A new synthetic methodology for the combinatorial preparation of C-terminus-modified Green and Red Fluorescent Protein chromophores is described. This method involves the modification of the previously reported [2+3] cycloaddition reaction scheme to incorporate new R2 groups in the imidate used in the final step. This is achieved through two primary routes: (a) the imidation of nitriles using hydrochloric acid gas and (b) the O-alkylation of amides using a variant of Meerwein's Salt to provide conjugated imidates. The preparation of fluorescent microcrystals and nanofibers from Green Fluorescent Protein chromophore derivatives via the reprecipitation method is also demonstrated. The properties of these microcrystals and nanofibers, especially in relation to the powder obtained from organic solvents, are also explored. Additionally, it is demonstrated that the size and shape of the microcrystals and nanofibers can be modulated with varying experimental conditions for RP. A new class of AIE-active GFP chromophores is reported. These chromophores contain a benzoxazole group on the phenyl ring and varying lengths of alkyl chains on the imidazolidinone nitrogen. These benzoxazole-based chromophores exhibit unique properties in the solid state not previously observed for GFP chromophore derivatives, namely, a broadening of the excitation spectrum and red-shifting of the emission, likely caused by excimer formation. The crystal structure also reveals a unique "hot-dog" stacking motif. Additionally, some projects which require further work are discussed at the end of the thesis. These include a stress-responsive GFP-based polymer and DNA-binding fluorophores.

Im Rahmen dieser Arbeit wurden neuartige, gemischte Tetrahydridoborate (Borhydride), die für die Wasserstoffspeicherung im Festkörper für die mobile Anwendung geeignet sein könnten, synthetisiert und vollständig charakterisiert. Entscheidende Materialanforderungen für die Kombination mit einer Tieftemperaturbrennstoffzelle sind die hohe Wasserstoffspeicherkapazität von min. 6 m% bei einer Wasserstoffdesorption unterhalb von 100°C. Um beide dieser Hauptkriterien zu erfüllen, wurden Li-Al- und Na-Al-Borhydrid entsprechend dem Konzept von Nakamori u.a. ausgewählt. Beide Borhydride desorbieren unterhalb von 100°C, wobei das synthetisierte Li-Al-Borhydrid aufgrund des hohen Wasserstoffgehalts (17,2 m% H2) die vielversprechendsten Eigenschaften zeigte. Beide Systeme wurden mittels Pulverdiffraktometrie am Synchrotron hinsichtlich Ihrer Struktur aufgeklärt, wobei die Struktur der einzelnen komplexen Ionen anhand von Schwingungsspektroskopie (Infrarot-, Ramanspektroskopie) ebenfalls bestätigt werden konnte. Mit Hilfe verschiedener kombinierter Desorptionsanalysen war es möglich den Zersetzungspfad, insbesondere die Bildung instabiler Desorptionsprodukte, aufzuklären. So erfolgt die Zersetzung des Li-Al-Borhydrids über die Bildung von Lithiumborhydrid in der Festphase, das mittels in-situ Ramanspektroskopie in einer speziellen Ramanzelle beobachtet werden konnte. Die Infrarotspektroskopie des Desorptionsgases zeigte zunächst die Freisetzung von Aluminiumborhydrid, dass wiederrum Diboran und Wasserstoff desorbiert. Weiterhin wurden verschiedene Möglichkeiten verfolgt, wie der Zusatz von Kohlenstoff oder das Nanoconfinement von Lithiumalanat, um den Zersetzungsweg hinsichtlich ausschließlicher Wasserstofffreisetzung zu modifizieren und somit Reversibilität zu ermöglichen. Es konnte jedoch kein reversibles System mit hoher gravimetrischer Wasserstoffspeicherdichte und Desorption unterhalb von 100°C erzeugt werden. / Aim of the work was the synthesis and characterisation of novel mixed tetrahydroborates (borohydrides) for solid state hydrogen storage suitable for mobile applications. The combination with a PEM fuel cell requires a material with at least 6 wt% hydrogen combined with hydrogen desorption below 100°C. To fulfill both criteria, Li-Al- und Na-Al-borohydride were selected according to Nakamori’s concept. Both mixed borohydrides desorb well below 100°C whereas the mixed Li-Al-borohydride showed the most promising properties due to its high gravimetric hydrogen content (17.2 wt% H2). The crystal structures were examined by powder diffraction with a synchrotron source. The symmetry of the containing complex cations and anions was confirmed with vibrational spectroscopy (infrared, raman spectroscopy). The desorption pathway was clarified using a variety of combined thermal analysis techniques. Especially the desorption of unstable products of the most promising Li-Al-borohydride was possible via spectroscopy. Hence the desorption of Li-Al-borohydride leads to the formation of lithium borohydride in the solid state which was monitored via in-situ raman spectroscopy in a special raman cell. Infrared spectroscopy of the desorbed gas showed the initial desorption of aluminium borohydride which desorbs diborane and hydrogen in the following. Different options were examined in order to modify this desorption pathway by carbon addition or nanoconfinement of lithium alanate. However, none of the materials showed high hydrogen content combined with exclusive hydrogen desorption below 100°C and reversibility.

