A poly-leucine transmembrane domain library was randomized at positions corresponding to contact surfaces for a right-handed crossing of two helices to determine the significance of small residues, GxxxG motifs, and hydrogen bonding residues in driving helix-helix interactions within membranes. About 10000 sequences, which include the interfaces of tightly interacting biological transmembrane domains, were subjected to increasing selection strength in the membrane interaction assay TOXCAT and surviving clones were sequenced to identify single site and pairwise amino acid trends. Statistical analysis identified a central glycine to be essential to strong dimerization. The next strongest statistical preference was for a phenylalanine three positions before the key glycine. Secondary to these residues, polar histidine and asparagine residues are also favored in strongly dimerizing sequences, but not to the exclusion of hydrophobic leucine and isoleucine. The analysis identifies novel pairwise combinations that contribute to or are excluded from strong dimerization, the most striking of which is that the biologically important GxxxGxxxG/A pattern is under-represented in the most strongly associating BNIP3-like transmembrane dimers. The variety of residue combinations that support strong dimerization indicates that not only key 'motif' residues, but also the residues that flank them, are important for strong dimerization. Because favorable pairwise combinations of flanking residues occur between both proximal positions and residues separated by two or more turns of helix, the complexity of how sequence context influences motif-driven dimerization is very high.

Catalytic ethylene oligomerization is a well understood industrially viable process. The large majority of scientific literature and patents concerning this process has been developed with the use of chromium catalysts. Commercial systems producing selective tri/tetramerization, non-selective oligomerization and polymerization are all based on this metal with the exception of a few systems based on other transition metals (Zr, Ti, Ni etc.). This versatility raises interesting questions about chromium’s unique behaviour. Essentially, selective or non-selective oligomerization and polymerization processes could be regarded as belonging to the same category of C-C bond forming reactions, though different mechanisms are involved. The first part of this thesis explores a variety of chromium complexes for ethylene oligomerization purposes. In order to gather further information about the unique behaviour of chromium, we have explored a variety of nitrogen and phosphorus containing ligands. We started with a simple bi-dentate anionic amidophosphine (NP) ligand and assessed the role of the ligand’s negative charge and number of donor atoms in determining the type of catalytic behaviour in relation to the metal oxidation state. This ligand proved capable of generating a series of chromium dimeric, tetrameric or polymeric and even heterobimetallic chromium-aluminate complexes in different valence states. This allowed us to isolate a “single component” self activating Cr(II) complex as well as a rare example of mixed valence Cr(I)/Cr(II) species. Additionally, each of these species acted as switchable catalyst depending on the type of co-catalyst

The largest class of cell surface receptors in mammalian genomes is the superfamily of G protein-coupled receptors (GPCRs) which are activated by a wide range of extracellular responses such as hormones, pheromones, odorants, and neurotransmitters. Drugs which have therapeutic effects on a wide range of diseases are act on GPCRs. In contrast to traditional idea, it is recently getting accepted that G-protein coupled receptors can form homo- and hetero-dimers and this interaction could have important role on maturation, internalization, function or/and pharmacology. Bimolecular fluorescence complementation technique (BiFC) / is an innovative approach based on the reassembly of protein fragments which directly report interactions. In our study we implemented this technique for detecting and visualizing the GPCR interactions in yeast cells. The enhanced green fluorescent protein (EGFP) fractionated into two fragments at genetic level which does not possess fluorescent function. The target proteins which are going to be tested in terms of interaction are modified with the non-functional fragments, to produce the fusion proteins. The interaction between two target proteins, in this study Ste2p receptors which are alpha pheromone receptors from Saccharomyces cerevisiae, enable the fragments to come in a close proximity and reassemble. After reassembly, EGFP regains its fluorescent function which provides a direct read-out for the detection of interaction. Further studies are required to determine subcellular localization of the interaction. Moreover, by using the fusion protein partners constructed in this study, effects of agonist/antagonist binding and post-translational modifications such as glycosylation and phosphorylation can be examined. Apart from all, optimized conditions for BiFC technique will guide for revealing new protein-protein interactions.

