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Thesis (Ph. D.)--University of Virginia, 2000. / Includes bibliographical references (leaves 104-139). Also available online through Digital Dissertations.

Interferon Regulatory Factor -1 (IRF-1) is a transcription factor that acts as a tumour suppressor in cancer cells. The inactivation or deletion of IRF-1 either in one or both allele has been frequently reported in leukaemia and myelodysplasia (MDS). On the other hand nucleophosmin (NPM), a nucleo-cytoplasmic shuttling phosphoprotein is also known to be aberrant in some form of leukaemia. NPM was first proposed as a binding partner of IRF-1 in 1997 and suggested to inactivate IRF-1 by inhibiting its DNA binding ability. No further researches on the interaction between IRF-1 and NPM1 was reported prior to the start of my PhD. In the research presented here the interaction and mechanism by which IRF-1 might be inactivated by NPM was studied. Under the context of both NPM and IRF-1 being frequently associated with leukaemia and MDS, the study was done to determine the role of NPM under its naïve condition and a most frequent mutated condition (NPMc+), where the C-terminal of NPM was frequently mutated to give rise to a cytoplasmic NPM in certain leukaemia. In this current research, the direct interaction between IRF1 and NPM was further confirmed both in vitro as well as within the cells. Following this, the effect of this interaction in respect to the leukaemic condition having NPMc+ mutation was done, by comparing the end results on AML2 (leukaemic cells with intact wild type NPM) and AML3 (leukaemic cells having a single NPM allele mutated to form NPMc+) cells. In this research, overexpression of wild type NPM (NPMwt) was found to increase IRF-1 transcriptional activity. On further analysis, the DNA binding activity of IRF-1 due to the presence of NPMwt or NPMc+ was not always inhibited, instead it shows a change in binding specificity, where NPMwt bound IRF-1, lacks DNA binding ability and DNA bound IRF-1 has a reduced binding towards NPM. This is being studied further in terms of NPM overexpression and increased IRF-1 transcriptional activity, as the order of addition (order of interaction in vivo) plays a major role in activating or deactivating IRF-1. This along with the increased transcriptional activity of IRF-1 suggests a novel function of NPM, where it could act in favour of IRF- 1 activity. Additionally, the NPM induced change in IRF-1 localisation was confirmed by the cytoplasmic localised IRF-1 in NPMc+ expressing cells and nucleolar sequestration in NPMwt overexpressing cells. This gives a novel mechanism by which NPM regulates IRF-1. Further, the NPMc+ specific colocalisation of IRF-1 urges to study the other proteins that may have been re-localised in AML cells due to the NPMc+ specific interaction. A mass spectrometric analysis on the cellular distribution of total proteins were analysed between AML2 (cells with NPMwt) and AML3 (cells containing NPMc+). Specific proteins related to cancer have been identified to be differentially distributed rather than being a random translocation. With this being said, a peptide phage display technology coupled with next generation sequencing was done to identify NPMwt binding peptides that can be used in drug discovery process or as small molecule inhibitors or activators. Three different peptides were selected at the end of the study that bind very effectively to NPMwt. These peptide can either aid or restrict NPM activity and need to be validated and studied in the future.

Thesis (Ph. D.)--Cornell University, January, 1998. / Vita. Includes bibliographical references (leaves 95-111).

abstract: In vitro selection technologies allow for the identification of novel biomolecules endowed with desired functions. Successful selection methodologies share the same fundamental requirements. First, they must establish a strong link between the enzymatic function being selected (phenotype) and the genetic information responsible for the function (genotype). Second, they must enable partitioning of active from inactive variants, often capturing only a small number of positive hits from a large population of variants. These principles have been applied to the selection of natural, modified, and even unnatural nucleic acids, peptides, and proteins. The ability to select for and characterize new functional molecules has significant implications for all aspects of research spanning the basic understanding of biomolecules to the development of new therapeutics. Presented here are four projects that highlight the ability to select for and characterize functional biomolecules through in vitro selection. Chapter one outlines the development of a new characterization tool for in vitro selected binding peptides. The approach enables rapid screening of peptide candidates in small sample volumes using cell-free translated peptides. This strategy has the potential to accelerate the pace of peptide characterization and help advance the development of peptide-based affinity reagents. Chapter two details an in vitro selection strategy for searching entire genomes for RNA sequences that enhance cap-independent initiation of translation. A pool of sequences derived from the human genome was enriched for members that function to enhance the translation of a downstream coding region. Thousands of translation enhancing elements from the human genome are identified and the function of a subset is validated in vitro and in cells. Chapter three discusses the characterization of a translation enhancing element that promotes rapid and high transgene expression in mammalian cells. Using this ribonucleic acid sequence, a series of full length human proteins is expressed in a matter of only hours. This advance provides a versatile platform for protein synthesis and is espcially useful in situations where prokaryotic and cell-free systems fail to produce protein or when post-translationally modified protein is essential for biological analysis. Chapter four outlines a new selection strategy for the identification of novel polymerases using emulsion droplet microfluidics technology. With the aid of a fluorescence-based activity assay, libraries of polymerase variants are assayed in picoliter sized droplets to select for variants with improved function. Using this strategy a variant of the 9°N DNA polymerase is identified that displays an enhanced ability to synthesize threose nucleic acid polymers. / Dissertation/Thesis / Doctoral Dissertation Biological Design 2015

