No description available.

The PsbQ protein (16.5 kDa) is an extrinsic protein found in the thylakoid membrane of higher plants and green algae. As a member of the Psb protein family, it is situated in the oxygen evolving center and takes part in the water splitting reaction. The stable oxygen production in photosystem II depends on the cooperation of PsbQ with other photosynthetic proteins, mainly PsbP. In order to identify the possible interaction sites, the tertiary structure in solution has to be determined. Although the X-ray crystallographic structure of PsbQ was determined previously, the conformation of residues 14-33 (so-called "missing link") was still unknown at the onset of this work. The initial backbone assignment as well as a secondary structure estimation were achieved recently. In this thesis the resonance assignment was extended and 15N as well as 13C NOESY-HSQC spectra were recorded to obtain structural constraints. The solution structure was determined using the program CYANA. The results obtained show that, while the four helix bundle domain is nearly identical compared to the available X-Ray crystallographic structure significant deviations occur in the N-terminal region. In particular, the residues 37-41, where a short ?-strand had been proposed in the crystal structure, exhibit high ?-helical propensity.

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Philosophiae Doctor - PhD / Retinoblastoma-binding protein 6 (RBBP6) is a multi-domain human protein known to play a role in mRNA splicing, cell cycle control and apoptosis. The protein interacts with tumour suppressor proteins p53 and pRb and recent studies have shown that it plays a role in the ubiquitination of p53 by interacting with Hdm2, the human homologue of mouse double minute protein 2 (Mdm2), in which the RING finger domain plays an essential role. Recently, RBBP6 has been shown to ubiquitinate the mRNA-associated proteinYB-1 through its RING finger domain, causing it to be degraded in the proteasome.RING (Really Interesting New Gene) fingers are small commonly-occurring domains of approximately 70 amino acids in length which coordinate two zinc ions in a cross-brace fashion.They are characterized by a conserved pattern of eight Cysteine or Histidine residues which are involved in coordinating the zinc ions. In terms of this conserved consensus, the RING finger from RBBP6 is expected to coordinate the zinc ions through eight Cysteine residues, making it a “C4C4” RING finger similar to those identified in transcription-associated proteins CNOT4(CCR4-NOT transcription complex, subunit 4) and p44 (interferon-induced protein 44). The amino acid sequence of the domain also shares many similarities with the U-box family of domains, which have an identical three-dimensional structure despite not requiring zinc ions in order to fold. This thesis reports the bacterial expression of a fragment containing the RING finger domain from human RBBP6, and determination of its structure using heteronuclear Nuclear Magnetic Resonance (NMR) spectroscopy. Preliminary NMR analysis of the fragment revealed that the domain was folded, but that it was preceded by an unstructured region at the N-terminus. A shortened fragment was therefore expressed and used for structural studies. Isotope-enriched protein samples were generated by growing bacteria in minimal media supplemented with 15NNH4Cl and 13C-glucose and purified using a combination of glutathione agarose affinity chromatography, anion exchange and size exclusion chromatography. A complete set of heteronuclear NMR data was collected at 600 MHz from which almost complete assignment of the backbone, side-chain and aromatic resonances was achieved. By exchange of Zn2+ with 113Cd2+ we managed to confirm that the domain binds two Zn2+ ions, and confirm that they are coordinated in the expected cross-brace manner. Structural data in the form of 2-Dimensional Nuclear Overhauser Enhancement Spectroscopy (2D-NOESY), 15N-separated NOESY and 13Cseparated NOESY spectra were recorded and used to determine the structure using restrained molecular dynamics on the Combined Assignment and Dynamics Algorithm for NMR Applications (CYANA) platform.As expected, the structure contains a triple-stranded β-sheet packing against an α-helix and two zinc-stabilized loops as found in all RING fingers. However, it also contains a C-terminal helix which packs against an N-terminal loop which is similar to that found in many U-box domains.A search using the DALI server revealed that the structure is most similar to the U-box from CHIP (C-terminus of Hsp70-interacting protein), an E3 ligase that cooperates with Hsp70 to degrade unfolded proteins that cannot be refolded. Using NMR we showed that the domain dimerizes with a KD of approximately 200 Μm, which means that it is dimeric at the concentrations used for NMR structure determination. Chemical shift analysis showed the dimerization interface to be very similar to that identified in U-box domains found in C-terminus of Hsp70 interacting proteins (CHIP).The structural similarities reported here between the RING finger from RBBP6 and the U-box family lead us to conclude that RBBP6 may, like CHIP, play a role in protein quality control.

