Dissertations / Theses on the topic 'Dissociation constant of inhibitor'

Cholera is an epidemic infectious diarrhoeal disease that for centuries has proven its frightening ability to cause rapid and widespread loss of human life. All symptoms associated with cholera are a result of rapid dehydration due to infection by pathogenic strains of the bacterium Vibrio cholerae. The damaging effects associated with cholera are mainly attributed to the toxin, which is secreted by the bacterium and infects cells lining the gastrointestinal tract. A sialidase, also secreted by the bacterium, is believed to facilitate toxin uptake by the gastrointestinal epithelium. V. cholerae sialidase is therefore a potential target for therapeutic intervention. A survey of the literature reveals that sialidases from different species share common features with respect to their structure, substrate specificity and catalytic mechanism. The unsaturated sialic acid, Neu5Ac2en, inhibits most exosialidases with a dissociation constant of inhibitor of -10-4 to-10-6 M and has frequently been used as a template in the design of more potent sialidase inhibitors. In the case of V. cholerae sialidase, there have been no inhibitors reported to date that are significantly more potent than Neu5Ac2en itself The present research aimed to develop a range of mimics of Neu5Ac2en, which contain various substituents to replace the C-6 glycerol side chain, as potential inhibitors of V cholerae sialidase. The x-ray crystal structure of V cholerae sialidase was used to explore potential interactions between active site residues and C-6 modified Neu5Ac2en mimetics of known inhibitory potency. Opportunities for interactions within the glycerol side chain pocket in the active site of V cholerae sialidase are discussed. A novel synthetic strategy was developed for the synthesis of a series of glucuronidebased Neu5Ac2en mimetics starting from readily available GIcNAc. This approach was employed for the preparation of Neu5Ac2en mimetics that contained an ether or thioether substituent as replacement of the glycerol side chain of Neu5Ac2en. Progress was also made towards the synthesis of a series of C-6 acylamino Neu5Ac2en mimetics. Analysis by 1H NMR spectroscopy showed that the acylamino derivatives adopted a half-chair conformation that was similar to the conformation of Neu5Ac2en but different to the conformation adopted by the ether and thioether derivatives prepared. The inhibitory activity of the C-6 ether and thioether Neu5Ac2en mimetics prepared was evaluated in vitro using an enzyme assay. It was found that most of the derivatives inhibited V. cholerae sialidase with a K1 of approximately 1O-4 M. The derivatives containing a hydrophobic side chain were found to be slightly more potent compared to derivatives with more hydrophilic side chains. A more detailed study of binding interactions between the C-6 thioether Neu5Ac2en mimetics and V cholerae sialdiase was carried out using STD 1H NMR spectroscopy and computational molecular modelling.

Cholera is an epidemic infectious diarrhoeal disease that for centuries has proven its frightening ability to cause rapid and widespread loss of human life. All symptoms associated with cholera are a result of rapid dehydration due to infection by pathogenic strains of the bacterium Vibrio cholerae. The damaging effects associated with cholera are mainly attributed to the toxin, which is secreted by the bacterium and infects cells lining the gastrointestinal tract. A sialidase, also secreted by the bacterium, is believed to facilitate toxin uptake by the gastrointestinal epithelium. V. cholerae sialidase is therefore a potential target for therapeutic intervention. A survey of the literature reveals that sialidases from different species share common features with respect to their structure, substrate specificity and catalytic mechanism. The unsaturated sialic acid, Neu5Ac2en, inhibits most exosialidases with a dissociation constant of inhibitor of -10-4 to-10-6 M and has frequently been used as a template in the design of more potent sialidase inhibitors. In the case of V. cholerae sialidase, there have been no inhibitors reported to date that are significantly more potent than Neu5Ac2en itself The present research aimed to develop a range of mimics of Neu5Ac2en, which contain various substituents to replace the C-6 glycerol side chain, as potential inhibitors of V cholerae sialidase. The x-ray crystal structure of V cholerae sialidase was used to explore potential interactions between active site residues and C-6 modified Neu5Ac2en mimetics of known inhibitory potency. Opportunities for interactions within the glycerol side chain pocket in the active site of V cholerae sialidase are discussed. A novel synthetic strategy was developed for the synthesis of a series of glucuronidebased Neu5Ac2en mimetics starting from readily available GIcNAc. This approach was employed for the preparation of Neu5Ac2en mimetics that contained an ether or thioether substituent as replacement of the glycerol side chain of Neu5Ac2en. Progress was also made towards the synthesis of a series of C-6 acylamino Neu5Ac2en mimetics. Analysis by 1H NMR spectroscopy showed that the acylamino derivatives adopted a half-chair conformation that was similar to the conformation of Neu5Ac2en but different to the conformation adopted by the ether and thioether derivatives prepared. The inhibitory activity of the C-6 ether and thioether Neu5Ac2en mimetics prepared was evaluated in vitro using an enzyme assay. It was found that most of the derivatives inhibited V. cholerae sialidase with a K1 of approximately 1O-4 M. The derivatives containing a hydrophobic side chain were found to be slightly more potent compared to derivatives with more hydrophilic side chains. A more detailed study of binding interactions between the C-6 thioether Neu5Ac2en mimetics and V cholerae sialdiase was carried out using STD 1H NMR spectroscopy and computational molecular modelling.
Thesis (PhD Doctorate)
Doctor of Philosophy (PhD)
School of Biomolecular and Physical Sciences
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O aminoácido selenocisteína (Sec) representa a principal forma biológica de selênio sendo requerida uma complexa maquinaria molecular para sua síntese e incorporação co-traducional em selenoproteínas. A Seril-tRNA sintetase (SerRS) inicia essa via, aminoacilando o Ser-tRNASec (SelC) com uma serina e também aminoacila os tRNAsSer. Sendo assim, um dos focos deste trabalho foi estudar a interação da SerRS de Trypanosoma brucei (T. brucei) com os tRNAsSer e o SelC utilizando a técnica de anisotropia de fluorescência para determinar suas constantes de dissociação. Em Kinetoplastidae, além da via de síntese de selenocisteína, há três selenoproteínas: SelT, SelK e SelTryp. No entanto, pouco se sabe a respeito das mesmas, sendo o estudo destas selenoproteínas o outro foco deste trabalho. Os fragmentos de DNA que codificam estas selenoproteínas foram subclonados em vetor de expressão pET 28a e 29a para posterior uso em células de Escherichia coli (E. coli). Para as proteínas SelK e SelTryp os ensaios de expressão apresentaram resultados insuficientes para dar continuidade aos experimentos planejados, pois o rendimento foi baixo e a purificação não foi possível. Já com a proteína SelT, devido à grande dificuldade encontrada para tornà-la solúvel, descobriu-se, no decorrer do trabalho, que tratava-se de uma proteína de membrana, ocasionando mudanças de alguns objetivos previamente propostos e consequentemente busca por novas estratégias. Conseguiu-se expressá-la na de forma solúvel e purificá-la por cromatografias. Ensaios realizados no SEC-MALLS mostraram uma estabilidade do complexo proteína-detergente. Com a TbSerRS é possível concluir que a organização de especificidade de ligação da enzima com seus ligantes se dá crescentemente: SelC>tRNASer7>tRNASer3a>tRNASer3b. E com as selenoproteínas do T. brucei faz-se necessários novas contruções para SelK e SelTryp e dar continuidade aos experimentos com a SelT tentando cristalizá-la, já que prototolo para a obtenção do complexo proteína-detergente está montado e estabilizado.
Selenocysteine (Sec) amino acid is the major biological form of selenium and requires a complex molecular machinery for its synthesis and co-translational incorporation into selenoproteins. The Seryl-tRNA synthetase (SerRS) starts this biosynthesis and matches the tRNASec (SELC) with a serine and the tRNAsSer, therefore the focus of this study is on SerRS of Trypanosoma brucei (T. brucei) and tRNAsSer and SELC interactions, with fluorescence anisotropy techinic to determinat dissociation constants. Three selenoproteins, namely SelT, SelK and SelTryp, besides the route of selenocysteine synthesis there be in Kinetoplastidae. DNA fragments that coding for these selenoproteins were subcloned in 28a and 29a to use into Escherichia coli (E. coli) cells. For Selk and SelTryp proteins, the expression protocol did not show an unsatisfactory result to continue the experiments. Many difficulties were encountered in studies with Selt protein, mainly in attempts to make it soluble. Our analyses revealed SelT was a membrane protein, therefore it could cause changes in some objectives and search for new strategies. It could be expressed and purified in cromatographis. SEC-MALLS assays showed a stability of the protein detergent complex. With TbSerRS is possible to conclude that the organization of binding specificity of the enzyme with its ligands occurs increasingly: SelC>tRNASer7>tRNASer3a>tRNASer3b. And selenoproteins in T. brucei, it is necessary for new constructions to SelK and SelTryp to continue the experiments trying to crystallizes SelT, since prototolo for obtaining the protein-detergent complex is assembled and stabilized.

