Spelling suggestions: "subject:"biomolecular"" "subject:"fiomolecular""
191 |
Production and Harvest of Microalgae in Wastewater Raceways with Resource RecyclingRoberts, Alexander Colin 01 December 2015 (has links) (PDF)
Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.
A pilot facility was operated with nine CO2-supplemented raceway ponds, each with a 33-m2 surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed primary-clarified municipal wastewater at either a 2-day or 3-day hydraulic residence time (HRT), and one set fed the clarified effluent of the 3-day pond set. This second pond-in-series was operated with a 3-day HRT.
Areal biomass productivity is reported as gross and net, the former based only on biomass in the pond effluents and the latter subtracting the volatile suspended solids in the influent from those in the effluent. An estimate was also made of autotrophic biomass productivity, as differentiated from heterotrophic growth.
Over a year, net productivity averaged 83 metric tons per hectare per year (MT/ha-yr) for the 2-day HRT ponds, 52 MT/ha-yr for the 3-day HRT ponds, and 44 MT/ha-yr for the 3-day HRT ponds receiving clarified effluent of the first set of 3-day HRT ponds (i.e., recycled water). The lower net productivity of the pond receiving water recycling was attributed to two factors. First, the relatively high influent suspended solids concentrations were subtracted from the effluent suspended solids concentrations before net productivity was calculated. Second, the recycled water contained less soluble organic matter than the primary-clarified wastewater leading to less heterotrophic biomass production. The accumulation of inhibitory allelochemicals is a possible third cause of lower productivity
, but no specific information was collected on allelopathy.
Algae were harvested from pond effluent by sedimentation, with harvest efficiency most affected by the extent of natural bioflocculation occurring in the ponds. Some forms of bioflocculation are thought to be mediated by bacteria, which often make-up a substantial fraction of the settled flocs. Pond samples settled in 1-L Imhoff cones averaged/L total suspended solids after 24 hours of settling; but all ponds fell short of meeting an averaged/L total suspended solids after a 2 hour interval which would be ideally achieved for wastewater effluent. No relationship was seen between settling performance and the bacterial content of flocs.
Soluble carbonaceous biochemical oxygen demand (scBOD5) removal by the raceway ponds was sufficient to meet wastewater treatment requirements year around. Influent scBOD5 concentrations averaged 83 mg/L, and the effluent averaged 5.1 mg/L and 4.2 mg/L for the 2-day and 3-day HRT pond sets, respectively.
The variable with the greatest influence on productivity in all pond sets, and settling performance in the recycled water pond set, was season (i.e., co-correlated variables of solar insolation and pond temperature). Neither productivity nor settling appeared to be related to prominent algae genera or prevalence of grazers.
The high net productivity achieved with a growth medium of primary clarifier effluent and the generally high settleability of algal-bacterial flocs indicate a good potential for algae wastewater treatment and biofuel production. However, the settling of algae grown on recycled water needs improvement to achieve the full potential of wastewater-grown algae biofuel production.
|
192 |
Temperature Influence and Heat Management Requirements of Microalgae Cultivation in PhotobioreactorsMehlitz, Thomas Hagen 01 February 2009 (has links) (PDF)
Microalgae are considered one of the most promising feedstocks for biofuel production for the future. The most efficient way to produce vast amounts of algal biomass is the use of closed tubular photobioreactors (PBR). The heat requirement for a given system is a major concern since the best algae growth rates are obtained between 25-30 °C, depending on the specific strain. A procedure to determine temperature influence on algal growth rates was developed for a lab-scale PBR system using the species Chlorella. A maximum growth rate of 1.44 doublings per day at 29 °C (optimal temperature) was determined. In addition, a dynamic mathematical model was developed to simulate heating and cooling energy requirements of tubular PBRs for any desired location. Operating the model with hourly weather data as input, heating and cooling loads can be calculated early in the planning stage of a project. Furthermore, the model makes it possible to compare the operation inside a greenhouse to the outdoor operations, and consequently provides fundamental information for an economic feasibility study. The best configuration for a specific location can be evaluated easily. The model was exemplary tested for a hypothetical 100,000 l photobioreactor located in San Luis Obispo, California, U.S.A. Average algae productivity rates of 23% and 67% for outdoor and indoor PBR operations, respectively, were obtained. Actual energy loads (heating and cooling) needed to maintain the PBR at optimal temperature were determined and compared. Sensitivity analyses had been performed for abrupt temperature and solar radiation steps, PBR row distances, ground reflectivities, and ventilation rates of the greenhouse. An optimal row distance of 0.75 m was determined for the specific PBR. The least amount of energy was needed for a ground reflectivity of 20%. The ventilation rate had no major influence on the productivity rate of the system. Results demonstrated the importance of a simulation model as well as the economic impact of a sophisticated heat management system. Energy savings due to an optimized heat management system will eventually increase proficiency of the systems, which will support a new sustainable industry and future developmental potential.
