Dentre as células ganglionares da retina existe uma pequena população de células que contem melanopsina e respondem diretamente à luz. Estas são as células ganglionares intrinsecamente fotossensíveis (ipRGCs), cujas funções são principalmente não visuais. Dentre as funções não visuais das ipRGCs sua influência na resposta pupilar dependente da luz foi o objeto central desta tese. Tanto a retina interna, através das ipRGCs, quanto a retina externa, através dos bastonetes e cones, fornecem uma informação neural que regula a resposta pupilar à luz (RPL). Este estudo avaliou a integridade das ipRGCs através do RPL em pacientes com glaucoma primário de ângulo aberto (GPAA), leve, moderado e avançado, e em pacientes com síndrome da apnéia obstrutiva do sono (SAOS), moderada e grave. Também foi avaliada a discriminação cromática e a sensibilidade ao contraste espacial de luminância (SC), a perimetria visual e a espessura da retina avaliada por tomografia de coerência óptica (OCT). Foram avaliados 98 participantes: 45 pacientes com GPAA ( 27, 18; idade média = 65,84 + 10,20), 28 pacientes com SAOS ( 14, 14; idade média = 52,93 + 7,13), e 25 controles ( 17, 8; idade média = 54,27 + 8,88). Após o exame oftalmológico foram avaliadas a SC de grades e a discriminação de cores através do Cambridge Colour Test (CCT). A avaliação do RPL foi feita apresentando-se flashes de 470 e 640 nm, de 1s de duração, em 7 luminâncias desde -3 até 2.4 log cd/m2 em um Ganzfeld Q450 SC (Roland Consult). O RPL foi registrado pelo sistema de eye tracker View Point System (Arrington Research Inc.). Os testes foram realizados em ambos os olhos, de forma monocular e no escuro. Para a comparação dos dados entre os grupos, utilizou-se um modelo de equações de estimação generalizada (GEE), para correção da dependência entre os dois olhos. O RPL dos pacientes com GPAA moderado e avançado apresentou redução significativa na amplitude do pico, dependente da severidade do glaucoma, nas diferentes luminâncias tanto para 470 nm quanto para 640 nm, evidenciando redução das contribuições dos cones e bastonetes ao RPL. As contribuições das ipRGCs ao RPL (avaliadas pela amplitude da resposta sustentada entre 6-8 s) foram também significativamente menores em GPAA moderado e avançado. No estado inicial do GPAA as contribuições das ipRGCs para o RPL encontram-se preservadas. No entanto, o GPAA parece afetar o processamento espacial desde o inicio da doença. Nos pacientes com GPAA leve foi observada uma perda acentuada nas faixas baixas de frequência espacial, compatível com prejuízo seletivo das células ganglionares do tipo M. A SC de pacientes com GPAA moderado e avançado mostrou perdas nas faixas baixas e altas de frequência espacial, apontando um prejuízo nas vias parvo- e margnocelulares. Uma perda significativa da discriminação de cores no eixo azul-amarelo foi observada em todos os estágios do GPAA. O RPL nos pacientes com SAOS está parcialmente preservado, não obstante, as respostas da amplitude do pico para o flash de 470 nm diminuem conforme aumenta a severidade da SAOS. As contribuições dos fotorreceptores da retina externa ao RPL, foram significativamente menores em algumas das luminâncias. Não foram observadas diferenças significativas de SC ou discriminação de cores nos pacientes com SAOS. Em conclusão, no estágio moderado e avançado do glaucoma tanto as contribuições das ipRGCs ao RPL quanto as vias M e P, se encontram mais afetadas do que no inicio do GPAA, quando a via parvocelular e as contribuições das ipRGCs ao RPL parecem estar mais preservadas / Among the retina ganglion cells there are a small population of cells containing melanopsin and which respond directly to light. They are the intrinsically photosensitive ganglion cells (ipRGCs), whose functions are mainly non-visual. Among these non-visual functions of the ipRGCs, their influence on the pupillary response as a function of light was the central subject of this thesis. Both the inner retina through the ipRGCs and the outer retina through the rods and cones, provide neural information that regulates the pupillary light response (PLR) to light. This study evaluated the integrity of ipRGCs through PLR in patients with Primary Open Angle Glaucoma (POAG), mild, moderate and advanced, and in patients with Obstructive Sleep Apnea Syndrome (OSAS), moderate and severe. We evaluated also the color discrimination and achromatic spatial contrast sensitivity (CS), visual perimetry and retinal thickness evaluated by Optical Coherence Tomography (OCT). 