This diploma thesis is focused on the study of dissociation behaviour of natural biocolloids, namely humic acids and fulvic acids. Humic and fulvic acids are natural, heterogeneous, high molecular weight substances which behave as weakly acidic polyelectrolytes and they have complex not exactly described structure. They are formed by biochemical transformations of organic residues (mainly plants). They are part of the soil, water, peat, sediments and coal. Solubility of humic acids is affected by pH value. The higher the pH value is the higher the solubility is. Fulvic acids are soluble in whole range of pH values. The aim of this diploma thesis is to determine the dissociation constant for the five kinds of humic acids and four kinds of fulvic acids, which have been isolated from various natural sources. These samples were purchased from IHSS. Dissociation constants were determined by the conductometric method and a combination of measurment pH and the content of acidic functional groups in Na2SO4. UV-VIS spectrophotometry method was used to characterize the quality of humic acids and fulvic acids.

Humic acids are natural substances belonging to the group of humic substances. They arise mainly decomposition of plant residues. They are contained in soils, peat, sediments, young coal, water and even in the air. Humic acids are only partially soluble in water with increasing pH increases their solubility. Diploma thesis focuses on the use of chronopotentiometric titration of humic research. This method is mainly used for the determination of trace concentrations of analytes. This work is focused on the determination of acidity by potentiometric titration and the determination of dissociation constants using chronopotentiometry with measurement of pH of prepared samples.

The scn1-1 mutants of Arabidopsis are characterised by spatially deregulated sites of root hair growth. This studydemonstrates that this phenotype is the result of the loss of regulation of members of the plant specific sub-family of Rho small GTPases by the Guanine nucleotide Dissociation Inhibitor (GDI), encoded by SCN1. The small GTPases R0P2, R0P4 and R0P5 of Arabidopsis are members of the I subset of type I ROPs that terminate with a conserved CXXL box and undergo 3 prenylation. These small GTPases are expressed in trichoblasts, and localize in patters suggestive of specific roles throughout root hair development. Loss-of function ROP2, R0P4 or ROP5 mutants display distinct root hair phenotypes lending support to the hypothesis that : R0P2, R0P4 and ROP5 control the establishment of the site of root hair initiation and subsequent tip-growth. Our findings also reveal SCNl/GDIl and R0P2 co-localize in a similiar pattern in developing root hairs in planta, but SCNl/GDIl is able to associate directly with ROP2, ROP4 and ROP5 in vitro.This suggests root hair morphogenesis relies on the negative regulation of ROP activity by SCNl/GDI 1 and is further supported by morphological phenotypes of scnl-l plants which can be rescued by the over expression of CFP:GD11 fusion placed under the control of the root hair specific PRP3 (Proline Rich Protein3) promoter. These observations imply that ROPs can be selectively sequestered away from the from plasma membrane of elongating root hairs during tip growth thereby promoting growth along a planar axis. Differences in the observed binding affinity of R0P2 in comparison to R0P4 and ROPS for SCNl/GDIl provides evidence that the CXXL box may play a critical role in ROP regulation, and that R0P2 and R0P4 are differentially prenylated.

Les biocapteurs sont des outils de détection et d'analyse puissants qui ont été largement utilisés dans les domaines de la santé, de la recherche biomédicale et de l’environnement. Cependant, différents biocapteurs utilisent différents transducteurs qui varient par la nature des substrats utilisés et par la chimie de surface. Tous ces paramètres peuvent avoir un effet sur les réactions biomoléculaires aux interfaces et conduire à des variations de la mesure de la constante de dissociation Kd. Dans ce contexte, ce travail de thèse visait à comparer trois techniques différentes : biopuce avec une détection par fluorescence, biocapteur à fluorescence par champ évanescent et biocapteur par résonance de plasmon de surface (SPR). Ces trois techniques ont été comparées pour la détermination de la constant de dissociation de l'hybridation de l'ADN. Pour la biopuce à fluorescence classique, le substrat est une lame de verre et la mesure est effectuée à la fin de l'expérience. Dans le cas du biocapteur à fluorescence à champ évanescent, le polystyrène est le substrat et une détection en temps réel est réalisée. La SPR est réalisée sur un film d'or mince. C'est une technique en temps réel et sans marquage. Les deux techniques basées sur la fluorescence nécessitent de marquer les cibles avec un fluorophore avant la mesure. Un facteur important déterminant la performance de l'analyse est la chimie de surface du capteur. Ici, nous avons optimisé la chimie de la surface de l'or pour le greffage d'ADN modifié thiol. Nous avons étudié deux méthodes de nettoyage: la solution de piranha et le plasma d'oxygène, dans le but d'obtenir une surface d'or propre sans oxydation de l'or. Ensuite, nous avons optimisé les paramètres lors de la mesure SPR comme par exemple la structure interfaciale du capteur, la force ionique .... Enfin, ces trois techniques ont été utilisées pour mesurer la constante de formation du duplex ADN/ADN. Les résultats ont montré que les Kd sont du même ordre de grandeur pour les trois techniques. De plus, pour les trois techniques, une augmentation de la densité de sonde de surface a entraîné une baisse d’affinité telle que mesurée
Biosensors are powerful detection and analysis tools that have been widely applied in pharmaceuticals, healthcare, biomedical research, and environmental monitoring. However different biosensors use different transducers and therefore different substrates and surface chemistries. All of these parameters may have an effect on the biomolecular reactions at the interface and lead to a deviation in dissociation constant Kd measurements. In this context, this PhD work aimed at comparing three different techniques: fluorescent microarray, evanescent field fluorescence biosensor and surface plasmon resonance (SPR) biosensor, to determine DNA hybridization Kd. For the classical fluorescence microarray, the substrate is a glass slide and the detection is performed at the end of the experiment. In the case of evanescent field fluorescence biosensor, polystyrene is the substrate and it permits a real-time detection. SPR is performed on thin gold film. It is a real-time and a label-free technique. The two fluorescent based techniques require to label the targets with fluorescent dyes prior to the measurements. One important factor determining the performance of the analysis is the surface chemistry of the sensor chip. Herein, we have optimized gold surface chemistry for thiol modified DNA grafting. We studied two cleaning methods: piranha solution and oxygen plasma, aiming at obtaining a clean gold surface without oxidation of the gold. Then, we optimized SPR assay parameters such as interfacial structure of sensor chip, ionic strength... After, these three techniques were used to measure the DNA hybridization Kd. The results showed that the Kds measured are similar for the three techniques. In addition, increasing surface probe density resulted in an increase of Kd of DNA hybridization

Le centrosome est le centre majeur d'organisation des microtubules dans les cellules eucaryotes. Le mecanisme de nucleation de la tubuline sur le centrosome est encore mal compris, bien que le modele le plus probable implique une liaison initiale des dimeres de la tubuline sur le centrosome. Ce travail demontre que la liaison tubuline-centrosome est specifique et que le centrosome possede en moyenne 25. 000 sites de liaison, avec une constante de dissociation (kd) d'environ 5,5 micromolaires. Une banque de peptides de tubuline produite par digestions endoproteasiques a ete utilisee, avec d'autres methodes biochimiques, pour rechercher le domaine de liaison dans la sequence de la tubuline

Mesmo com o grande número de estudos relacionados à proteases do subtipo B e de como suas mutações podem interferir na estrutura, na resistência a inibidores e na eficiência catalítica da enzima, existe ainda uma lacuna de como as mudanças polimórficas de proteases de HIV de outros subtipos de HIV-1 interferem nesses fatores. Nesse contexto insere-se esse trabalho, que utilizou proteases de HIV-1 isoladas de pacientes brasileiros HIV-1 infectados com o subtipo F, e outros dois mutantes, sendo que um do subtipo F e outro do subtipo B para ensaios frente a seis inibidores comercialmente disponíveis: amprenavir, indinavir, lopinavir, nelfinavir, ritonavir e saquinavir. Nossos resultados experimentais revelam que os seis inibidores comerciais estudados são significantemente menos ativos para o subtipo F e para as mutantes quando comparados ao subtipo B. Além disso, os valores de vitalidade dessas proteases também são considerados maiores que os obtidos para a proteína selvagem do subtipo B. O acúmulo de mutações comumente detectadas e o polimorfismo natural tornam a protease selvagem do subtipo F cataliticamente suficiente para manter a viabilidade do vírus e garantir alto grau de resistência cruzada frente a todos os inibidores estudados.
Despite years of intense research around the world, HIV continues to represent considerable therapeutical challenge. In order to gain more insights into resistance of polymorphic mutations of existing HIV subtypes toward commercially available pharmaceutics, we studied inhibition of subtypes B and F HIV proteases (PRs) [native and two mutant enzymes clinically identified in Brazilian patients] by six commercial inhibitors (amprenavir, indinavir, lopinavir, nelfinavir, ritonavir and saquinavir). Our results show that all these inhibitors have significantly higher Ki values for the subtype F HIV PR (Fwt) and both mutant enzymes than that for the B subtype HIV PR (Bwt). Furthermore, the biochemical fitnesses of these proteases, or their vitalities, are also considerably higher than that of Bwt. The accumulation of commonly detected resistant mutations in HIV PRs with natural polymorphisms turns Fwt sufficiently catalytically active to guarantee the virus viability and confers it a large degree of cross resistance against all studied inhibitors.

