The function of G protein-coupled receptors is intrinsically linked to their conformational dynamics. In conjugation with site-directed spin labeling, electron paramagnetic resonance (EPR) spectroscopy provides powerful tools to study the highly dynamic conformational states of these proteins. Here, we explored positions for nitroxide spin labeling coupled to single cysteines, introduced at transmembrane, intra- and extra-cellular sites of the human neuropeptide Y2 receptor. Receptor mutants were functionally analyzed in cell culture system, expressed in Escherichia coli fermentation with yields of up to 10 mg of purified protein per liter expression medium and functionally reconstituted into a lipid bicelle environment. Successful spin labeling was confirmed by a fluorescence assay and continuous wave EPR measurements. EPR spectra revealed mobile and immobile populations, indicating multiple dynamic conformational states of the receptor. We found that the singly mutated positions by MTSL ((1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl) methyl methanesulfonothioate) have a water exposed immobilized conformation as their main conformation, while in case of the IDSL (bis(1-oxyl-2,2,5,5-tetramethyl-3-imidazolin-4-yl) disulfide) labeled positions, the main conformation are mainly of hydrophobic nature. Further, double cysteine mutants were generated and examined for potential applications of distance measurements by double electron–electron resonance (DEER) pulsed EPR technique on the receptor.

Many biological functions of peptides are mediated through G protein-coupled receptors (GPCRs). Upon ligand binding, GPCRs undergo conformational changes that facilitate the binding and activation of multiple effectors. GPCRs regulate nearly all physiological processes and are a favorite pharmacological target. In particular, drugs are sought after that elicit the recruitment of selected effectors only (biased ligands). Understanding how ligands bind to GPCRs and which conformational changes they induce is a fundamental step toward the development of more efficient and specific drugs. Moreover, it is emerging that the dynamic of the ligand–receptor interaction contributes to the specificity of both ligand recognition and effector recruitment, an aspect that is missing in structural snapshots from crystallography. We describe here biochemical and biophysical techniques to address ligand–receptor interactions in their structural and dynamic aspects, which include mutagenesis, crosslinking, spectroscopic techniques, and mass-spectrometry profiling. With a main focus on peptide receptors, we present methods to unveil the ligand–receptor contact interface and methods that address conformational changes both in the ligand and the GPCR. The presented studies highlight a wide structural heterogeneity among peptide receptors, reveal distinct structural changes occurring during ligand binding and a surprisingly high dynamics of the ligand–GPCR complexes.

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[EN] The Selective Catalytic Reduction of nitrogen oxides (SCR-NOx) is nowadays a very relevant process for reducing NOx emissions in diesel vehicles, which must comply with increasingly restrictive European regulations. In this thesis the reaction mechanism and active centers in Cu-zeolite catalysts with different structures has been investigated. For his purpose two in situ spectroscopic techniques were mainly used, being Nuclear Magnetic Resonance NMR and Electron Paramagnetic Resonance EPR, which allowed the detection of reaction intermediates and identification of Cu active species. In particular we have studied the SCR-NOx reaction using NH3 as the reducing agent and Cu-zeolites catalysts with the chabazite structure. The preliminary study of the interaction of the catalysts with NH3 has shown the formation of several Cu-NH3 complexes with different stability. At SCR typical reaction temperatures (250 ° C), ammonia forms NH4+ ions in Brønsted acids centers of the zeolite and stable Cu+-(NH3) complexes, while Cu2+ remains isolated at the 6R plane, which is precisely the active site. However, when studying species formed on Cu-zeolites in the presence of the reaction mixture NH3/NO/O2, it appears that NH4+ ions are consumed during reaction and the formation of various intermediates including nitrite/nitrate species that decompose at T > 250 ° C to the reaction products (N2 and H2O). We also investigated the mechanism of the SCR-NOx reaction using C3H8 as the reducing agent and Cu-zeolites of different topology with medium and large pore systems. The results show the formation of a hydrocarbon activated species in the Cu2+ which is related to the catalytic activity. Furthermore, isolated Cu2+ is an active site that is reduced to