A fosfatase Cdc25B atua na progressão do ciclo celular através da ativação de complexos Cdk/Ciclina. Atualmente, nos modelos estruturais propostos do domínio catalítico da Cdc25B não estão incluídos os últimos 16 resíduos da região C-terminal. Este segmento tem importante papel no reconhecimento do substrato proteico e pode estar envolvido na complexação de pequenas moléculas com a Cdc25B. Assim, o principal objetivo desta tese foi avaliar a flexibilidade conformacional do domínio catalítico completo da Cdc25B em solução através de simulações computacionais e por medidas experimentais de ressonância magnética nuclear (RMN). A similaridade entre as estruturas cristalográficas e em solução foi confirmada pela previsão de ângulos diedrais φ/ψ da cadeia principal a partir dos deslocamentos químicos (CS) e pela concordância entre os acoplamentos dipolares residuais (RDC) medidos e calculados a partir da geometria cristalina. Medidas de parâmetros de relaxação de 15N e RDC evidenciaram a presença de desordem conformacional na região C-terminal, em acordo com a ausência de densidade eletrônica desse segmento no experimento de difração de raios-X. Através da comparação entre CS experimentais e previstos de simulações de dinâmica molecular (DM) longas (total de 6µs de duração) foram apontados artefatos de cristalização, possíveis erros nos campos de força usados nas simulações, falhas na composição do sistema simulado e estados conformacionais populados pela Cdc25B em solução distintos da geometria cristalográfica. De maneira geral, os CS previstos a partir das simulações para a flutuação estrutural dos resíduos da região C-terminal desordenada estão em acordo com os valores experimentais, sugerindo que os estados conformacionais deste segmento foram razoavelmente bem amostrados nas simulações. Em particular, verificou-se que o contato tipo cátion-π entre as cadeias laterais dos resíduos 550W do C-terminal desordenado e 482R do núcleo proteico, ausente na estrutura cristalográfica, pode ser importante em solução. A formação desse contato na simulação de DM também está de acordo com medidas experimentais de perturbação de deslocamentos químicos (CSP) entre construções completa e truncada do domínio catalítico da Cdc25B. Assim, através do uso conjunto de simulações computacionais e medidas experimentais foi possível obter uma representação mais completa e realista da flexibilidade conformacional do domínio catalítico da Cdc25B em solução, incluindo a determinação de possíveis contatos intramoleculares entre a região C-terminal desordenada e o núcleo proteico. Essas informações poderão ser usadas na construção de um ensemble conformacional da Cdc25B. / Cdc25B phosphatase acts on the progression of cell cycle through the activation of Cdk/Cyclin complexes. Currently, the proposed structural models of Cdc25B catalytic domain lack the last 16 residues from the C-terminal region. This segment is important for protein substrate recognition and might be involved in small molecule binding to Cdc25B. Thus, the main goal of this thesis was to evaluate the conformational flexibility of the complete catalytic domain from Cdc25B through computer simulations and experimental nuclear magnetic resonance (NMR) measurements. Similarity between crystal and in solution structures was confirmed by the prediction of backbone φ/ψ dihedral angles from chemical shifts (CS) and by the agreement between observed and back-calculated residual dipolar couplings (RDC). 15N relaxation and RDC measurements pointed to the conformational disorder of the C-terminal region, in agreement with the X-ray diffraction experiment where this segment showed no electronic density. Comparison between experimental and predicted CS from long molecular dynamics (MD) simulations (6µs total running time) pointed to the presence of crystallographic artifacts, possible deficiencies in simulation force fields, inaccurate composition of the simulated system and conformational states visited by Cdc25B in solution that were not observed in the crystallographic geometry. Generally, CS predicted from simulations for the structural fluctuation of the disordered C-terminal region were in agreement with experimental values, suggesting that the simulations sampled the conformational states populated by this segment reasonably well. In particular, a cation-π contact not observed in the crystal structure between side chains of residue 550W from the disordered C-terminal tail and residue 482R from the protein core might be important in solution. This contact is also in agreement with experimental chemical shift perturbations (CSP) measured between complete and truncated constructs of Cdc25B catalytic domain. Therefore, the joint use of computer simulations and experimental measurements allowed the achievement of a more complete and realistic representation of the conformational flexibility of the Cdc25B catalytic domain in solution, including intramolecular contacts between the disordered C-terminal region and the protein core. This information might be used to obtain a conformational ensemble of Cdc25B.