Ce travail est présenté en 2 parties. La première partie aborde la synthèse stéréocontrôlée de 2 séries de carbonucléosides de structures méthylènecyclopropane. Les molécules cibles sont des analogues de l’entécavir, une prodrogue utilisée en trithérapie pour lutter contre le VHB. Les synthèses des carbonucléosides cibles de la série I utilisent un chiron commun, un alcool obtenu par désymétrisation enzymatique d’un diol méso. La transformation chimique de cet intermédiaire clé permet d’obtenir le carbonucléoside (+)-17 en 8 étapes mettant en œuvre comme étapes cruciales un réarrangement de Curtius et la construction de la base uracile avec un rendement global de 23%. Le carbonucléoside appartenant à la série II, a été synthétisé en 10 étapes mettant en jeu une réaction de Mitsunobu, une acylation chimique et contrairement à l’approche précédente, la désymétrisation enzymatique d’un diol méso n’a pas permis d’obtenir le carbonucléoside cible énantiopure. La seconde partie est consacrée à l’activation et l’homolyse des alcoxyamines pour une application en théranostique. La synthèse de l’alcoxyamine modèle présente un groupement vinyl pyridine et un nitroxyde SG1. L’activation est réalisée par protonation, oxydation, méthylation et benzylation de la partie pyridyle et met en évidence l’importance de la polarité. Elle a permis d’obtenir des espèces hautement labiles qui libèrent un radical alkyle et le nitroxyde SG1, avec notamment des valeurs de la constante de dissociation kd plus élevées et donc des énergies d’activation Ea plus faibles par rapport à l’alcoxyamine non activée
This work is presented in 2 parts. The first part is dedicated to the stereocontrolled synthesis of 2 series of carbonucleosides of methylenecyclopropane structure. The target molecules are analogs of entecavir, a prodrug used in triple therapy to fight against HBV. The syntheses of the carbonucleosides targets of the series I use a common chiron, an alcohol obtained by enzymatic desymmetrization of meso-diol. For example, the chemical transformation of this key intermediate allows to obtain carbonucleoside (+)-16 in 8 steps as crucial steps involving a Curtius rearrangement and the construction of the uracil base with 23% overall yield. The carbonucleoside belonging to the series II was first synthesized in 10 steps involving a reaction of Mitsunobu, a chemical acylation. Howerer the enzymatic desymmetrization of a meso-diol did not get the target carbonucleoside in an enantiopur form. The second part is dedicated to the activation and the homolysis of the alcoxyamines for a theranostic application. The synthesis of the model alcoxyamine is made from vinyl pyridine and nitroxide SG1. Activation is carried out by protonation, oxidation, methylation and benzylation of the pyridyl part and highlights the importance of polarity. It allowed getting highly labile species that release an alkyl radical and nitroxide SG1, with notably higher kd dissociation constant values and therefore activation energies Ea lower compared to the alcoxyamine not enabled

This diploma thesis deals with acid-base and electrolytic behavior of hyaluronan solutions at different ionic strength. Acid-base behavior of hyaluronan was investigated by acid-base titrations which were carried out with two different methods, acid and alkaline acid-base titration. Dissociation constants at different ionic strength at zero degree of dissociation and at 50% degree of dissociation were evaluated from the results of acid-base titrations. Dissociation constants obtained from acid acid-base titrations have values between 3,0 and 3,6. Dissociation constants obtained from alkaline acid-base titrations are not very informative because their values are much higher than the expected values. The study of degradation of hyaluronan during acid-base titration was performed to complete study of acid-base behavior. Electrolytic behavior of hyaluronan solution was performed by conductometric titrations in three different environments.

Cette these repose sur l'application de la chromatographie d'affinite (zonale) conventionnelle (cac) et haute performance (cahp) a l'etude des interactions de la lipase (ou ses isolipases, ou sa sequence c terminale) d'une part, et la colipase, d'autre part. Les constantes de dissociations k::(d) du complexe calculees en cac et cahp sont voisines des valeurs mesurees par d'autres techniques non chromatographiques dans des conditions operatoires similaires. La cahp est une technique qui permet de determiner rapidement la stabilite du complexe lipase/colipase. L'influence de parametres physiques et physico-chimiques montre que la nature des interactions lipase/colipase est mixte, de type hydrophobe et ionique. En cahp les isolipases a et c presentent une affinite plus faible que l'isolipase b pour le cofacteur immobilise. Le peptide b, region c terminale de l'enzyme, engage des interactions specifiques avec la colipase, ce qui laisse supposer que le site d'association de la lipase avec son cofacteur se situe dans la region 336-449

