Proteins can often adsorb irreversibly at fluid/fluid interfaces; the understanding of the adsorption mechanism has relevance across a variety of industrial (e.g. the creation of stable emulsions) and biological (e.g. biofilm formation) processes. I performed molecular dynamics simulations of two surfactant proteins as they interact with air/water and oil/water interfaces, describing the origin of the surface activity, the adsorption dynamics and the conformational changes that these proteins undergo at the interface. BslA is an amphiphilic protein that forms a highly hydrophobic coat around B. subtilis biofilms, shielding the bacterial community from an external aqueous solution. By investigating the behaviour of BslA variants at oil/water interfaces via coarse-grained molecular dynamics, I show that BslA represents a biological example of an ellipsoidal Janus nanoparticle, whose surface interactions are controlled by a local conformational change. All-atom molecular dynamics simulations then reveal the details of the conformational change of the protein upon adsorption, and the self-assembly into a two-dimensional interfacial crystal. Ranaspumin-2 is one of the main components of the tungara frog foam nest. Contrary to most surfactant proteins, its structure lacks any sign of amphiphilicity. All-atom simulations show that the adsorption proceeds via a two-step mechanism where firstly the protein binds to the interface through its flexible N-terminal tail and then it undergoes a large conformational change in which the hydrophobic core becomes exposed to the oil phase. I then developed a simple structure-based coarse-grained model that highlights the same adsorption mechanism observed in all-atom simulations, and I used it to compare the dynamics of adsorption and the underlying free energy landscape of several mutants. These results agree with and are used to rationalise the observations from Langmuir trough and pendant drop experiments. Colloids can often be considered simpler versions of proteins that lack conformational changes. I performed coarse-grained simulations of the compression of interfacial monolayers formed by rod-like particles. These simulations show a rich behaviour characterised by the flipping of adsorbed rods, nematic ordering and bilayer formation. I report the series of transitions that take place as the rod aspect ratio is increased from 3 to 15.

Um estudo experimental sobre os aspectos estruturais e dinâmicos de um complexo hidratado de fragmentos de DNA (150 pb) e fases lamelares de lipídios zwitteriônicos é apresentado. Variando-se a hidratação, é possível controlar o confinamento imposto por essa matriz hospedeira sobre os nucleotídeos inseridos na camada aquosa. O arranjo supramolecular do complexo é investigado por difração de raios X e técnicas de microscopia óptica e eletrônica. Um rico polimorfismo de mesofases é observado em função do confinamento. No regime mais hidratado, os fragmentos se distribuem segundo uma orientação nemática entre as membranas. À medida que a quantidade de água diminui, o confinamento das bicamadas sobre os nucleotídeos aumenta e correlações transmembranares aparecem, dando origem a fases altamente organizadas, com simetrias hexagonais 2D de DNA entre as lamelas. A incorporação completa de nucleotídeos é observada apenas quando grandes quantidades de DNA estão presentes. Esse fato aponta para importância maior de interações de volume excluído. Uma análise do parâmetro de Caillé mostra que as flutuações das membranas diminuem com a inserção de DNA. A partir dessas observações,é sugerido que a alteração das interações entre membranas, aliada à aparição de efeitos interfaciais entre DNA e membranas, é um mecanismo relevante no comportamento de fase. As propriedades dinâmicas dos nucleotídeos são investigadas através da técnica de FRAP (fluorescence recovery after photobleaching). Um modelo recentemente desenvolvido para análise de difusão anisotrópica é testado com sucesso, demonstrando estreita correlação entre estrutura e dinâmica. / An experimental study on the structural and dynamical properties of a hydrated DNA zwitterionic lipids complex is presented. By varying the water amount, it is possible to control the connement imposed by this host matrix over the organization of the nucleotides inserted within the water layers. The supramolecular assembly is investigated by X-rays diraction and techniques involving both optical and electron microscopy. A rich polymorphism of mesophases is observed as a function of connement. In the more hydrated regime, the fragments are distributed according to nematic orientation in-between lamellae. As the water amount decreases, the connement of bilayers over the particles increases and transmembrane correlations appear, giving raise to highly-ordered phases, with 2D-hexagonal symmetries of DNA embodied in the lamellar phase. The full incorporation of nucleotides by the lamellar phase is observed only in the presence of large amounts of DNA. This nding points to the major importance of excluded volume interactions. An analysis of the Caillé parameter shows that the insertion of DNA reduces the fluctuations of membranes. From these observations, it is suggested that changes in the interactions between bilayers, together with the appearance of interfacial eects between DNA and membranes, are a relevant mechanism for the phase behavior of these systems. The dynamical properties of nucleotides are investigated through the fluorescence recovery after photobleach (FRAP). A model recently developed for analyses of anisotropic difusion is sucessfully tested, demonstrating a close relationship between structure and dynamics.