The specific interactions of macromolecules along with the activity of enzymes are central to all aspects of biology. It is well recognized that when the relative concentration or activity of macromolecules is perturbed, it can lead to human diseases. Thus, the development of simple methods for the detection of macromolecules and the activity of enzymes in complex environments is important for understanding biology. Moreover, the development of methods for measuring interactions allows for the testing of inhibitors that can be used as tools or drugs for improving human health. Towards this goal, a promising new method has been developed, which is the focus of this thesis, called split-protein reassembly or protein fragment complementation. In this method, a protein reporter, such as the green fluorescent protein or firefly luciferase, is dissected into two fragments, which are attached to designed adaptor proteins. The designed split-protein systems only produce a measurable signal, either fluorescence or luminescence, when a specific macromolecular interaction or activity is present. In this thesis, I have extended previous research on the direct detection of DNA using split-protein sensors utilizing a red fluorescent protein, dsRED from Discosoma that allows for multiplexed DNA detection. I have designed a new split-luciferase based sensor for detection of poly (ADP-ribose) or PAR, which plays a key role in the response to DNA damage and have applied it for monitoring the activity of poly (ADP-ribose) glycohydrolase that controls PAR levels in the cell. Furthermore, I have significantly expanded upon a three-hybrid split-luciferase system for identifying protein kinase inhibitors. I have designed and tested two orthogonal peptide based chemical inducers of dimerization based on BAD and p53mt conjugates. I have studied these chemically induced dimerization systems in detail in order to begin to provide a theoretical basis for the observed experimental results. Finally, in a less related area, I have developed methods for producing water soluble semiconductor nanoparticles called Quantum Dots (QDs), with potential application in biological imaging. I have developed methods for functionalizing the QDs with orthogonal peptides, which can be potentially used for the assembly of high affinity non-covalent QD targeted proteins.

Somatostatin (SST) is a peptide hormone that was originally identified in the hypothalamus and subsequently found throughout the central nervous system and in various peripheral organs. Generally classified as an inhibitory factor, SST is secreted by endocrine, neuronal and immune cells and acts to regulate cell secretion, neurotransmission and cell proliferation. There are five receptor-subtypes known to engage SST, termed SSTR1-5, all belonging to the superfamily of G-protein coupled receptors (GPCRs). Within the past few years, there has been a prepondef8:llce of evidence to suggest the importance of GPCR dimerization in receptor-biogenesis, regulation and pharmacology. It has been previously reported in our laboratory, that human (h) SSTR5 homo- and heterodimerizes with hSSTR1 in an agonist-regulated manner. However, it was unclear as to the contribution of each subtype in the formation of the hSSTR1/hSSTR5 heterodimer, the possible molecular determinants involved and the effects of heterodimerization on the pharmacology of the receptors. Furthermore, the dimerization properties of other hSSTRs including their heterodimerization remain undetermined. Here, we demonstrate that agonist binding to hSSTR5 and not hSSTR1 modulates the formation of the heterodimer, with particular emphasis on its carboxyl-terminal tail in specifying the interaction. We also determined the mechanics of the hSSTR2 homodimer, unlike the previous hSSTRs investigated, forms constitutive dimers that dissociate into monomers following activation with agonist. This feature is important for receptor trafficking, as preventing their dissociation impairs agonist-mediated endocytosis. Lastly, we investigated the heterodimerization of hSSTR2 and hSSTR5, an interaction that, like the hSSTR1/hSSTR5 heterodimer, is subtype-specific, requiring selective-activation of hSSTR2 and not hSSTR5. The heterodimer exhibited enhanced signalling characteristics including, prolonged activation of MAP kinases and an increase in the induction of the cyclin-dependent kinase inhibitor p27Kip1. These enhanced properties of the heterodimer conferred an extended growth inhibitory response. Dimerization of GPCRs, with particular emphasis on heterodimers, generates novel receptors with unique properties distinct from those of the individual receptor monomers/homodimers. An understanding on the mechanisms involved in GPCR dimerization could provide a rationale in future drug design.