Vias redox são importantes reguladores da homeostase e sinalização celular, mas o entendimento dos mecanismos desses processos é incompleto. Tiol-proteínas como a dissulfeto isomerase proteica (PDI) podem ser moduladores dessas vias. A PDI(PDIA1) é o protótipo da família das PDIs, cuja função canônica é o enovelamento redox de proteínas no retículo endoplasmático. Além disso, PDI exerce regulação de NADPH oxidases, as principais fontes de oxidantes celulares, e é necessária para ativação de RhoGTPases, organização do citoesqueleto e migração de células vasculares. No estudo de mecanismos pelos quais a PDI regula RhoGTPases, mostramos, em redes computacionais e em experimentos de co-imunoprecitação, associação entre PDIA1 e o regulador de RhoGTPases RhoGDIalfa. Além disso, identificamos forte proximidade entre os genes codificando estas proteínas. Neste estudo, caracterizamos o perfil e implicações desta sintenia gênica.A análise bioinformática pelos programs Ensembl, NCBI e UCSC evidencia um padrão de sintenia entre diferentes isoformas destas duas famílias: PDIA1 (P4HB), PDIA2 (PDIP) e PDIA8 (Erp27) são vizinhos, respectivamente, a RhoGDIbeta, RhoGDIy e RHOGDIalfa, com correspondentes regiões intergênicas de 7.1, 2.9 e 0.14 kb em distintos cromossomos em H. sapiens. O padrão dessa sintenia foi fortemente conservado emC. elegans, alguns peixes e uniformemente em anfíbios, répteis, aves e mamíferos. Leveduras expressam no mesmo cromossomo , porém em locais distantes (i.emacrossintenia) ortólogos da PDIA1 e RhoGDI?, mas não expressam outras PDIs e RhoGDIssintênicasnos eucariotos complexos. No entanto, sintenia entre PDI e RhoGDI foi também observada na planta A. thaliana, sem evidência de um ancestral comum. Os pares sintênicos associam-se a blocos vizinhos conservados, porém diversos para cada par, enquanto cada bloco contem um gene codificando um distinto regulador da PP1 (fosfatase proteica-1). Análise filogenética mostrou topologia semelhante entre as duas famílias.Análise dos dados do estudo ENCODE e predição pelo Softberry identificou sítios de ligação a fatores de transcrição comuns entre os distintos pares, cuja ontologia indicou principalmente desenvolvimento, processos metabólicos e resposta imune. O estudo de possíveis implicações funcionais dessa sintenia mostrou que manipulações da expressão proteica de PDIA1 não promovem mudança consistente na expressão proteica de RhoGDIalfa, tanto in vitro (silenciamento da PDI por siRNA e superexpressão por vetor lentiviral induzível) como in vivo (camundongo transgênico com superexpressão constitutiva da PDIA1). No entanto, as mudanças da expressãogênica de ambos os genes na camada íntima de artérias carótidas de camundongo durante remodelamento induzido por fluxo foram fortemente correlacionadas. Experimentos de coimunoprecipitação e co-localização à microscopia confocal sugeriram interação física entre PDIA1 e RhoGDIAalfa. Deste modo, estes dados mostram um intrigante padrão de conservação evolutiva da proximidade gênica entre PDIs e RhoGDIs, não usual em eucariotos. Genes sintênicos frequentemente codificam proteínas que tendem a interagir física e/ou funcionalmente. Com efeito, nosso dados sugerem co-regulação e interação física entre PDIA1 e RhoGDIAalfa, corroborando a convergência entre essas proteínas como possível mecanismo envolvido na regulação redox do citoesqueleto pela PDIA1
Redox pathways are important regulators of homeostasis and cell signaling, but the understanding of the mechanisms of these processes is incomplete. Thiol proteins such as protein disulfide isomerase (PDI) can be modulators of these pathways. PDI (PDIA1) is the prototype of the family of PDIs whose canonical function is a redox protein folding in the endoplasmic reticulum. In addition, PDI exerts regulatory NADPH oxidase, the main sources of cellular oxidant, and is required for activation RhoGTPases, cytoskeletal organization and migration of vascular cells. In the study of mechanisms by which regulates PDI RhoGTPases, we showed in computer networks and co-imunoprecitation experiments association between PDIA1 and the regulator of RhoGTPases, RhoGDI?. In addition, we identified strong proximity of the genes encoding these proteins. In this study, we characterize the profile and implications of this synteny. .A bioinformatic analysis by programs Ensembl, NCBI and UCSC shows a pattern of synteny between different isoforms of these two families: PDIA1 (P4HB), PDIA2 (PDIP) and PDIA8 (Erp27) are neighbors , respectively RhoGDIalfa, and RhoGDIy RHOGDIbeta with corresponding intergenic regions 7.1, 2.9 and 0:14 kb in different chromosomes of H. sapiens. The pattern of this synteny was strongly maintained in C. elegans, some fish and evenly amphibians, reptiles, birds and mammals. Yeasts express on the same chromosome, but in distant places (i.e macrosintenia) orthologs of PDIA1 and RhoGDI?, but do not express other syntenics PDIs and RhoGDIs in complex eukaryotes. However, synteny between PDI and RhoGDI was also observed in the plant A. thaliana, no evidence of a common ancestor. The syntenic pairs are associated with the stored neighboring blocks, but different for each pair, while each block contains a gene encoding a regulator of distinct PP1 (protein phosphatase-1). Phylogenetic analysis showed similar topology between the two famílias. The identified binding sites common transcription factors between different pairs, which mainly indicated ontology development, metabolic and immune response. The study of possible functional implications of synteny showed that manipulations of PDIA1 protein expression do not promote consistent change in protein expression RhoGDI, both in vitro (silencing of PDI by siRNA and overexpression of inducible lentiviral vector) and in vivo (transgenic mice overexpressing constitutive of PDIA1). The study of possible functional implications of synteny showed that manipulations of PDIA1 protein expression do not promote consistent change in protein expression RhoGDIalfa, both in vitro (silencing of PDI by siRNA and overexpression of inducible lentiviral vector) and in vivo (transgenic mice overexpressing constitutive of PDIA1). However, changes of gene expression of both genes in the intima of mouse carotid arteries during remodeling induced by flow were strongly correlated. Immunoprecipitation experiments and co-location to confocal microscopy suggested physical interaction between PDIA1 and RhoGDIAalfa. Thus, these data show an intriguing pattern of evolutionary conservation of gene proximity between POIs and RhoGDIs not common in eukaryotes. sintênicos genes often encode proteins that tend to interact physically and / or functionally. Indeed, our data suggest co-regulation and physical interaction between PDIA1 and RhoGDIAalfa, supporting the convergence of these proteins as a possible mechanism involved in redox regulation of cytoskeleton by PDIA1

Die Reaktionspfade und Reaktionsdynamik photoinduzierter bimolekularer Ladungstransferreaktionen werden mit Hilfe der ultraschnellen polarisationsabhängigen UV-Pump/IR-Probe-Spektroskopie charakterisiert. Allgemein akzeptierte Modelle zur Beschreibung von bimolekularen Elektrontranserreaktionen nehmen an, dass Ladungstrennung in polaren Lösungsmitteln zu zwei Arten von Ionenpaaren führt, den lockeren (LIPs) und den engen Ionenpaaren (TIPs). TIPs und LIPs können durch die Beobachtung von Schwingungsmoden spektroskopisch unterschieden werden. Allerdings deuten die multiplen Zeitskalen sowohl für die Bildung von TIPs als auch LIPs darauf hin, dass eine Unterscheidung in zwei Arten von Ionenpaaren mit definierter Geometrie eine erhebliche Vereinfachung ist. TIPs und LIPs sind vielmehr als Grenzfälle zu betrachten, zwischen derer eine kontinuierliche Verteilung verschiedener Ionenpaare existiert. Die Natur der Ionenpaare wird durch die Verteilung der neutralen Reaktionspaare vor Initiation der Reaktion bestimmt. Außerdem wird gezeigt, dass TIPs höchst anisotrop sind. Die Wichtigkeit der beidseitigen Orientierung der Reaktanten wird dabei offengelegt. Weiterhin wird erstmalig ein femtosekundenspektroskopischer Beweis für die Existenz von Kohlensäure in wäßriger Lösung präsentiert. Eine Photosäure wurde verwendet, um die ultraschnelle Protonierung von Bikarbonat optisch auszulösen. Kohlensäure wurde bisher als Feststoff in Eismatrizen und in der Gasphase detektiert. Da Kohlensäure als Intermediat zwischen Kohlenstoffdioxid und Bikarbonat postuliert wird, ist ihre Charakterisierung von immenser Bedeutung für das Verständnis grundlegender Säure-Base Chemie von Karbonaten in wäßriger Lösung. Die Analyse der zeitabhängigen Signale unter Verwendung eines theoretischen Modells erlaubt die Bestimmung der bimolekularen Reaktionsdynamik. Dies ermöglicht einen Einblick in die Säure-Base Chemie von Kohlensäure.
The reaction pathways and dynamics of photoinduced bimolecular charge transfer reactions are characterised with ultrafast polarisation-sensitive UV-pump/IR-probe-spectroscopy. Generally accepted models for bimolecular electron transfer reactions suppose that charge separation in polar solvents leads to two geminate ion pairs, namely loose (LIPs) and tight ion pairs (TIPs). By monitoring vibrational marker modes TIPs and LIPs can be distinguished spectroscopically. However, multiple time scales for the formation of TIPs and LIPs indicate that a distinction between two kinds of ion pairs with well-defined geometries is a considerable simplification. TIPs and LIPs should rather be regarded as limiting cases, as there is a continuous distribution of different ion pairs between these two limits. The crucial parameter governing the nature of the ion pairs is the distribution of neutral reaction pairs subsequent to initiation of the reaction. Furthermore, TIPs are found to be highly anisotropic, revealing the importance of mutual orientation of the reactants. This thesis also presents for the first time femtosecond infrared spectroscopic results proving the existence of carbonic acid in aqueous solution. A photoacid is used to optically trigger the ultrafast protonation of bicarbonate. Carbonic acid has only been detected as solid existing in ice matrices and in the gas phase, so far. Because carbonic acid is often postulated as intermediate between carbon dioxide and bicarbonate its characterisation is of substantial support in understanding fundamental acid-base chemistry of carbonates in aqueous solution as well as in biophysical situations. Analysing the time-dependent signals using a theoretical model to describe bimolecular reaction dynamics an on-contact proton transfer reaction rate is derived. This gives an insight into the acid-base chemistry of carbonic acid.

Les constantes d'inhibition reversible de la butylcholinesterase par une serie de 16 phosphoramides aliphatiques ont ete determinees par spectrophotometrie et par microcalorimetrie. L'activite des substituants amines augmente avec la lipophilie. L'inhibition irreversible de la butylcholinesterase par le thio-tepa et le methyl-parathion a ete etudiee en suivant l'hydrolyse d'une faible concentration de substrat en presence de l'inhibiteur