98 participants were evaluated, 45 patients with POAG ( 27 18; mean age = 65.84 + 10.20), 28 with OSAS ( 14 14; mean age = 52.93 + 7.13) and 25 controls ( 17 8; mean age = 54.27 + 8.88). After the ophthalmological exam it was evaluated the contrast sensitivity and color discrimination measures using the Cambridge Colour Test (CCT). Pupil responses were elicited by Ganzfeld (Q450 SC, Roland Consult) presentation of 1-sec flashes of 470- and 640-nm at 7 luminance from -3 to 2.4 log cd/m2. PLR was measured with the eye tracker system View Point (Arrington Research Inc.). The tests were performed monocularly, on both eyes, in a darkened room. In order to compare data across groups, we used a General Estimating Equations (GEE) to adjust for within subject inter-eye correlations. Patients with moderate and advanced POAG had a significantly decreased PLR that depends on the severity of the glaucoma, for both the 470- and 640-nm stimuli, making evident the reduction of the contributions of the cones and rods to the PLR. The contributions of ipRGCs to PLR (assessed by the amplitude of the sustained response between 6 8 sec) were also significantly lower in patients with moderate and advanced POAG. In the initial and mild stages of POAG the contribution of ipRGCs to the PLR is preserved. However, POAG appears to affect spatial processing from the early stages of the disease. Mild-POAG patients showed a marked loss in the low spatial frequency bands, compatible with selective loss of magnocellular ganglion cells. The CS of patients with moderate and advanced POAG showed losses at both low and high spatial frequencies, suggesting a loss in both parvo- and margnocellular channels. A significant loss of color discrimination along the blue-yellow axis was observed in all stages of POAG. The PLR in patients with OSAS is partially preserved, however the peak amplitude responses for the 470-nm flash decreased with increased severity of OSAS. The contributions of the photoreceptors of the outer retina to the PLR were significantly lower at some of the luminance. Significant differences in CS or color discrimination were not observed in patients with OSAS. In conclusion, in moderate and advanced stages of glaucoma, both the contributions of ipRGCs to PLR as well as the M- and P channels, were found more affected than at the beginning of POAG, in contrast the parvocellular channel and the contributions of ipRGCs on the PLR would be more preserved

Proteins are an important component of living organisms, composed of one or more polypeptide chains, each containing hundreds or even thousands of amino acids of 20 standard types. The structure of a protein from the sequence determines crucial functions of proteins such as initiating metabolic reactions, DNA replication, cell signaling, and transporting molecules. In the past, proteins were considered to always have a well-defined stable shape (structured proteins), however, it has recently been shown that there exist intrinsically disordered proteins (IDPs), which lack a fixed or ordered 3D structure, have dynamic characteristics and therefore, exist in multiple states. Based on this, we extend the mapping of protein sequence not only to a fixed stable structure but also to an ensemble of protein conformations, which help us explain the complex interaction within a cell that was otherwise obscured. The objective of this dissertation is to develop effective ab initio methods and tools for protein un/structure prediction by developing effective statistical energy function, conformational search method, and disulfide connectivity patterns predictor. The key outcomes of this dissertation research are: i) a sequence and structure-based energy function for structured proteins that includes energetic terms extracted from hydrophobic-hydrophilic properties, accessible surface area, torsion angles, and ubiquitously computed dihedral angles uPhi and uPsi, ii) an ab initio protein structure predictor that combines optimal energy function derived from sequence and structure-based properties of proteins and an effective conformational search method which includes angular rotation and segment translation strategies, iii) an SVM with RBF kernel-based framework to predict disulfide connectivity pattern, iv) a hydrophobic-hydrophilic property based energy function for unstructured proteins, and v) an ab initio conformational ensemble generator that combines energy function and conformational search method for unstructured proteins which can help understand the biological systems involving IDPs and assist in rational drugs design to cure critical diseases such as cancer or cardiovascular diseases caused by challenging states of IDPs.

