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Shakedown of porous materials / Adaptation plastique des matériaux poreuxZhang, Jin 28 September 2018 (has links)
Cette thèse est consacrée à la détermination des états limites de l'adaptation des matériaux ductiles poreux sur la base du théorème de Melan et en considérant le modèle de la sphère creuse. Dans un premier temps, nous proposons le critère analytique macroscopique d'adaptation avec la matrice de von Mises sous deux charges particuliers, alterné et pulsé. Le critère analytique dépend des première et seconde invariants des contraintes macroscopiques, du signe du troisième et du coefficient de Poisson. Ensuite, ce critère est étendu aux charges cycliques répétées générales par la construction d'un champ de contraintes résiduelles d'essai plus approprié permettant simultanément des calculs analytiques et l'amélioration du modèle précédent. De plus, il est également utilisé pour les matériaux ductiles poreux avec une matrice de Drucker-Prager.L'idée repose d'abord sur la solution exacte pour le charge purement hydrostatique. Il s'avère que la ruine se produit par fatigue. Ensuite, des champs de contrainte d'essai appropriés sont construits avec des termes supplémentaires pour capter les effets de cisaillement. Le domaine de sécurité, défini par l'intersection du domaine d'adaptationet celui d'analyse limite (la ruine survenant brusquement par formation d'un mécanisme au premier cycle), est entièrement comparé avec des simulations élasto-plastique incrémentales et des calculs directs simplifiés.Enfin, nous fournissons une méthode numérique directe pour prédire le domaine de sécurité de l'adaptation des matériaux poreux soumis à des charges variant de manière indépendante en considérant le chemin critique du domaine de chargement au lieu de l'histoire entière. Le problème de l'adaptation est transformé en un problème d'optimisation de grande taille, qui peut être résolu efficacement par l'optimiseur non-linéaire IPOPT pour donner non seulement le facteur de charge limite, mais aussi le champ de contrainte résiduelle correspondant à l'état d'adaptation. / This thesis is devoted to the determination of shakedown limit states of porous ductile materials based on Melan's static theorem by considering the hollow sphere model, analytically and numerically. First of all, we determine the analytical macroscopic shakedown criterion of the considered unit cell with von Mises matrix under alternating and pulsating special loading cases. The proposed macroscopic analytical criterion depends on the first and second macroscopic stresses invariants, the sign of the third one and Poisson's ratio. Then, the procedure is extended to the general cyclically repeated loads by the construction of a more appropriate trial residual stress field allowing analytical computations and the improvement of the previous model simultaneously. Moreover, this approach is applied to porous materials with dilatant Drucker-Prager matrix.The idea relies firstly on the exact solution for the pure hydrostatic loading condition. It turns out that the collapse occurs by fatigue. Next, suitable trial stress fields are built with additional terms to capture the shear effects. The safety domain, defined by the intersection of the shakedown limit domain and the limit analysis domain corresponding to the sudden collapse by development of a mechanism at the first cycle, is fully compared with step-by-step incremental elastic-plastic simulations and simplified direct computations. At last, we provide a direct numerical method to predict the shakedown safety domain of porous materials subjected to multi-varying independent loadings by considering the critical loading path of the load domain instead of the whole history. The shakedown problem is transformed into a large-size optimization problem, which can be solved efficiently by the non-linear optimizer IPOPT to give out not only the limit load factor, but also the corresponding residual stress field for the shakedown state.