A doença de Chagas, causada pelo protozoário flagelado Trypanosoma cruzi, é uma doença tropical que enseja morte/morbidade de milhões de pessoas na América Latina. Por processos migratórios, vem-se estendendo ao sul dos Estados Unidos, Canadá, Europa, Austrália e Japão. Essa doença tem sido considerada super-negligenciada pela indústria farmacêutica, já que os dois fármacos disponíveis para o seu tratamento foram introduzidos há mais de quarenta anos e apresentam baixa eficácia com vários efeitos colaterais severos. Mais recentemente, a Organização Mundial da Saúde considerou a doença de Chagas, dentre outras, como a doença da pobreza! Com esse cenário completamente desfavorável aos portadores da doença, é necessária a descoberta, desenvolvimento e introdução de novos fármacos para o tratamento eficiente e seguro da doença de Chagas.
Dentro desse contexto, este trabalho representa uma importante contribuição para o entendimento das razões moleculares da ação farmacológica de substâncias químicas bioativas de interesse à farmacoterapia da doença de Chagas. Ao nível molecular, a enzima pertencente à via de síntese de novo de nucleotídeos de pirimidinas, diidroorotato desidrogenase do Trypanosoma cruzi (TcDHODH), é um alvo promissor para a descoberta e desenvolvimento de candidatos a fármacos de interesse para o tratamento da doença de Chagas.
Os conceitos e ferramentas da química medicinal computacional, tais como os ensaios virtuais in silico, foram usados para a identificação de inibidores da TcDHODH. Vinte e seis substâncias inéditas como inibidores da TcDHODH foram adquiridos comercialmente e avaliados experimentalmente através da Calorimetria de Titulação Isotérmica (ITC) para a determinação do mecanismo de inibição e da constante cinética de afinidade (Kiapp).
Na etapa de docagem molecular, o objetivo era identificar moléculas que apresentassem uma boa afinidade pelo sítio ativo da enzima TcDHODH. A primeira série de ligantes selecionados dos métodos in silico, apresentou inibição enzimática na concentração de micromolar com eficiência média de ligante de 0,50 kcal mol-1 átomo-1. Devido à baixa massa molecular (aproximadamente 200 kDa) e a alta eficiência de ligante, essa série foi considerada como constituída de excelentes substâncias com elevado poder de reconhecimento biomolecular. Por isso, foram caracterizadas como substâncias passíveis de otimização no processo do-ligante-para-substância matriz.
As enzimas TcDHODH e DHODH de Leishmania major (LmDHODH) têm sítios ativos com elevado grau de similaridade. Portanto, usando a enzima LmDHODH como padrão de substituição da TcDHODH é possível fazer a descrição do modo de interação do co-complexo TcDHODH-inibidor. O modo de ação descrito através da resolução da estrutura cristalográfica de raios-X, além de validar ortogonalmente os resultados cinéticos obtidos por ITC - que identificou as substâncias como inibidores competitivos (por interação direta no sítio ativo da enzima TcDHODH), geraram hipóteses farmacofóricas para a busca de novas moléculas (chamadas de segunda geração), agora com padrão superior de reconhecimento molecular do sítio da TcDHODH. Para validar complementarmente a hipótese, foi demonstrado que os inibidores da TcDHODH inibem, similarmente, a LmDHODH.
Uma análise cuidadosa da estrutura tridimensional da enzima TcDHODH, demostrou a possibilidade de ocupação do sítio S2 que se estende além da região do sítio catalítico S1, permitindo assim o aumento da afinidade biomolecular com os inibidores. Além disso, o sítio S2 não é encontrado na estrutura da proteína de humanos (HsDHODH), podendo ser uma região passível de seletividade frente à enzima TcDHODH.
O emprego adequado dessa hipótese resultou na otimização dos ligantes identificados previamente para substâncias mais potentes que inibiram a enzima de forma competitiva em relação ao substrato diidroorotato (DHO) em valores Kiapp de 121 ± 14 nM e 190 ± 10 nM.
A técnica de ITC foi fundamental no processo de descoberta de inibidores enzimáticos, pois se mostrou extremamente susceptível à determinação da interação intermolecular enzima-inibidor, permitindo acompanhar a cinética da reação e obter os valores da constante de afinidade de maneira precisa e acurada. Com isso, a taxa de acerto obtida nesta tese foi de 46%, considerando-se apenas as substâncias com valores de Ki app < 100 µM. Esse é um número favoravelmente apreciável, já que na literatura ele gira em torno de 1-10% quando o planejamento in silico é realizado, quando comparado às taxas de acerto dos métodos de ensaio em larga escala (HTS), entre 0-2 %, os resultados alcançados neste trabalho são ainda mais significativos.
Além disso, as substâncias químicas selecionadas através da integração de métodos in silico e biocalorimétricos apresentam elevado grau de complexidade no processo biomolecular de interação enzima-ligante, que permite classificá-las para as fases seguintes da gênese planejada de fármacos.
American trypanosomiasis or Chagas disease, caused by the haemoflagellate Trypanosoma cruzi, is a tropical disease that affects millions of people in Latin America. Epidemiology of Chagas disease in non-endemic countries is attained by immigration as the disease also affects people in the United States, Canada, Europe, Australia and Japan. However, the United States are not to be written off as an area of nonendemicity for Chagas disease like Europe or Asia because the southern states have enzootic T. cruzi transmission that involves triatomine species and hosts such as raccoons, opossums, and domestic dogs. Even though, this disease has been considered as a super-neglected from the big Pharma Industry viewpoint since the only available drugs for its treatment were introduced in the market more than forty years ago and worsen is that they have low efficacy and cause various severe side effects.
Although the current clinical scenario is of course discouraging and is far from being even a soothing treatment for those who suffer from the disease, it prompt ones to set efforts towards the need of discovering and developing new efficacious and safe drugs to treat Chagas disease.
Our research group covers the concept of enzymes acting as targets for the action of drugs. Once T. cruzi has many druggable targets, the dihydroorotate dehydrogenase enzyme (TcDHODH) that belongs to the de novo pyrimidine nucleotide synthetic pathway has been chosen for the search of new inhibitors that may be of use in the treatment of Chagas disease. To accomplish with this and considering that inhibitors are molecules that decrease enzyme activity leading to parasite death, we used the concepts and tools of modern computational medicinal chemistry such as in silico screening of small molecules that bind to the active site of the TcDHODH.
After a thoroughly program of virtually screening thousands of compounds, 26 were purchased from commercially available sources and experimentally assayed against the TcDHODH using Isothermal Titration Calorimetry (ITC) in order to determine the mechanism of inhibition and the kinetic affinity constant (Kiapp).
The first series of inhibitors selected from our in silico strategy were evaluated by ITC to yield compounds that inhibited the TcDHODH in the micromolar concentration range with an average of 0.50 kcal mol-1 atom-1 ligand efficiency (LE). Because the assayed compounds have low molecular weight (ca. 200 kDa) and high LE, which bring them to the specific bimolecular pattern recognition all of them were considered good inhibitors capable of being selected to enter the hit-to-lead optimization process.
The detailed description of the ligand-enzyme mode of binding (MOB) is thoroughly accomplished by solving the X ray crystal structure of the surrogate Leishmania major DHODH enzyme (LmDHODH), which has a high degree of similarity with the enzyme TcDHODH. The MOB credited to be in the active site of the TcDHODH orthogonally validated the ITC kinetic experimental data obtained for all ligands as competitive inhibitors that interact at the active site of the TcDHODH and helped to generate pharmacophoric hypotheses for the search of new second generation molecules acting against the enzyme TcDHODH.  Analyzing the 3D structure of the TcDHODH along with its surrogate LmDHODH, we envisaged the possibility of compounds to extend their side chain beyond the region of the catalytic site (called S1), and interacting in a region called S2, so to increase binding affinity. Moreover, the TcDHODH S2 site that is not found in the 3D protein structure of humans (HsDHODH) is likely to offer new insights for the search of inhibitors whose binding to this S2 site can pave the roads towards the needed structural basis for selective inhibition of TcDHODH.
The most potent compounds inhibited the enzyme competitively with respect to the substrate dihydroorotate (DHO) at Kiapp values of 121 ± 14 nM and 190 ± 10 nM, which constitutes high affinity TcDHODH inhibitors. The ITC technique was pivotal to this process of enzyme inhibitors discovery, because it proved to be extremely sensitive thus allowing to monitor the kinetics of the reaction and to obtain precise and accurate values of affinity constants.
The hit rate obtained in this work, considering only those compounds with Kiapp < 100 µM, was 46%. This is a really high number, since literature values range from 1 to 10% when the planning new inhibitors via in silico methods when compared to the success rates obtained by the methods of testing on large scales (HTS), 0-2 %, the results achieved in this work are even more significant. Moreover, the compounds selected through the integration of in silico and calorimetric methods showed a high degree of complexity in the process of bimolecular enzyme-ligand recognition, which allows to pass them to the next phase of the drug design process.

Specific and non-specific interactions of solutes with immobilized biomembranes were studied using chromatographic methods. Liposomes, proteoliposomes and red blood cell (RBC) membrane vesicles were immobilized by a freeze-thawing procedure, whereas whole RBCs were adsorbed in the gel beds using electrostatic interaction, binding to wheat germ agglutinin (WGA) or the streptavidin-biotin interaction.

Superporous agarose gel with coupled WGA was the most promising matrix for RBC adsorption and allowed frontal chromatographic analyses of the cells for about one week. Dissociation constants for the binding of cytochalasin B and glucose to the glucose transporter GLUT1 were determined under equilibrium conditions. The number of cytochalasin B-binding sites per GLUT1 monomer was calculated and compared to corresponding results measured on free and immobilized membrane vesicles and GLUT1 proteoliposomes. This allowed conclusions about the protein´s binding state in vitro and in vivo.