The extracellular matrix (ECM) provides mechanical and biochemical support to tissues and cells. It is crucial for cell attachment, differentiation, and migration, as well as for ailment-associated processes such as angiogenesis, metastases and cancer development. An approach to study these phenomena is through emulation of the ECM by synthetic gels constructed of natural polymers, such as collagen and fibronectin, or simple but tunable materials such as poly(ethylene glycol) (PEG) crosslinked with short peptide sequences susceptible to digestion by metalloproteases and cell-binding domains. Our lab uses PEG gels to study cell behavior in three dimensions (3D). Although this system fosters cell attachment and crosslinking peptides mentioned, the regenerative process of the ECM has not been mimicked yet in 3D synthetic gels. In an attempt to build in this functionality to PEG-based gels, I performed phage display to identify short oligopeptides that bind either collagen or fibronectin to assess them as potential nucleation points for crosslinking elements in order to emulate the in vivo reconstitution process. A phage display is a library of random oligopeptides expressed on a M13 bacteriophage that allows identification of a phenotype and a genotype with a single screening step. This inexpensive strategy could yield a short oligopeptide with high specificity. I identified the conditions under which phage display is compatible with our targets, and I isolated and identified five peptide candidates for fibronectin binding and two for collagen. Future work includes assessing whether these candidates could facilitate the formation of cell-created crosslinking in 3D synthetic hydrogels.

