Determination of Biomolecular Interdomain Motions using Nuclear Magnetic Resonance

Biological macromolecules can rearrange interdomain orientations when binding to various partners. Interdomain dynamics serve as a molecular mechanism to guide the transitions between orientations. However, our understanding of interdomain dynamics is limited because a useful description of interdomain motions requires an estimate of the probabilities of interdomain conformations, increasing complexity of the problem.

Staphylococcal protein A (SpA) has five tandem protein-binding domains and four interdomain linkers. The domains enable Staphylococcus aureus to evade the host immune system by binding to multiple host proteins including antibodies. Here, I present a study of the interdomain motions of two adjacent domains in SpA. NMR spin relaxation experiments identified a 6-residue flexible interdomain linker and interdomain motions. To quantify the anisotropy of the distribution of interdomain orientations, we measured residual dipolar couplings (RDCs) from the two domains with multiple alignments. The N-terminal domain was directly aligned by a lanthanide ion and not influenced by interdomain motions, so it acted as a reference frame to achieve motional decoupling. We also applied {\it de novo} methods to extract spatial dynamic information from RDCs and represent interdomain motions as a continuous distribution on the 3D rotational space. Significant anisotropy was observed in the distribution, indicating the motion populates some interdomain orientations more than others. Statistical thermodynamic analysis of the observed orientational distribution suggests that it is among the energetically most favorable orientational distributions for binding to antibodies. Thus, the affinity is enhanced by a pre-posed distribution of interdomain orientations while maintaining the flexibility required for function.

The protocol described above can be applied to other biological systems in general. Protein molecule calmodulin and RNA molecule trans-activation response element (TAR) also have intensive interdomain motions with relative small intradomain dynamics. Their interdomain motions were studied using our method based on published RDC data. Our results were consistent with literature results in general. The differences could be due to previous studies' use of physical models, which contain assumptions about potential energy and thus introduced non-experimental information into the interpretations.

Synthetic Studies of Azulenyl and Pseudoazulenyl Nitrones

Free radicals have been implicated in various pathological conditions such as, stroke, aging and ischemic heart disease (IHD), as well as neurodegenerative diseases like Alzheimer’s, Parkinson’s, and Huntington’s disease. The role of antioxidants in protection from the harmful effects of free radicals has long been recognized. Trapping extremely reactive free radicals and eliminating them from circulation has been shown to be effective in animal models. Nitrone-based free radical traps have been extensively explored in biological systems. Examples include nitrones such as PBN, NXY-059, MDL-101,002, DMPO and EMPO. However, these nitrones have extremely high oxidation potentials as compared to natural antioxidants such as Vitamin E (á-tocopherol), and glutathione. Becker et al. (1995) synthesized novel azulenyl nitrones, which were shown to have oxidation potentials much lower than that of any of the previously reported nitrone based spin traps. Another azulenyl nitrone derivative, stilbazulenyl nitrone (STAZN), was shown to have an even lower oxidation potential within the range of natural antioxidants. STAZN, a second generation free radical trap, was found to be markedly superior than the two most studied nitrones, PBN and NXY-059, in animal models of cerebral ischemia and in an in vitro assay of lipid peroxidation. In this study, a third generation azulenyl nitrone was synthesized with an electron donating group on the previously synthesized STAZN derivative with the aim to lower the oxidation potential even more. Pseudoazulenes, because of the presence of an annular heteroatom, have been reported to possess even lower oxidation potential than that of the azulenyl counterpart. Therefore, pseudoazulenyl nitrones were synthesized for the first time by extracting and elaborating valtrate from the roots of Centranthus ruber (Red valerian or Jupiter’s beard). Several pseudoazulenyl nitrones were synthesized by using a facile experimental protocol. The physical and biological properties of these pseudoazulenyl nitrones can be easily modified by simply changing the substituent on the heteroatom. Cyclic voltammetry experiments have shown that these pseudoazulenyl nitrones do indeed have low oxidation potentials. The oxidation potential of these nitrones was lowered even more by preparing derivatives bearing an electron donating group at the 3-position of the five membered ring of the pseudoazulenyl nitrone.