The recent advances in the Materials Engineering have led to the development of new materials with customized microstructure in which the properties of its constituents and their geometric distribution have a considerable effect on determination of the macroscopic properties of the substance. Direct inclusion of the material microstructure in the analysis on a macro level is challenging since spatial meshes created for the analysis should have enough resolution to be able to accurately capture the geometry of the microstructure. In most cases this leads to a huge finite element model which requires a substantial amount of computational resources. To circumvent this limitation a number of homogenization techniques were developed. By considering a small element of the material, referred to as Representative Volume Element (RVE), homogenization methods make it possible to include the effects of a material’s microstructure on the overall properties at the macro level. However, complexity of the microstructure geometry and the necessity of satisfying periodic boundary conditions introduce additional difficulties into the analysis procedure. In this dissertation we propose a hybrid homogenization method that combines Asymptotic homogenization with MeshFree Solution Structures Method (SSM). Our approach allows realistic inclusion of complex geometry of the microstructure that can be captured from micrographs or micro CT scans. In addition to unprecedented flexibility in handling complex geometries, this method also provides a completely automatic analysis procedure. Using meshfree solution structures simplifies meshing to creating a simple cartesian grid which only needs to contain the domain. This also eliminates manual modifications which usually needs to be performed on meshes created from image data. A computational platform is developed in C++ based on meshfree/asymptotic method. In this platform also a novel meshfree solution structure is designed to provide exact satisfaction of periodic boundary conditions for boundary value problems such as homogenization. Performance of the developed platform is tested over 2D and 3D domains against previously published data and/or conventional finite element methods. After getting satisfactory results, homogenized properties are used to compute localized stress and strain distributions over inhomogeneous structures. Furthermore, effects of geometric features of pores/inclusions on homogenized mechanical properties is investigated and it is demonstrated that the developed platform could provide an automated quantitative analysis tool for studying effects of different design parameters on homogenized properties.

In this work, a pioneering application of the Solution Structure Method (SSM) for structural dynamics problems is presented. Vibration analysis is an important aspect of any design-analysis cycle for which reliable computational methods are required. Unlike many meshfree methods, SSM is capable of {\it exact treatment of all prescribed boundary conditions}. In addition, the method is capable of using basis functions which do not conform to the shape of the geometric model. Together, this defines an unprecedented geometric flexibility of the SSM. This work focused on the development of numerical algorithms for 2D in-plane and 3D natural vibration analysis and 2D in-plane dynamic response. The convergence and numerical properties of the method were evaluated by comparing meshfree results with those obtained using traditional Finite Element Analysis implemented in Solidworks and ANSYS. The numerical experiments presented in this work illustrate that the Solution Structure Method possesses good convergence and in some cases, such as geometries with partially fixed boundaries, this method converges much more rapidly than traditional FEA. Finally, in addition to complex boundary conditions, this method can easily handle complex geometries without losing favorable convergence properties.

Protein solution structures were analyzed by horizontal attenuated total reflectance (ATR) FTIR spectroscopy. Secondary structure compositions determined from analyses of amide-I and II region and amide-III region difference spectra were compared. Data for proteins of known solution structure, cytochrome c, concanavalin A and lysozyme, were compared with those reported in the iiterature. Melittin, a peptide from bee venom whose secondary structural configuration varies depending upon solution conditions was also examined. Acyl-carrier protein (ACP) is a small protein of recognized dynamic structure that in its diverse physiologic roles interacts specifically with numerous different proteins. Horizontal ATR FTIR analysis of ACP's secondary structure indicated a predominately helical structure best defined as a combination of ordered and disordered helices. The FTIR-derived structural composition agreed with those determined for ACP by other techniques. Comparison of independent analyses of the amide-I and III regions to determine protein configuration compositions was a useful method of verifying the internal consistency of the calculated structural compositions of dynamically-structured proteins.