Partitioning of drugs into biomembranes was quantified and the system was suggested as a screening method to test for possible intestinal absorption of drug candidates. We also studied how membrane partitioning of drugs is affected by the presence of integral membrane proteins or of charged phospholipids.

An attempt to combine the theory for specific binding and membrane partitioning of solutes in a single equation is briefly presented.

The human glucose transporter GLUT1 is abundant in red blood cells, the blood-brain barrier and epithelial cells, where it mediates the transport of the energy metabolite, glucose. In the present work some properties of GLUT1, including affinity binding of both substrates and inhibitors, transport rates as well as permeabilities of aromatic amino acids and drug-membrane interactions were analyzed by chromatographic methods.

Reconstitution by size-exclusion chromatography on Superdex 75 from a detergent with a low CMC that provides monomeric GLUT1 was examined regarding D-glucose- and CB binding as well as D-glucose transport. Upon steric immobilization in Superdex 200 gel beads, residual detergent could be washed away and dissociation constants in the same range as reported for binding to GLUT1 reconstituted from other detergents were obtained. The transport rate into the GLUT1 proteoliposomes was low, probably due to residual detergent. Binding to GLUT1 at different pH was analyzed and the affinity of glucose and GLUT1 inhibitors was found to decrease with increasing pH (5–8.7). The average number of cytochalasin B-binding sites per GLUT1 monomers was, in most cases, approximately 0.4. GLUT1 may work as a functional monomer, dimer or oligomer. To determine whether GLUT1 was responsible for the transport of the aromatic amino acids tyrosine and tryptophan, uptake values and permeabilities of these amino acids into liposomes and GLUT1 proteoliposomes were compared to the permeabilities of D- and L- glucose in the same systems. Dihydrocytochalasin B was identified to be a new inhibitor of tyrosine and tryptophan transport into red blood cells. Ethanol turned out to inhibit the specific binding between CB and GLUT1 and also to decrease the partitioning of CB and drugs into lipid bilayers. A capacity factor for drug partitioning into membranes that allows comparison between columns with different amount of immobilized lipids was validated, and turned out to be independent of flow rate, amount of lipids and drug concentration in the ranges tested.

This work investigates the correlation of structural and photovoltaic properties of dyes used in dye-sensitized solar cells. Experimental methods, including ultraviolet-visible spectroscopy, fluorescence spectroscopy, cyclic voltammetry and electrochemical impedance spectroscopy are employed to study optical and electrochemical properties of dye molecules. Computational methods, including density functional theory and time-dependent density functional theory, are used to validate and predict the optical and electronic properties of dye molecules, in their isolated state and once embedded into a working electrode device environment that comprises a dye...TiO2 interface. The results chapters begin with the presentation of a series of quinodimethene dyes that are experimentally validated for their photovoltaic application, and associated computational studies reveal that an inner structural factor - a phenyl ring rotation occurring during the optical excitation process - leads to the competitive photovoltaic device performance of these dyes. Carbazole-based dyes are then systematically studied by computation, especially considering charge transfer paths and binding modes of these dyes on a titania surface. The theoretical models for the basic building block of this chemical family of dyes, known as MK-44, successfully support and explain structural discoveries from X-ray diffraction and reflectometry that impact of their function. A benzothiadiazole-based dye, RK-1, is then systematically studied by both experimental and computational methods, and the results show that the π-bridge composed of thiophene, benzothiadiazole and benzene rings leads to excellent charge separation; and the rotation of these rings during the optical excitation process may well be consistent with the fluorescence spectrum. Finally, the well-known ruthenium-based dyes are theoretically studied to determine the properties of different ligands connected to the metal core of the complex. Conformations with different NCS ligands are calculated in terms of energy and explain well the corresponding results from X-ray diffraction. Acid-base properties of carboxyl groups connected to pyridine ligands in N3 and N749 are theoretically calculated based on thermodynamics and density functional theory. Implicit and explicit models are both adopted to predict these acid dissociative constant values, which are generally in a good agreement with the reported experimental data. The thesis concludes with conclusions and a future outlook.

Aus den frühen Bindungsstudien des globalen Regulators AbrB mit der ausgedehnten phyC-Promotorregion von Bacillus amyloliquefaciens FZB45 konnte ein mehrstufiger kooperativer Bindungsprozess abgeleitet werden. Dabei verlangt die AbrB-vermittelte Repression von phyC nach Integrität zweier großer Bindungsstellen, ABS1 und ABS2, die 162 bp voneinander entfernt liegen. In der vorliegenden Arbeit wurden die ersten Echtzeitkinetiken zur DNA-AbrB-Interaktion mittels der Oberflächenplasmonresonanz (SPR) gemessen und analysiert. AbrB zeigte hohe Affinitäten zu den 40 bp langen Oligonukleotiden, die den beiden Bindungsstellen entstammen. Dabei verursachten alle Oligonukleotide der ABS2 und nur eine kurze Region innerhalb der ABS1 bei der Bindung von AbrB Konformationsänderungen im Protein und in der DNA (CD - Zirkulardichroismusspektroskopie) und wiesen eine Kooperativität von 2
In previous binding studies it could be demonstrated that a global regulator AbrB and the extensive phyC promoter region of Bacillus amyloliquefaciens FZB45 interact in a complex manner. AbrB binding is a multistep cooperative process. The integrity of both binding sites, ABS1 and ABS2, which are separated by 162 bp, is crucial for the AbrB-mediated repression of phyC. This work presents the first real-time binding kinetics of the AbrB-DNA interaction using surface plasmon resonance (SPR). AbrB exhibited high affinities to all analyzed 40-bp oligonucleotides that were derived from the ABSs of phyC. All parts of the ABS2, but only a small region within ABS1, were bound cooperatively to AbrB with a stoichiometry of 2 DNA to 1 AbrB tetramer and with 2

The kinetic inhibitor Poly Vinyl Caprolactam (PVCap) was added as a kinetic inhibitor to the gas-water system. Different hydrate formers were used in order to obtain formation of the different hydrate structures (sI, sII and sH). All hydrate structures were formed with PVCap. The effect of applying different melting rates was investigated. The isochoric technique was used to obtain dissociation temperatures and corresponding pressures. The melting rate was found to be a parameter influencial for the dissociation temperature. Even for very slow melting rates such as 0.0125 Kelvin per hour, the final dissociation temperature was significantly higher that the dissociation temperature for the corresponding non-inhibited system.

-5- ABSTRACT A huge effort has been put in determining the mechanism of the development of tolerance and dependence in context of clinical use of morphine for treatment of severe pain. Understanding of this mechanism would help to design new and more efficient pharmaceuticals. This diploma paper discus the opiate receptors with a special focus on long-term effect of chronic morphine treatment, which was determined using a radioligand binding assays with a non-selective antagonist [3 H]Diprenorphine. One of the goals of this work was to create and optimise a method for preparation of pure plasma membranes from rat cortex using percoll gradient. There were five groups, which differed in the length of morphine treatment: ten days (M-10), twenty-eight days (M-28), ten days with seven days of regression (RM-10 twenty-eight days with seven days of regression (RM-28) and a control group (K). The loss of total opioid receptor number was noticeable after ten days and grew slightly during continuous morphine treatment and kept lowering in the period of regression. The total loss was approximately 30% of the control binding. The equilibrium dissociation constant (Kd), thus the affinity of [3 H]Diprenorphine wasn't significantly different among the groups. Morphine acts through µ-opioid receptor, that's why there was a...

Inhibitor containing systems were investigated for hydrate structures I and II. The kinetic inhibitor PVCap was added to the water phase for each hydrate structure. Dissociation temperatures were determined for various formation temperatures and PVCap concentrations. Obtained dissociation temperatures were compared with corresponding values calculated with CSMHYD. Differences between experimental and calculated values were compared for various formation temperatures and inhibitor concentrations. Comparison revealed that these parameters (formation temperature and concentration) had an effect on the dissociation temperature. Dissociation temperatures for hydrates formed at low degrees of subcooling were higher than for hydrates formed at large subcooling. The effect depended on the system pressure; apparently decreasing or vanishing with increasing pressure. Furthermore, the temperature of dissociation increased with the inhibitor dose.