ENVIRONMENTAL INFLUENCES AND EPIGENETIC MECHANISMS IN RISK FOR DEPRESSION

Genetic and environmental factors interact to influence vulnerability for internalizing psychopathology, including Major Depressive Disorder (MDD). The mechanisms that account for how environmental stress can alter biological systems are not yet well understood yet are critical to develop more accurate models of vulnerability and targeted interventions. Epigenetic influences, and more specifically, DNA methylation, may provide a mechanism by which stress could program gene expression, thereby altering key systems implicated in depression, such as frontal-limbic circuitry and its critical role in emotion regulation. This thesis investigated the role of environmental factors from infancy and throughout the lifespan affecting the serotonergic (5-HT) system in the vulnerability to and treatment of depression and anxiety and potential underlying DNA methylation processes. First, we investigated the contributions of additive genetic vs. environmental factors on an early trait phenotype for depression (negative emotionality) in infants and their stability over time in the first 2 years of life. We provided evidence of the substantial contributions of both genetic and shared environmental factors to this trait, as well as genetically- and environmentally- mediated stability and innovation. Second, we studied how childhood environmental stress is associated with peripheral DNA methylation of the serotonin transporter gene, SLC6A4, as well as long-term trajectories of internalizing behaviours. There was a relationship between childhood psychosocial adversity and SLC6A4 methylation in males, as well as between SLC6A4 methylation and internalizing trajectory in both sexes. Third, we investigated changes in emotion processing and epigenetic modification of the SLC6A4 gene in depressed adolescents before and after Mindfulness-Based Cognitive Therapy (MBCT). The alterations from pre- to post-treatment in connectivity between the ACC and other network regions and SLC6A4 methylation suggested that MBCT may work to optimize the connectivity of brain networks involved in cognitive control of emotion as well as also normalize the relationship between SLC6A4 methylation and activation patterns in frontal-limbic circuitry. Our results from these three studies strengthen the theory that environmental influences are critical in establishing early vulnerability factors for MDD, driving epigenetic processes, and altering brain processes as an individual undergoes treatment, or experiences relapse.

A hierarchical approach to defining marine heatwaves

Marine heatwaves (MHWs) have been observed around the world and are expected to increase in intensity and frequency under anthropogenic climate change. A variety of impacts have been associated with these anomalous events, including shifts in species ranges, local extinctions and economic impacts on seafood industries through declines in important fishery species and impacts on aquaculture. Extreme temperatures are increasingly seen as important influences on biological systems, yet a consistent definition of MHWs does not exist. A clear definition will facilitate retrospective comparisons between MHWs, enabling the synthesis and a mechanistic understanding of the role of MHWs in marine ecosystems. Building on research into atmospheric heatwaves, we propose both a general and specific definition for MHWs, based on a hierarchy of metrics that allow for different data sets to be used in identifying MHWs. We generally define a MHW as a prolonged discrete anomalously warm water event that can be described by its duration, intensity, rate of evolution, and spatial extent. Specifically, we consider an anomalously warm event to be a MHW if it lasts for five or more days, with temperatures warmer than the 90th percentile based on a 30-year historical baseline period. This structure provides flexibility with regard to the description of MHWs and transparency in communicating MHWs to a general audience. The use of these metrics is illustrated for three 21st century MHWs; the northern Mediterranean event in 2003, the Western Australia ‘Ningaloo Niño’ in 2011, and the northwest Atlantic event in 2012. We recommend a specific quantitative definition for MHWs to facilitate global comparisons and to advance our understanding of these phenomena.

A hierarchical approach to defining marine heatwaves

Marine heatwaves (MHWs) have been observed around the world and are expected to increase in intensity and frequency under anthropogenic climate change. A variety of impacts have been associated with these anomalous events, including shifts in species ranges, local extinctions and economic impacts on seafood industries through declines in important fishery species and impacts on aquaculture. Extreme temperatures are increasingly seen as important influences on biological systems, yet a consistent definition of MHWs does not exist. A clear definition will facilitate retrospective comparisons between MHWs, enabling the synthesis and a mechanistic understanding of the role of MHWs in marine ecosystems. Building on research into atmospheric heatwaves, we propose both a general and specific definition for MHWs, based on a hierarchy of metrics that allow for different data sets to be used in identifying MHWs. We generally define a MHW as a prolonged discrete anomalously warm water event that can be described by its duration, intensity, rate of evolution, and spatial extent. Specifically, we consider an anomalously warm event to be a MHW if it lasts for five or more days, with temperatures warmer than the 90th percentile based on a 30-year historical baseline period. This structure provides flexibility with regard to the description of MHWs and transparency in communicating MHWs to a general audience. The use of these metrics is illustrated for three 21st century MHWs; the northern Mediterranean event in 2003, the Western Australia ‘Ningaloo Niño’ in 2011, and the northwest Atlantic event in 2012. We recommend a specific quantitative definition for MHWs to facilitate global comparisons and to advance our understanding of these phenomena.

