertation improves the understanding of how proteins recognize complex carbohydrates by analysis of structural thermodynamics, which might lead to reliable algorithms for predictions of protein-carbohydrate-interactions. As model system for this work the tailspike protein (TSP) from coliphage HK620 was used. This phage recognizes specifically the surface O-antigen of its E. coli host by its TSP. HK620TSP does not only bind the O-antigen of host lipopolysaccharide (LPS), but also cleaves the polysaccharide (PS) by its endo-N-acetylglusaminidase activity. HK620TSP binds hexasaccharide fragments of this PS with low affinity (KD ~ 130 μM). However, single amino acid exchanges generated a set of high-affinity mutants with submicromolar dissociation constants (KD ~ 100 nM). Strikingly, at room temperature association is driven by enthalpic and entropic contributions emphasizing major solvent rearrangements upon complex formation. Regardless of their affinity towards hexasaccharide the TSP complexes showed only minor conformational differences in crystal structure analysis accept of mutant D339N. The extended sugar binding site can be subdivided into two regions: Firstly, there is a hydrophobic pocket at the reducing end with minor affinity contributions. Surprisingly, access to this site is blocked by a single exchange of aspartate to asparagine (D339N) without major loss in hexasaccharide affinity. Secondly, there is a region where specific exchange of glutamate for glutamine (E372Q) creates a site for an additional water molecule. Upon sugar binding side chain rearrangements lead to displacement of this water molecule and additional hydrogen bonding. Thereby this region of the binding site is defined as the high affinity scaffold. HK620TSP is not only specific for the O18A1-antigen, but also the lacking of the branching glucose in the O18A1-antigen can be tolerated so that the accordant O18A PS can be bound and cleaved by HK620TSP as well. Surprisingly, in binding studies with the smallest O-antigen units of these PS the O18A pentasaccharide was bound by TSP variants with nearly the same affinity or even a slightly increased one compared to the O18A1 hexasaccharide. However, there is a change in thermodynamic contributions to binding: the lack of the glucose moiety leads to a less entropically favored binding compared to binding of O18A1-hexasaccharide (Δ (-TΔS) ~ 10 kJ/mol). In contrast the enthalpic contribution to the binding is more favorable (ΔΔH ~ -10 kJ/mol) for the binding of O18A pentasaccharide. The side-chain glucose contributes to entropy by the release of four water molecules out of a hydrophobic pocket. The binding of this branching glucose is paid by an enthalpic penalty because of the breakup of hydrogen bonding of displaced water molecules and destabilizing contacts between sugar and protein in this hydrophobic pocket. Therefore the binding of the glucose in this pocket does not account for generating affinity and an evolutionary relation of HK620TSP to an O18A-antigen binding protein is presumed. Finally, the infection mechanism of phage HK620 was studied as well. In analogy to the related phage P22 the DNA-ejection could be triggered by incubation of HK620 with the host LPS in vitro. The morphology and chain length of the LPS as well as the activity of HK620TSP towards the LPS are crucial for this in vitro DNA-ejection. Thus, the DNA-ejection could also be induced by LPS from bacteria of serogroup O18A which can be bound and hydrolyzed by HK620TSP. These results stress the role of TSP for the recognition of host LPS-receptors as a crucial step of infection by podoviruses P22 and HK620.

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