碩士
國立陽明大學
生物化學研究所
93
Beta-2-glycoprotein I (β2-GPI) is a human plasma protein mainly produced by the liver. Although various pathological properties have been attributed to this protein, its biological role and intracellular distribution still remain unclear. In our previous study, β2-GPI was proved to protect cells from apoptosis in J774A.1 macrophages and human coronary artery smooth muscle cells (HCASMCs) treated with nitric oxide donors. The aim of this study was to investigate the proteomic profile in β2-GPI over-expressed cells, and to clarify the role of β2-GPI in apoptosis. The differentially expressed proteins in the β2-GPI over-expressed Huh7 cells were analyzed by the two dimension gel electrophoresis analysis and subsequent MALDI-TOF / Q-TOF. We identified a β2-GPI upregulated-protein, Rho guanine nucleotide dissociation inhibitor-α (RhoGDI-α), as the Rho family protein regulator. Rac1 activity seemed to be down-regulated by RhoGDI-α in the β2-GPI over-expressed Huh7 cells. Overexpression of β2-GPI was also shown to result in reorganization of filamentous-actin (F-actin) in Huh7 cells under confocal microscopic observation. In addition, the contribution of β2-GPI to apoptosis was investigated in Huh7 hepatoma cells treated with TNF-α by cell viability assay, Hoechst33258 staining, and detection of caspase-3 and poly(ADP-ribose)- polymerase (PARP). This study shows the involvement of β2-GPI in the regulation of RhoGDI-α, Rac1, F-actin organization, and apoptosis. The result may lay the foundation for future refinements in the exploration of novel function of β2-GPI.

1. Abstract Charles University in Prague Faculty of Pharmacy in Hradec Kralove Department of Biophysics and Physical Chemistry Candidate: Miroslav Suchy Supervisor: Ing. Vladimir Kubicek, CSc. Title of Diploma Thesis: Physico-Chemical properties of drugs To test physico-chemical properties of new molecules is necessary during drug development. It could be helpful to understand or predict the pharmacokinetic parametres of a new drug in vivo/in vitro experiments. One of this parameters is a dissociation constant (pK). Dissociation constant is defined as " Number on pH scale, wherein is just fifty percent of molecule in a ionization condition". In real case this number can help us to know where in the gastro-intestinal tract (GIT) the drug will be absorbed. In GIT only molecules exhibiting pK from 3 to 11 could be absorbed. Out of this range it is not possible. In this work I would like to introduce the ways of experimental measurement of pK values. I was working with two methods to measure the pK values of water-soluble compounds. The spectrophotometric method and the potentiometric one. I had to find out, that potentiometric titration is primary method which gets us good and accurate results. Based on my measurement I evaluated the spectrophotometric method as the secondary method. Spectrophotometric method...

碩士
國立陽明大學
生物藥學研究所
101
Megakaryocytes are the precursors of platelets and thus play an essential role in blood clotting. K562 is a human leukemia cell line that can be induced by PMA (phorbol 12-myristate 13-acetate) to undergo megakaryocytic (MK) differentiation and has been used as a cell model for studying MK differentiation. The Rho family belongs to the small GTPase superfamily and GDP-dissociation inhibitor α (RhoGDIα) suppresses the activity of Rho. Our previous study has shown that RhoGDIα promoted MK differentiation. RhoGDIα has been reported to contain three di-methylated arginines (R111, R152 and R180) however their function is not reported. In addition, our previous results also showed that protein arginine methyltransferase 6 (PRMT6) played a positive role in MK differentiation. This study thus aimed to investigate the functional role of arginine methylation of RhoGDIα and whether PRMT6 mediates methylation of RhoGDIα. In this study, the arginine residues (R111, R152 and R180) were mutated to lysines to mimic the non-methylated state. By ectopic expression, my results showed that single, double and triple mutations lost, to different extent, their stimulatory effects on MK differentiation of K562 cells. Besides R180K, all the mutants appeared to have a dominant negative effect. In the RhoGDIα knockdown (KD) cells, R111K and R152K single mutants still promoted MK differentiation however to a lower degree than wild type did. R111/152K and R111/152/180K double mutants completely lost their stimulatory effects. R111/180K and R152/180K had a similar effect to R111K and R152K single mutants. Together, these results suggest methylation on R111 and R152 plays a more significant role than R180 in promoting MK differentiation. Overexpression of PRMT6 in RhoGDIα KD cells could no longer promoted MK differentiation. When co-expressed with RhoGDIα, PRMT6 regains its ability to promote differentiation in RhoGDIa knockdown cell; while co-expression with RhoGDIα R111/152K did not help regaining the ability. Notably, PRMT6 methylated RhoGDIα in in vitro methylation. These results suggest that PRMT6 may be responsible for methylation of R111 and R152 of RhoGDIα which then promote PMA-induced megakaryocytic differentiation of K562 cells. This study provides links suggesting a positive role of RhoGDIα arginine methylation in MK differentiation.

Laboratory tests have been performed using a stirred cell where SI and SII gas hydrates have been formed under the presence of the kinetic inhibitor Poly Vinyl Caprolactam (PVCap) and INHIBEX. The latter is a mixture containing 50wt% PVCap 2k and 50wt% butyl glycol. The effect of PVCap is enhanced by the presence of butyl glycol; the latter acts as a synergist for the former. Dissociation temperatures were obtained and compared for hydrates formed 1) in presence of PVCap and 2) in presence of INHIBEX. The effect of INHIBEX concentration on the temperature of dissociation was also investigated. Systems containing INHIBEX dissociated at lower temperatures than the corresponding systems with only PVCap present. Furthermore, 3000 ppm INHIBEX mixtures were found to have higher dissociation temperatures than 1500 ppm INHIBEX mixtures.

碩士
國立陽明大學
生物藥學研究所
99
The mitogen-activated protein kinase (MAPK) pathways regulate various cellular functions, including differentiation. Activation of Erk MAPK pathway promotes megakaryocytic (MK) differentiation and p38 MAPK pathway plays a negative role in MK differentiation. K562 is a multipotent human leukemia cell line which can be induced to differentiate into various lineages including megakaryocytes. Upon PMA (phorbol 12-myristate 13-acetate) treatment, K562 cells display characteristics of MK and are often used as a model cell line. Our previous study demonstrated that PRMT1 (protein arginine methyltransferase 1) inhibited PMA-induced MK differentiation of K562 cells via activation of p38? MAPK. However, the molecular mechanism is unclear. The activity of the p38 MAPK pathway is regulated by the upstream MAPKK and MAPKKK and small G proteins such as Rho family. The Rho GDP-dissociation factor ? (RhoGDI?? is known to inhibit activity of Rho GTPases and has been shown to contain three arginine residues that can be dimethylated. This study showed that RhoGDI? plays a positive role in PMA-induced MK differentiation of K562 cells as demonstrated by changes in cytological characteristics. Activation of p38 was enhanced in RhoGDI? knockdown cells by Western blot analysis. Suppression of MK differentiation in RhoGDI? knockdown cells was reverted upon treatment of p38 inhibitor (SB203580). RhoGDI? could reverse the MK differentiation in p38β knockdown cells but not in p38? knockdown cells. In context with PRMT1, promotion of MK differentiation by RhoGDI? was reversed. Mutations at Arg111 or Arg152, which are known to be methylated in cells, abolished the promotion of MK differentiation by RhoGDI?? Together, our results suggest, for the first time, that RhoGDI? and the potential role of methylation regulates PMA-induced megakaryocytic differentiation of K562.

The inhibitor and steam injection methods have been examined using a laboratory-prepared methane hydrate bearing sediment. New experimental apparatuses have been designed and constructed. In the case of inhibitor injection, the measurement of gas production vs. time suggested that the inhibitor increased dissociation rate. Core temperature decreased upon the inhibitor injection, in contrast to that in the case of pure water injection. The observed pressure differentials between the inlet and outlet of the core sample suggest that the inhibitor effectively prevented the hydrate reformation within the dissociating core sample. In the case of steam injection coupled with depressurization, it can be seen that the effect of steam (or hot water) injection was clear in the later stage of dissociation, compared with that in the case of depressurization alone. The inner (core) temperature change indicates that the coupling of depressurization and steam injection induces MH dissociation from upstream and downstream to the center of the sample. However, it starts from an upstream region and continues downstream steadily in the case of steam (hot water) injection alone.