A fosfatase Cdc25B atua na progressão do ciclo celular através da ativação de complexos Cdk/Ciclina. Atualmente, nos modelos estruturais propostos do domínio catalítico da Cdc25B não estão incluídos os últimos 16 resíduos da região C-terminal. Este segmento tem importante papel no reconhecimento do substrato proteico e pode estar envolvido na complexação de pequenas moléculas com a Cdc25B. Assim, o principal objetivo desta tese foi avaliar a flexibilidade conformacional do domínio catalítico completo da Cdc25B em solução através de simulações computacionais e por medidas experimentais de ressonância magnética nuclear (RMN). A similaridade entre as estruturas cristalográficas e em solução foi confirmada pela previsão de ângulos diedrais φ/ψ da cadeia principal a partir dos deslocamentos químicos (CS) e pela concordância entre os acoplamentos dipolares residuais (RDC) medidos e calculados a partir da geometria cristalina. Medidas de parâmetros de relaxação de 15N e RDC evidenciaram a presença de desordem conformacional na região C-terminal, em acordo com a ausência de densidade eletrônica desse segmento no experimento de difração de raios-X. Através da comparação entre CS experimentais e previstos de simulações de dinâmica molecular (DM) longas (total de 6µs de duração) foram apontados artefatos de cristalização, possíveis erros nos campos de força usados nas simulações, falhas na composição do sistema simulado e estados conformacionais populados pela Cdc25B em solução distintos da geometria cristalográfica. De maneira geral, os CS previstos a partir das simulações para a flutuação estrutural dos resíduos da região C-terminal desordenada estão em acordo com os valores experimentais, sugerindo que os estados conformacionais deste segmento foram razoavelmente bem amostrados nas simulações. Em particular, verificou-se que o contato tipo cátion-π entre as cadeias laterais dos resíduos 550W do C-terminal desordenado e 482R do núcleo proteico, ausente na estrutura cristalográfica, pode ser importante em solução. A formação desse contato na simulação de DM também está de acordo com medidas experimentais de perturbação de deslocamentos químicos (CSP) entre construções completa e truncada do domínio catalítico da Cdc25B. Assim, através do uso conjunto de simulações computacionais e medidas experimentais foi possível obter uma representação mais completa e realista da flexibilidade conformacional do domínio catalítico da Cdc25B em solução, incluindo a determinação de possíveis contatos intramoleculares entre a região C-terminal desordenada e o núcleo proteico. Essas informações poderão ser usadas na construção de um ensemble conformacional da Cdc25B. / Cdc25B phosphatase acts on the progression of cell cycle through the activation of Cdk/Cyclin complexes. Currently, the proposed structural models of Cdc25B catalytic domain lack the last 16 residues from the C-terminal region. This segment is important for protein substrate recognition and might be involved in small molecule binding to Cdc25B. Thus, the main goal of this thesis was to evaluate the conformational flexibility of the complete catalytic domain from Cdc25B through computer simulations and experimental nuclear magnetic resonance (NMR) measurements. Similarity between crystal and in solution structures was confirmed by the prediction of backbone φ/ψ dihedral angles from chemical shifts (CS) and by the agreement between observed and back-calculated residual dipolar couplings (RDC). 15N relaxation and RDC measurements pointed to the conformational disorder of the C-terminal region, in agreement with the X-ray diffraction experiment where this segment showed no electronic density. Comparison between experimental and predicted CS from long molecular dynamics (MD) simulations (6µs total running time) pointed to the presence of crystallographic artifacts, possible deficiencies in simulation force fields, inaccurate composition of the simulated system and conformational states visited by Cdc25B in solution that were not observed in the crystallographic geometry. Generally, CS predicted from simulations for the structural fluctuation of the disordered C-terminal region were in agreement with experimental values, suggesting that the simulations sampled the conformational states populated by this segment reasonably well. In particular, a cation-π contact not observed in the crystal structure between side chains of residue 550W from the disordered C-terminal tail and residue 482R from the protein core might be important in solution. This contact is also in agreement with experimental chemical shift perturbations (CSP) measured between complete and truncated constructs of Cdc25B catalytic domain. Therefore, the joint use of computer simulations and experimental measurements allowed the achievement of a more complete and realistic representation of the conformational flexibility of the Cdc25B catalytic domain in solution, including intramolecular contacts between the disordered C-terminal region and the protein core. This information might be used to obtain a conformational ensemble of Cdc25B.