Die vorliegende Dissertation befasst sich mit der theoretischen Vorhersage neuer Materialien. Ein evolutionärer Algorithmus, der zur Lösung dieses globalen Optimierungsproblems Konzepte der natürlichen Evolution imitiert, wurde entwickelt und ist als Programmpaket EVO frei verfügbar. EVO findet zuverlässig sowohl bekannte als auch neuartige Kristallstrukturen. Beispielsweise wurden die Strukturen von Germaniumnitrofluorid, einer neue Borschicht und mit dem gekreuzten Graphen einer bisher unbekannte Kohlenstoffstruktur gefunden. Ferner wurde in der Arbeit gezeigt, dass das reine Auffinden solcher Strukturen der erste Teil einer erfolgreichen Vorhersage ist. Weitere aufwendige Berechnungen sind nötig, die Aufschluss über die Stabilität der hypothetischen Struktur geben und Aussagen über zu erwartende Materialeigenschaften liefern.

DNA polymerase epsilon (Pol ε) is a multi-subunit B-family DNA polymerase that is involved in leading strand DNA replication in eukaryotes. DNA Pol ε in yeast consists of four subunits, Pol2, Dpb2, Dpb3, and Dpb4. Pol2 is the catalytic subunit and Dpb2, Dpb3, and Dpb4 are the accessory subunits. Pol2 can be further divided into an N-terminal catalytic core (Pol2core) containing both the polymerase and exonuclease active sites and a C-terminus domain. We determined the X-ray crystal structure of Pol2core at 2.2 Å bound to DNA and with an incoming dATP. Pol ε has typical fingers, palm, thumb, exonuclease, and N-terminal domains in common with all other B-family DNA polymerases. However, we also identified a seemingly novel domain we named the P-domain that only appears to be present in Pol ε. This domain partially encircles the nascent duplex DNA as it leaves the active site and contributes to the high intrinsic processivity of Pol ε. To ask if the crystal structure of Pol2core can serve as a model for catalysis by Pol ε, we investigated how the C-terminus of Pol2 and the accessory subunits of Pol ε influence the enzymatic mechanism by which Pol ε builds new DNA efficiently and with high fidelity. Pre-steady state kinetics revealed that the exonuclease and polymerization rates were comparable between Pol2core and Pol ε. However, a global fit of the data over five nucleotide-incorporation events revealed that Pol ε is slightly more processive than Pol2 core. The largest differences were observed when measuring the time for loading the polymerase onto a 3' primer-terminus and the subsequent incorporation of one nucleotide. We found that Pol ε needed less than a second to incorporate the first nucleotide, but it took several seconds for Pol2core to incorporate similar amounts of the first nucleotide. B-family polymerases have evolved an extended β-hairpin loop that is important for switching the primer terminus between the polymerase and exonuclease active sites. The high-resolution structure of Pol2core revealed that Pol ε does not possess an extended β-hairpin loop. Here, we show that Pol ε can processively transfer a mismatched 3' primer-terminus between the polymerase and exonuclease active sites despite the absence of a β-hairpin loop. Additionally we have characterized a series of amino acid substitutions in Pol ε that lead to altered partitioning of the 3'primer-terminus between the two active sites. In a final set of experiments, we investigated the ability of Pol ε to displace the downstream double-stranded DNA while carrying out DNA synthesis. Pol ε displaced only one base pair when encountering double-stranded DNA after filling a gap or a nick. However, exonuclease deficient Pol ε carries out robust strand displacement synthesis and can reach the end of the templates tested here. Similarly, an abasic site or a ribonucleotide on the 5'-end of the downstream primer was efficiently displaced but still only by one nucleotide. However, a flap on the 5'-end of the blocking primer resembling a D-loop inhibited Pol ε before it could reach the double-stranded junction. Our results are in agreement with the possible involvement of Pol ε in short-patch base excision repair and ribonucleotide excision repair but not in D-loop extension or long-patch base excision repair.