Transition metal complexes of some N4-phenylsemicarbazones: crystal structures and spectral studies

The work embodied in this thesis was carried out by the author in the Department of Applied Chemistry, CUSAT, Kochi, during the period 2009-2012. The thesis is an introduction to our attempts to evaluate the coordination behavior of some compounds of our interest. The biological activities of semicarbazones and their metal complexes have been an active area of research during the past years because of their significant role in naturally occurring biological systems. Tridentate NNO and ONO semicarbazone systems formed from heterocyclic and aromatic carbonyl compounds and their transition metal complexes are wellauthenticated compounds in this field and their synthesis, crystal structures and spectral studies are well desirable. Hence, we decided to develop a research program aimed at the syntheses, crystal structures and spectral studies of new N4- phenylsemicarbazones derived from 2-formylpyridine and 3-ethoxysalicylaldehyde and their transition metal complexes and new transition metal complexes of 2- benzoylpyridine-N4-phenylsemicarbazone. In addition to various physicochemical methods of analysis, single crystal X-ray diffraction studies were also used for the characterization of the complexes.

Fibronectin/phosphorylcholine coatings on fluorocarboned surfaces: a study upon adsorption and grafting processes

Depuis ces dernières décennies, le domaine des biomatériaux a connu un essor considérable, évoluant de simples prothèses aux dispositifs les plus complexes pouvant détenir une bioactivité spécifique. Outre, le progrès en science des matériaux et une meilleure compréhension des systèmes biologiques a offert la possibilité de créer des matériaux synthétiques pouvant moduler et stimuler une réponse biologique déterminée, tout en améliorant considérablement la performance clinique des biomatériaux. En ce qui concerne les dispositifs cardiovasculaires, divers recouvrements ont été développés et étudiés dans le but de modifier les propriétés de surface et d’améliorer l’efficacité clinique des tuteurs. En effet, lorsqu’un dispositif médical est implanté dans le corps humain, son succès clinique est fortement influencé par les premières interactions que sa surface établit avec les tissus et les fluides biologiques environnants. Le recouvrement à la surface de biomatériaux par diverses molécules ayant des propriétés complémentaires constitue une approche intéressante pour atteindre différentes cibles biologiques et orienter la réponse de l’hôte. De ce fait, l’élucidation de l’interaction entre les différentes molécules composant les recouvrements est pertinente pour prédire la conservation de leurs propriétés biologiques spécifiques. Dans ce travail, des recouvrements pour des applications cardiovasculaires ont été créés, composés de deux molécules ayant des propriétés biologiques complémentaires : la fibronectine (FN) afin de promouvoir l’endothélialisation et la phosphorylcholine (PRC) pour favoriser l’hémocompatibilité. Des techniques d’adsorption et de greffage ont été appliquées pour créer différents recouvrements de ces deux biomolécules sur un polymère fluorocarboné déposé par traitement plasma sur un substrat en acier inoxydable. Dans un premier temps, des films de polytétrafluoroéthylène (PTFE) ont été utilisés en tant que surface modèle afin d’explorer l’interaction de la PRC et de la FN avec les surfaces fluorocarbonées ainsi qu’avec des cellules endothéliales et du sang. La stabilité des recouvrements de FN sur l’acier inoxydable a été étudiée par déformation, mais également par des essais statiques et dynamiques sous-flux. Les recouvrements ont été caractérisés par Spectroscopie Photoéléctronique par Rayons X, immunomarquage, angle de contact, Microscopie Électronique de Balayage, Microscopie de Force Atomique et Spectrométrie de Masse à Ionisation Secondaire à Temps de Vol (imagerie et profilage en profondeur). Des tests d’hémocompatibilité ont été effectués et l’interaction des cellules endothéliales avec les recouvrements a également été évaluée. La FN greffée a présenté des recouvrements plus denses et homogènes alors que la PRC quant à elle, a montré une meilleure homogénéité lorsqu’elle était adsorbée. La caractérisation de la surface des échantillons contenant FN/PRC a été corrélée aux propriétés biologiques et les recouvrements pour lesquels la FN a été greffée suivie de l’adsorption de la PRC ont présenté les meilleurs résultats pour des applications cardiovasculaires : la promotion de l’endothélialisation et des propriétés d’hémocompatibilité. Concernant les tests de stabilité, les recouvrements de FN greffée ont présenté une plus grande stabilité et densité que dans le cas de l’adsorption. En effet, la pertinence de présenter des investigations des essais sous-flux versus des essais statiques ainsi que la comparaison des différentes stratégies pour créer des recouvrements a été mis en évidence. D’autres expériences sont nécessaires pour étudier la stabilité des recouvrements de PRC et de mieux prédire son interaction avec des tissus in vivo.