Parmi les voies de signalisation, la voie hedgehog (HH) intervient dans la formation de la polarité segmentaire. Si elle est défectueuse, elle entraine plusieurs malformations. De nombreux cancers présentent une suractivation de cette voie. La voie HH activée par la fixation du ligand HH sur le récepteur Patched (hPtc) et fait intervenir plusieurs partenaires cytoplasmiques dont Supressor of Fused (SUFU).Peu de données moléculaires et structurales sont disponibles pour cette voie et pourtant, ces données sont nécessaires pour comprendre sans ambiguïté son fonctionnement. De plus, la voie HH a été proposée comme pouvant être la cible de traitements chimio thérapeutiques mais, la protéine hPtc est impliquée dans l’efflux des drogues anticancéreuses. Une inhibition de hPtc par la fixation de son ligand entraine l’inhibition de l’efflux de drogues. Néanmoins, le site de fixation de HH sur son récepteur n’a pas encore été déterminé.Durant cette thèse, les travaux effectués ont permis l’étude structurale de la protéine hPtc notamment la détermination du site de fixation de HH. Dans un deuxième volet de cette thèse, j’ai effectué des études structurales de certaines protéines SUFU.Dans un premier temps, je me suis concentrée sur les domaines extracellulaires de hPtc qui ont été décrits comme nécessaires pour la fixation du ligand HH. J’ai cloné une protéine chimère constituée de ces deux domaines liés par le lysozyme du phage T4 (hPtcD1D2). Cette construction a été exprimée dans la bactérie E.coli. Les conditions d’expression testées permettent d’obtenir la protéine sous forme de corps d’inclusion dans le cytoplasme de la bactérie. Dans un deuxième temps, j’ai cloné la protéine dans un vecteur d’expression en levure. De manière concomitante, j’ai exprimé la protéine hPtc tronquée de ses régions N et C terminales (hPtcΛNΛC). Ce sont des régions intrinsèquement désordonnées qui ne permettraient pas une bonne cristallisation de la protéine. L’expression a été effectuée dans la levure. La solubilisation de cette protéine membranaire est en cours d’expérimentation.Ce travail a permis de poser les bases de l’expression de hPtcD1D2 et de hPtcΛNΛC. Ceci va notamment permettre la surexpression de la protéine et sa cristallisation afin de déterminer sa structure 3D et de caractériser le site de fixation de son ligand.Enfin, j’ai entrepris des études structurales des protéines SUFU. Un nouveau site de fixation du Zn a été caractérisé. En effet, après purification de la protéine, j’ai effectué des mesures d’affinité à l’aide d’un composé colorimétrique, le PAR et des expériences de spectroscopie d’émission atomique dans lesquelles j’ai fait varier le pH et la concentration en Zn. Ainsi, j’ai pu déterminer que SUFU a une affinité nanomolaire pour le Zn meilleure à pH 8 qu’à pH 6,5. La fixation du Zn se ferait donc sur un site basique. La structure de SUFU a été publiée en 2013 par deux équipes, je me suis inspirée des conditions de cristallisation de ces deux articles, pour cristalliser SUFU en présence de Zn. Les expériences de dichroïsme circulaire ont permis d’affirmer que ces protéines sont organisées en hélices α et en feuillets β. De plus, grâce à la diffusion des rayons X aux petits angles, j’ai pu déterminer que dSUFU, hSUFU et zSUFU n’ont pas la même conformation en solution. Alors que SUFU de drosophile est un monomère globulaire, les protéines humaine et de poisson zèbre seraient plutôt allongées et dimériques. La région N-terminale potentiellement impliquée dans la dimérisation de hSUFU a été tronquée et hSUFUΛ30 présente des différences d’état d’oligomérisation. / The hedgehog (HH) signalling pathway is involved in the segmentary polarity formation. A dysfunction of this pathway is involved in several malformations. Many cancers are caused by an overactivation of this pathway. The HH signalling pathway is activated by the binding of HH on the receptor Patched (hPtc) and included many cytoplasmic partners such as Suppressor of Fused (SUFU). Few molecular and structural