We have synthesized dimethyl derivatives of the GFP chromophore (p-HOBDI) and several of its derivatives, and their photochemistry and photophysics were investigated using various steady-state and time-resolved techniques as follows. We first consider the effect of the £]-barrel on the optical properties of the GFP chromophore (p-HOBDI) experimentally by selective variation of the protonation state of chromophores and different solvents. Each of these forms shows a complex solvatochromic behavior and is governed by both polar and acid/base properties of the solvents. In contrast to their solution behavior, some O-alkyl GFP chromophore (alkoxy-BDI) derivatives exhibit large fluorescent enhancement in the solid state. The color of the crystalline BDI is tuned by substituent-mediated crystal packing, showing the potential applications in optoelectronic devices. Using femtosecond polarization-sensitive infrared (IR) spectrosceopy of the C=O stretching mode of the HOBDI, we have then discovered a near complete twisting around the ethylenic bridge between the phenolate and imidazolidinone groups upon electronic excitation. Cis/trans isomerization induced by the rotation around the bridge is thought to be responsible for the behavior of blinking in fluorescent protein; however, the mechanism of the thermal reverse isomerization is more problematic. Thus we synthesized BDI derivatives with decreasing para-donating ability, HO, CH3O, CH3, H, and Cl, and used a Hammett plot for the rate study. With a positive â value, we conceived, for the first time, a novel nucleophilic addition/elimination mechanism. Finally, the GFP chromophore falls into the general category of hydroxyarene photoacids, which exhibit high excited-state acidities but neutral ground states. A hydroxyl substituent at the meta position shows enhanced charge transfer and greater acidity in the excited state. As a result, we have demonstrated that the fast quenching of the excited state by internal conversion to the ground state is much slower in meta- than in para-HOBDI derivatives. This allows studies of this ultrafast intermolecular ESPT that competes with isomerization. The photoinduced dynamics of the meta isomer of GFP chromophore was further investigated using femtosecond transient absorption and fluorescence upconversion spectroscopies.