|
193 |
Cellular and Computational Evaluation of the Structural Pharmacology of Delta Opioid ReceptorsYazan J Meqbil (14210360) 05 December 2022 (has links)
<p>G-protein coupled receptors (GPCRs) are membrane proteins that constitute ~30% of the FDA-approved drug targets. Opioid receptors are a subtype of GPCRs with four different receptor types: delta, kappa, mu, and nociception opioid receptors. Opioids such as morphine have been used for thousands of years and are deemed the most effective method for treating pain. However, opioids can have detrimental effects if used illicitly or over an extended period of time. Intriguingly, most of the clinically used opioids act on the mu opioid receptor (µOR). Hence, efforts in recent decades have focused on other opioid receptors to treat pain and other disorders. The delta opioid receptor (δOR) is one of four opioid receptors expressed in the central and peripheral nervous system. The δOR has attracted much attention as a potential target for a multitude of diseases and disorders including substance and alcohol use disorders, ischemia, migraine, and neurodegenerative diseases. However, to date, no δOR agonists, or drugs that act directly at the δOR, have been successful as clinical candidates. Nonetheless, the therapeutic potential of the δOR necessitates the targeting its pharmacologically. In this dissertation, I highlight peptide-based modulation as well as the identification of novel agonists at the δOR. I report research findings in the context of biased agonism at δOR, which is a hypothesized cellular signaling mechanism with potential therapeutic benefits. The focus on this work is the molecular determinants of biased agonism, which were investigated using a combination of cellular and computational approaches. </p>
|
194 |
TYROSINE PHOSPHORYLATION MEDIATED REMODELING OF THE ERYTHROCYTE MEMBRANE IN SICKLE CELL DISEASEJohn M Hausman (14043162) 04 November 2022 (has links)
<p>The pathological hallmarks of sickle cell disease originate from a single mutation of the beta hemoglobin gene resulting in a valine at position 6 instead of the canonical glutamic acid. This small change perpetuates many factors, manifesting into chronic embolic processes in the microvasculature, causing painful vaso-occlusive episodes and eventual organ failure. There have been numerous therapies developed to reduce the mortality of sickle cell ranging from agents to induce production of fetal hemoglobin to chronic blood transfusions. Although each of these options are effective at improving the quality of life for sickle cell patients, they only treat one aspect of the disease and, for some, become ineffective over time. In the hope of producing a better therapy, a better understanding of the pathogenesis of vaso-occlusive episodes is needed. While many models have been offered to account for these vaso-occlusive events, one recently proposed mechanism stems from the elevated tyrosine phosphorylation of the cytoplasmic domain of the major erythrocyte membrane protein, Band 3. Band 3 serves as a hub for many critical proteins in the red cell. It binds ankyrin, which associates the spectrin cortical cytoskeleton to the red cell membrane, deoxygenated hemoglobin, the kinases Wnk1 and OSR1, which regulate cation transport, and a glycolytic enzyme metabolon that regulates the production of ATP and glutathione. When Band 3 is tyrosine phosphorylated, each of these proteins dissociate, causing significant changes to red cell homeostasis. These changes include an accumulation of reactive oxygen species, vesiculation and release of prothrombotic microvesicles, leakage of cell free hemoglobin, and a decrease in cell volume. Normally, Band 3 exists in a predominantly unphosphorylated state, however, in sickle cell disease, Band 3 is abundantly tyrosine phosphorylated. Reduction in the tyrosine phosphorylation of Band 3 has been documented to prevent the release of microvesicles and hemoglobin from sickle cell red blood cells. Because these microvesicles and cell free hemoglobin contribute to the vaso-occlusive episodes in sickle cell patients, inhibiting the mechanism for their release offers a potential therapeutic option. But to accomplish this, the molecular cause for the elevated tyrosine phosphorylation in sickle cell disease must be identified. Since tyrosine phosphorylation is performed by a tyrosine kinase and removed by a tyrosine phosphatase, the elevation in phosphorylation must be due to changes in both of these processes. Unfortunately, the identity and nature of these kinases and phosphatases are poorly understood. In this dissertation, I identified the tyrosine kinases Syk, Lyn, and Src attributed to Band 3</p>