In the present work we performed electronic structure calculations within the Kohn-Sham scheme of the density functional theory (DFT). We studied two molecules with potential applications in life sciences and medicine: ferrioxamine B and 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H (TMPyP) porphyrin. We used different methods and different exchange and correlation functionals, analyzing optical and vibrational properties and hyperfine interactions. In the case of ferrioxamine B, results in the crystalline phase (molecular crystal), and gas phase were compared with experimental results obtained using Mössbauer spectroscopy from the literature. We analyzed hyperfine parameters such as the electric quadrupole splitting, asymmetry parameter, hyperfine field and isomer shift. In the case of TMPyP porphyrin we analyzed vibrational properties in the gas phase and optical properties. For the electronic absorption, solvent effects and electronic charges states were analyzed. / In the present work we performed electronic structure calculations within the Kohn-Sham scheme of the density functional theory (DFT). We studied two molecules with potential applications in life sciences and medicine: ferrioxamine B and 5,10,15,20-tetrakis(1-methyl-4-pyridyl)-21H,23H (TMPyP) porphyrin. We used different methods and different exchange and correlation functionals, analyzing optical and vibrational properties and hyperfine interactions. In the case of ferrioxamine B, results in the crystalline phase (molecular crystal), and gas phase were compared with experimental results obtained using Mössbauer spectroscopy from the literature. We analyzed hyperfine parameters such as the electric quadrupole splitting, asymmetry parameter, hyperfine field and isomer shift. In the case of TMPyP porphyrin we analyzed vibrational properties in the gas phase and optical properties. For the electronic absorption, solvent effects and electronic charges states were analyzed.

Orientador: Sônia Maria Alves Bueno / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Química / Made available in DSpace on 2018-08-17T11:27:09Z (GMT). No. of bitstreams: 1 Bresolin_IgorTadeuLazzarotto_D.pdf: 3279874 bytes, checksum: b2f9ab93ce7e5036f95f0da584a42017 (MD5) Previous issue date: 2010 / Resumo: Dentre os hemoderivados disponíveis comercialmente, as imunoglobulina do isotipo G (IgG) recebem destaque pelo seu uso em aplicações terapêuticas. Por esta razão são requeridas com elevado grau de pureza. Várias técnicas vêm sendo investigadas para a purificação de IgG a partir do soro ou plasma humano, desde a precipitação até métodos mais seletivos, como os cromatográficos. Neste trabalho, investigou-se o efeito de agentes quelantes de IMAC (cromatografia por íons metálicos imobilizados) como Tris-2(aminoetil)amina (TREN) e o-fosfoserin (OPS) como grupos ionogênicos (sem íon metálico imobilizado), além do aminoácido L-Lisina e seu polímero poli-L-Lisina (PLL) como ligantes visando a purificação de IgG a partir do soro humano. Para tanto, foram realizados experimentos de adsorção em diferentes sistemas tamponantes. A seletividade dos adsorventes foi verificada por eletroforese SDS-PAGE e análise nefelométrica. As melhores condições, para cada caso, foram utilizadas em experimentos de curvas de ruptura e isotermas de adsorção de albumina de soro humano (HSA) e IgG. No caso dos ligantes TREN e PLL, 73% e 86% da IgG alimentada foi recuperada nas frações não-retidas (cromatografia negativa) apresentado pureza superior a 90%. Quando o ligante OPS foi utilizado, por sua vez, a recuperação de IgG ocorreu nas frações retidas juntamente com IgM. Experimentos de curva de ruptura mostraram que um fator de purificação de 4.9 foi atingido, sendo a IgG recuperada com pureza de 88%. Este ligante se mostrou eficiente quando se deseja purificar IgG humana que possui pontos isoelétricos na faixa de 7,8 a 8,5. Para todos os ligantes, a recuperação de IgG a partir soro humano pode ser alcançado sob condições brandas de pH, baixa força iônica, e temperatura ambiente. De um ponto de vista de processo em larga escala, todos os ligantes apresentados neste trabalho apresentam potencial para serem usados como uma das etapas em um processo industrial de recuperação e purificação de IgG / Abstract: Among the commercially available hemoderivatives or blood products, the immunoglobulin G (IgG) is