Nonlinear Dynamics Near the Cell Membrane of Chara Corallina

The phenomenon of patterned distribution of pH near the cell membrane of the algae Chara corallina upon illumination is well-known. In this paper, we develop a mathematical model, based on the detailed kinetic analysis of proton fluxes across the cell membrane, to explain this phenomenon. The model yields two coupled nonlinear partial differential equations which describe the spatial dynamics of proton concentration changes and transmembrane potential generation. The experimental observation of pH pattern formation, its period and amplitude of oscillation, and also its hysteresis in response to changing illumination, are all reproduced by our model. A comparison of experimental results and predictions of our theory is made. Finally, a mechanism for pattern formation in Chara corallina is proposed.

Competition-related factors directly influence preferences for facial cues of dominance in allies

Alliance formation is a critical dimension of social intelligence in political, social and biological systems. As some allies may provide greater ‘leverage’ than others during social conflict, the cognitive architecture that supports alliance formation in humans may be shaped by recent experience, for example in light of the outcomes of violent or non-violent forms intrasexual competition. Here we used experimental priming techniques to explore this issue. Consistent with our predictions, while men’s preference for dominant allies strengthened following losses (compared to victories) in violent intrasexual contests, women’s preferences for dominant allies weakened following losses (compared to victories) in violent intrasexual contests. Our findings suggest that while men may prefer dominant (i.e. masculine) allies following losses in violent confrontation in order to facilitate successful resource competition, women may ‘tend and befriend’ following this scenario and seek support from prosocial (i.e. feminine) allies and/or avoid the potential costs of dominant allies as long-term social partners. Moreover, they demonstrate facultative responses to signals related to dominance in allies, which may shape sex differences in sociality in light of recent experience and suggest that intrasexual selection has shaped social intelligence in humans.

Monitoring pollutants in occupied spaces.

There is increasing evidence of a causal link between airborne particles and ill health and this study monitored the exposure to both airborne particles and the gas phase contaminants of environmental tobacco smoke (ETS) in a nightclub. The present study followed a number of pilot studies in which the human exposure to airborne particles in a nightclub was assessed and the spatio-temporal distribution of gas phase pollutants was evaluated in restaurants and pubs. The work reported here re-examined the nightclub environment and utilized concurrent and continuous monitoring using optical scattering samplers to measure particulates (PM10) together with multi-gas analysers. The analysis illustrated the highly episodic nature of both gaseous and particulate concentrations in both the dance floor and in the bar area but levels were well below the maximum recommended exposure levels. Short-term exposure to high concentrations may however be relevant when considering the possible toxic effects on biological systems. The results give an indication of the problems associated with achieving acceptable indoor air quality (IAQ) in a complex space and identified some of the problems inherent in the design and operation of ventilation systems for such spaces.