Le virus d'immunodéficience humaine 1 (VIH-1) cible spécifiquement les cellules CD4+ et empêche ainsi l'activation de cellules T cytotoxiques et B lors d'une infection secondaire. Le VIH-1 antagonise également la plupart des facteurs de restriction de l'hôte, y compris la tétherine. En l'absence de la protéine virale Vpu, la tétherine inhibe le relarguage de particules virales et provoque leur dégradation. La tétherine est également capable d'induire une signalisation pro-inflammatoire en réponse au bourgeonnement viral ainsi que d'activer le récepteur de cellules dendritiques ILT7. L'objectif principal de cette étude consistait à élucider les bases structurales de l'interaction entre la tétherine et ILT7. Malgré de nombreuses difficultés rencontrées dans la production recombinante de ILT7, on a pu déterminer la structure cristallographique du domaine N-terminale du récepteur. La ligation de la tétherine à l'ectodomaine entier de ILT7, mais pas au domaine N-terminal, a également été montré. Ces résultats constituent une base solide pour la caractérisation plus détaillée de l'interaction. / Human immunodeficiency virus 1 (HIV-1) specifically infects CD4+ T cells, thereby preventing an appropriate activation of cytotoxic T cells and B cells in response to opportunistic pathogens. In addition, HIV-1 antagonises host restriction factors, including tetherin. In the absence of the viral protein Vpu, tetherin potently inhibits virus particle release from infected cells. Tetherin also triggers proinflammatory signaling upon sensing virus assembly, and activates the dendritic cell receptor ILT7. The principal objective of this thesis was to elucidate the structural details underlying the interaction of tetherin with ILT7. Despite difficulties in the production of recombinant ILT7, the crystal structure of the N-terminal ILT7 domain could be determined. Furthermore, binding of tetherin to full-length ILT7, but not to the N-terminal domain, could be confirmed by SPR. These results provide a solid basis for the more detailed characterisation of the interaction.

Title: Structure and magnetic properties of f-electron compounds and their hydrides Author: Silvie Mašková Department: Deparment of Condensed Matter Physics Supervisor: Doc. RNDr. Ladislav Havela, CSc., Deparment of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Prague, The Czech Republic Abstract: Magnetic properties were studied in several types of actinide- and lanthanide-based ternary compounds. We have shown indirect that anisotropy of compressibility and thermal expansion can be related to the direction of magnetic moments at U-compounds with "soft" directions (where the closest U-U links are) perpendicular to the moments direction. Comparison of U and RE compounds of the 2-2-1 type indicates that contrary to U compounds, RE compounds can absorb much more hydrogen. The involvement of the f-states in metallic bond, which takes place at actinides and not in lanthanides, makes the U-based compounds apparently more stable against hydrogenation. Basic electronic properties were established for ζ -Pu19Os, which is a close analogy to β-Pu, and for its low-temperature variety η -Pu19Os. The results confirm that the volume is not the main parameter driving Pu properties, as β-Pu with intermediate volume is the most strongly correlated Pu phase. Keywords: uranium compounds,...

Les ribosomes sont des complexes ribo-nucléoprotéiques qui lisent l'ARNm pour synthétiser les protéines. Il a été démontré que les inhibiteurs de la synthèse des protéines eucaryotes ont un potentiel thérapeutique important pour traiter un large éventail de cancers humains. Récemment, nous avons publié une étude multidisciplinaire dans laquelle nous démêlons le mécanisme d'action du chlorolissoclimide (CL), un composé qui partage la similarité chimique avec le cycloheximide (CHX), mais qui présente une cytotoxicité inférieure prometteuse. Nous nous sommes intéressés aux nouveaux types d'interactions de CL avec le ribosome et nous avons donc résolu une nouvelle structure cristalline du complexe S.cerevisiae 80S en complexe avec un autre composé de lissoclimide à une résolution de 3.1 Å. Le couplage de structures à haute résolution avec la conception de médicaments axée sur le calcul et l'analyse FRET guidera davantage la conception d'inhibiteurs plus sélectifs et moins cytotoxiques. / Ribosomes are ribo-nucleoprotein complexes that read mRNA to synthesize proteins. This is important to consider in the case of cancer cells, which show a global increase in protein synthesis to support their hyper-proliferative behaviour. Inhibitors of eukaryotic protein synthesis have been shown to have significant therapeutic potential to treat a wide range of human cancers. Recently we published a multidisciplinary study in which we unravel the mechanism of action of chlorolissoclimide (CL), a compound sharing chemical similarity to cycloheximide (CHX), but showing promising lower cytotoxicity. We were interested in the new types of interaction of CL with the ribosome and therefore we solved a new crystal structure of the S.cerevisiae 80S in complex with another lissoclimide compound at 3.1 Å resolution. The coupling of high-resolution structures with computationally-driven drug design and FRET analysis will further guide the design of more selective and less cytotoxic inhibitors.