The goal of this study was to characterize the binding sites on the surface of wheat roots, Triticum turgidum, involved in the adsorption of protons and metals, and quantify the thermodynamic constants needed for a surface complexation model to predict metal binding. The adsorption of protons, Cd(II), Cu(II), and Ni(II) to the root surface as a function of pH and ionic strength in single metal exposure scenarios was quantitatively described using potentiometric titrations, batch metal adsorption experiments, and the least squares fitting program FITEQL. Model predictions from single metal exposures were compared to measured metal adsorption concentrations when roots were exposed to binary and ternary combinations of the metals. Proton dissociation was a function of three discrete monoprotic acid sites on the root surface with log proton dissociation constants of -4.50, -6.23, and -7.37 respectively, upon which varied ionic strength had no effect. The total proton binding capacities for the three sites were 2.58 x 10-4, 1.29 x 10-4, and 2.58 x 10-4 M, respectively. Metal complexation was best described by a two-site model having conditional stability constant log values of 3.04 and 3.30 for Cd(II), 3.21 and 3.25 for Cu(II), and 2.83 and 2.84 for Ni(II) at ionic strength 0.01M. At ionic strength 0.1 M the conditional stability constants log values were 2.37 and 3.36 for Cd(II), 3.11 and 2.56 for Cu(II), and 2.18 and 3.00 for Ni(II). When roots were exposed to binary or ternary mixtures of the metals, the two monoprotic acid single metal model did not provide ideal fits to the data indicating that adsorption in a metal mixture scenario cannot be considered additive and is dependent on the combination of metals present in the exposure environment. The experimentally determined proton dissociation constants and metal stability constants could be used in commercial geochemical speciation programs such as Visual MINTEQ to predict metal adsorption to plants.
Natural Sciences and Engineering Research Council of Canada, The Mining Association of Canada, Ontario Power Generation, Environment Canada.

The dependencies of electrophoretic mobility on pH were measured for a set of 14 markers used for isoelectric focusing that were developed by the group of Šlais and that are based on substitutions on the nitrophenol core, and for a kit consisting of 5 pI markers developed by Shimura, which have an oligopeptide structure. The dissociation constants and limiting electrophoretic mobilities of these compounds were obtained from the dependencies with the use of the program AnglerFish. The isoelectric point values of the compounds were consequently calculated using the obtained data. A comparison of the obtained pI values with the values that have been declared in literature, albeit gained by different analytical methods, has been made. Key Words capillary zone electrophoresis, isoelectric focusing, pI markers, isoelectric point, thermodynamic dissociation constant, limiting ionic mobility

Knowledge of the dissociation constants of the ionizable protons of weak acids in aqueous media is of fundamental importance in many areas of chemistry and biochemistry. The pKa value, or equilibrium dissociation constant, of a molecule determines the relative concentration of its protonated and deprotonated forms at a specified pH and is therefore an important descriptor of its chemical reactivity. Considerable efforts have been devoted to the determination of pKa values by deferent experimental techniques. Although in most cases the determination of pKa values from experimental is straightforward, there are situations where interpretation is difficult and the results ambiguous. It is, therefore, not surprising that the capability to provide accurate estimates of the pKa value has been a central goal in theoretical chemistry and there has been a large effort in developing methodologies for predicting pKa values for a variety of chemical systems by differing quantum chemical techniques. A prediction accuracy within 0.5 pKa units of experiment is the desirable level of accuracy. This is a non-trivial exercise, for an error of 1 kcal/mol in estimates of the free energy value would result in an error of 0.74 pKa units. In this thesis ab initio Car-Parrinello molecular dynamics (CPMD) has been used for investigating the Brϕnsted acid-base chemistry of weak acids in aqueous solution. A key issue in any dissociation event is how the solvating water molecules arrange themselves spatially and dynamically around the neutral and dissociated acid molecule. Ab initio methods have the advantage that all solvent water molecules can, in principle, be con- sidered explicitly. One of the factors that has inhibited the widespread use of ab initio MD methods to study the dissociation reaction is that dissociation of weak acids are rare events that require extremely long simulation times before one is observed. The metady- namics formalism provides a solution to this conundrum by preventing the system from revisiting regions of configuration space where it has been in the past. The formalism allows the system to escape the free-energy minima by biasing the dynamics with a history dependent potential (or force) that acts on select degrees of freedom, referred to as collective variables. The bias potentials, modeled by repulsive inverted Gaussians that are dropped during propagation, drive the system out of any free-energy minima and allow it to explore the configuration space by a relatively quick and efficient sampling. The the- sis deals with a detailed investigation of the Brϕnsted acid-base chemistry of weak acids in aqueous solutions by the CPMD-metadynamics procedure. In Chapter 1, current approaches for the theoretical estimation of pKa values are summarized while in Chapter 2 the simulation methodology and the metadynamics sampling techniques used in thisstudy are described. The potential of the CPMD-metadynamics procedure to provide estimates of the acid dissociation constant (pKa) is explored in Chapter 3, using acetic acid as a test sys- tem. Using the bond-distance dependent coordination number of protons bound to the dissociating carboxylic groups as the collective variable, the free-energy profile for the dissociation reaction of acetic acid in water was computed. Convergence of the free-energy profiles and barriers for the simulations parameters is demonstrated. The free-energy profiles exhibit two distinct minima corresponding to the dissociated and neutral states of the acid and the deference in their values provides the estimate for pKa. The estimated value of pKa for acetic acid from the simulations, 4.80, is in good agreement with the experiment at value of 4.76. It is shown that the good agreement with experiment is a consequence of the cancellation of errors, as the pKa values are computed as the difference in the free energy values at the minima corresponding to the neutral and dissociated state. The chapter further explores the critical factors required for obtaining accurate estimates of the pKa values by the CPMD-metadynamics procedure. It is shown that having water molecules sufficient to complete three hydration shells as well as maintaining water density in the simulation cell as close to unity is important. In Chapter 4, the CPMD-metadynamics procedure described in Chapter-3 has been used to investigate the dissociation of a series of weak organic acids in aqueous solutions. The acids studied were chosen to highlight some of the major factors that influence the dissociation constant. These include the influence of the inductive effect, the stabilization of the dissociated anion by H-bonding as well as the presence of multiple ionizable groups. The acids investigated were aliphatic carboxylic acids, chlorine-substituted carboxylic acids, cid and trans-butenedioic, the isomers of hydroxybenzoic acid and phthalic acids and its isomers. It was found that in each of these examples the CPMD-metadynamics procedure correctly estimates the pKa values, indicating that the formulism is capable of capturing these influences and equally importantly indicating that the cancellation of errors is indeed universal. Further, it is shown that the procedure can provide accurate estimates of the successive pKa values of polypro tic acids as well as the subtle deference in their values for deterrent isomers of the acid molecule. Changes in protonation-deprotonation of amino acid residues in proteins play a key role in many biological processes and pathways. It is shown that CPMD simulations in conjunction with metadynamics calculations of the free energy profile of the protonation- deprotonation reaction can provide estimates of the multiple pKa values of the 20 canonical α-amino acids in aqueous solutions in good agreement with experiment (Chapter 5). The distance-dependent coordination number of the protons bound to the hydroxyl oxygen of the carboxylic and the amine groups is used as the collective variable to explore the free energy profiles of the Brϕnsted acid-base chemistry of amino acids in aqueous solutions. Water molecules, sufficient to complete three hydration shells surrounding the acid molecule were included explicitly in the computation procedure. The method works equally well for amino acids with neutral, acidic and basic side chains and provides estimates of the multiple pKa values with a mean relative error with respect to experimental results, of 0.2 pKa units. The tripeptide Glutathione (GSH) is one of the most abundant peptides and the major repository for non-protein sulfur in both animal and plant cells. It plays a critical role in intracellular oxidative stress management by the reversible formation of glutathione disulfide with the thioldisulfide pair acting as a redox buffer. The state of charge of the ionizable groups of GSH can influences the redox couple and hence the pKa value of the cysteine residue of GSH is critical to its functioning. In Chapter 6, it has been reported that ab initio Car-Parrinello Molecular Dynamics simulations of glutathione solvated by 200 water molecules, all of which are considered in the simulation. It is shown that the free-energy landscape for the protonation - deprotonation reaction of the cysteine residue of GSH computed using metadynamics sampling provides accurate estimates of the pKa and correctly predicts the shift in the dissociation constant values as compared to the isolated cysteine amino acid. The dissociation constants of weak acids are commonly determined from pH-titration curves. For simple acids the determination of the pKa from the titration curves using the Henderson-Hasselbalch equation is relatively straightforward. There are situations, however, especially in polypro tic acids with closely spaced dissociation constants, where titration curves do not exhibit clear inflexion and equivalence stages and consequently the estimation of multiple pKa values from a single titration curve is no longer straightfor- ward resulting in uncertainties in the determined pKa values. In Chapter 7, the multiple dissociation constant of the hexapeptide glutathione disulfide (GSSG) with six ionizable groups and six associated dissociation constants has been investigated. The six pKa values of GSSG were estimated using the CPMD-metadynamics procedure from the free-energy profiles for each dissociation reaction computed using the appropriate collective variable. The six pKa values of GSSG were estimated and the theoretical pH-titration curve was then compared with the experimentally measured pH-titration curve and found to be in excellent agreement. The object of the exercise was to establish whether interpretation of pH-titration curves of complex molecules with multiple ionizable groups could be facilitated using results of ab initio molecular dynamics simulations.