Sampling strategies for characterization of neuropeptides using mass spectrometry and functional implications into cell-cell signaling

In this dissertation, there are developed different analytical strategies to discover and characterize mammalian brain peptides using small amount of tissues. The magnocellular neurons of rat supraoptic nucleus in tissue and cell culture served as the main model to study neuropeptides, in addition to hippocampal neurons and mouse embryonic pituitaries. The neuropeptidomcis studies described here use different extraction methods on tissue or cell culture combined with mass spectrometry (MS) techniques, matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI). These strategies lead to the identification of multiple peptides from the rat/mouse brain in tissue and cell cultures, including novel compounds One of the goals in this dissertation was to optimize sample preparations on samples isolated from well-defined brain regions for mass spectrometric analysis. Here, the neuropeptidomics study of the SON resulted in the identification of 85 peptides, including 20 unique peptides from known prohormones. This study includes mass spectrometric analysis even from individually isolated magnocellular neuroendocrine cells, where vasopressin and several other peptides are detected. At the same time, it was shown that the same approach could be applied to analyze peptides isolated from a similar hypothalamic region, the suprachiasmatic nucleus (SCN). Although there were some overlaps regarding the detection of the peptides in the two brain nuclei, different peptides were detected specific to each nucleus. Among other peptides, provasopressin fragments were specifically detected in the SON while angiotensin I, somatostatin-14, neurokinin B, galanin, and vasoactive-intestinal peptide (VIP) were detected in the SCN only. Lists of peptides were generated from both brain regions for comparison of the peptidome of SON and SCN nuclei. Moving from analysis of magnocellular neurons in tissue to cell culture, the direct peptidomics of the magnocellular and hippocampal neurons led to the detection of 10 peaks that were assigned to previously characterized peptides and 17 peaks that remain unassigned. Peptides from the vasopressin prohormone and secretogranin-2 are attributed to magnocellular neurons, whereas neurokinin A, peptide J, and neurokinin B are attributed to cultured hippocampal neurons. This approach enabled the elucidation of cell-specific prohormone processing and the discovery of cell-cell signaling peptides. The peptides with roles in the development of the pituitary were analyzed using transgenic mice. Hes1 KO is a genetically modified mouse that lives only e18.5 (embryonic days). Anterior pituitaries of Hes1 null mice exhibit hypoplasia due to increased cell death and reduced proliferation and in the intermediate lobe, the cells differentiate abnormally into somatotropes instead of melanotropes. These previous findings demonstrate that Hes1 has multiple roles in pituitary development, cell differentiation, and cell fate. AVP was detected in all samples. Interestingly, somatostatin [92-100] and provasopressin [151-168] were detected in the mutant but not in the wild type or heterozygous pituitaries while somatostatin-14 was detected only in the heterozygous pituitary. In addition, the putative peptide corresponding to m/z 1330.2 and POMC [205-222] are detected in the mutant and heterozygous pituitaries, but not in the wild type. These results indicate that Hes1 influences the processing of different prohormones having possible roles during development and opens new directions for further developmental studies. This research demonstrates the robust capabilities of MS, which ensures the unbiased direct analysis of peptides extracted from complex biological systems and allows addressing important questions to understand cell-cell signaling in the brain.