<p>15</p>
<p>phosphorylation that facilitates the release of microvesicles and hemoglobin in sickle cell red blood cells. Inhibition of Syk or one of the two Src family kinases is sufficient to prevent the destabilization of the red blood cell membrane. These kinases function in a hierarchy, where one of the three Src family kinase, Lyn phosphorylates Syk, activating it, and promoting the phosphorylation of Band 3 at tyrosines 8 and 21. Prevention of either phosphorylation event prevents the release of microvesicles and cell free hemoglobin. I also report the identification of PTP1B as the tyrosine phosphatase responsible for maintaining Band 3 in an unphosphorylated state. Interestingly, in sickle cell disease, this tyrosine phosphatase is proteolytically cleaved, resulting in a reduction in dephosphorylating potential. It has been reported previously that PTP1B is a substrate of the calcium dependent protease, calpain and that calpain inhibitors improve the cell morphology of sickle erythrocytes. Inhibition of this proteolytic process may offer an additional therapeutic option for the treatment of sickle cell disease.</p>
|
195 |
CELLULAR AND BEHAVIORAL CHARACTARIZATION OF δ-OPIOID RECEPTOR MEDIATED ß-ARRESTIN SIGNALINGArryn T Blaine (13154670) 26 July 2022 (has links)
<p>The following thesis will focus on understanding the downstream behavioral effects of δORmediated β-arrestinsignaling. δORagonists have been implicated as effective targets for a variety of diseases, however detrimental side effects of opioid-targeting agonists limit their clinical use. δORagonists specifically can induce seizures, however the underlying mechanism contributing to this behavior is unknown. We review this phenomenon in more detail, highlighting current agonists known to induce seizures and potential circuits and pathways involved. Our work suggests β-arrestinsignaling is involved, specifically β-arrestin2 mediated signaling may be largely contributing to δORagonist-induced seizure behavior. As it is possible the β-arrestinisoforms have unique roles in seizure behavior, we also analyzed methods in which to provoke β-arrestinisoform bias of δORtargeting compounds. Though the full mechanism relating δORagonists with seizures remains unknown, our work provides foundational detail of this behavior, implicating the importance of β-arrestinisoform signaling through δOR; allowing for future studies to full define this seizure pathway and develop δORsafer agonists. </p>
|
196 |
Discovering, Understanding, and Targeting Lipid Metabolism and Cytoskeleton Structural Changes in Stress-Adaptive Cancer CellsGil A Gonzalez (19176721) 19 July 2024 (has links)
<p dir="ltr">Cancer biological mechanisms are a vastly researched area in the field, yet they are not well understood in the various contexts in which cancer is found. Cancerous tumors often exist in harsh, stressful environments for normal cells, but cancer cells can thrive in these conditions. The tumor microenvironment (TME) typically has low oxygen levels (hypoxia), high acidity, and low nutrition. Exposure to the TME leads to many metabolic changes in the cells, enabling cancer to continue proliferating and migrating. However, these metabolic changes are not well understood, especially at the single-cell level. The ability to monitor cells in real time to determine the physical characteristics they undergo is critical to understanding the impact of these metabolic changes. Conventional methods focus on determining the genomic and proteomic changes in large numbers of cells, which may be overlooked if the changes are homogeneous across samples. In this work, we demonstrate the power of using multiple imaging techniques in combination with biochemical methods to visualize metabolic changes and determine the causes in various cancer cells under extreme hypoxia conditions.