highlighted by its use in therapeutic applications, which need high purity IgG. Several techniques are being investigated aiming at the purification of IgG from human serum or plasma, usually starting with precipitation and then using more selective methods such as chromatography. In this study, we evaluated the effect of Tris-2 (aminoethyl) amine (TREN) and o-phosphoserine (OPS) - two chelating agents used in immobilized metal ion chromatography (IMAC) - as ionogenic groups (without immobilized metal ion), and the amino acid L-lysine and its polymer poly-L-lysine (PLL) as ligands aiming at the purification of IgG from human serum. For this purpose, adsorption experiments were performed using different buffering systems. The selectivity of the adsorbents was checked by SDS-PAGE and nephelometric analysis. The best conditions for each adsorbent were used in experiments of breakthrough curves and adsorption isotherms of human serum albumin (HSA) and IgG. In the case of TREN and PLL, 73% and 86% of IgG fed was recovered in the non-retained fractions (negative chromatography) with purity higher than 90%. When the ligand OPS was used, IgG was recovered in retained fractions. Experiments of breakthrough curve showed that a purification factor of 4.9 was reached, and IgG was recovered with a purity degree 88% (with IgM). This ligand is efficient when it is desired to purify human IgG with isoelectric points ranging from 7.8 to 8.5. For all ligands, the recovery of IgG from human serum was achieved under mild conditions of pH, low ionic strength and temperature. All ligands presented in this study have potential to be used in an industrial downstream processing of IgG from human serum / Doutorado / Desenvolvimento de Processos Biotecnologicos / Doutor em Engenharia Química

Este trabalho apresenta a síntese e a caracterização de quatro complexos trinucleares de acetato de rutênio, de fórmula geral [Ru3O(CH3COO)6(L)2(CO)] nos quais L são ligantes N-heterocíclicos 4-aminopiridina, isonicotinamida, 4-(dimetil)aminopiridina e 2,6-dimetilpirazina com características -aceptoras ou -doadoras. Os derivados de rutênio foram sintetizados de acordo com adaptações de rotas sintéticas já reportadas na literatura, e caracterizados por meio de técnicas de cunho espectroscópico, eletroquímico e outras, a saber: análise elementar, 1H RMN, absorção UV-vis, infra-vermelho, voltametria cíclica e difração de raios-X. Foi investigada a liberação fotoinduzida de monóxido de carbono proveniente dos complexos trinucleares em acetonitrila, por meio de acompanhamento espectrofotométrico. O rendimento quântico envolvido na liberação do CO foi calculado por meio de actinometria química. Foi estudada a interação entre os complexos com as biomoléculas HSA e o DNA de timo de bezerro por meio das técnicas espectroscópicas de fluorescência, UV-vis e dicroísmo circular. Além disso, foram realizados ensaios preliminares in vitro para avaliar a citotoxicidade dos complexos frente a uma linhagem de células de melanoma murinho (B16F10) e foi avaliada a atividade tripanocida dos complexos sobre a forma amastigota do parasita Tripanossoma cruzi. / This work describes the synthesis and characterization of four ruthenium trinuclear complex of general formula [Ru3O(CH3COO)6(CO)(L)2] where L = 2,6-dimethylaminopyridine; isonicotinamide; 4-aminopyridine and 4-dimethylpyrazine (N-heterocyclic ligands with -acceptor or -donor characteristics). The ruthenium derivatives were synthesized according to adaptations of synthetic routes already reported in literature and characterized by spectroscopic and electrochemical techniques such as nuclear magnetic ressonance (NMR), UV-vis, infrared, cyclic voltammetry, X-ray diffraction and elemental analysis. The photoinduced release of carbon monoxide in acetonitrile was investigated by means of spectrophotometric monitoring. The quantum yield involved in the CO release was calculated by chemical actinometry. It was studied the interaction between the complexes with the biomolecules HSA and calf thymus DNA by spectroscopic techniques of fluorescence, UV-vis and circular dichroism. In addition, preliminary tests were performed in vitro in order to evaluate the cytotoxicity of the complexes against a murine melanoma cell line (B16F10) and trypanocidal activity of the complexes over the amastigote form of the parasite Trypanosoma cruzi.

