Injury to the bronchial epithelium in respiratory diseases such as asthma and COPD results in the loss of barrier function and an elevated sensitivity to environmental insults. An increased release of the endogenous cannabinoid, anandamide in response to inhalation of allergen in asthmatic patients has been reported. In contrast, previous clinical trial findings suggest anti-inflammatory and broncho-relaxant properties of the phytocannabinoid, ∆9-tetrahydrocannabinol (THC). The aim of this study was, therefore, to determine the effects of endocannabinoids and phytocannabinoids on bronchial epithelial cell permeability and to investigate the mechanisms involved. Calu-3 human bronchial epithelial cells were cultured at air-liquid interface to allow development of tight junctions. Changes in transepithelial electrical resistance (TEER), a reflection of epithelial permeability, were measured at various time points post-treatment. The endogenous cannabinoid anandamide produced a significant reduction in TEER, which was unaffected by cannabinoid receptor antagonists, but attenuated by URB597, an inhibitor of fatty acid amide hydrolase, and by a combination of cyclooxygenase and lipooxygenase blockade. Subsequent immunoblotting data revealed that the expression of tight junction proteins, occludin and ZO-1, were also reduced by anandamide. Inhibition of ERK activation by MEK1/2 inhibitors, PD98059 and U0126, prevented the anandamide-induced reduction in TEER and prevented the reduction in occludin expression. Thus, ERK activation is likely to mediate these effects by altering the expression of tight junction proteins. Treatment with THC prevented TNFα-induced decrease in TEER and increased in paracellular permeability. CB1 and CB2 receptor-like immunoreactivity was found in Calu-3 cells. Subsequent pharmacological blockade of either cannabinoid receptor inhibited the THC effect. In comparison, stimulation of both or either CB1 or CB2 receptors displayed similar effect to that of THC. Western immunoblotting also revealed reproducible decreases in occludin and ZO-1 expression in TNFα-treated cells, whereas cells pre-incubated with THC alone or in combination with TNFα did not alter expression levels. Phosphorylation of myosin-phosphatase target protein at threonine 696 residue by TNFα was attenuated in the presence of THC, indicating the involvement of RhoA/ROCK cascade. Selective stimulation of either cannabinoid receptor in TNFα-treated cells suggests THC-induced inhibitory effect on RhoA/ROCK signalling was mediated through CB2 receptor, and not CB1. In summary, these data suggest that the reduction in transepithelial resistance by anandamide, indicative of increased epithelial permeability, is caused by its metabolites rather than anandamide itself. Inhibition of anandamide degradation might provide a novel approach to treat airway inflammation. Conversely, THC reverses the reduction in transepithelial resistance caused by TNFα, through an effect at CB1 and CB2 receptors. Hence, THC, or perhaps other cannabinoid receptor ligands may have potential therapeutic roles in inflammation-induced changes in airway epithelial cell permeability, such as asthma and COPD.

Iron containing metalloenzymes are an extremely important class of biocatalysts conserved throughout evolution because of their vital role in the biochemistry of life. Here we discuss a specific class of these enzymes that use molecular oxygen binding to enable there activity. We also attempt to describe synthetic analogues whose chemistry is based on that seen in those natural systems. This dissertation will highlight how computational research can illuminate specific aspects of the reaction mechanisms that these systems catalyse, which in many cases are unable to be understood purely experimentally. We report on two combined QM/MM and density functional theory (DFT) projects, which describe the AlkB demethylation enzyme and the SyrB2 halogenase; both highlight the strengths and weaknesses of each method. Our DFT work on an i-propyl-bis(imino)pyridine, an equatorial tridentate ligand, developed by one of the papers’ co-authors (Badiei, Siegler et al. 2011) exampifies superoxo chemistry based on the dioxygenases. Our other projects focus on monooxygenase catalysed chemistry one based on the biomimic [FeIV(O)(TPA)Cl]+ reports on a halogenase mimic that shows exciting chemoselectivity in halogenation vs. hydroxylation. I also report on publications examining two other biomimetic ligands. A imido-bridged diiron-oxo phtalocyanine complex capable of hydroxylating methane and a nonheme iron system which gives us a good deal of insight into the effects of secondary coordination sphere chemistry [FeII(N4Py2Ph)(NCCH3)](BF4)2. My computational studies have given insight into the chemical properties of metal-oxo oxidants and their reactivity patterns with substrate and have been utilized to explain experimentally observed data.