data are available on this pathway even if these data are important to fully understand the pathway functioning. Furthermore, the HH signalling pathway maybe be the target of chemotherapy treatments. However, hPtc is involved in drugs efflux. Inhibition of hPtc by the binding of its ligand HH may lead to this efflux inhibition. Yet, the binding site of HH on its receptor hPtc is not yet determined.During this thesis, the structural study of hPtc have been engaged especially the study of the binding site of HH. On the second hand, I have structurally studied some SUFU proteins.First of all, I have expressed the extracellular domains of hPtc. These domains have been described as necessary for HH binding. I have cloned a chimeric protein made by the extracellular domains of hPtc associated with the lysozyme T4 (hPtcD1D2). This protein have been expressed in the E.Coli bacteria. The protein expressed in inclusion bodies in the cytoplasm of the bacteria. In the other hand, I have cloned the protein in a yeast expression vector. Part of this, I have also expressed the protein hPtc without its N and C terminus regions (hPtcNC). These regions are intrinsically disrupted. They may lead to crystallization problems. The protein has been expressed in yeast.This work permits to expressed hPtcD1D2 and hPtcΛNΛC. This will lead to the expression of the protein and its crystallisation in order to determine its 3D structure and to characterize its ligand binding site.Finally, I structurally studied the protein SUFU. A novel Zn binding site has been characterized. In fact, after the protein purification, I have made affinity measures using a colorimetric compound, PAR. I also performed spectroscopic experiments in which I varied the pH and the Zn concentration. I determined the SUFU has a nanomolar affinity for the Zn best at pH 8 than pH 6.5. Indeed, the Zn binding site may be basic.The SUFU 3D structure has been published in 2013 by two teams. Inspired by their crystallization conditions, I crystallized SUFU with Zn. Circular dichroism experiments permitted to know that the proteins are organized in  helices and  sheets. Moreover, small angles X ray spectroscopy experiments show that dSUFU, hSUFU and zSUFU did not have the same conformation in solution. Drosophila SUFU is globular and human and zebrafish SUFU are long and dimeric. The N-terminal region involved in hSUFU has been removed and hSUFUΛ30 is present in different oligomerization forms.

RNA recognition motifs (RRMs) are a ubiquitous class of proteins which bind RNA in a sequence-specific fashion, often with high affinity. The mechanisms through which this single protein domain recognizes diverse RNA sequences is not fully understood. High-resolution three-dimensional structures are particularly important in understanding the structural features required for RNA recognition and binding. This work presents the structure of an expanded RRM domain from the Drosophila melanogaster Bruno protein. The Bruno protein is involved in establishing proper body patterning during development. This is accomplished through the translational repression of several mRNAs, in particular, the oskar mRNA. Previous work has identified an expanded RRM domain within the Bruno protein. This RRM requires an additional forty amino acids prior to the start of the canonical RRM domain for high affinity RNA binding. The protein was found to contain a canonical RRM domain comprised of four anti-parallel [beta] strands and two [alpha] helices. The RRM is preceded by a ten amino acid loop that interacts with [alpha]₁ and [beta]₂, while the remaining amino acids are flexible in solution. Interestingly, the deletion of these residues does not alter the fold or stability of the RRM domain. Thus, these additional residues must be involved in RNA binding, as they are not required for structure. From these studies, the Bruno RRM represents a new example of protein features required for recognition and high affinity binding of RNA. / text

No description available.