Host cellular regulatory networks in dengue virus-human interactions

Dengue fever is one of the most important mosquito-borne diseases worldwide and is caused by infection with dengue virus (DENV). The disease is endemic in tropical and sub-tropical regions and has increased remarkably in the last few decades. At present, there is no antiviral or approved vaccine against the virus. Treatment of dengue patients is usually supportive, through oral or intravenous rehydration, or by blood transfusion for more severe dengue cases. Infection of DENV in humans and mosquitoes involves a complex interplay between the virus and host factors. This results in regulation of numerous intracellular processes, such as signal transduction and gene transcription which leads to progression of disease. To understand the mechanisms underlying the disease, the study of virus and host factors is therefore essential and could lead to the identification of human proteins modulating an essential step in the virus life cycle. Knowledge of these human proteins could lead to the discovery of potential new drug targets and disease control strategies in the future. Recent advances of high throughput screening technologies have provided researchers with molecular tools to carry out investigations on a large scale. Several studies have focused on determination of the host factors during DENV infection in human and mosquito cells. For instance, a genome-wide RNA interference (RNAi) screen has identified host factors that potentially play an important role in both DENV and West Nile virus replication (Krishnan et al. 2008). In the present study, a high-throughput yeast two-hybrid screen has been utilised in order to identify human factors interacting with DENV non-structural proteins. From the screen, 94 potential human interactors were identified. These include proteins involved in immune signalling regulation, potassium voltage-gated channels, transcriptional regulators, protein transporters and endoplasmic reticulum-associated proteins. Validation of fifteen of these human interactions revealed twelve of them strongly interacted with DENV proteins. Two proteins of particular interest were selected for further investigations of functional biological systems at the molecular level. These proteins, including a nuclear-associated protein BANP and a voltage-gated potassium channel Kv1.3, both have been identified through interaction with the DENV NS2A. BANP is known to be involved in NF-kB immune signalling pathway, whereas, Kv1.3 is known to play an important role in regulating passive flow of potassium ions upon changes in the cell transmembrane potential. This study also initiated a construction of an Aedes aegypti cDNA library for use with DENV proteins in Y2H screen. However, several issues were encountered during the study which made the library unsuitable for protein interaction analysis. In parallel, innate immune signalling was also optimised for downstream analysis. Overall, the work presented in this thesis, in particular the Y2H screen provides a number of human factors potentially targeted by DENV during infection. Nonetheless, more work is required to be done in order to validate these proteins and determine their functional properties, as well as testing them with infectious DENV to establish a biological significance. In the long term, data from this study will be useful for investigating potential human factors for development of antiviral strategies against dengue.

Studies on the synthesis of novel PP2A inhibitors and a GPCR detergent

Chapter 1 While targeting kinases in oncology research has been explored extensively, targeting protein phosphatases is currently in its infancy. However, a number of pharmaceutical companies are currently looking to expand their research efforts in this area. PP2A has been shown to down-regulate ERK5, a mitogen-activated protein kinase (MAPK) that has been shown to be important in driving the invasive phenotype of prostate cancer. Fostriecin and its related structural analogues PD 113,270 and 113,271 have been shown to inhibit a mitotic entry checkpoint in cell growth through the potent and selective inhibition of protein phosphatases PP1, PP2A, and PP4 (IC50 of 45 μM, 1.5 nM, and 3 nM respectively). Fostriecin is one of the most selective protein phosphatase inhibitors disclosed to date with a 104 fold selectivity for PP2A/PP4 versus PP1. Unfortunately, fostriecin and its analogues are very unstable, and this instability has effectively prevented them from being used as effective therapeutic leads. The microcystins and nodularins on the other hand, exhibit significant inhibitory activity against PP1 and PP2A (IC50 = 26 pM and 1.8 nM respectively), but their high toxicity has prevented any therapeutic application. Truncation of the ADDA chain from these polypeptides completely attenuates PP inhibitory activity. Simpler analogues incorporating the N-acylated ADDA chain and D-Ala retain moderate activity against PP1 and PP2A (IC50 = 1.0 μM and 0.17 μM respectively). The generation of a new series of fostriecin analogues to further expand its structure-activity relationship is envisaged with a view to creating new more stable PP2A inhibitors. It was hoped that by incorporating some of the more stable structural features of ADDA into fostriecin that stability and activity could be reconciled. With that in mind a series of PP2A inhibitors were synthesised and biologically evaluated. Chapter 2 GPCRs are an important area of research and are the targets of a quarter of the drugs on the market (2005). As a result, GPCRs continue to be at the forefront of research in both small and large drug companies. However one of the difficulties in studying this diverse class of membrane proteins is their tendency to denature in aqueous solution. As a result there is a pressing need to develop new detergents to solubilise, stabilise and crystallise GPCRs in their native form for further study. Cholesterol analogues have been shown to be important for stabilising membrane proteins and preventing their thermal inactivation. In addition the β2-adrenergic receptor, a GPCR membrane protein, has been crystallised in the active state with two cholesterol molecules bound between the I, II, III and IV helices of the protein. This appears to represent a distinct cholesterol binding pocket on the membrane protein that is speculated to be conserved across up to 44% of the rhodopsin class of GPCRs. CHOBIMALT is a cholesterol-based detergent that has been shown to exhibit promising GPCR-stabilising properties. When benchmarked against other cholesterol based detergents it was found to be superior to all others tested except for cholesteryl hemisuccinate.1 CHOBIMALT has an aggregation number of roughly 200 and forms 210 ± 30 kDa micelles, which are significantly larger than those of most detergents used for biological systems which is likely due to the packing constraints associated with CHOBMALT’s large polar headgroup.2 As a result, CHOBIMALT is used mostly as an additive to other commercially available detergents in order to decrease micelle size. A branched dimaltoside motif is common in recently synthesised detergents by Chae and co-workers. These detergents have shown promising detergent properties, for example the maltose neopentyl glycol (MNG) detergent synthesised by Chae. This branched dimaltoside detergent was shown to be able to solubilise and stabilise the very labile light harvesting complex I (LHI) from Rhodopsin capsulatus in its active form for 20 days with little loss of protein conformation.3 A cholesterol-based detergent was envisaged that combines the cholesterol framework of CHOBIMALT but replaces its linear tetrasaccharide with a branched dimaltoside. This detergent would then be investigated to assess its ability to solubilise, stabilise and crystallise GPCR proteins. This cholesterol-based detergent (shown below) was eventually synthesised in 9 linear steps from cholesterol.