L'objectif de cette thèse est de développer un nouvel instrument de chromatographie de partage centrifuge (CPC) dédié à la purification de molécules très polaires. La CPC est une technique préparative permettant la séparation des molécules grâce à l'utilisation d'un système solvant constitué de deux liquides non miscibles. Ce manuscrit expose dans un premier temps les différentes techniques de purification de protéines utilisées dans le cas d'un procédé industriel de production. Un focus est réalisé sur l'utilisation de systèmes biphasiques aqueux pour la purification des biomolécules, qui représente un réel avenir dans l'industrie du fait de son faible coût, de sa facilité de montée en échelle et surtout de l'environnement favorable qu'il fournit aux biomolécules. Ainsi en se basant sur les avantages de ces systèmes solvants dits Aqueous Two Phase Systems (ATPS), la CPC pourrait apporter une efficacité supplémentaire permettant de purifier les protéines à moindre coût. Pour pouvoir répondre à cet enjeu industriel, il est nécessaire de développer à la fois des méthodes chromatographiques innovantes et de nouveaux instruments dédiés. En effet, les instruments de CPC actuels ne sont pas compatibles avec les Bonne Pratique de Fabrication du fait de la présence de joints téflons qui empêche la possibilité de stériliser les instruments. La fabrication d'un nouvel instrument monobloc entièrement en titane a été réalisée grâce à la technologie de l'impression 3D pour répondre à cette problématique. L'objet de cette thèse est l'évaluation poussée des performances de cette nouvelle colonne afin de déterminer son applicabilité à la purification des biomolécules. Un focus sera également apporté à l'injection de volumes très faibles d'échantillon afin de faciliter le développement de méthodes / The aim of this thesis is to develop a new centrifugal partition chromatography (CPC) instrument in order to purify highly polar molecules. CPC is a preparative technique for the separation of molecules using a solvent system composed of two immiscible liquids. This manuscript describes the different protein purification techniques used in industrial production process. A focus is made on the use of aqueous biphasic systems for the purification of biomolecules, which represents a real trend in the industry thanks to its low cost, scaling simplicity and especially the favorable environment that it provides to biomolecules. Thus, based on the advantages of these solvent systems known as Aqueous Two Phase Systems (ATPS), CPC could provide additional performances to purify proteins at lower cost. To respond to this industrial challenge, it is necessary to develop both innovative chromatographic methods and new devoted instruments. Indeed, current CPC instruments are not compatible with Good Manufacturing Practices due to the presence of Teflon seals which prevents the possibility of sterilizing the instruments. The manufacture of a new monobloc instrument entirely made of titanium was achieved thanks to the 3D printing technology. The purpose of this thesis is the evaluation of this new column performance in order to determine its applicability to biomolecules purification. A special attention is also provided to the injection of very small sample volumes in order to facilitate method development

HSP70 is one of the most important families of molecular chaperone that regulate the folding and transport of client proteins in an ATP dependent manner. The ATPase activity of HSP70 is stimulated through an interaction with its family of HSP40 co-chaperones. There is evidence to suggest that specific partnerships occur between the different HSP40 and HSP70 isoforms. While some of the residues involved in the interaction are known, many of the residues governing the specificity of HSP40-HSP70 partnerships are not precisely defined. It is not currently possible to predict which HSP40 and HSP70 isoforms will interact. We attempted to use bioinformatics to identify residues involved in the specificity of the interaction between the J domain from HSP40 and the ATPase domain from the HSP70 isoforms from humans. A total of 49 HSP40 and 13 HSP70 sequences from humans were retrieved and used for subsequent analyses. The HSP40 J domains and HSP70 ATPase domains were extracted using python scripts and classified according to the subcellular localization of the proteins using localization prediction programs. Motif analysis was carried out using the full length HSP40 proteins and Multiple Sequence Alignment (MSA) was performed to identify conserved residues that may contribute to the J domain – ATPase domain interactions. Phylogenetic inference of the proteins was also performed in order to study their evolutionary relationship. Homology models of the J domains and ATPase domains were generated. The corresponding models were docked using HADDOCK server in order to analyze possible putative interactions between the partner proteins using the Protein Interactions Calculator (PIC). The level of residue conservation was found to be higher in Type I and II HSP40 than in Type III J proteins. While highly conserved residues on helixes II and III could play critical roles in J domain interactions with corresponding HSP70s, conserved residues on helixes I and IV seemed to be significant in keeping the J domain in its right orientation for functional interactions with HSP70s. Our results also showed that helixes II and III formed the interaction interface for binding to HSP70 ATPase domain as well as the linker residues. Finally, data based docking procedures, such as applied in this study, could be an effective method to investigate protein-protein interactions complex of biomolecules.