The work presented in this thesis has two parts. The first part deals with methodological developments in the area of solid-state NMR, relevant to the study of partially ordered systems. Liquid crystals are best examples of such partially ordered systems and they are easily oriented by the magnetic field used for the NMR study. They provide spectra rich in information useful for the study of structure and dynamic s of the oriented molecule. Dipolar couplings and anisotropic chemical shifts are relatively easy to obtain for these systems. However, the methodologies used for extracting the required information are constantly undergoing change, with newer ideas being used for optimal use of the technique and increasing the sensitivity of the methodology. In this thesis, existing methods used for obtaining dipolar couplings from oriented liquid crystalline samples are examined in detail and conditions for optimal use of the methods are investigated. Different approaches for enhancing the sensitivity of the techniques are also proposed. Estimation of chemical shift anisotropy of carbons for a molecule that is used as a building block for several mesogens has been obtained and its utility for estimating the order parameters of the system have been examined. The second part of the thesis deals with the application of solid state NMR methods to the study of a number of novel liquid crystalline systems and for the estimation of dynamics, order and orientation of the mesogenic molecules in the magnetic field. Chapter-2 deals with a detailed and systematic study to improve the sensitivity of cross-polarization based separated local field (SLF) NMR spectroscopy techniques such as PISEMA(Polarization Inversion Spin Exchange at the Magic Angle) and PDLF(Pro-ton Detected Local Field). The chapter has been further divided into three sections. Section-A describes the optimization procedure for cross-polarization period for reducing zero-frequency peaks in SLF experiments. Polarization Inversion(PI) is one of the important components of PISEMA and plays a crucial role in enhancing the dipolar cross-peaks and suppressing the axial-peaks. Shortening this period has the advantage of less r.f. power input into the system, thus less susceptibility to sample heating. Therefore it is crucial to arrive at the optimum condition for which maximum sensitivity and resolution are obtained. A detailed experimental investigation of the role of the initial po1arization period has been carried out for two different samples of static oriented liquid crystalline material at two different temperatures and a contact time of 2ms has been found to be optimal for such samples. Insection-B of this chapter, the initial preparation period of the experiment is considered as a possible means of increasing the sensitivity of the experiment. Thus the use of cross-polarization via the dipolar bath by the use of a diabatic demagnetization in the rotating frame(ADRF-CP) has been proposed to be incorporated into PISEMA. To understand the CP dynamics, magnetization in double-and zero-quantum reservoirs of an ensemble of spin-1/2 nuclei and their role in determining the sensitivity the experiments have been theoretically examined. Experimentally, a modification incorporating ADRF-CP is shown to result in enhancement of signal-to-noise by as much as 90% in the case of rigid single crystals of a model peptide and up to 50% in non-rigid, partially ordered liquid crystalline systems. In section-C another useful SLF technique known as PDLF spectroscopy has also been examined. In this case a sweep of one of the r.f. amplitudes(RAMP-CP),rather than ADRF is found to work well. The reason for the different behaviours has been discussed. Chapter-3 highlights two experimental approaches used to extract the chemical shift anisotropy(CSA) tensor information from rotating solids. Section-A is devoted to the measurement of the CSA values of thiophene by using MAS side band analysis, by extracting the principal values from the intensities of just a few spinning side bands. Experiments have been performed on thiophene-2 carboxylic acid and thiophene-3 carboxylic acid samples and the carbon CSA values have been obtained. In section-B, CSA values of carbons of the core unit of the liquid crystal4- hexyloxybenzoic acid (HBA) have been obtained by using the recoupling pulse sequence SUPER(Separation of Undistorted Powder patterns by Effortless Recoupling).HBA belongs to an important class of thermotropic liquid crystals which are structurally simple and often used as starting materials for many novel mesogens. As this molecule could serve as an ideal model compound, high resolution13C NMR studies of HBA in solution, solid and liquid crystalline phases have been also undertaken. The CSA values obtained from the 2D SUPER experiment showed good agreement to those computed by DFT calculations. The CSA values were used for obtaining the order parameter of the system at different temperatures. These matched well the order parameter obtained from the 13C-1 H dipolar couplings in the nematic phase determined by SLF spectroscopy at various temperatures. A knowledge of the CSA of the carbons is thus very useful, as they can be used for gaining knowledge about the system