Cu+ during reaction, and then re-oxidized to Cu2+ in the presence of O2. Finally, the hydrothermal stability of Cu-zeolites has been studied, since it is a prerequisite for its application as SCR catalysts, comparing the very hydrothermally stable Cu-SSZ-13 zeolite and the Cu-ZSM-5 which is completely disabled after hydrothermal treatment. The findings suggest the origin of the deactivation to be a change in the coordination of isolated Cu2+ in the Cu-ZSM-5 type to form CuAlOx species which are inactive in the SCR-NOx reaction. / [ES] La Reducción Catalítica Selectiva de óxidos de nitrógeno, SCR-NOx (acrónimo del inglés Selective Catalytic Reduction of NOx) es un proceso muy importante actualmente para la reducción de las emisiones de NOx en vehículos diésel, que deben ajustarse a nuevas normativas europeas más restrictivas. En la presente tesis doctoral se ha investigado el mecanismo de reacción y los centros activos en catalizadores de Cu en zeolitas (Cu-zeolitas) con distintas estructuras. Para ello se han utilizado fundamentalmente dos técnicas espectroscópicas in situ, la resonancia magnética nuclear RMN y la resonancia paramagnética electrónica EPR, que han permitido la detección de intermedios de reacción y la identificación de especies de Cu activas. En concreto se ha estudiado la reacción SCR-NOx utilizando NH3 como reductor y catalizadores Cu-zeolitas con estructura chabazita. Los resultados obtenidos en el estudio preliminar de la interacción del catalizador con el NH3 muestran la formación de distintos complejos de Cu-NH3 con diferente estabilidad. A la temperatura de reacción (250 °C), el amoniaco forma iones NH4+ en centros ácidos Brønsted de la zeolita y complejos Cu+(NH3) estables, y el Cu2+ permanece aislado en el plano de los anillos 6R, que es precisamente el centro activo. Sin embargo, cuando se estudian las especies formadas con la mezcla de reacción NH3/NO/O2 en las Cu-zeolitas, se observa que los iones NH4+ se consumen en el transcurso de la reacción y la formación de varios intermedios incluyendo nitritos/nitratos que descomponen a T > 250 °C a los productos de reacción (N2 y H2O). También se ha investigado el mecanismo de la reacción SCR-NOx utilizando C3H8 como reductor y Cu-zeolitas de distinta topología con tamaños de poros medio y grande. Los resultados obtenidos evidencian la formación de una especie activada del hidrocarburo en el Cu2+ que está relacionada con la actividad catalítica. Además el Cu2+ aislado es un centro activo que se reduce a Cu+ en el transcurso de la reacción, y se re-oxida posteriormente a Cu2+ en presencia de O2. Finalmente, se ha estudiado la estabilidad hidrotermal de las zeolitas con cobre, puesto que es una condición indispensable para su aplicación como catalizadores SCR, comparando la zeolita Cu-SSZ-13 muy estable hidrotermalmente, y la Cu-ZSM-5 que se desactiva por completo tras el tratamiento hidrotermal. Los resultados obtenidos apuntan que el origen de la desactivación es el cambio en la coordinación del Cu2+ en la Cu-ZSM-5 para formar especies tipo CuAlOx inactivas en la reacción. / [CA] La reducció catalítica selectiva d'òxids de nitrogen, SCR-NOx (acrònim del anglès Selective Catalytic Reduction of NOx) és un procés molt important actualment per a la disminució de les emissions de NOx en vehicles dièsel, que deuen ajustar-se a les normatives europees més restrictives. En la present tesi doctoral s'ha investigat el mecanisme de reacció i els centres actius en catalitzadors de Cu en zeolites (Cu-zeolites) amb diferents estructures. Per a dur a terme aquesta tasca s'han utilitzat fonamentalment dos tècniques espectroscòpiques in situ, la ressonància magnètica nuclear RMN i la ressonància paramagnètica electrònica EPR, les quals han permès la detecció d'intermedis de reacció i la identificació d'espècies de Cu actives. Concretament s'ha estudiat la reacció SCR-NOx emprant NH3 com a reductor i catalitzadors Cu-zeolita amb estructura chabacita. Els resultats obtinguts en l'estudi preliminar de la interacció del catalitzador amb NH3 mostren la formació de diversos complexes de Cu-NH3 amb diferent estabilitat. A la temperatura de reacció (250 °C), l'amoníac forma ions NH4+ en centres àcids Brønsted de la zeolita i complexes Cu+(NH3) estables, a més, el Cu2+ roman aïllat en el plànol dels anells 6R, que és precisament el centre actiu. No obstant, quan s'estudien les espècies formades amb la mescla de reacció, NH3/NO/O2 en les Cu-zeolites, s'observa que els ions NH4+ es consumeixen durant la reacció i la formació de diversos intermedis incloent nitrits/nitrats que descomponen, a T > 250 °C, als productes de la reacció (N2 y H2O). També s'ha estudiat el mecanisme de la reacció SCR-NOx utilitzant C3H8 com a reductor i Cu-zeolites amb diferent topologia amb mides de porus