No description available.

The group 2 late embryogenesis abundant (LEA) proteins, also known as the dehydrins, are intrinsically disordered proteins that are expressed in plants experiencing extreme environmental conditions such as drought or low temperature. In this work, we study the potential roles that dehydrins may have in stabilizing membranes and actin microfilaments during cold stress. We have cloned and expressed in E. coli two dehydrins from Thellungiella salsuginea, denoted TsDHN-1 (acidic) and TsDHN-2 (basic). These proteins were expressed as SUMO-fusion proteins for in vitro phosphorylation by casein kinase II (CKII), and for structural analysis by CD and Fourier transform infrared (FTIR) spectroscopy. We show using transmission-FTIR spectroscopy that ordered secondary structure is induced and stabilized in these proteins by association with large unilamellar vesicles emulating the lipid compositions of plant plasma and organellar membranes. The increase in secondary structure by membrane association is further facilitated by the presence of Zn2+. Lipid composition and temperature have synergistic effects on the secondary structure. Our single molecule force spectroscopy studies also suggest tertiary folding of both TsDHN-1 and TsDHN-2 induced by association with lipids. From Langmuir-Blodgett monolayer compression studies, and from topographic studies using atomic force microscopy at variable temperature, we conclude that TsDHN-1 stabilizes the membrane at lower temperatures. Finally, we show that the conformations of TsDHN-1 and TsDHN-2 are affected by pH, interactions with cations and membranes, and phosphorylation. Actin assembly by these dehydrins was assessed by sedimentation assays, and viewed by transmission electron and atomic force microscopy. Phosphorylation enabled both dehydrins to polymerize actin filaments, a phenomenon that may occur in the cytosols of plant cells undergoing environmental stress. These results support the hypothesis that dehydrins stabilize plant organellar membranes and/or the cytoskeleton in conditions of stress, and further that phosphorylation may be an important feature of this stabilization. / NSERC

Dentre as células ganglionares da retina existe uma pequena população de células que contem melanopsina e respondem diretamente à luz. Estas são as células ganglionares intrinsecamente fotossensíveis (ipRGCs), cujas funções são principalmente não visuais. Dentre as funções não visuais das ipRGCs sua influência na resposta pupilar dependente da luz foi o objeto central desta tese. Tanto a retina interna, através das ipRGCs, quanto a retina externa, através dos bastonetes e cones, fornecem uma informação neural que regula a resposta pupilar à luz (RPL). Este estudo avaliou a integridade das ipRGCs através do RPL em pacientes com glaucoma primário de ângulo aberto (GPAA), leve, moderado e avançado, e em pacientes com síndrome da apnéia obstrutiva do sono (SAOS), moderada e grave. Também foi avaliada a discriminação cromática e a sensibilidade ao contraste espacial de luminância (SC), a perimetria visual e a espessura da retina avaliada por tomografia de coerência óptica (OCT). Foram avaliados 98 participantes: 45 pacientes com GPAA ( 27, 18; idade média = 65,84 + 10,20), 28 pacientes com SAOS ( 14, 14; idade média = 52,93 + 7,13), e 25 controles ( 17, 8; idade média = 54,27 + 8,88). Após o exame oftalmológico foram avaliadas a SC de grades e a discriminação de cores através do Cambridge Colour Test (CCT). A avaliação do RPL foi feita apresentando-se flashes de 470 e 640 nm, de 1s de duração, em 7 luminâncias desde -3 até 2.4 log cd/m2 em um Ganzfeld Q450 SC (Roland Consult). O RPL foi registrado pelo sistema de eye tracker View Point System (Arrington Research Inc.). Os testes foram realizados em ambos os olhos, de forma monocular e no escuro. Para a comparação dos dados entre os grupos, utilizou-se um modelo de equações de estimação generalizada (GEE), para correção da dependência entre os dois olhos. O RPL dos pacientes com GPAA moderado e avançado apresentou redução significativa na amplitude do pico, dependente da severidade