Cytochrome P450 (P450) enzymes are found in all kingdoms of life, catalysing a wide range of biosynthetic and metabolic processes. They are, in fact, of particular interest in a variety of applications such as the design of agents for the inhibition of a particular P450 to combat pathogens or the engineering of enzymes to produce a particular activity. Bacterial P450BM3 is of particular interest as it is a self-sufficient multi-domain protein with high reaction rates and a primary structure and function similar to mammalian isoforms. It is an attractive enzyme to study due to its potential for engineering catalysts with fast reaction rates which selectively produce molecules of high value.In order to study this enzyme in detail and characterise intermediate species and reactions, the first step was to design a general hybrid quantum mechanical /molecular mechanics (QM/MM) computational method for their investigation. Two QM/MM approaches were developed and tested against existing experimental and theoretical data and were then applied to subsequent investigations.The dissociation of water from the water-bound resting state was scrutinised to determine the nature of the spin conversion that occurs during this transformation. A displacement of merely 0.5 Å from the starting state was found to trigger spin crossing, with no requirement for the presence of a substrate or large conformational changes in the enzyme.A detailed investigation of the sulfoxidation reaction was undertaken to establish the nature of the oxidant species. Both reactions involving Compound 0 (Cpd0) and Compound I (CpdI) confirmed a concerted pathway proceeding via a single-state reactivity mechanism. As the reaction involving Cpd0 was found to be unrealistically high, the reaction proceeds preferentially via the quartet state of CpdI. This QM/MM study revealed that the preferred spin-state and the transition state structure for sulfoxidation are influenced by the protein environment. P450cam and P450BM3 were found to have CpdI species with different Fe-S distances and spin density distributions, and the latter having a larger reaction barrier for sulfoxidation.A novel P450 species, the doubly-reduced pentacoordinated system, was characterised using gas-phase and QM/MM methods. It was discovered to have a heme radical coupled to two unpaired electrons on the iron centre, making it the only P450 species to have similar characteristics to CpdI. Calculated spectroscopic parameters may assist experimentalists in the identification of the elusive CpdI.

Modelling the human eye provides a great challenge in both the field of mathematical medicine and in engineering. Four different problems regarding flow and deformation in the eyeball are considered, showing how changes in both the fluid and solid mechanicsof the human eye contribute to the development of pathological states. Firstly,a mathematical model is presented for the flow of aqueous humour through the trabecular meshwork and into the Schlemm canal. This predicts the intraocular pressure and investigates how this influences primary open angle glaucoma. Secondly, paradigm problems concerning the development of rhegmatogeneous retinal detachment are presented. A two-dimensional model of pressure driven fluid flow between rigid walls, and between one rigid and one moving wall is presented and followed by a three-dimensional model concerning liquefied vitreous humour flow induced by saccadic eye motion. The purpose of these models is to examine the flow behaviour and the deformation of the detached retina. Thirdly, a mathematical model of aqueous humour flow, driven by buoyancy effects through the detached descemet membrane in the anterior chamber, has been developed to analyse the fluid mechanics concerning the progression of descemet membrane detachment. Lastly, mathematical models studying the effects of a tonometer and a scleral buckle on the shape of the eyeball membrane are presented. The modelling of fluid flow in these studies is based on the lubrication theory limit of the Navier-Stokes equations. However, the full Navier-Stokes equations have been used in the development of a three-dimensional model of retinal detachment. In the modelling of the tonometry and scleral buckling the membrane theory of spherical shells has been used. The results of these models predict changes in the intraocular pressure as well as examining the fluid flow behaviour and the deformation of the detached retina. The modelling of descemet membrane detachment is shown to explain the progress of the spontaneous reattachment and redetachment of descemet membrane may be controlled under the correct conditions. The results of the modelling of the tonometer cast doubt on the Imbert-Fick law, but the results of the scleral buckle may prove useful to predict changes in the focal length of the eye when a scleral buckle is present.

