The research in this dissertation examines the chemistry and applications of dendrimers in homogeneous catalysis. We examined interactions between dendrimers and charged probe molecules, prepared dendrimer-encapsulated metal nanoparticles in organic solvents, studied size-selectivity of dendrimer-encapsulted catalysts, and designed molecular rulers as in-situ probes to measure the location of dendrimer-encapsulted metal nanoparticles. The intrinsic proton binding constant and a constant that characterizes the strength of electrostatic interactions among occupied binding sites in poly(amidoamine) (PAMAM) dendrimers have been obtained by studying the effect of solution pH on the protonation of the dendrimers. The significant finding is that these two factors are greatly modulated by the unique and hydrophobic microenvironment in the dendrimer interior. Hydrophilic poly(propylene imine) (PPI) dendrimers were modified with various hydrophobic alkyl chains through an amide linkage and were then used as templates for preparing intradendrimer copper nanoclusters. The main driving force for encapsulating metal-ions was found to be the differences in metal-ion solubility between the solvent and the interior of the dendrimer. Nanometer-sized metal particles are synthesized and encapsulated into the interior of dendrimers by first mixing together the dendrimer and metal ion solution and then reducing the composite chemically, and the resulting dendrimer-encapsulated metal nanoparticles can then be used as catalysts. By controlling the packing density on the dendrimer periphery using either different dendrimer generations or dendrimer surface functionalities, it is possible to control access of substrates to the encapsulated catalytic nanoparticle. Molecular rulers consisting of a large molecular "stopper", a reactive probe and a linker were designed as in-situ probes for determining the average distance between the surface of dendrimer-encapsulated palladium nanoparticles and the periphery of their fourth-generation, hydroxyl-terminated PAMAM dendrimer hosts. By doing so, we avoid having to make assumptions about the nanoparticle size and shape. The results suggest that the surface of the encapsulated nanoparticle is situated 0.7 ± 0.2 nm from the surface of the dendrimer.

Tripeptidyl-peptidase II (TPP II) is a subtilisin-like serine peptidase that forms a gigantic homooligomeric complex, and is involved in the degradation of peptides in the cytosol. In addition, TPP II has been implicated in specific cellular processes, such as apoptosis control and adipogenesis, but if this is dependent on its endo- or exopeptidase activity remains to be determined. This work is devoted to the structure and function of TPP II, and to finding connections between the two. Evolutionarily conserved regions of TPP II have been identified, and sequence signatures have been constructed as an aid in identification of TPP II homologues. The conserved regions highlight amino acid residues of potential importance to structure, function or both. In addition, the first TPP II homologue in a prokaryote has been documented, which was likely the result of a horizontal gene transfer. Substrate binding for the exopeptidase activity of TPP II has been studied through mutagenesis of Glu-331, which revealed a molecular ruler mechanism that positions substrates for cleavage at the third peptide bond from the N-terminus. Thus, the well-known tripeptidyl-releasing property of TPP II could be explained. The exopeptidase activity was also probed by pH dependence studies, which revealed that a substrate with a smaller residue in the P1 position could bind non-productively to the active site. Furthermore, a difference in the pH dependence of KM between TPP II from Drosophila and homologues from mammals indicated a difference in the configuration of the binding pockets between these species. The endopeptidase activity of TPP II has also been investigated, and was found to differ from the exopeptidase activity. The endopeptidase activity appeared to be promiscuous and the preference for basic amino acid residues in the P1 position reported earlier could not be substantiated. In conclusion, many structural and mechanistic features have been observed in this work. This might be of value to future drug discovery efforts towards TPP II, and in elucidating the physiological role of this gigantic enzyme. / Felaktigt tryckt som Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 721

Le transfert d'énergie par résonance de type Förster (FRET) est un transfert d'énergie non radiatif d'un donneur à un accepteur à proximité. En raison de sa dépendance de la distance extrêmement sensible entre env. 1 et 20 nm, FRET joue un rôle important dans la nanobiotechnologie. Ainsi FRET peut être utilisé comme système de transduction du signal, mais aussi pour l'estimation de la distance entre le donneur et l'accepteur.Les accepteurs de FRET utilisés dans ce travail étaient des nanocristaux semi-conducteurs (quantum dots, QD). Ce type de luminophore est bien connu pour ses propriétés photophysiques supérieures. Leur absorption forte et spectralement large, et leur photoluminescence (PL) brillante et spectralement fine et de l'accordabilité spectrale de la PL sont idéalement adaptés aux applications de FRET. La combinaison des QDs comme accepteurs de FRET avec des complexes luminescents de terbium (CLT) comme donneurs permet des grandes distances de FRET (> 10 nm). La distance de FRET est caractéristique d'une paire FRET et décrit la distance à laquelle l'efficacité de FRET est égale à 50%. CLT sont idéal comme donneurs de FRET parce qu'ils fournissent des longues durées de vie des états excités à l'ordre de la milliseconde. Cette longue période de décroissance de PL permet de mesurer en temps décalé pour une répression d’autofluorescence et la PL des QDs directement excités, ce qui augmente fortement la sensibilité de détection. Les bandes d'émission de PL structurés de CLT et la PL accordable de QDs sont idéales pour l'application dans le diagnostic multiplexé.La thèse se compose de deux parties. Dans la première le couple FRET CLT-QD a été utilisé dans des