mitges i grans. Els resultats obtinguts evidencien la formació d'una espècie en forma activa del hidrocarbur al Cu2+ que està relacionada amb l'activitat catalítica. A més a més, el Cu2+ aïllat és un centre actiu que és redueix amb el transcurs de la reacció, i es re-oxida posteriorment a Cu2+ en presència de O2. Finalment, s'estudia l'estabilitat hidrotermal de les zeolites amb coure, puix que és una condició indispensable per a la seua aplicació com a catalitzadors SCR, comparant la zeolita Cu-SSZ-13 que és molt estable hidrotermalment, i Cu-ZSM-5 que es desactiva completament després del tractament hidrotermal. Els resultats obtinguts indiquen que la causa de la desactivació és el canvi en la coordinació del Cu2+ en Cu-ZSM-5 per a formar espècies tipus CuAlOx que són inactives a la reacció. / Moreno González, M. (2015). APLICACIÓN DE TÉCNICAS ESPECTROSCÓPICAS IN SITU AL ESTUDIO DE REACCIONES DE INTERÉS MEDIOAMBIENTAL: ELIMINACIÓN DE ÓXIDOS DE NITRÓGENO [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/52601

The Parkinsonian Syndrome-inducing effects of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) on the body have been well-documented since its discovery. However, its mechanism of oxidation by monoamine oxidase B (MAO B) has been debated for just as long. Proponents of the single electron transfer (SET) pathway of oxidation faced severe critiques in that the hypothesized radical intermediates arising from the SET pathway were never directly observed. Work performed herein provides that exact evidence using biomimetics of MAO B. The first section of the dissertation will highlight the ability of one such biomimetic, 3-methyllumiflavin (3MLF), to provide a chemical model for the oxidation of -unsaturated tetrahydropyridines. Using a nontoxic analog of MPTP, 1-methyl-4-(1-methyl-1-H-pyrrol-2-yl)-1,2,3,6-tetra-hydropyridine (MMTP), reactions with 3MLF were performed under both aerobic and anaerobic conditions. The anaerobic studies of these reactions proved to be the key to the direct observations (by 1H NMR and EPR) of flavin-derived radical behavior. Armed with the knowledge of how to prepare reactions for the direct observation of flavin radical intermediates, studies of N-cyclopropyl substrate derivatives were subsequently conducted to gather evidence for the formation of radical substrate intermediates. If the hypothesized SET is the first step of the reaction mechanism, then the resulting aminyl radical cation could undergo a cyclopropyl ring opening. Several products derived from the substrate were observed; among them were ring-opened variations suggesting that the reaction does begin with a SET. Thermodynamically, this process is unfavorable, leading to the hypothesis that this reaction step may be better described as a proton-coupled electron transfer (PCET). The kinetics of this process were studied at length. Finally, to provide a more compelling argument for the fundamental reactivities, two other flavin biomimetics are investigated. Their reactions with tetrahydropyridines were put under the same scrutiny as 3MLF, leading to the conclusion that the chemistry discussed herein is not unique to 3MLF, but is much more broadly applicable to other flavin biomimetics and MAO B. / Doctor of Philosophy / First reported in 1982, Parkinsonian Syndrome related to the injection of the designer drug meperidine was linked to an impurity in the drug, 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine, MPTP. That compound was able to be oxidized in the brain by the enzyme monoamine oxidase B (MAO B) to form the neurotoxin 1-methyl-4-phenylpyridinium (MPP+). For many years, the way that oxidation occurred remained a mystery as MPTP is chemically very different than typical substrates of MAO B. One type of reaction, single electron transfer (SET), which involves the production of high-energy intermediates called radicals, was largely overlooked as it seemed chemically implausible, especially in a biological system. This dissertation will focus on providing evidence for the SET oxidation of MPTP-like molecules using a class of compounds called flavins. Flavins are biomimetics of MAO B, meaning they behave in reaction vessels the same way that MAO B behaves biologically. Evidence for the SET pathway comes primarily in two forms: nuclear magnetic resonance (1H NMR) and electron paramagnetic resonance (EPR). Each of these techniques allow us to "see" exactly what species are present in solution. In the case of 1H NMR, we will be able to see the "normal" molecules, while EPR allows us to see the high energy radical species in solution. Using these techniques, several substrate and flavin analogs were investigated to uncover a universal reaction mechanism by which MPTP and related compounds are oxidized by MAO B.