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Lentigo maligno microinvasivoCamboim, Denise Cruz January 2016 (has links)
Orientador: Mariângela Esther Alencar Marques / Resumo: O uso da imuno-histoquímica pode aumentar a acurácia na detecção de melanócitos neoplásicos na derme. Com o objetivo de pesquisar microinvasão, cento e nove casos previamente diagnosticados como lentigo maligno (LM) foram resgatados dos arquivos do Departamento de Patologia da Faculdade de Medicina de Botucatu, da Universidade Estadual Paulista (FMB/UNESP) no período de 01/01/2002 a 01/01/2014. As lâminas histológicas de todos os casos foram revisadas pelos autores para confirmação do diagnóstico e seleção do bloco mais representativo para realização de estudo imuno-histoquímico com Melan-A e MITF. Em 25 casos (22,9%) foi observada invasão focal da derme por melanócitos neoplásicos claramente imunomarcados pelo Melan-A. Nos locais onde se evidenciou invasão foi realizada a medida da espessura de Breslow que variou de 0,1 a 0,45 mm. A coloração imuno-histoquímica com MITF evidenciou positividade focal na derme, porém a identificação das células coradas não permitiu a mesma segurança da coloração pelo Melan-A. Todas as lâminas de imuno-histoquímica foram contracoradas pelo Giemsa para diferenciar positividade para o anticorpo testado e melanina. O presente estudo permitiu identificar microinvasão dérmica em 22,9% dos casos de lentigo maligno, mostrando a possibilidade de estadiamento e tratamento inadequado quando utilizada a técnica de rotina. Os achados são um alerta para os patologistas e clínicos, especialmente em lesões de grandes dimensões e associadas com infiltrado linf... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: The use of immunohistochemistry can enhance the accuracy in detecting neoplastic melanocytes in the dermis. In order to search for microinvasion, one hundred and nine cases previously diagnosed as lentigo maligna (LM) were retrieved from the archives of the Department of Pathology, Faculty of Medicine of Botucatu, Universidade Estadual Paulista (FMB / UNESP) in the period of 01/01 / 2002 to 01/01/2014. The histological slides of all cases were reviewed by the authors to confirm the diagnosis and selection of the most representative block for performing immunohistochemical study with Melan-A, and MITF. In 25 cases (22.9%) was observed focal dermal invasion by neoplastic melanocytes clearly immunostained for Melan-A. In these cases the Breslow thickness ranged between 0.1 and 0.45mm. Immunohistochemical staining showed MITF focal positivity in the dermis, but did not allow the same certainty of Melan-A staining. In order to distinguish melanin in macrophage cytoplasm from brown-staining melanocytes, the slides were counterstained by Giemsa. This study identified dermal microinvasion in 22.9% cases of lentigo maligna, showing the possibility of inadequate staging and treatment when using the routine technique. The findings are a warning for pathologists and clinicians, especially in large lesions and associated with lymphocytic infiltrate that obscures their limits. / Doutor
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Utvärdering av en immunhistokemisk panel för malignt melanomKarlsson, Sofie January 2016 (has links)
För att diagnostisera malignt melanom och dess undergrupper används immunhistokemi för att färga in celler som uttrycker specifika protein. Särskilt desmoplastiska melanom kan initialt felbedömas baserat på utseendet som ärr, och det är därför viktigt att ha sensitiva antikroppar för att diagnostisera dem. Elva arkiverade patientprover (varav tre epiteloida melanom, fyra spolcelliga, tre desmoplastiska och ett akralt lentiginöst) färgades in med antikroppar mot CK18, HMB-45, Melan-A, S100, SOX10 och synaptophysin. Alla prover var negativa för CK18, nio var positiva för HMB-45 och Melan-A (de negativa var båda desmoplastiska melanom) och alla var positiva för S100 och SOX10. Synaptophysin var positiv i alla epiteloida melanom och det akralt lentiginösa melanomet, två av de fyra spolcelliga melanomen och negativ i alla desmoplastiska melanom. Fördelarna med SOX10, som tidigare studier i ämnet har påvisat, observerades inte i denna studie, troligen på grund av begränsningen i patientmaterial. Trots det verkar SOX10 vara ett användbart tillägg i melanompanelen, eller kanske till och med kan ersätta S100, baserat på tidigare studier.