from the chemical shifts obtained from a simple 1D spectrum. In chapter-4, 1-and 2-dimensional13CNMR techniques have been utilized to obtain extensive information about some novel mesogenic molecules. Four molecules of different structure and topology have been taken up for study. These molecules have the following features. Mesogen-1 has a terminal hydroxyl group. Such systems with further modification can result in mesogenic monomers for side chain liquid crystalline polymers. Mesogen-2 has a dimethyl amino group at one end and has three phenyl groups connected by appropriate linking units that form the core. In the third case, mesogen-3, the terminal hydroxyl group of mesogen-1 is replaced with a hydrogen such that13C-1 H dipolar couplings provide directly information on molecular ordering and orientation. In the fourth case, mesogen-4, the core is built with four phenyl rings. Here the fourth ring is linked to other three rings via a flexible chain unit. In each of these cases the 2DSLFNMR experiments have been carried out where13C-1 H dipolar couplings as well as13C chemical shifts were used for obtaining the order parameters of various segments of the molecule. The data provide useful insight into the phase behaviour, ordering and orientation of the molecules. Chapter-5 discusses the applications of the natural abundance 13CNMR techniques to thiophene based mesogens, that have the potential for use in molecular electronics material. Typically, these molecules consist of phenyl rings appropriately connected by linking units with thiophene. Different core units as well as different linking units to thiophene have been considered. The six mesogens thus obtained have been investigated in detail using 1D and 2D NMR methods.13C-1 H dipolar couplings have been used to obtain ordering information, that show interesting correlation to the molecular orientation and dynamics.

No description available.

La mesure de couplage dipolaire permet d’accéder à la structure tridimensionnelle d’un composé solide. Cependant, en présence d’une forte densité de spins couplés, le phénomène de troncature dipolaire rend difficile l’obtention de ces informations par RMN du solide. Ce problème peut être affranchi par l’étude de spins rares en abondance naturelle. En effet, avec une abondance naturelle de 1.1 %, la probabilité que trois 13C soient couplés, et avec elle la troncature dipolaire, devient négligeable. Une méthodologie basée sur la séquence de recouplage dipolaire POST-C7 permet d’accéder à des informations structurales d’échantillons en abondance naturelle sensibles à la fois à la conformation moléculaire et à l’empilement cristallin par mesure de couplages dipolaires 13C-13C. La sensibilité de détection des signaux RMN 13C est augmentée à l’aide la polarisation dynamique nucléaire ce qui permet de réduire considérablement les temps d’expériences. De plus, la séquence de recouplage R20_9_2 aidée de supercycles s’est montrée être plus robustes que POST-C7 face à de fortes anisotropies de déplacement chimique ou de forts couplages hétéronucléaires 1H-13C. La seconde problématique abordée concerne l’attribution de signaux 13C. En effet, il existe seulement quelques exemples de détermination de connectivités 13C -13C en abondance naturelle. Nous montrons ici que des spectres de corrélations dipolaires 13C-13C peuvent être obtenus en quelques jours à l’aide de la séquence de recouplage R20_9_2. Contrairement aux méthodologies basées sur le couplage J, notre séquence requiert un temps d’excitation DQ plus court ce qui la rend adaptée à l’étude de solides désordonnés. / Measurment of dipolar coupling provides 3D structural information of powder samples. However, in practice, the high density of spins in organic compounds prevents the measurements of long-range dipolar couplings in solid-state NMR by the so-called dipolar truncation effect. The study of rare spins on natural abundance allows to overcome this problem. In fact, with a natural abundance of 1.1 %, the probability for three 13C to be coupled is negligible. We developed a methodology based either on the dipolar recoupling NMR pulse sequence POST-C7 or on the dramatic increase in sensitivity provided by dynamic nuclear polarization. We demonstrated that its methodology provides a measure of 13C-13C dipolar couplings in natural abundance powder samples and that the so-obtained distance information is sensitive to both molecular conformation and crystal packing of powder samples. Moreover, we show that the recoupling pulse sequence R20_9_2 is more robust to strong chemical shift anisotropy and also to strong 1H-13C heteronuclear dipolar couplings than POST-C7. The second challenge involves 13C signal assignment for natural abundance. In fact, there are only a few examples of 13C-13C correlation spectra obtained for natural abundance samples. Here, we show that 13C-13C correlation spectra sequence based on the reintroduction of 13C−13C dipolar couplings can be obtained with standard MAS probe and within few days using R20_9_2 pulse sequence. Contrary to pulse sequences based on 13C-13C J coupling, our pulse sequence requires shorter DQ excitation time and hence, is more suitable for samples having short T2 relaxation times such as amorphous solids.