Cette thèse est consacrée à l'étude expérimentale et théorique des corrélations quantiques en variables continues.<br />La question de la caractérisation de ces corrélations est largement abordée, en particulier dans le cas des états gaussiens. Le formalisme mathématique des matrices de covariance, particulièrement adapté à cette étude, est développé ; et les différents critères existants sont répertoriés.<br />Ces critères permettent de caractériser le degré d'intrication des faisceaux générés par le dispositif expérimental au cœur de cette thèse : un Oscillateur Paramétrique Optique auto-verrouillé en phase. Au-dessous du seuil, les faisceaux, de valeur moyenne nulle, présentent une séparabilité de 0,33. Le système viole de manière apparente l'inégalité de Heisenberg de 58%. Au-dessus du seuil, les faisceaux brillants obtenus sont également fortement non classiques : la séparabilité vaut 0,76 et l'inégalité de Heisenberg est violée en apparence de 24%.<br />Une application originale de ce dispositif est proposée : il est montré théoriquement qu'un OPO à deux cristaux auto-verrouillé en phase génère deux faisceaux intriqués en polarisation, ce qui devrait faciliter le transfert de l'intrication de la lumière à la matière.

The outcome of chemical reactions proceeding via radical pair (RP) intermediates can be influenced by the magnitude and direction of applied magnetic fields, even for interaction strengths far smaller than the thermal energy. Sensitivity to Earth-strength magnetic fields has been suggested as a biophysical mechanism of animal magnetoreception and this thesis is concerned with simulations of the effects of such weak magnetic fields on RP reaction yields. State-space restriction techniques previously used in the simulation of NMR spectra are here applied to RPs. Methods for improving the efficiency of Liouville-space spin dynamics calculations are presented along with a procedure to form operators directly into a reduced state-space. These are implemented in the spin dynamics software Spinach. Entanglement is shown to be a crucial ingredient for the observation of a low field effect on RP reaction yields in some cases. It is also observed that many chemically plausible initial states possess an inherent directionality which may be a useful source of anisotropy in RP reactions. The nature of the radical species involved in magnetoreception is investigated theoretically. It has been shown that European Robins are disorientated by weak radio-frequency (RF) fields at the frequency corresponding to the Zeeman splitting of a free electron. The potential role of superoxide and dioxygen is investigated and the anisotropic reaction yield in the presence of a RF-field, without a static field, is calculated. Magnetic field effect data for Escherichia coli photolyase and Arabidopsis thaliana cryptochrome 1, both expected to be magnetically sensitive, are satisfactorily modelled only when singlet-triplet dephasing is included. With a view to increasing the reaction yield anisotropy of a RP magnetoreceptor, a brief study of the amplification of the magnetic field experienced by a RP from nearby magnetite particles is presented. Finally in a digression from RPs, Spinach is used to determine the states expected to be immune from relaxation and therefore long-lived in NMR experiments on multi-spin systems.