do glaucoma, nas diferentes luminâncias tanto para 470 nm quanto para 640 nm, evidenciando redução das contribuições dos cones e bastonetes ao RPL. As contribuições das ipRGCs ao RPL (avaliadas pela amplitude da resposta sustentada entre 6-8 s) foram também significativamente menores em GPAA moderado e avançado. No estado inicial do GPAA as contribuições das ipRGCs para o RPL encontram-se preservadas. No entanto, o GPAA parece afetar o processamento espacial desde o inicio da doença. Nos pacientes com GPAA leve foi observada uma perda acentuada nas faixas baixas de frequência espacial, compatível com prejuízo seletivo das células ganglionares do tipo M. A SC de pacientes com GPAA moderado e avançado mostrou perdas nas faixas baixas e altas de frequência espacial, apontando um prejuízo nas vias parvo- e margnocelulares. Uma perda significativa da discriminação de cores no eixo azul-amarelo foi observada em todos os estágios do GPAA. O RPL nos pacientes com SAOS está parcialmente preservado, não obstante, as respostas da amplitude do pico para o flash de 470 nm diminuem conforme aumenta a severidade da SAOS. As contribuições dos fotorreceptores da retina externa ao RPL, foram significativamente menores em algumas das luminâncias. Não foram observadas diferenças significativas de SC ou discriminação de cores nos pacientes com SAOS. Em conclusão, no estágio moderado e avançado do glaucoma tanto as contribuições das ipRGCs ao RPL quanto as vias M e P, se encontram mais afetadas do que no inicio do GPAA, quando a via parvocelular e as contribuições das ipRGCs ao RPL parecem estar mais preservadas / Among the retina ganglion cells there are a small population of cells containing melanopsin and which respond directly to light. They are the intrinsically photosensitive ganglion cells (ipRGCs), whose functions are mainly non-visual. Among these non-visual functions of the ipRGCs, their influence on the pupillary response as a function of light was the central subject of this thesis. Both the inner retina through the ipRGCs and the outer retina through the rods and cones, provide neural information that regulates the pupillary light response (PLR) to light. This study evaluated the integrity of ipRGCs through PLR in patients with Primary Open Angle Glaucoma (POAG), mild, moderate and advanced, and in patients with Obstructive Sleep Apnea Syndrome (OSAS), moderate and severe. We evaluated also the color discrimination and achromatic spatial contrast sensitivity (CS), visual perimetry and retinal thickness evaluated by Optical Coherence Tomography (OCT). 98 participants were evaluated, 45 patients with POAG ( 27 18; mean age = 65.84 + 10.20), 28 with OSAS ( 14 14; mean age = 52.93 + 7.13) and 25 controls ( 17 8; mean age = 54.27 + 8.88). After the ophthalmological exam it was evaluated the contrast sensitivity and color discrimination measures using the Cambridge Colour Test (CCT). Pupil responses were elicited by Ganzfeld (Q450 SC, Roland Consult) presentation of 1-sec flashes of 470- and 640-nm at 7 luminance from -3 to 2.4 log cd/m2. PLR was measured with the eye tracker system View Point (Arrington Research Inc.). The tests were performed monocularly, on both eyes, in a darkened room. In order to compare data across groups, we used a General Estimating Equations (GEE) to adjust for within subject inter-eye correlations. Patients with moderate and advanced POAG had a significantly decreased PLR that depends on the severity of the glaucoma, for both the 470- and 640-nm stimuli, making evident the reduction of the contributions of the cones and rods to the PLR. The contributions of ipRGCs to PLR (assessed by the amplitude of the sustained response between 6 8 sec) were also significantly lower in patients with moderate and advanced POAG. In the initial and mild stages of POAG the contribution of ipRGCs to the PLR is preserved. However, POAG appears to affect spatial processing from the early stages of the disease. Mild-POAG patients showed a marked loss in the low spatial frequency bands, compatible with selective loss of magnocellular ganglion cells. The CS of patients with moderate