No description available.

Les molécules se trouvent très rarement isolées, ceci implique qu'une modélisation de leur environnement doit être faite lors du calcul de propriétés physiques ou chimiques. Il est possible de considérer l'environnement par plusieurs méthodes de chimie théorique. Le modèle du continuum polarisable est un exemple dont les premières applications ont maintenant plus de 30 ans. Ce modèle permet de reproduire l'influence d'un solvant mais n'est pas capable de représenter des milieux fortement anisotropes tels que les macro-molécules. Afin de représenter de tels environnements, des méthodes couplant la mécanique quantique, pour le traitement de la partie d'intérêt chimique ou physique, et la mécanique moléculaire pour la représentation de l'environnement, ont été développées. Cette thèse est consacrée à l'étude de complexes de ruthénium en interaction avec l'ADN. Leurs spectres d'émission présentent des particularités trés intéressantes dues à cette interaction. Nous montrons que les propriétés photophysiques calculées doivent prendre en compte l'environnement. En particulier, nous avons utilisé une méthode permettant de modéliser la réponse électronique de l'environnement lors de transitions électroniques verticales. Les états triplets de ces complexes intercalés entre deux paires de bases de l'ADN sont également étudiés. En effet, les propriétés d'émission sont liées à la nature de ces derniers et il est important de modéliser de façon correcte le double-brin pour comprendre les mécanismes mis en jeu. Nous avons ainsi donné une interprétation physique à l'effet light-switch / Molecules are rarely isolated and a modelisation of their environment must be carried out when computing their physical or chimical properties. Quantum chemistry offers various ways to take into account this environment. For instance, polarizable continuum model is available for more than 30 years. This model is able to reproduce the influence of a solvent upon a solute but while the environment is becoming less isotropic, serious limitations are found for the model. In order to represent such environments, methods coupling quantum mechanics, for the treatment of the physically or chemically interesting part, and molecular mechanics for the environment have been developped. This thesis is dedicated to the study of ruthenium complexes in interaction with DNA. Moreover, their emission spectra are strongly modified by this interaction. We show that the photophysical properties calculated must take into account the environment. Eventually, we used a methodology able to include effects linked to the electronic response of the surroundings when computing vertical transitions. Triplets of these complexes intercalated between 2 DNA base pairs are also studied. Indeed, emission properties are linked to the nature of these and it is necessary to modelize correctly the double-strand to better understand mecanisms involved. The light-switch effect is then elucidated

Neste trabalho estudamos as propriedades estruturais e eletrônicas do CO2 supercrítico, iniciando com a avaliação de campos de força balizados por aplicações anteriores de simulação quântica do tipo Dinâmica Molecular de Born-Oppenheimer (BOMD). A aplicação principal é a descrição do espectro de absorção da paranitroanilina (pNA) em CO2 supercrítico. O CO2 supercrítico pode ser considerado como uma ``alternativa verde para os solventes orgânicos convencionais e a busca por solventes mais seguros, juntamente com a crescente consciência sobre a questão ambiental, tem levado a uma ``química verde com o intuito de se buscar soluções sustentáveis. A princípio estudamos três campos de força tradicionais para o CO2, aplicados na região supercrítica. Estes campos de força podem ser validados por meio de simulação de primeiros principios. Iniciamos considerando a condição supercrítica para o CO2 como T = 315 