Les molécules classiques du CMH de classe II sont responsables de la présentation de peptides exogènes par les cellules présentatrices d’antigène aux lymphocytes T CD4+. Cette présentation antigénique est essentielle à l’établissement d’une réponse immunitaire adaptative. Cependant, la reconnaissance d’auto-antigènes ainsi que l’élimination des cellules du Soi sont des problèmes à l’origine de nombreuses maladies auto-immunes. Notamment, le diabète et la sclérose en plaque. D’éventuels traitements de ces maladies pourraient impliquer la manipulation de la présentation antigénique chez les cellules dont la reconnaissance et l’élimination engendrent ces maladies. Il est donc primordial d’approfondir nos connaissances en ce qui concerne les mécanismes de régulation de la présentation antigénique. La présentation antigénique est régulée tant au niveau transcriptionnel que post-traductionnel. Au niveau post-traductionnel, diverses cytokines affectent le processus. Parmi celles-ci, l’IL-10, une cytokine anti-inflammatoire, cause une rétention intracellulaire des molécules du CMH II. Son mécanisme d’action consiste en l’ubiquitination de la queue cytoplasmique de la chaîne bêta des molécules de CMH II. Cette modification protéique est effectuée par MARCH1, une E3 ubiquitine ligase dont l’expression est restreinte aux organes lymphoïdes secondaires. Jusqu’à tout récemment, il y avait très peu de connaissance concernant la structure et les cibles de MARCH1. Considérant son impact majeur sur la présentation antigénique, nous nous sommes intéressé à la structure-fonction de cette molécule afin de mieux caractériser sa régulation ainsi que les diverses conditions nécessaires à son fonctionnement. Dans un premier article, nous avons étudié la régulation de l’expression de MARCH1 au niveau protéique. Nos résultats ont révélé l’autorégulation de la molécule par formation de dimères et son autoubiquitination. Nous avons également démontré l’importance des domaines transmembranaires de MARCH1 dans la formation de dimères et l’interaction avec le CMH II. Dans un second article, nous avons investigué l’importance de la localisation de MARCH1 pour sa fonction. Les résultats obtenus montrent la fonctionnalité des motifs de localisation de la portion C-terminale de MARCH1 ainsi que la présence d’autres éléments de localisation dans la portion N-terminale de la protéine. Les nombreux mutants utilisés pour ce projet nous ont permis d’identifier un motif ‘‘VQNC’’, situé dans la portion cytoplasmique C-terminale de MARCH1, dont la valine est requise au fonctionnement optimal de la molécule. En effet, la mutation de la valine engendre une diminution de la fonction de la molécule et des expériences de BRET ont démontré une modification de l’orientation spatiale des queues cytoplasmiques. De plus, une recherche d’homologie de séquence a révélé la présence de ce même motif dans d’autres ubiquitines ligases, dont Parkin. Parkin est fortement exprimée dans le cerveau et agirait, entre autre, sur la dégradation des agrégats protéiques. La dysfonction de Parkin cause l’accumulation de ces agrégats, nommés corps de Lewy, qui entraînent des déficiences au niveau du fonctionnement neural observé chez les patients atteints de la maladie de Parkinson. La valine comprise dans le motif ‘’VQNC’’ a d’ailleurs été identifiée comme étant mutée au sein d’une famille où cette maladie est génétiquement transmise. Nous croyons que l’importance de ce motif ne se restreint pas à MARCH1, mais serait généralisée à d’autres E3 ligases. Ce projet de recherche a permis de caractériser des mécanismes de régulation de MARCH1 ainsi que de découvrir divers éléments structuraux requis à sa fonction. Nos travaux ont permis de mieux comprendre les mécanismes de contrôle de la présentation antigénique par les molécules de CMH II. / Classical MHC class II molecules are responsible for the presentation of exogenous peptides to CD4+ T cells, which is essential for the establishment of the adaptive immune response. However, problems with recognition of auto-antigens and the subsequent cell elimination are at the root of numerous autoimmune diseases. Manipulation of the antigen presentation pathway in order to eliminate cells that present self-antigens could serve as potential treatments of many autoimmune disorders. It is therefore essential to deepen our knowledge regarding the mechanisms regulating antigen presentation. Antigen presentation is regulated both transcriptionally and post-translationally. Whereas many cytokines affect the latter, IL-10, an anti-inflammatory cytokine, causes the intracellular retention of MHC II molecules. This phenotype is the result of the ubiquitination of MHC II -chain cytoplasmic tail by MARCH1. MARCH1 is an E3 ubiquitin ligase expressed in secondary lymphoid organs. Until recently, little was known about the structure-function and the targets of MARCH1. Considering its major impact on antigen presentation, we were interested to study this E3 ligase in order to reveal how it is regulated and what are the required conditions for its function. In a first report, we have investigated the regulation of MARCH1’s protein expression. Our results revealed its autoregulation via dimer formation and autoubiquitination. In addition, we have demonstrated the involvement of MARCH1’s transmembrane domains for dimerization and MHC II interaction. In a second article, we highlighted the importance of MARCH1 localization for its function. Our results indicated that localization motifs in the C-terminal portion of MARCH1 were functional and revealed the presence of some sorting elements in the N-terminal portion of the molecule. A panel of mutant were used and allowed us to identify a ‘’VQNC’’ motif, located in the C-terminal cytoplasmic portion of MARCH1, in which the valine is central for the molecule’s function. Indeed, point-mutation of the valine led to a decrease in MARCH1 ability to relocate MHC II whereas BRET experiments revealed a modification in the spatial organization of the cytoplasmic tails. Moreover, a blast of sequence homology showed the presence or that same motif in others ubiquitine ligases, one of which is Parkin. Parkin is highly expressed in the brain and seems to be implicated in protein aggregates’ degradation. It was reported that malfunction of Parkin leads to the accumulation of aggregates, called Lewy bodies, responsible for the neural functions deficiencies observed in patients with Parkinson disease. Interestingly, a family for which the sickness was genetically transmitted has a mutated valine in the VQNC motif. We believe that the importance of this motif is not restricted to MARCH1 and could be generalized to others E3 ubiquitin ligases. This project enabled us to characterize the regulation mechanisms of MARCH1. In addition, we discovered various structural elements required for its function. Altogether, our data allows for a better understanding of the mechanisms controlling MHC II molecules antigen presentation.