immunodosages de FRET homogènes pour la détection de marqueurs biologiques antigène prostatique spécifique (TPSA), énolase specifique des neurones (NSE), antigène carcino-embryonnaire (CEA), et le récepteur du facteur de croissance épidermique (EGFR). La sensibilité du dosage immunologique a été optimisé en utilisant des différents types d'anticorps IgG, F (ab')2, F (ab), et pour EGFR un anticorps de chaîne lourde unique. Des limites de détection picomolaires étaient réalisées en utilisant des échantillons de sérum de petit volume et des mesures sur des lecteurs de microplaques cliniques. Une étude détaillée des différents systèmes de FRET en utilisant la spectroscopie résolue en temps a été réalisée pour étudier l'influence des différents anticorps sur la distance, la fonctionnalité, et la sensibilité des immunodosages. L'étude a été complétée par la mesure de NSE et CEA dans un format duplexé et des échantillons réels de patients.Dans la deuxième partie le FRET pour des mesures de distance nanométriques (réglette moléculaire ou spectroscopique) étaient étudiés. FRET en résolution temporelle a permis de calculer la distance entre le donneur et l’accepteur. Par conséquent, deux stratégies de liaisons différentes ont été étudiées pour établir une proximité entre le CLT et le QD : la reconnaissance biotine-streptavidine et l’auto-assemblage médié par polyhistidine. Une étude en résolution temporelle détaillée a été effectuée avec des QDs de différentes tailles, formes et revêtements de surface combiné avec des CLT liés à trois différentes biomolécules. L'analyse des courbes de décroissance multiexponentielle des donneurs et accepteurs permettait à obtenir des informations sur la taille, la forme et la biofonctionnalité des bioconjugués CLT-QD. Les résultats étaient en accord avec d'autres méthodes d'analyse de structure, telles que la microscopie électronique à transmission (MET) ou la diffusion de lumière dynamique (DLS), mais avec l'avantage d'une mesure homogène à la résolution 3-dimensionelle (impossible pour le MET), sans l'inclusion d'une couche d'hydratation (l’inconvénient de DLS) et en faible concentration dans le même environnement que celui utilisé pour l'application biologique. / Förster resonance energy transfer (FRET) is a non-radiative energy transfer from a donor to an acceptor in close proximity. Due to its extremely sensitive distance dependence in the 1 – 20 nm range, FRET plays an important role in nanobiotechnology. Thereby FRET can be used as signal transduction system but also for the distance estimation between donor and acceptor. The selected FRET acceptors in this work were semiconductor nanocrystals (quantum dots, QDs). This type of luminophore is well known for its superior photophysical properties. Their strong and broad absorption and their bright, narrow-band, and size-tunable photoluminescence (PL) emission make QDs ideally suited for FRET application. Combing QDs as FRET acceptors with luminescent terbium complexes (LTC) as FRET donors offers exceptionally large Förster distances of more than 10 nm. The Förster distance is characteristic of a FRET pair and is the distance at which the FRET efficiency equals 50 %. A large Förster distance is desirable as it offers the detection of biological interactions over large distances. LTC are suitable FRET donors for QDs because they provide long excited-state lifetimes in the millisecond range. This long PL decay time enables time-gated measurements for the suppression of autofluorescence and PL of directly excited QDs, which strongly increases the detection sensitivity. Additionally, the structured PL emission bands of LTCs together with the size-tunable PL emission bands of QDs make this FRET pair ideal for the application in multiplexed diagnostics, which is the measurement of multiple biomarkers in a single sample.The PhD thesis consists of two parts. In the first part the LTC-QD FRET pair was used within homogeneous FRET immunoassays for the detection of the biomarkers prostate specific antigen (TPSA), neuron-specific enolase (NSE), carcinoembryonic antigen (CEA), and epidermal growth factor receptor (EGFR). The immunoassay sensitivity was optimized using different types of antibodies IgG, F(ab’)2,F(ab), and for EGFR single heavy chain antibodies, which differ largely in their size. The use of small-volume serum samples and measurements on clinical as well customized fluorescence plate readers result in picomolar detection limits for all measured biomarkers. In addition to these QD-based in vitro diagnostic tests, a detailed study of the different FRET-systems using time-resolved spectroscopy was performed. The investigation revealed the influence of the different antibodies on distance, functionality, and sensitivity of the FRET immunoassays. The study was completed by the measurement of NSE and CEA in a duplexed format and real patient samples were investigated.The second part was to use FRET for nanometric distance measurements as molecular or spectroscopic ruler. Time-resolved FRET measurements enabled the calculation of the distance between donor and acceptor. Therefore two different binding strategies were investigated to establish a close proximity between the LTC-donor to the QD-acceptor, namely biotin-streptavidin recognition and polyhistidine mediated self-assembly. A detailed time-resolved study was performed of QDs with different sizes, shapes, and surface coatings in combination with LTC bound to three different host biomolecules, which also possessed different sizes, shapes, orientations, and binding conditions. The analysis of the multi-exponential decay curves of donor and acceptor allowed to obtain information about the size, shape, and biofunctionality of the investigated QD bioconjugates. The results were in agreement with other structural analysis methods, such as transmission electron microscopy (TEM) or dynamic light scattering (DLS), but with the advantage of a homogeneous measurement with three-dimensional resolution (not possible for TEM), without the inclusion of a hydration shell (drawback for DLS), and at low concentration in the same environment as used for the biological application.