Orientadores: Everson Alves Miranda, Adriano Rodrigues Azzoni / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Engenharia Química / Made available in DSpace on 2018-08-18T15:34:36Z (GMT). No. of bitstreams: 1 Bonturi_Nemailla_M.pdf: 2076232 bytes, checksum: e3f4e56f400891ab77fe029e0c1f0899 (MD5) Previous issue date: 2011 / Resumo: O número de estudos em terapia gênica com vetores plasmídiais (pDNA) têm aumentado nestes últimos anos. Como resultado, a demanda para preparações de pDNA em conformidade com as recomendações das agências reguladoras (EMEA, FDA) também aumentou. O DNA plasmidial é frequentemente obtido através da fermentação de Escherichia coli transformada e purificada por uma série de operações unitárias, incluindo a cromatografia. Este trabalho teve como objetivo o desenvolvimento de um processo cromatográfico para a recuperação e purificação do pDNA superenovelado (sc pDNA) a partir do lisado neutralizado. Os ligantes fenil (hidrofóbico) e mercaptopirimidina (tiofílico) foram imobilizados em matrizes de agarose e celulose. A seletividade destes ligantes para com o sc pDNA foi determinada através de estudos de adsorção utilizando citrato de sódio 1,5 mol/L e fosfato de potássio 2,0 mol/L como tampões de adsorção. A cromatografia com o adsorvente fenil-agarose e o citrato de sódio 1,5 mol/L permitiu recuperar 58% do pDNA sem contaminação por gDNA, proteínas e endotoxinas, sendo uma alternativa potencial para a recuperação primária do sc pDNA. O resultado mais promissor foi obtido com a cromatografia com o adsorvente mercaptopirimidina-agarose e fosfato de potássio 2,0 mol/L como tampão de adsorção. Este sistema tampão de adsorção/adsorvente permitiu a obtenção de pDNA com 100% de pureza e dentro das recomendações das agências reguladoras no tocante à contaminação por RNA e endotoxinas. Assim, este trabalho lançou as bases para o desenvolvimento de dois métodos cromatográficos para a recuperação primária ou purificação de pDNA diretamente do lisado neutralizado, ambos potencialmente aplicáveis em larga escala / Abstract: The number of studies in gene therapy with plasmid vectors (pDNA) has witnessed an increase in the recent years. As result the demand for preparations of pDNA in compliance with recommendations of the regulatory agencies (EMEA, FDA) has also increased. Plasmid DNA is oftenly obtained through fermentation of transformed Escherichia coli and purified by a series of unit operations, including chromatography. This work aimed the development of a chromatographic process for the recovery and purification of supercolied pDNA (sc pDNA) directly from neutralized cell lysate. Phenyl (hydrophobic) and mercaptopyrimidine (thiophilic) molecules immobilized in agarose and cellulose matrices were the ligands used to capture the pDNA. Their selectivity towards sc pDNA was evaluated through adsorption studies using sodium citrate 1.5 mol/L and potassium phosphate 2.0 mol/L as the adsorption buffers. The chromatography with the adsorbent phenyl-agarose and sodium citrate 1.5 mol/L was able to recover 58% of sc pDNA without gDNA, proteins and endotoxins contamination, being an potential alternative for the primary recovery of sc pDNA. The most promising result was obtained with the chromatography with mercaptopyrimidine-agarose and potassium phosphate 2.0 mol/L adsorpition buffer. With the latter buffer/adsorbent system it was possible to obtain in a single step pDNA with 100% purity and within the recommendations of regulatory agencies with regard to contamination by RNA and endotoxins. Thus, this work laid the basis for the development of two chromatographic process for the recovery or purification of pDNA directly from the neutralized lysate, both potentially applicable in larger scale / Mestrado / Desenvolvimento de Processos Biotecnologicos / Mestre em Engenharia Química