Im Rahmen der vorliegenden Arbeit, wird ein neuartiges Markierungsschema für die Festkörper-NMR-Spektroskopie vorgestellt, das sogenannte Reduced Adjoining Protonation (RAP) Schema, welches die Protonendetektion sämtlicher Aliphaten erlaubt. Hochaufgelöste, 1H-detektierte 1H,13C Korrelationsspektren wurden erhalten. Des Weiteren wurde der Vorteil von hohen MAS-Frequenzen untersucht. 1H- und 13C-detektierte 3D Zuordnungsexperimente wurden implementiert, welche uns die Zuordnung von 90% aller aliphatischen Resonanzen von alpha-Spektrin SH3 erlaubten. Da die chemische Verschiebung abhängt vom Strukturmotiv, kann sie verwendet werden, um Sekundärstruktur-Informationen abzuleiten. Darüber hinaus wurde ein 1H-detektiertes H(H)CH 3D Experiment entwickelt, um weitreichende 1H,1H Kontakte zu ermitteln, welche für die Bestimmung der Tertiärstruktur genutzt werden können. Um artefaktfreie Relaxationsdaten zu erhalten, wurde das RAP-Markierungsschema modifiziert, um 1H- und 13C-verdünnte Proben zu erhalten, in denen Spindiffusion unterdrückt ist. Für die Untersuchung von Sub-Mikrosekunden-Dynamik werden Experimente vorgestellt zur Bestimmung von 13C T1 Relaxationszeiten und 1H,13C dipolaren Kopplungstensoren für Rückgrat- und Seitenketten-Resonanzen. Des weiteren zeigen wir, dass das RAP-Markierungsschema auf nicht-kristalline Systeme, wie Amyloidfibrillen des Abeta1-40 Peptids der Alzheimer-Krankheit, angewendet werden kann. Unter Verwendung von 1H-Detektion, erhielten wir hochaufgelöste 1H,13C Korrelationsspektren. Schließlich wurde der Perdeuterierungsansatz auf den L7Ae-box C/D Protein-RNA Komplex aus P. furiosus angewendet. Wir erhielten hochaufgelöste, 1H-detektierte 1H,15N, sowie 13C,13C Korrelationsspektren des Protein-RNA Komplexes. Weiterhin haben wir eine Methode zur Bestimmung genauer Abstands- und Winkelinformationen für die Protein-RNA Schnittstelle etabliert und schlagen Ansätze vor, für die Zuordnung der chemischen Verschiebungen von RNA-Resonanzen. / In this thesis, a novel labeling scheme for solid-state NMR spectroscopy, the Reduced Adjoining Protonation (RAP) scheme, is introduced, which allows proton detection of all aliphatic sites, as shown for the microcrystalline SH3 domain of alpha-spectrin. These samples yield high-resolution, 1H-detected 1H,13C correlation spectra. In addition, the benefit of high MAS frequencies was investigated. 1H- and 13C-detected 3D assignment experiments are implemented, which allowed us to assign 90% of all aliphatic resonances of alpha-spectrin SH3. As the chemical shift is dependent on the structural motif, it can be employed to derive secondary structure information. Furthermore, a 1H-detected H(H)CH 3D experiment is introduced, to obtain long-range 1H,1H contacts, which can be used for the determination of the tertiary structure. To obtain artifact-free relaxation data, the RAP labeling scheme was modified to obtain sparsely proton labeled, 13C dilute samples, in which spin diffusion is suppressed. To probe sub-microsecond dynamics, we report experiments to determine 13C T1 relaxation times and 1H,13C dipolar coupling tensors for backbone and side chain resonances, respectively. Furthermore, we show, that the RAP labeling scheme can be applied to non-crystalline systems, such as amyloid fibrils of the Alzheimer’s disease peptide Abeta1-40. Using 1H-detection, we obtained high-resolution 1H,13C correlation spectra. Finally, we applied the perdeuteration approach to the L7Ae-box C/D protein-RNA complex from P. furiosus. We obtained high-resolution, 1H-detected 1H,15N, as well as 13C,13C correlation spectra of the protein-RNA complex. In addition, we established a methodology to determine accurate distance and angular restraints for the protein-RNA interface and propose approaches for the chemical shift assignment of RNA resonances.