</p><p dir="ltr">The changes in the microtubule network that occur under hypoxia at the single-cell level are not widely researched. The use of confocal fluorescence microscopy can determine microtubule polymerization in conjunction with eGFP-transfected EB3, a protein that assists in microtubule polymerization. We have determined that hypoxic HeLa cells produce finger-like protrusions when exposed to hypoxia that help with cell migration and, ultimately, cancer cell metastasis. The formation of these protrusions is facilitated by localized mitochondria activities in the protrusions.</p><p dir="ltr">The metabolic changes in lipid droplets (LDs) under hypoxia at the single-cell level remain an elusive topic. The use of stimulated Raman spectroscopy (SRS) and coherent anti-Stokes Raman scattering (CARS) can determine the quantity and spatial-temporal distribution of LDs in cancer cells. We have found that LDs redistribute to the endoplasmic reticulum (ER) and increase in intensity in hypoxic MIA PaCa-2 and A549 cells. Time-lapse CARS microscopy revealed a release-accumulate process of these LDs on ER in hypoxia. We also studied the impact of carbon sources on LD formation and found that MIA PaCa2 cells prefer direct lipid uptake while glucose is also essential to reduce lipotoxicity. The use of hyperspectral stimulated Raman scattering (hSRS) also reveals that the content of the LDs changes to include less cholesteryl ester and a decrease in lipid saturation level.</p><p dir="ltr">Collectively, these findings shed new light on the understanding of cytoskeleton dynamics and lipid metabolism in hypoxic conditions. The discoveries made within this research would lead to better treatment strategies for effective treatment of hypoxia-resistant cancer cells.</p>
|
197 |
MASS SPECTROMETRY FOR CHEMICAL REACTIONS: SYNTHESIS, ANALYSIS, AND APPLICATIONSKai-Hung Huang (19649191) 13 September 2024 (has links)
<p dir="ltr">Mass spectrometry (MS) has long been recognized as a technology for bioanalysis. However, this thesis focuses on exploiting mass spectrometry for chemical reactions. The work described here covers the (a) investigation of chemistry at interfaces by MS, (b) utilization of MS to accelerate drug discovery processes, and (c) applications of MS techniques for organic synthesis. MS techniques are used to scrutinize the distinctive chemistry and super acidity mechanisms at the gas/liquid interfaces by reacting carbon dioxide (gas phase) with amines (solution, in droplets). The intriguing trace water effect in creating this unique environment at the interfaces is described. A systematic survey of reactions promoted by glass microspheres at liquid/solid interfaces is conducted, revealing that glass surface can act as strong base to speed up reactions. Additionally, the ability of glass surface to degrade biomolecules is revealed, which has implications for bioanalysis. Desorption electrospray ionization (DESI), an ambient ionization method, can be used as a rapid analytical technique for the direct analysis of complex reaction mixtures or bioassays without sample workup. Moreover, DESI can also be used as a small-scale synthetic tool due to accelerated reactions in generated microdroplets. These characteristics make DESI a core technology for high-throughput (HT) experimentation that prioritizes speed to achieve three major roles. <b>(i) HT reaction screening</b> leverages the reaction acceleration phenomenon for rapid chemical space exploration, especially for the late-stage diversification of drug molecules. The entire process, from sampling the reaction mixture by droplets to on-the-fly chemical transformation during millisecond timescales to analysis by MS, achieves an overall throughput of one reaction per second in an integrated fashion. Diverse chemical transformations for various functional groups were achieved, with over 10<sup>4</sup> reactions explored and over 10<sup>3</sup> analogs identified within three hours. <b>(ii) HT synthesis</b> is achieved using an automated homebuilt array-to-array transfer system. The synthetic system uses DESI microdroplets for transferring reaction mixtures from a precursor array to products on a product array. High conversions of diverse reactions with synthetic throughput of 0.2-0.02 Hz and scale of ng-µg (pmole-nmole) in a spatially resolved manner are demonstrated. Hundreds of modified bioactive molecules are generated in an array format, and the spatial distribution of the products is visualized by mass spectrometry imaging. <b>(iii) HT bioassays</b> are demonstrated by combining the label-free nature of MS with the high-speed analysis of DESI. The contactless