Human Immunodeficiency Virus type I genome consists of two identical RNA molecules that are non-covalently linked to form a dimer. HIV-1 immature and mature genomic RNA (gRNA) dimers were found in protease defective (PR -) and wild type virions, respectively, and the 5'untranslated region (5' UTR) was shown to play key roles during the genome dimerization process; but the dimerization mechanism still remains to be clarified My research project is to characterize the dimerization process and the role of 5' UTR in genome dimerization in virions produced by tissue culture cells. I'll firstly show the dimer maturation processes of HIV-1 gRNA isolated from newly released to grown-up (≥10h old) wild type, PR-, and SL1 defective (DeltaIDS) virions respectively. The results showed that HIV-1 gRNA dimer maturation process was protease-dependent and involved multiple steps: from low to high dimerization level and dimer thermostability, and from low dimer mobility to intermediate and high mobility. PR- virions did not freeze gRNA conformation in the primordial nascent state and gRNA changed from monomeric in newly released virions to half dimeric in grown-up virions, which showed that genome was packaged in the form of monomeric RNA or fragile dimers, more thermolabile than immature dimers in grown-up PR- virions. DeltaDIS inhibited gRNA dimerization by about 50% in newly released virions, though grown-up DeltaDIS gRNA was fully dimeric, which indicated that the DIS played the initiation role in gRNA dimerization in HIV-1 virions. The gRNA dimerization rate in PR- or DeltaDIS virions was much slower than that in wild type virions. These results show for the first time the whole process of dimer maturation after virion release, the gRNA conformation rearrangement in PR- virions, and the initiation role of the DIS in HIV-1 virions. Next, I'll provide a rather systematic search for the contribution of different regions in 5' UTR to HIV-1 gRNA dimerization by studying selected mutations singly or together with defective SL1. The results showed that the 5'trans-activation response element (5'TAR) was directly involved in gRNA dimerization, and a long distance base-pairing interaction between a sequence in U5 region (nts105-1l5) and another around the initiation codon of the gag gene (nts334-344) was structurally contributive to gRNA dimerization. Deletions of sequences around the 3'end of Primer Binding Site (PBS) stem-loop moderately decreased gRNA dimerization level. Other sequences in 5' UTR except DIS/SL1, which was previously known to play important roles, didn't show any systematic role. Here the results suggested that the absence of inhibition on gRNA dimerization level with defective DIS might be the compensation of the direct role of 5'TAR; and wild type-like dimerization level of DeltaTAR must be the direct contribution of the DIS.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (leaves 132-138).