Ce travail a pour objectif de contribuer à l'étude du magnétisme dans les oxydes isolants de type AB_2O_6 (A= Fe, Co, Ni; B= Ta, Sb). Ces composés cristallisent dans une structure trirutile et présentent une variété très riche de phases magnétiques. Tous les ordres observés peuvent être classés comme antiferromagnétiques mais diffèrent d'un ordre simple de type Néel. En outre, les substitutions comme Fe_xCo_{1-x}Ta_2O_6, Fe_xNi_{1-x}Ta_2O_6 et Co_xNi_{1-x}Ta_2O_6 conduisent à des domaines de coexistence de phases magnétiques et à des points bicritiques dans les diagrammes de phases T(x). Une caractéristique particulièrement intéressante de ces composés est le caractère quasi-bidimensionnel de leur magnétisme, puisque les ions de métaux de transitions A apparaissent dans des réseaux plans séparés par deux plans d'ions non magnétiques B. Une forte anisotropie de champ cristallin est observée sur les sites magnétiques, résultant de la distorsion axiale des octaèdres d'oxygènes qui entourent ces ions A. Nous avons abordé deux aspects complémentaires: théorique et expérimental. Du point de vue théorique, une reformulation du modèle bidimensionnel jusqu'à present utilisée pour décrire la susceptibilité paramagnétique nous a permi d'obtenir des constants d'échange compatibles avec les types d'ordre magnétique planaire observés. Considérant que le caractère tridimensionnel des structures magnétiques révélées par diffraction neutronique indique l'importance du couplage entre plans, quoique faible, à basse température, nous proposons un modèle tridimensionnel coherent avec les ordonnements observés aussi dans le plan ab qu'au long de l'axe c. Du point de vue expérimental, nous faisons des substitutions sur le site non magnétique pour modifier de façon systematique l'espacement entre les plans magnétiques et, en consequence, le couplage entre eux. En particulier, nous avons synthétisé des composés du type ANb_xTa_{2-x}O_6 avec A = Fe, Ni et Co, restant dans le domaine de stabilité de la phase quadratique, puisque la présence de Nb favorise une phase orthorhombique. Une caractérisation structurale et magnétique de ces systèmes est faite par diffraction de rayons X et de neutrons, complétées par des mesures de susceptibilité magnétique, chaleur spécifique et aimantation en fonction du champ appliqué. Nous étudions également des séries avec Sb à la place de Nb où nous avons également effectué des remplacements sur le site magnétique. / This work aims to contribute to the study of magnetism in insulating oxides of the type AB_2O _6 (A = Fe, Co, Ni, Ta = B, Sb). These compounds crystallize in a trirutile structure and present a rich variety of magnetic phases. All the observed orderings can be classified as antiferromagnetic, but they differ from a simple Néel type order. Moreover, substitutions such as Fe_xCo_{1-x}Ta_2O_6, Fe_xNi_{1-x}Ta_2O_6 and Co_xNi_{1-x}Ta_2O_6 produce several regions of phase coexistence and bicritical points in the phase diagram T vs. x. A particularly interesting characteristic of these compounds is the quasi-two-dimensional nature of their magnetism, since the transition-metal ions A appear in layers separated by two planes of the non-magnetic ions B. They also show strong crystal-field anisotropy on the magnetic sites due to axial distortion of the oxygen octahedra surrounding the A ions. Our approach involves two complementary aspects: theoretical and experimental. From the theoretical point of view, a reformulation of the two-dimensional model used until now to describe the paramagnetic susceptibility allows us to obtain exchange parameters compatible with the observed planar magnetic orderings. Considering that the three-dimensional character the magnetic structures revealed by neutron diffraction indicates that the coupling between planes, although weak, plays an important role to low temperatures, we propose a three-dimensional model consistent with the observed orderings both in the ab plane and along the c axis. From the experimental point of view, we make substitutions on the non-magnetic sites, in order to systematically modify the spacing between planes and, consequently, the coupling between them. In particular, we have synthesized compounds of type ANb_xTa_{2-x}O_6 with A = Fe, Ni and Co, remaining in the stability region of tetragonal phase, since the presence of Nb favors an orthorhombic phase. The structural and magnetic characterization of the systems is done via the X-ray and neutron diffraction as well as measurements of magnetic susceptibility, specific heat, and magnetization as a function of the applied field. We also study series with Sb in place of Nb where we additionally include substitutions in the magnetic site.