feature, with high tolerance towards complex mixtures, allows direct bioassays with minimal sample preparation. An opioid receptor binding assay is described with an evaluation of the binding affinity of synthesized opioid analogs. An on-surface enzymatic assay is developed for measuring the bioactivity of deposited molecules <i>in situ</i>. The consolidation of (i) HT reaction screening, (ii) HT synthesis, and (iii) HT bioassays by a single but versatile technique, HT-DESI, can expedite the early drug discovery process. For applications, MS technologies are utilized to probe reactive intermediates and the reaction mechanisms of palladium-catalyzed coupling reactions. MS is also used to explore chemical reactions for natural products, rapidly generating analogs for bioactivity evaluation and benefiting bioanalysis through the discovery of derivatization reactions. HT tandem MS is demonstrated to be powerful for structural elucidation and reaction site identification.</p>
|
198 |
5’-PHOSPHOROTHIOESTER LINKED CYCLIC DINUCLEOTIDES AS NOVEL STING AGONISTSKofi Simpa Yeboah (20372145) 03 December 2024 (has links)
<p dir="ltr">Over the last century, cancer immunotherapy has become an attractive field due to the popularity of checkpoint blockades and adoptive cell therapy. Though these new frontier therapeutics are effective for certain populations, they’ve had either adverse effects on others or are non-efficacious when used to treat “cold tumors”. Hence, newer strategies are needed to sensitize cold tumors into immune-responsive “hot tumors”, which synergize with checkpoint blockades. The cyclic GMP-AMP synthase-Stimulator of INterferon Genes (cGAS-STING) pathway has been identified as a pathway that can initiate T cell infiltration and turn cold tumors into hot tumors. Therefore, STING agonists have been identified as potential remedies that could help bend the curve to increase the survival rate of cancer patients if combined with anti-PD1 and anti-CTLA4 therapies.</p><p dir="ltr">2’3’-cGAMP is a master regulator of the innate immune system and is produced by cGAS upon cancer deregulation as well as bacterial and viral infection. Although 2’3’-cGAMP is a nanomolar affinity binder to STING and has vast immunostimulatory potential, it is plagued by several limitations that prevent its use in vivo. Most medicinal chemists have focused on making phosphorothioate derivatives which circumvents 2’3’-cGAMP’s limitations, but synthesizing these analogs presents a synthetic challenge. Also, these derivatives are commonly administered via intratumoral injection, which is not an attractive mode of delivery. This dissertation tries to address some of these challenges and provide a newer platform to develop CDN-based STING agonists.</p><p dir="ltr">We describe a novel class of phosphorothioester-linked cyclic dinucleotides (endo-S-CDNs) as excellent STING agonists. Showing through structural-activity relationship (SAR) which groups are tolerated or detrimental for STING binding and cellular activity. Also, determining that these 5’-phosphorothioester-linked CDNs are resistant to cleavage by clinically relevant phosphodiesterases (PDEs). Finally, we discuss how this novel class of CDNs is suitable for subcutaneous dosing to clear tumors in different mouse models.</p>
|
199 |
Touching the Essence of Life : Haptic Virtual Proteins for LearningBivall, Petter January 2010 (has links)
This dissertation presents research in the development and use of a multi-modal visual and haptic virtual model in higher education. The model, named Chemical Force Feedback (CFF), represents molecular recognition through the example of protein-ligand docking, and enables students to simultaneously see and feel representations of the protein and ligand molecules and their force interactions. The research efforts have been divided between educational research aspects and development of haptic feedback techniques. The CFF model was evaluated in situ through multiple data-collections in a university course on molecular interactions. To isolate possible influences of haptics on learning, half of the students ran CFF with haptics, and the others used the equipment with force feedback disabled. Pre- and post-tests showed a significant learning gain for all students. A particular influence of haptics was found on students reasoning, discovered through an open-ended written probe where students' responses