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Immunhistologische Untersuchungen an primären Melanomen und deren Metastasen mit SM5-1, einem neuen monoklonalen AntikörperReinke, Susanne 18 October 2004 (has links)
Der monoklonale Antikörper SM5-1 wurde in Vorarbeiten mittels eines Immunisierungsprotokolls (Kooperation Prof. Guo, Cleveland, USA) von einer humanen Melanom-Zell-Linie gewonnen. In der vorliegenden Arbeit wurde an nicht-melanozytären benignen Geweben, 16 Nävi, 84 nicht-melanozytären Tumoren sowie 745 Melanomproben das Färbeverhalten von SM5-1 mittels Immunhistochemie charakterisiert. SM5-1 wurde zunächst mit HMB-45 und anti-S100 an 250 primären und 151 metastasierten Melanomen und in einer zweiten Stichprobe mit Antikörpern gegen Melan-A/MART-1 (A103) und Tyrosinase (T311) an 101 primären und 243 metastasierten Melanomen verglichen. Es zeigte sich, dass SM5-1 für normale Zellen negativ ist. SM5-1, anti-S100 und HMB-45 färbten 100% der Nävi und 97 - 99% der 250 primären Melanome. Während SM5-1 und anti-S100 96% der 151 Melanommetastasen korrekt identifizierten, waren für HMB-45 nur 83% der Proben positiv. Alle HMB-45 negativen Metastasen reagierten mit SM5-1. Weder SM5-1 noch HMB-45 färbten nicht-melanozytäre Tumore, wohingegen der unspezifischere Antikörper anti-S100 21 von 84 dieser Tumore färbte. Insgesamt wurde beim primären und metastasierten Melanom für SM5-1 eine Sensitivität von 98%, für HMB-45 von 93% und für anti-S100 von 97% beobachtet. Im Vergleich der Antikörper SM5-1, A103 und T311 färbten SM5-1 92,4%, A103 82,9% und T311 71,2% der insgesamt 344 primären und metastasierten Melanome. SM5-1 zeigte innerhalb einer Tumorzellpopulation ein homogeneres Färbeverhalten und eine höhere Färbeintensität bei den 243 Melanommetastasen als A103 und T311. Der monoklonale Antikörper SM5-1 zeigte gegenüber den gebräuchlichen Antikörpern erhebliche Vorteile bei der immunhistochemischen Beurteilung des Melanoms, insbesondere bei dessen Metastasen. Somit kann er als Marker der ersten Wahl bei der immunhistochemischen Diagnostik von Melanomen empfohlen werden. Um die Rolle des durch SM5-1 erkannten Antigens zu verstehen, sind jedoch noch weitere Untersuchungen notwendig. / Antibodies such as HMB-45 and anti-S100 protein have been widely used as markers of malignant melanoma. Using a subtractive immunization protocol in preliminary works (cooperation Prof. Guo, Cleveland, USA), the monoclonal antibody SM5-1 was generated from a mouse model of human melanoma. The immunhistochemical staining of SM5-1 was studied in paraffin-embedded specimens of normal non-melanocytic tissue, melanocytic nevi of the skin (n = 16), non-melanocytic neoplasms (n = 84) and 745 melanomas. 250 primary melanomas and 151 metastases were compared with HMB-45 and anti-S100 staining. Further 101 primary melanomas and 243 metastases were compared with Melan-A/MART-1 (A103) and tyrosinase (T311). Staining of normal cells for SM5-1 was found to be negative. SM5-1, anti-S100 and HMB-45 reacted with nevi and 97 - 99% of 250 primary melanomas. Whereas SM5-1 and anti-S100 showed a high degree of positive staining in 96% of 151 metastases, only 83% reacted with HMB-45. All HMB-45-negative melanoma metastases were found to be positive for SM5-1. Whereas neither SM5-1 nor HMB-45 stained any of 84 specimens from non-melanocytic neoplasms, anti-S100 was positive in 21/84. Altogether SM5-1 has a sensitivity of 98%, HMB-45 of 93% and anti-S100 of 97% for primary and metastatic melanomas. SM5-1 stained 92,3%, A103 82,9% and T311 71,2% of 344 primary and metastatic melanomas. SM5-1 showed a stronger and more homogeneous reactivity as A103 und T311 in metastases (n = 243). All tested antibodies had a comparable staining intensity for primary melanomas (n = 101). The monoclonal antibody SM5-1 appears to have advantages for the immunhistochemical analysis of melanoma over currently available antibodies, especially for melanoma metastases. Therefore it is useful as a first line reagent in immunohistochemistry of melanoma. Further studies are needed to elucidate the exact nature of the antigen recognized by SM5-1.