K, = 0.81 g/cm³ e o campo de força clássico de Zhang e Duan. Depois fizemos uma análise consistindo de uma alteração de cargas e também da geometria do CO2, que seria um caso não linear no qual foi considerado um ângulo (O-C-O) = 176° . O estudo do solvatocromismo da pNA em CO2 supercrítico foi feito considerando todas estas situações descritas para o campo de força, avaliando os resultados experimentais e teóricos já existentes. A simulação gera estruturas usando Monte Carlo e são usadas em cálculos de Mecânica Quântica do tipo DFT (CAM-B3LYP). Por fim, para verificar a importância da geometria do sistema, ou seja, a propriedade estrutural, consideramos uma outra geometria para a pNA, diferente da geometria que utilizamos a princípio nas simulações com o CO2 supercrítico. Essa ``geometria modificada\" da pNA foi obtida de uma simulação existente de Born-Oppenheimer e a utilizamos numa simulação Monte Carlo com o caso não linear para o CO2 supercrítico. Os resultados de todas essas simulações nos indicaram que a alteração das cargas e por consequência a alteração da polarização do solvente, não possui muita importância na mudança do espectro de absorção da pNA. Ao se considerar o CO2 não linear, obtivemos resultados um pouco melhor, mas não muito, comparados com a previsão teórica. Mas os resultados mais significativos são os obtidos para a situação em que utilizamos a geometria modificada da pNA. Uma parte do deslocamento do máximo da banda de absorção no espectro da pNA vem com a contribuição eletrostática da interação soluto-solvente e a outra parte vem da mudança estrutural. / In this work we study the structural and electronic properties of CO2 supercritical starting with the evaluation of force fields based on previous ab initio Born-Oppenheimer molecular dynamics (BOMD). The main application is the description of the absorption spectrum of paranitroanilina (pNA) in supercritical CO2. The supercritical CO2 is considered a ``green alternative\" to conventional organic solvents and the search for safer solvents, along with the increasing awareness of environmental issues has led to the interest in ``green chemistry\", seeking sustainable solutions. At first we studied three traditional force fields for CO2, applied in the supercritical region. These force fields can be validated by first principles simulation. We considered the supercritical condition for CO2 as T=315K, =0.81g/cm³ and the classical force field of Zhang and Duan. We also did an analysis consisting of a change of the atomic point charges and the geometry of CO2, including a non-linear case in which an angle (O-C-O)=176° was considered. The study of the solvatochromism of pNA in supercritical CO2 was made considering all these situations, evaluating the theoretical outcome and the experimental results. The simulation generates structures using Monte Carlo and are used in quantum mechanics calculations of DFT (CAM-B3LYP). To verify the importance of geometry in the system, that is, the structural property, we considered another geometry for the pNA geometry different from that we used initially in the simulations with supercritical CO2. This ``modified geometry\" of pNA was obtained from a previous Born-Oppenheimer simulation and was used in a Monte Carlo simulation with the non-linear case for supercritical CO2. The results of all these simulations indicated that the alterations of charge and thus the change in the polarization of the solvent, has no great importance in the change of the absorption spectrum of the pNA. When considering the nonlinear CO2, we obtained slightly better results. But the most significant results are obtained for the situation in which we use the modified geometry of pNA. Part of the shift in the absorption spectrum of the pNA comes with the electrostatic contribution of solute-solvent interaction and the other part comes from the structural change.