Identificação dos produtos de oxidação de glicosfingolípidos por espectrometria de massa

O stress oxidativo está associado ao envelhecimento e a inúmeras patologias, nomeadamente a doenças neurodegenerativas e cardiovasculares, e a diversos outros fatores. O stress oxidativo leva à oxidação de importantes biomoléculas como os lípidos e, ao contrário da maior parte dos produtos de oxidação de fosfolípidos e ácidos gordos insaturados (PUFAS), os produtos de oxidação de glicosfingolípidos (GSLs) têm sido escassamente estudados. Os glicosfingolípidos são moléculas muito diversificadas estruturalmente e com importantes funções, essencialmente no sistema nervoso central (SNC) onde estão localizados maioritariamente. Deste modo, alterações na estrutura dos GSLs conduzirão a consequente comprometimento das suas funções e ao possível desenvolvimento de patologias. Assim para identificar as modificações oxidativas que ocorrem em glicosfingolípidos e pressupor consequentes efeitos biológicos nas células sob stress oxidativo, prepararamse sistemas modelo biomiméticos com diferentes GSLs os quais foram expostos a radicais hidroxilo gerados sob condições da reação de Fenton (H2O2 e Fe2+) e as reações foram monitorizadas por diferentes metodologia utilizando a espectrometria de massa. Os resultados obtidos com este estudo permitiram-nos identificar vários produtos de oxidação produzidos durante a oxidação desta classe de lípidos. Os produtos de oxidação observados em comum, em todos os GSLs estudados (C16:0GalCer, C24:1GalCer, C24:1LacCer e GM1) foram as suas correspondentes ceramidas. Estas atuam como agentes pro-apoptóticos e podem in vivo promover a neurodegeneração nas células sob stress oxidativo. Também foi possível observar produtos com inserção de oxigénio junto às duplas ligações ou na cadeia de esfingosina (no caso do GM1) ou na cadeia de ácido gordo monoinsaturada (no caso da C24:1GalCer, C24:1LacCer), corroborando o facto de que ácidos gordos saturados não são susceptíveis à oxidação por radicais. Interessantemente em ambos os GSLs de cadeias glicosiladas compostas com mais de um açúcar (C24:1LacCer e GM1) observou-se a despolimerização oxidativa da porção glicosilada por quebra das correspondentes ligações glicosídicas. Esta degradação leva à formação de GlcCer no caso de oxidação de LacCer ou na formação de outros gangliósidos (GM2, GM3, asialoGM1 e asialoGM2) e glicolípidos (LacCer e GlcCer), no caso de oxidação de GM1. A formação por via radicalar não enzimática destes GSLs leva a distúrbios no perfil lipídico. Previamente, em certas doenças, foram observadas variações na concentração do perfil de gangliósidos e de ceramidas. Estes dados permitem sugerir que em células em condições de stress oxidativo, a acumulação de gangliósidos mais simples e ceramidas poderá ter uma contribuição de produtos da degradação oxidativa dos gangliósidos e GSLs mais complexos. Este trabalho contribui assim para uma melhor compreensão das modificações estruturais que ocorrem em alguns glicosfingolípidos em condições de stress oxidativo. Os produtos de oxidação aqui identificados suportam a sua possível futura deteção em sistemas biológicos.