and advanced POAG showed losses at both low and high spatial frequencies, suggesting a loss in both parvo- and margnocellular channels. A significant loss of color discrimination along the blue-yellow axis was observed in all stages of POAG. The PLR in patients with OSAS is partially preserved, however the peak amplitude responses for the 470-nm flash decreased with increased severity of OSAS. The contributions of the photoreceptors of the outer retina to the PLR were significantly lower at some of the luminance. Significant differences in CS or color discrimination were not observed in patients with OSAS. In conclusion, in moderate and advanced stages of glaucoma, both the contributions of ipRGCs to PLR as well as the M- and P channels, were found more affected than at the beginning of POAG, in contrast the parvocellular channel and the contributions of ipRGCs on the PLR would be more preserved

La protéine NS5A est essentielle pour la réplication et l'assemblage du virus de l'hépatite C (VHC), et elle constitue une cible thérapeutique prometteuse pour le développement d'antiviraux. Cependant, aucune fonction claire n'a encore été décrite pour NS5A, et les connaissances structurales restent limitées. Ainsi, nous avons caractérisé l'état intrinsèquement désordonné des domaines D2 et D3 de NS5A en décrivant leurs espaces conformationnels et leurs potentialités de repliement en combinant différentes méthodes biophysiques. Nous avons aussi mis en évidence la variabilité structurale du domaine D2 au sein des génotypes du VHC, ce qui pourrait être en rapport avec les différences de pathogénie et d'efficacité des thérapies observées selon les génotypes. L'interaction de D2 et D3 avec la cyclophiline humaine A (CypA) a été étudiée par résonance plasmonique de surface (SPR). Bien que des mutations au sein du domaine D2 rendent la réplication du VHC moins dépendante de la présence de CypA, ces mutations n'empêchent pas la liaison entre D2 et CypA. En revanche, elles induisent des perturbations structurales qui pourraient affecter la cinétique d'interconversion des conformères de D2. Nous avons montré par SPR que D2 et D3 interagissent avec le domaine de fixation à l'ADN du récepteur nucléaire FXR. Cette interaction pourrait inhiber la fixation de FXR sur sa cible ADN, suggérant une implication de NS5A dans la modulation de l'activité transcriptionnelle de ce récepteur nucléaire. L'ensemble de ces informations, nous a permis de proposer un modèle de la structure globale de NS5A permettant une meilleure compréhension des propriétés structurales et fonctionnelles de cette protéine énigmatique / NS5A is essential for HCV replication and particle assembly, and constitutes a very promising drug target. However, no clear function has yet been described for NS5A, and structural knowledge remains limited. We characterized the intrinsically disordered nature of NS5A domains D2 and D3, and describe their folding propensity and their overall conformational behaviour by combining different biophysical methods. We also highlighted the structural variability of D2 domain in HCV genotypes, which might be correlated with the disparities observed between genotypes in terms of pathogenesis and efficiency of therapies. The interactions between D2 and D3 with human cyclophilin A (CypA) was analysed by surface plasmon resonance (SPR). We showed that mutations in the D2 domain conferring resistance of HCV replication to CypA inhibitors did not prevent the interaction between D2 and CypA. However, they induce structural perturbations that may affect the kinetics of conformers interconversion of D2. We also showed by SPR that D2 and D3 interact with the of DNA-binding domain of the nuclear receptor FXR (farnesoid X receptor alpha). This interaction reduce the binding of FXR to its DNA target, suggesting an involvement of NS5A in the modulation of the transcriptional activity of FXR. All this data led us to propose a model of the overall structure of NS5A, which provides a useful template for a better understanding of structural and functional properties of this enigmatic protein

No description available.