Orientador: Glaucia Maria Pastore / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia de Alimentos / Made available in DSpace on 2018-08-18T17:50:02Z (GMT). No. of bitstreams: 1 Barros_FranciscoFabioCavalcante_D.pdf: 2000120 bytes, checksum: f060d84f3896d913e5e93d9a39dd6b0f (MD5) Previous issue date: 2011 / Resumo: Um notável desenvolvimento dos bioprocessos tem sido alcançado nas últimas décadas. Entre os principais objetivos da aplicação desses processos está a obtenção de compostos de elevado valor agregado. Somado a isso há, atualmente, uma crescente demanda por materiais e energia, fato que resulta em desequilíbrios ambientais, especialmente quando esses bens são produzidos a partir de fontes não renováveis como o petróleo, por exemplo. Entre as diferentes estratégias para o desenvolvimento desses bioprocessos estão a coprodução, onde a partir de um mesmo processo são obtidos mais de um produto simultaneamente, e o uso resíduo e subprodutos agroindustriais como meios de cultura ou substrato de reações bioquímicas. Neste trabalho, foi realizado o estudo do processo fermentativo realizado pela bactéria Bacillus subtilis usando como meio de cultura a manipueira, um resíduo da industrialização de mandioca. Esse processo resultou na produção simultânea de biomoléculas de interesse industrial, no caso: lipopeptídios biossurfactantes, os compostos voláteis acetoína e diacetil e as enzimas do grupo das amilases e proteases. Adicionalmente, foi usado o método previamente descrito na literatura de recuperação primária de biossurfactantes baseado nos princípios da coluna de espuma. Esse procedimento possibilitou o arraste dos bioprodutos sem que fosse necessário o uso de compostos sintéticos, como solventes, ou a modificação dos parâmetros de fermentação / Abstract: A notable bioprocesses development was achieved in recent decades. Among the objectives of these processes is the production of high added value compounds. Moreover, there is a growing demand for materials and energy, which results in negative environmental issues, especially when those supplies are produced from non-renewable sources such as petroleum. Some of these different strategies for the bioprocesses development are co-production and the use of agro-industrial waste and by-products. The aim of this work was to study the fermentation process carried out by the bacterium Bacillus subtilis developed in manipueira that is a residue of the cassava industrialization. This process resulted in the simultaneous production of industrial interest biomolecules: lipopeptide biosurfactants, volatile compounds (acetoin and diacetil), and enzymes (amylases and proteases). It was used the primary recovery method of biosurfactants based on the principles of the column of foam. This procedure enabled the drag of bioproducts without the use of synthetic chemicals such as solvents, or modification of the fermentation parameters / Doutorado / Ciência de Alimentos / Doutor em Ciência de Alimentos

High-throughput technologies have continuously driven the generation of different biomolecular data, including the genomics, epigenomics, transcriptomics, and other omics data in the last two decades. The developments and advances have revolutionized medical research. In this dissertation, a collection of computational analyses and tools, based on different types of biomolecular data with particular applications on human diseases are presented including 1) a cascade ensemble model based on the Dirichlet process mixture model for reconstructing tumor subclonality from tumor DNA sequencing data; 2) a meta-analysis of gene expression and DNA methylation data from prefrontal cortex samples of patients with neuropsychiatric disorders indicating a stress-related epigenetic mechanism; 3) 2DImpute, an imputation algorithm that is designed to alleviate the sparsity problem in single-cell RNA-sequencing data; and 4) a pan-cancer transformation from adipose-derived stromal cells to metastasis-associated fibroblasts revealed by single cell analysis.