Produção e extração da enzima anidrase carbônica e de ficobiliproteínas a partir de microalgas

Muito interesse tem sido focado no potencial biotecnológico das microalgas, principalmente devido à identificação de diversas substâncias sintetizadas por estes organismos, dentre elas a anidrase carbônica e as ficobiliproteínas. A anidrase carbônica é uma metaloenzima que catalisa a hidratação reversível do CO2 em bicarbonato com alta eficiência, sendo utilizada para captação de CO2 através de sistemas biológicos. A C-ficocianina e a aloficocianina, corantes naturais, são os dois principais componentes das ficobiliproteínas em cianobactérias e apresentam diversas aplicações dentro da indústria alimentícia, cosmética e farmacêutica. O objetivo principal desta tese foi avaliar a produção e a extração da anidrase carbônica e das ficobiliproteínas a partir de diferentes microalgas. Para isso, primeiramente foi realizado uma investigação da produção da anidrase carbônica pela microalga Dunaliella tertiolecta, onde foi estudada a extração da enzima e sua aplicação em sistemas de captura enzimática de CO2. Posteriormente foi avaliada a produção da enzima ao longo do cultivo de diferentes microalgas marinhas e dulcícolas (Dunaliella tertiolecta, Tetraselmis sueccica, Phaeodactylum tricornutum, Nannochloropsis oculata, Isochysis galbana, Chlorella vulgaris e Scenedesmus obliquus). A produção da enzima e de ficobiliproteínas, também, foi estudada para as cianobactérias Spirulina platensis LEB 52, Spirulina sp. LEB 18 e Synechococcus nidulans. Todos os cultivos foram acompanhados em termos de biomassa e pH. Por último, foi realizado um estudo de extração da enzima de P. tricornutum e extração conjunta da anidrase carbônica e de ficobiliproteínas da cianobactéria S. sp. LEB 18. Os cultivos foram realizados em frascos erlenmeyer contendo os meios Conway (marinhas), BG-11 (dulcícolas) e Zarrouk 20% (cianobactérias). Na avaliação da ruptura celular foram testadas as técnicas de maceração em gral e pistilo, agitação em vórtex com pérolas de vidro, sonicação com pérolas de vidro, homogeneizador ultrassônico, secagem, congelamento e descongelamento e a combinação de tratamentos. Maiores rendimentos de extração da enzima a partir da microalga D. tertiolecta foram obtidos utilizando tratamento ultrassônico, juntamente com baixas concentrações de biomassa úmida (0,1 e 0,2 g/L), e a mesma apresentou potencial para aplicação em processos de captação enzimática do CO2. Durante os cultivos, a microalga C. vulgaris se destacou como maior produtora da enzima anidrase carbônica, atingindo valores de atividade enzimática de 44,0 U/L. As cianobactérias apresentaram valores de atividade entre 41,6 e 45,9 U/L, sendo que a S. sp. LEB 18 foi a que apresentou maiores produções de C-ficocianina e aloficocianina no ponto de máxima atividade volumétrica, 65,9 e 82,2 µg/mL, respectivamente. A enzima extraída da biomassa de S. platensis LEB 52 catalisou a hidratação do CO2 que precipitou na forma de CaCO3. Maiores rendimentos de extração da enzima a partir das microalgas P. tricornutum e S. sp. LEB 18 foram obtidos utilizando homogeneizador ultrassônico, que foram 31,3 U/g e 25,5 U/g, respectivamente. A biomassa de S. sp. LEB 18, também apresentou potencial para a extração de ficobiliproteínas, obtendo- se altas concentrações de C-ficocianina (100,5 mg/g) e aloficocianina (69,9 mg/g). Através dos resultados obtidos, pode-se verificar a potencialidade das microalgas e das cianobactérias para produção da enzima anidrase carbônica e das ficobiliproteínas, biomoléculas de alto valor industrial. Este trabalho apresenta processos eficientes para a extração da enzima e de ficobiliproteínas tanto para escala laboratorial como industrial.