contained elaborate descriptions of the molecular recognition process. Students' interactions with the system were analyzed using customized information visualization tools. Analysis revealed differences between the groups, for example, in their use of visual representations on offer, and in how they moved the ligand molecule. Differences in representational and interactive behaviours showed relationships with aspects of the learning outcomes. The CFF model was improved in an iterative evaluation and development process. A focus was placed on force model design, where one significant challenge was in conveying information from data with large force differences, ranging from very weak interactions to extreme forces generated when atoms collide. Therefore, a History Dependent Transfer Function (HDTF) was designed which adapts the translation of forces derived from the data to output forces according to the properties of the recently derived forces. Evaluation revealed that the HDTF improves the ability to haptically detect features in volumetric data with large force ranges. To further enable force models with high fidelity, an investigation was conducted to determine the perceptual Just Noticeable Difference (JND) in force for detection of interfaces between features in volumetric data. Results showed that JNDs vary depending on the magnitude of the forces in the volume and depending on where in the workspace the data is presented.
|
200 |
Structure of bio-macromolecular complexes by solid-state Nuclear Magnetic Resonance / Structure de complexes biologiques macromoléculaires par Résonance Magnétique Nucléaire du solideBarbet-Massin, Emeline 03 May 2013 (has links)
La RMN du solide a récemment émergé en tant que technique très puissante en biologie structurale, permettant de caractériser au niveau atomique des systèmes qui ne peuvent être étudiés par d’autres méthodes. Des protocoles spécifiques à la RMN du solide sont à présent bien établis pour la préparation des échantillons, l’attribution des spectres et l’acquisition de contraintes structurales. Ensemble, ces protocoles ont ouvert la voie aux premières déterminations de structures tridimensionnelles de molécules biologiques à l’état solide avec une résolution atomique, et ce non seulement pour des échantillons protéiques microcristallins, mais également pour des systèmes plus complexes tels que des fibrilles ou des protéines membranaires.La détermination structurale de tels systèmes est cependant encore loin d’être une routine, et des avancées de plus large ampleur sont attendues grâce à des développements aux niveaux méthodologique et matériel. Pour cette raison, une majeure partie du travail présenté dans cette thèse a été consacrée au développement d’expériences à la fois nouvelles et sophistiquées pour améliorer la sensibilité et la résolution des méthodes déjà existantes pour attribuer les spectres et élargir les possibilités offertes par la RMN du solide en vue d’étudier la structure de systèmes protéiques plus larges. Ces développements reposent notamment sur l’utilisation de champs magnétiques très intenses et sur la rotation des échantillons à l’angle magique dans la gamme des très hautes vitesses angulaires. Nous montrons que dans ce cadre, il est possible de concevoir des expériences utilisant uniquement des champs radiofréquences à faible puissance ainsi que d’utiliser des transferts sélectifs, l’acquisition de corrélations à travers les liaisons chimiques et la détection proton.En particulier, nous montrons que des expériences de corrélation homonucléaire reposant sur des transferts scalaires deviennent une alternative compétitive aux expériences basées sur des transferts dipolaires. Deux nouvelles séquences d’impulsion permettant de détecter des corrélations 13C-13C à travers les liaisons chimiques avec une excellente résolution sont présentées; couplées à des transferts 15N-13C, elles permettent l’attribution des résonances de la chaîne principale des protéines avec une grande sensibilité.De plus, nous démontrons qu’il est possible d’obtenir des raies très fines pour les résonances de protons dans des protéines complètement protonées à l’état solide grâce à la rotation à l’angle magique à ultra-haute vitesse, sans avoir recours à la deutération. Dans ce contexte, nous avons développé de nouvelles stratégies permettant d’attribuer rapidement et de façon fiable les