A proteína ribossomal L10 (RP L10) é uma forte candidata a ser incluída na classe de proteínas supressoras de tumor. Também denominada QM, a proteína em questão é conhecida por participar da ligação das subunidades ribossomais 60S e 40S e da tradução de mRNAs. Possui massa molecular entre 24 a 26 kDa e ponto isoelétrico (pI) 10,5. A seqüência da proteína QM é bastante conservada em mamíferos, plantas, invertebrados, insetos e leveduras indicando que esta possui funções críticas na célula. Com função supressora de tumor, a proteína RP L10 foi estudada em linhagens de tumor de Wilm (WT-1) e em células tumorais de estômago, nas quais se observou uma diminuição na quantidade de seu mRNA. Mais recentemente a RP L10 foi encontrada em baixas quantidades nos estágios iniciais de adenoma de próstata e com uma mutação em câncer de ovário, indicando uma participação no desenvolvimento destas doenças. Como proteína, já foi descrito que esta interage com as proteínas c-Jun e c-Yes, inibindo a ação ativadora de fatores de crescimento e divisão celular. Este trabalho tem um papel importante no estabelecimento da expressão desta proteína solúvel, para estudos posteriores que tenham como objetivo avaliar a ação de regiões específicas que atuam na ligação das subunidades ribossomais 60S e 40S e tradução, bem como nas regiões que se ligam a proto-oncogenes. O cDNA para proteína QM foi amplificado por PCR e clonado no vetor de expressão periplásmica p3SN8. A proteína QM foi expressa em E.coli BL21 (DE3) no citoplasma e periplasma bacteriano e na melhor condição, a expressão de QM de bactérias transformadas pelo plasmídeo recombinante p1813_QM em 25°C ou 30°C, a proteína foi obtida solúvel e com quantidad es muito pequenas de contaminantes. Os ensaios de estrutura secundária demonstraram que a proteína QM tem predominância de a-hélice, mas quando do seu desenovelmento, essa condição muda e a proteína passa a ter característica de folhas β. / The ribosomal protein L10 (RP L10) is a strong candidate to be included in the class of tumor suppressor proteins. This protein, also denominated as QM, is known to participate in the binding of ribosomal subunits 60S and 40S and the translation of mRNAs. It has a molecular weight that varies between 24 and 26 kDa and an isoelectric point of (pI) 10.5. The sequence of the protein QM is highly conserved in mammals, plants, invertebrates, insects and yeast which indicates its critical functions in a cell. As a tumor suppressor, RP L10 has been studied in strains of Wilm\'s tumor (WT-1) and tumor cells in the stomach, where was observed a decrease in the amount of its mRNA. More recently, the RP L10 was found in low amounts in the early stages of prostate adenoma and showed some mutation in ovarian cancer, what indicates its role as a suppressor protein in the development of these diseases. It has also been described that this protein interacts with c-Jun and c-Yes inhibiting growth factors and consequently, cell division. This work has an important role on the establishment of soluble expression of QM to give base information for further studies on expression that aim to evaluate the specific regions where it acts binding the 60S and 40S ribossomal subunits and translation, as well as its binding to proto-oncogenes. The cDNA for QM protein was amplified by PCR and cloned into periplasmic expression vector p3SN8. The QM protein was expressed in E. coli BL21 (DE3) in the region of cytoplasm and periplasm, the best condition was obtained from the expression of the recombinant plasmid QM p1813_QM at 25°C or 30°C, the soluble protein was obtained with small amounts of contaminants. The assays of secondary structure showed that the QM protein is predominantly alpha-helix, but when it loses the folding, this condition changes and the protein is replaced by β- sheet feature.