Orientadores: Flávia Maria Netto, Maria Teresa Bertoldo Pacheco / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-22T00:05:18Z (GMT). No. of bitstreams: 1 Caetano-Silva_MariaElisa_M.pdf: 1696296 bytes, checksum: 13e371ea02446fff6b254e550f086832 (MD5) Previous issue date: 2013 / Resumo: A deficiência de ferro é um dos principais problemas nutricionais no mundo, sendo a suplementação de alimentos com sais de ferro uma importante estratégia para combater essa deficiência. Porém, nessa forma, o mineral apresenta baixa biodisponibilidade e pode causar dor de estômago, diarreia, alterações de sabor e aparência dos produtos. Quelatos ferro-peptídeos têm sido apontados como uma promissora fonte de ferro mais biodisponível e com redução desses efeitos adversos. O presente estudo teve por objetivo avaliar o potencial de quelação de ferro dos peptídeos obtidos da hidrólise enzimática de isolado proteico de soro de leite (IPS) com as enzimas alcalase (HA), pancreatina (HP) ou flavourzyme (HF). Os hidrolisados foram ultrafiltrados (membrana de corte de 5 kDa) e as frações permeada (< 5 kDa) e retida (> 5 kDa) foram liofilizadas. Os hidrolisados e suas frações foram caracterizados quanto ao perfil aminoacídico, perfil de hidrofilicidade por cromatografia líquida de alta eficiência em fase reversa (CLAE-FR), perfil de massa molecular (MM) por cromatografia líquida de alta eficiência de exclusão molecular (CLAE-EM) e eletroforese SDS-PAGE Tricina. As frações foram avaliadas quanto à sua capacidade quelante de ferro, utilizando-se FeCl2 na proporção 40:1 proteína:Fe, pH 7,0, 25±2 °C/1h sob agitação, seguida de centrifugação. Para avaliação do ferro livre e/ou fracamente ligado aos peptídeos, o pH dos sobrenadantes da reação de quelação foi ajustado para 3,5 e o Fe2+ solúvel foi determinado. Foi selecionado o hidrolisado com maior capacidade quelante (frações HP > 5 kDa e HP < 5 kDa) para o prosseguimento do trabalho. Para avaliação da estabilidade do quelato, essas frações foram submetidas à digestão gástrica in vitro e posterior neutralização (pH 7,0), seguida de centrifugação. Os peptídeos das amostras selecionadas foram isolados por cromatografia de afinidade por íons metálicos imobilizados (IMAC-Fe3+). Os peptídeos com afinidade pelo ferro foram sequenciados por espectrometria de massas (MS/MS). O grau de hidrólise (GH) dos hidrolisados HA, HP e HF foi 16,8%, 16,4% e 9,1%, respectivamente. O perfil eletroforético das frações < 5 kDa não apresentou bandas, enquanto as frações > 5 kDa apresentaram bandas de MM inferior; porém, por CLAE-EM, foi verificado que todas as frações apresentaram peptídeos de MM aparente superior a 5 kDa, sugerindo que nas condições usadas houve formação de agregados. Na reação de quelação, HP > 5 kDa reteve 70,6% do ferro em solução, enquanto as demais frações variaram entre 37,4% e 66,1%. A fração HP > 5 kDa apresentou maior teor de ferro precipitado em pH 3,5 (65,3%), sugerindo maior interação peptídeos-ferro. A mesma amostra, após digestão gástrica, apresentou solubilidade do ferro inicialmente presente entre 57,8 e 59,0% em pH 7,0, sugerindo que a digestão com ou sem pepsina não desfez totalmente o complexo formado. Esse teor foi superior ao obtido com HP < 5 kDa (40,1 a 43,0%), bem como ao ensaio controle com FeCl2 (9,9%). No isolamento de peptídeos por IMAC-Fe3+, verificou-se maior teor de peptídeos com capacidade quelante de ferro na fração HP > 5 kDa (70%) do que na fração HP < 5 kDa (50%). O sequenciamento por MS/MS mostrou, em todos os fragmentos, presença de Glu e/ou Asp, cujos grupos carboxílicos estão entre os principais sítios de ligação com o ferro. Os resultados sugerem que a hidrólise do IPS com pancreatina origina peptídeos com alta capacidade quelante de ferro. Esses peptídeos podem ser usados para obtenção de quelatos Fe2+-peptídeos que, futuramente, sejam aplicados para fortificação de alimentos no intuito de elevar a biodisponibilidade do ferro, além de potencialmente reduzir seus efeitos pró-oxidantes / Abstract: Iron deficiency is one of the major nutritional problems in the world, being the food supplementation with iron salts an important strategy to combat this deficiency. However, in salt form, this mineral has low bioavailability and may lead to stomachache, diarrhea and even cause changes in flavor and appearance of food products. Iron-peptides chelates have been suggested as a promising source of more bioavailable iron, reducing these side effects. This study aimed at evaluating the iron-binding ability of peptides obtained from enzymatic hydrolysis of whey protein isolate (WPI) with alcalase (AH), pancreatin (PH) or flavourzyme (FH). Hydrolysates were ultrafiltered in 5 kDa membrane and permeate (< 5 kDa) and retentate (> 5 KDa) fractions were lyophilized. Hydrolysates and their fractions were characterized by aminoacidic profile, hydrophilicity profile by reversed-phase high performance liquid chromatography (RP-HPLC), molecular weight (MW) profile by size-exclusion high performance liquid chromatography (SE-HPLC) and SDS-PAGE Tricine). Fractions were evaluated by iron-binding ability using FeCl2 (40:1 protein:Fe ratio) at pH 7.0 and 25±2 °C for 1h under stirring, followed by centrifugation. For evaluation of free and/or weakly bound iron, the pH of the supernatant from the chelation reaction was adjusted to 3.5 and soluble Fe2+ was determined. The hydrolysate with higher iron-binding ability was selected (fractions PH > 5 kDa and PH < 5 kDa) for further proceeds. To evaluate the chelate stability, these fractions were subjected to in vitro gastric digestion and further neutralization, followed by centrifugation. The peptides of selected samples were isolated by immobilized metal affinity chromatography (IMAC-Fe3+). The peptides with iron-binding affinity were sequenced by mass spectrometry (MS/MS). The degree of hydrolysis (DH) of hydrolysates AH, PH and FH was 16.8%, 16.4% and 9.1%, respectively. Electrophoretic profile of fractions < 5 kDa did not present any band, while fractions > 5 kDa presented peptides with lower MW. However, by SE-HPLC, it was verified peptides with apparent MW above 5 kDa for all samples, suggesting that, under the conditions studied, there was aggregates formation. In the chelation reaction, PH > 5 kDa retained 70.6% of iron in solution, while other samples ranged from 37.4% to 66.1%. PH > 5kDa showed higher content of precipitated iron in pH 3.5 (65.3%), suggesting greater peptide-iron interaction. After gastric digestion, the same sample showed initial iron solubility ranging from 57.8 and 59.0% in pH 7.0, suggesting that digestion with or without pepsin was not able to completely break the complex formed. This content was higher than that obtained in both PH < 5 kDa (40.1 to 43.0%) and the control assay with FeCl2 (9.9%). IMAC-Fe3+ isolation showed higher content of iron-binding peptides in PH > 5 kDa (70%) than in PH < 5 kDa (50%). The MS/MS sequencing showed Glu and/or Asp in all fragments, which carboxylic groups are among the main iron-binding sites. The results suggest that WPI hydrolysis with pancreatin yields peptides with high iron-binding ability. These peptides may be used for obtaining iron-peptide chelates, which, in future, may be applied in food fortification in order to increase iron bioavailability and potentially reduce its pro-oxidant effects / Mestrado / Nutrição Experimental e Aplicada à Tecnologia de Alimentos / Mestre em Alimentos e Nutrição