résonances des spins 1H, 15N, 13CO, 13CA et 13CB dans différentes classes de protéines, ainsi que pour mesurer des contraintes structurales à partir des distances entre protons. L’approche proposée repose sur la haute sensibilité des protons et accélère donc considérablement les processus d’attribution et de détermination structurale des protéines à l’état solide, comme illustré sur la protéine beta-2-microglobuline.Enfin, nous avons appliqué cette nouvelle approche pour réaliser l’attribution et l’étude structurale et fonctionnelle de trois catégories de complexes protéiques: les fibrilles amyloidogènes formées par beta-2-microglobuline, les nucléocapsides du virus de la rougeole, et les nucléocapsides d’Acinetobacter phage205. Nous avons également utilisé la technique de Polarisation Nucléaire Dynamique pour obtenir des informations sur l’ARN des nucléocapsides du virus de la rougeole.Nous considérons que les résultats présentés dans cette thèse représentent une avancée substantielle dans le domaine de la RMN du solide appliquée à la biologie structurale. Grâce aux progrès actuels dans ce domaine, l’impact de la RMN biomoléculaire à l’état solide promet d’augmenter dans les prochaines années. / Solid-state NMR has recently emerged as a key technique in modern structural biology, by providing information at atomic level for the characterization of a wide range of systems that cannot be investigated by other atomic-scale methods. There are now well established protocols for sample preparation, resonance assignment and collection of structural restraints, that have paved the way to the first three-dimensional structure determinations at atomic resolution of biomolecules in the solid state, from microcrystalline samples to fibrils and membrane-associated systems. These determinations are however still far from being routine, and larger breakthroughs are expected with further methodological and hardware developments. Accordingly, most of the work presented in this thesis consists of the development of new, sophisticated NMR experiments to improve the sensitivity and resolution of the currently existing schemes for resonance assignment and to extend the capabilities of solid-state NMR in terms of structural investigation of proteins for the analysis of large substrates. These developments notably rely on the use of very high magnetic fields and ultra-fast magic-angle spinning (MAS). We show the great potential of this particular regime, which enables the use of low-power experiments and the acquisition of selective cross-polarization transfers, through-bond correlations and 1H-detected correlations.In particular, we show that homonuclear correlation experiments based on through-bond transfers become competitive alternatives to dipolar transfer schemes. Two new pulse sequences that detect sensitive and resolved 13C-13C through-bond correlations are introduced, which coupled to 15N-13C dipolar transfer steps provide sensitive routes for protein backbone resonance assignment.Furthermore, we demonstrate that narrow 1H NMR line widths can be obtained for fully protonated proteins in the solid state under ultra-fast MAS, even without perdeuteration. In this context, we have developed new strategies for extensive, robust and expeditious assignments of the 1H, 15N, 13CO, 13CA and 13CB resonances of proteins in different aggregation states, and new schemes for the measurements of site-specific 1H-1H distance restraints. This approach relying on the very high sensitivity of 1H spins remarkably accelerates the processes of assignment and structure determination of proteins in the solid state, as shown by the assignment and de novo structure determination of native beta-2-microglobulin. Finally, we apply this new approach to perform resonance assignment and to study structural and dynamic features of three complex protein aggregates: amyloid fibrils formed by native and D76N beta-2-microglobulin, Acinetobacter phage 205 nucleocapsids and measles virus (MeV) nucleocapsids. We also used Dynamic Nuclear Polarization to obtain the first information about RNA in MeV nucleocapsids.We believe that the results presented in this thesis represent a substantial step forward for solid-state NMR in structural biology. With all the current advances in the field, the impact of biomolecular solid-state NMR is likely to increase in the next years.
|
Page generated in 0.0598 seconds