Orientador: Douglas Soares Galvão / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-12T10:36:43Z (GMT). No. of bitstreams: 1 ValegaMackenzie_FidelOrlando_M.pdf: 2711520 bytes, checksum: 6eef4b8eb7c976af1efdb0f0bb711dd0 (MD5) Previous issue date: 2008 / Resumo: Nesta dissertação foram estudados, utilizando um enfoque semiempírico e de primeiros princípios, a estrutura e as propriedades eletrônicas de alguns precursores de alomelaninas. As alomelaninas fazem parte de uma classe de pigmentos escuros presentes numa grande variedade de organismos e seus precursores são formados por unidades monoméricas de o-benzoquinona e catecol. Devido à limitada disponibilidade de dados experimentais realizamos inicialmente uma comparação das diferentes grandezas, como momentos de dipolo e entalpias de formação, obtidas a partir de diversas metodologias dentro as quais se incluem Hartree-Fock e DFT, para escolher um modelo semiempírico que descreva melhor o comportamento eletrônico da o-benzoquinona e do catecol. Os modelos semiempíricos utilizados foram o AM1 e o PM3, onde o primeiro parece oferecer melhores resultados reproduzindo as estruturas determinadas pelos métodos ab initio, assim como os dados experimentais disponíveis. Consideramos a formação de dímeros a partir de ligações carbono-carbono e carbono-oxigênio-carbono entre diferentes monômeros. Em geral estas estruturas resultaram ser boas aceitadoras de um e até dois elétrons. Nenhum tipo de régio-seletividade foi observada nos dímeros. É provável que a falta de sítios preferenciais na dimerização resulte no fato das alomelaninas serem amorfas. Os espectros de absorção para as formas neutras e iônicas dos precursores também foram simulados / Abstract: In this work we studied, on the basis of a semiempirical and ab initio approaches, the structure and electronic properties of some allomelanins precursors. Allomelanins are part of an ubiquitous class of dark pigments known as melanins and their precursors are formed by monomers of catechol and o-benzoquinone units. Due to the lack of extensive experimental data we first compared different quantities such as dipole moment and enthalpy of formation obtained from several methodologies including Hartree-Fock and DFT, in order to choose a semiempirical model that better describes the electronic behavior of o-benzoquinone and catechol. The semiempirical models used were AM1 and PM3, where the former seems to better reproduce the structures found by ab initio methods as well as the limited available experimental data. We have investigated monomers and some dimers formed through carbon-carbon and carbon-oxygen-carbon linkages from different monomers. In general those structures resulted to be good electron acceptors, accepting one, and in some cases, two electrons. No regioselectivity was found for the dimers. Perhaps the nonexistence of preferential dimerization sites can explain why allomelanins are amorphous. Absorption spectra for neutral and ionic forms of the precursors were also simulated / Mestrado / Física / Mestre em Física

Abstract This study concentrates on the preparation and characterization of some ionic liquids and their use in dimerization reaction of 2-methylpropene. Ionic liquids consist of cations and anions, and are commonly understood as green solvents. By definition their melting points should be lower than 100 °C. Prepared ionic liquids were used as catalytic solvents in dimerizations of 2-methylpropene to a high octane compound, isooctene. The monograph consists of two parts: the literature survey and the practical work. The literature survey reviews the preparation and characterization of ionic liquids as well as their environmental aspects, such as toxicity, biodegradability and recyclability. In addition, the acid catalyzed dimerization of butenes is discussed together with the dimerizations of light olefins carried out in ionic liquids. The practical work consists of three entities: The environmentally benign preparation of 1-alkyl-3-methylimidazolium-based ionic liquids under microwave activation, the characterization of ionic liquids and the use of the ionic liquids in the dimerization reaction. Ionic liquids absorb efficiently microwave irradiation and the most beneficial aspect in the microwave-assisted preparations was the considerably shortened reaction time compared to the conventional methods. In addition to the microwave-assisted preparations, [Cnmim][InCl4] ionic liquids were prepared successfully without microwave irradiation. A special attention was paid to the characterization of ionic liquids since impurities are known to affect on the properties of the ionic liquids. Ionic liquids were analysed with the following methods: 1H and 13C NMR, MS(ESI+ and ESI-), GC and elemental analysis. Characterization of ionic liquids was done by determining the thermal stability, the melting point and the crystal structure of each solid ionic liquid. The determination of the liquid range of ionic liquid is necessary in order to know the temperature limits for each ionic liquid. Novel InCl3-based ionic liquids revealed to be the more efficient than Brønsted acidic ILs as a catalytic reaction media in the dimerization of 2-methylpropene. It was preferable to apply [C6mim]Cl/InCl3 (x(InCl3) = 0.55) as a catalytic IL since then the conversion of 2-methylpropene and the product distribution revealed to be good. In order to maximize the production and the separation of dimers reaction should be carried out continuously at temperature high enough, such as 160 °C. Neutral InCl3-based ionic liquid did not catalyze reaction of 2-methylpropene, but it had to be acidic x(InCl3) > 0.5. Excess of InCl3 did not leach out from the IL and the recycling of IL was possible.