A proteína ribossomal L10 (RP L10) é uma forte candidata a ser incluída na classe de proteínas supressoras de tumor. Também denominada QM, a proteína em questão é conhecida por participar da ligação das subunidades ribossomais 60S e 40S e da tradução de mRNAs. Possui massa molecular entre 24 a 26 kDa e ponto isoelétrico (pI) 10,5. A seqüência da proteína QM é bastante conservada em mamíferos, plantas, invertebrados, insetos e leveduras indicando que esta possui funções críticas na célula. Com função supressora de tumor, a proteína RP L10 foi estudada em linhagens de tumor de Wilm (WT-1) e em células tumorais de estômago, nas quais se observou uma diminuição na quantidade de seu mRNA. Mais recentemente a RP L10 foi encontrada em baixas quantidades nos estágios iniciais de adenoma de próstata e com uma mutação em câncer de ovário, indicando uma participação no desenvolvimento destas doenças. Como proteína, já foi descrito que esta interage com as proteínas c-Jun e c-Yes, inibindo a ação ativadora de fatores de crescimento e divisão celular. Este trabalho tem um papel importante no estabelecimento da expressão desta proteína solúvel, para estudos posteriores que tenham como objetivo avaliar a ação de regiões específicas que atuam na ligação das subunidades ribossomais 60S e 40S e tradução, bem como nas regiões que se ligam a proto-oncogenes. O cDNA para proteína QM foi amplificado por PCR e clonado no vetor de expressão periplásmica p3SN8. A proteína QM foi expressa em E.coli BL21 (DE3) no citoplasma e periplasma bacteriano e na melhor condição, a expressão de QM de bactérias transformadas pelo plasmídeo recombinante p1813_QM em 25°C ou 30°C, a proteína foi obtida solúvel e com quantidad es muito pequenas de contaminantes. Os ensaios de estrutura secundária demonstraram que a proteína QM tem predominância de a-hélice, mas quando do seu desenovelmento, essa condição muda e a proteína passa a ter característica de folhas β. / The ribosomal protein L10 (RP L10) is a strong candidate to be included in the class of tumor suppressor proteins. This protein, also denominated as QM, is known to participate in the binding of ribosomal subunits 60S and 40S and the translation of mRNAs. It has a molecular weight that varies between 24 and 26 kDa and an isoelectric point of (pI) 10.5. The sequence of the protein QM is highly conserved in mammals, plants, invertebrates, insects and yeast which indicates its critical functions in a cell. As a tumor suppressor, RP L10 has been studied in strains of Wilm\'s tumor (WT-1) and tumor cells in the stomach, where was observed a decrease in the amount of its mRNA. More recently, the RP L10 was found in low amounts in the early stages of prostate adenoma and showed some mutation in ovarian cancer, what indicates its role as a suppressor protein in the development of these diseases. It has also been described that this protein interacts with c-Jun and c-Yes inhibiting growth factors and consequently, cell division. This work has an important role on the establishment of soluble expression of QM to give base information for further studies on expression that aim to evaluate the specific regions where it acts binding the 60S and 40S ribossomal subunits and translation, as well as its binding to proto-oncogenes. The cDNA for QM protein was amplified by PCR and cloned into periplasmic expression vector p3SN8. The QM protein was expressed in E. coli BL21 (DE3) in the region of cytoplasm and periplasm, the best condition was obtained from the expression of the recombinant plasmid QM p1813_QM at 25°C or 30°C, the soluble protein was obtained with small amounts of contaminants. The assays of secondary structure showed that the QM protein is predominantly alpha-helix, but when it loses the folding, this condition changes and the protein is replaced by β- sheet feature.

El Premio Nobel de Química de 2013 ha sido otorgado a A. Warshel, M. Levitt y M. Karplus debido al desarrollo de métodos híbridos de cálculo para química computacional. En este artículo se presentará una breve introducción del uso de los métodos de química computacional. Se describirá cómo se desarrollaron, y por qué, los métodos híbridos de cálculo, conocidos como QM/MM (Quantum Mechanics/Molecular Mechanics) para el estudio de sistemas macromoleculares, sobre todo para el caso de su aplicación en enzimas y bioquímica. Finalmente, se comentarán los alcances y expectativas futuras para estos métodos, desarrollados en los años 70. / The 2013 Nobel Prize in chemistry was awarded to A.Warshel, M.Levitt and M.Karplus for their contribution to the development of hybrid methods for computational chemistry. In this article a brief introduction about computational chemistry methods is presented. This paper will show the order in which the QM/MM (Quantum Mechanics/Molecular Mechanics) methods were developed for the study of macromolecular systems and specially their application in enzymes and biochemistry. Finally, the reach and future prospects of these methods originally developed by A. Warshel, M.Levitt and M. Karplus in the seventies will be discussed.