Le travail de thèse consistera à explorer et caractériser l'ensemble conformationnel de protéines intrinsèquement désordonnées (IDPs) en utilisant plusieurs techniques complémentaires, notamment des simulations avancées de dynamique moléculaire et la diffusion des rayons X aux petits angles (SAXS). Les IDPs sont des protéines possédant une ou plusieurs régions n'ayant pas de structures secondaires stables lorsqu'elles sont isolées, mais pouvant en adopter lors de leur association avec de multiples autres protéines. La question, à laquelle ce travail souhaite répondre dans le cas de trois IDPs, est de savoir si ces éléments de structures secondaires, formés à l'interfaces des complexes protéine-protéine, pré-existent de façon transitoire, ou non, à l'état non-lié des IDPs en solution. S'il est possible d'identifier et de caractériser ces éléments de reconnaissance moléculaire dans les IDPs isolées, alors les résultats de ce travail permettront de guider par la suite la détermination des structures de complexes protéiques impliquant des IDPs. / The PhD work will consist in exploring and characterizing the conformational ensemble of intrinsically disordered proteins (IDPs), by using several complementary methods, including enhanced molecular dynamics simulations and small angle X-ray scattering (SAXS). IDPs are proteins having one or several regions that lack stable secondary structures in the unbound state, but which can adopt various structured conformations to bind other proteins. In the case of three IDPs, the project aims to answer the question of whether these secondary structures formed at the protein-protein interfaces transiently pre-exist or not in the unbound state of solvated IDPs. If it is possible to identify and characterize these molecular recognition features (MoRFs) in the IDP unbound state, then the results of this work will subsequently help to determine the structures of protein complexes involving IDPs.

Morphogenesis of the intricate patterns of diatom silica cell walls is a protein-guided process, yet to date only very few such silica biomineralization proteins have been identified. Therefore, it is currently unknown whether all diatoms share conserved proteins of a basal silica forming machinery, and whether unique proteins are responsible for the morphogenesis of species-specific silica patterns. To answer these questions, we extracted proteins from the silica of three diatom species (Thalassiosira pseudonana, Thalassiosira oceanica, and Cyclotella cryptica) by complete demineralization of the cell walls. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) analysis of the extracts identified 92 proteins that we name ‘soluble silicome proteins’ (SSPs). Surprisingly, no SSPs are common to all three species, and most SSPs showed very low similarity to one another in sequence alignments. In-depth bioinformatics analyses revealed that SSPs could be grouped into distinct classes based on short unconventional sequence motifs whose functions are yet unknown. The results from the in vivo localization of selected SSPs indicates that proteins, which lack sequence homology but share unconventional sequence motifs may exert similar functions in the morphogenesis of the diatom silica cell wall.

Indiana University-Purdue University Indianapolis (IUPUI) / Intrinsically disordered proteins are proteins characterized by lack of stable tertiary structures under physiological conditions. Evidence shows that disordered proteins are not only highly involved in protein interactions, but also have the capability to associate with more than one partner. Short disordered protein fragments, called “molecular recognition features” (MoRFs), were hypothesized to facilitate the binding diversity of highly-connected proteins termed “hubs”. MoRFs often couple folding with binding while forming interaction complexes. Two protein disorder mechanisms were proposed to facilitate multiple partner binding and enable hub proteins to bind to multiple partners: 1. One region of disorder could bind to many different partners (one-to-many binding), so the hub protein itself uses disorder for multiple partner binding; and 2. Many different regions of disorder could bind to a single partner (many-to-one binding), so the hub protein is structured but binds to many disordered partners via interaction with disorder. Thousands of MoRF-partner protein complexes were collected from Protein Data Bank in this study, including 321 one-to-many binding examples and 514 many-to-one binding examples. The conformational flexibility of MoRFs was observed at atomic resolution to help the MoRFs to adapt themselves to various binding surfaces of partners or to enable different MoRFs with non-identical sequences to associate with one specific binding pocket. Strikingly, in one-to-many binding, post-translational modification, alternative splicing and partner topology were revealed to play key roles for partner selection of these fuzzy complexes. On the other hand, three distinct binding profiles were identified in the collected many-to-one dataset: similar, intersecting and independent. For the similar binding profile, the distinct MoRFs interact with almost identical binding sites on the same partner. The MoRFs can also interact with a partially the same but partially different binding site, giving the intersecting binding profile. Finally, the MoRFs can interact with completely different binding sites, thus giving the independent binding profile. In conclusion, we suggest that protein disorder with post-translational modifications and alternative splicing are all working together to rewire the protein interaction networks.