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / The molecular study by X-ray diffraction of β-aminovinyl ketones [R3C(O)CH=C(R1)N(R4R5), onde R3 = CF3, CCl3, CHCl2; R1 = H, Me; R4 = H; R5 = benzyl, Ph, 5-methylisoxazol-3-yl; R4, R5 = -(CH2)4-, -(CH2)2O(CH2)2-], methyl 5- hydroxy-5-trihalomethyl-4,5-dihydro-1H-pyrazole-1-carboxylate [3-(R1), 4-(R2), and 5- (R3) substituted, where R1 = H, Me; R2 = H, Me; R3 = CCl3, CF3], 1-cyanoacetyl-5- trifluorometyl-5-hydroxy-4,5-dihydro-1H-pyrazole [3-(R1) and 4-(R2) substituted, where R1 = H, Ph; R1, R2 = -(CH2)4-, R2 = H] and 5-triclorometyl-5-hydroxy-4,5- dihydroisoxazole [3-(R1) substituted, where R1 = Ph, 4Br-Ph, tien-2-yl] were reported. The β-aminovinyl ketones have showed the fragment O=C-C=C-N essentially plane, as well as, the heterocyclic rings 4,5-dihydropyrazole and 4,5-dihydroisoxazole. The shorter bond lengths of b-aminovinyl ketones indicated an eletronic resonance effect in the conjugated system O=C-C=C-N. This effect also was encountered in the double bond N2=C3 of the rings 4,5-dihydropyrazole and 4,5-dihydroisoxazole and the substituent of the 3-position of this rings, when this substituent was an aromatic ring. In general, the molecules studied have its crytalline packing governed by intraand intermolecular hydrogen bond. / Neste trabalho foi descrito o estudo molecular por difração de raios-X de β- aminovinil cetonas [R3C(O)CH=C(R1)N(R4R5), onde R3 = CF3, CCl3, CHCl2; R1 = H, Me; R4 = H; R5 = benzila, Ph, 5-metilisoxazol-3-ila; R4, R5 = -(CH2)4-, -(CH2)2O(CH2)2- ], 1-metilcarboxilato-5-trialometil-5-hidróxi-4,5-diidropirazóis [3-(R1), 4-(R2) e 5-(R3) substituídos, onde R1 = H, Me; R2 = H, Me; R3 = CCl3, CF3], 1-cianoacetil-5- trifluormetil-5-hidróxi-4,5-diidropirazóis [3-(R1) e 4-(R2) substituídos, onde R1 = H, Ph; R1, R2 = -(CH2)4-, R2 = H] e 5-triclorometil-5-hidróxi-4,5-diidroisoxazóis [3-(R1) substituído, onde R1 = Ph, 4-BrPh, tien-2-ila]. As b-aminovinil cetonas apresentaram o fragmento O=C-C=C-N e os anéis heterocíclicos, 4,5-diidropirazol e 4,5- diidroisoxazol, essencialmente planos. Os dados relacionados aos comprimentos de ligações do sistema conjugado O=C-C=C-N indicaram um efeito de ressonância eletrônica nas β-aminovinil cetonas. Esse efeito foi encontrado também na ligação dupla N2=C3 dos anéis 4,5-diidropirazóis e 4,5-diidroisoxazóis e o substituinte da posição-3 dos mesmos, quando este fosse um anel aromático. De maneira geral, as moléculas estudadas têm seu empacotamento cristalino governado por ligações de hidrogênio intra- e intermoleculares.