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Die Modulation des Ubiquitin-Proteasom-Systems als Immunevasionsmechanismus des malignen MelanomsKeller, Martin 13 August 2009 (has links)
Die effiziente Präsentation von Tumorepitopen stellt einen kritischen Faktor zur Eliminierung von Tumorzellen durch die CD8+ cytotoxische T-Lymphozyten (CTL) vermittelte Immunantwort dar. Eine wichtige Rolle spielt in diesem Zusammenhang die effiziente Generierung von Tumorepitopen durch das Ubiquitin-Proteasom-System (UPS). Veränderungen von Komponenten des UPS, die an der Degradation und Prozessierung von Antigenen beteiligt sind, können daher zur Immunevasion von Tumorzellen gegenüber CTL führen. In der vorliegenden Arbeit wurden zwei unterschiedliche UPS-assoziierte Immunevasionsmechanismen des malignen Melanoms identifiziert, die auf einer ineffizienten Präsentation des immundominanten Tumorepitops Melan-A26-35 basieren. Ein Mechanismus beruht auf den unterschiedlichen katalytischen Eigenschaften von Proteasomsubtypen, deren Expression durch INFgamma induziert wird. Proteasomen, die einerseits die Immunountereinheiten beta1i und/oder beta2i beinhalten, oder anderseits mit dem Proteasomaktivator 28 (PA28) assoziiert sind, führen zu einer drastisch reduzierten Generierung des Tumorepitops Melan-A26-35. In beiden Fällen ist dies auf eine ineffiziente Prozessierung des N-Terminus des Epitops zurückzuführen. Der andere Immunevasionsmechanismus steht im Zusammenhang mit der ER-assoziierten Degradation (ERAD), die den retrograden Transport von Proteinen aus dem Endoplasmatischen Retikulum (ER) ins Cytosol zur proteasomalen Degradation beinhaltet. Durch Immunselektion mittels Melan-A26-35-spezifischen CTL wurden cytolyseresistente Melanomzellen identifiziert, deren Resistenz auf eine defiziente ER-assoziierte Degradation zurückzuführen ist. Dieser Defekt beruht auf einer verminderten Expression von ERAD-Komponenten, deren Reduktion die Verfügbarkeit des Antigens Melan-A zur proteasomalen Degradation und Generierung des immundominanten Epitops Melan-A26-35 wesentlich limitiert. / Efficient presentation of tumor epitopes by MHC class I molecules on the cell surface is a prerequisite for the elimination of tumor cells by cytotoxic CD8+ T lymphocytes. The generation of these epitopes requires the degradation and processing of proteins by the ubiquitin proteasome system (UPS). Therefore alterations of UPS components can lead to tumor escape from immune recognition as a result of decreased epitope generation. In the present thesis two different UPS connected immune escape mechanisms of melanoma cells were identified. Both are based on an impaired generation of the immunodominant epitope Melan-A26-35 derived from Melan-A/MART-1 tumor antigen. One mechanism is mediated by the expression of different INFgamma-inducible proteasome immunosubunits leading to the formation of intermediate proteasome subtypes, which differ in their cleavage site preferences. Purified proteasomes harboring the immunosubunits beta1i and/or beta2i show a dramatic decrease in the generation of the Melan-A26-35 epitope. In addition, the INFgamma induced association of proteasomes with the proteaosome activator 28 (PA28) results in a reduced epitope generation. Both mechanisms are induced by an inefficient processing of the epitope’s N-terminus. The second immune escape mechanism is caused by defects of the ER-associated degradation pathway (ERAD). ERAD mediates the transport of ER-proteins back to the cytosolic compartment for proteasomal degradation. Via immunselection of tumor cells with Melan-A26-35 specific CTL, cytolysis resistant cells were identified. Resistance to CTL mediated lysis was shown to be connected to a decreased expression of ERAD components. This defect of the ERAD pathway limits the availability of the Melan-A protein and as consequence the generation of the immunodominant Melan-A26-35 epitope by proteasomes.
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Étude du rôle des lymphocytes T chez les receveurs pédiatriques de greffe de sang de cordon ombilicalMerindol, Natacha 11 1900 (has links)
La transplantation de sang de cordon ombilical (TSCO) est utilisée pour traiter les enfants atteints de maladies hématologiques en l’absence de donneurs apparentés compatibles. Elle est associée avec des risques plus élevés d’échec de greffe et d’infections opportunistes dans les premiers mois qui suivent la transplantation en comparaison avec une greffe de moelle osseuse. Par contre, la TSCO comporte un risque plus faible de maladie du greffon contre l’hôte et une incidence comparable de rechute de leucémie. Ces quatre complications impliquent directement les lymphocytes T. Dans le but de mieux comprendre le schéma particulier des évènements qui suivent la TSCO et d’améliorer le pronostic des patients, nous avons étudié le potentiel fonctionnel, la persistance et la reconstitution antivirale des lymphocytes T au sein d’un groupe d’enfants transplantés de sang de cordon ombilical (SCO). Étant donné que le SCO contient une majorité de lymphocytes T naïfs, nous avons étudié les lymphocytes T spécifiques au HLA-A2:Melan-A26-35 A27L; seul répertoire naïf et abondant caractérisé chez l’homme. Nous avons observé que les lymphocytes T du SCO se différencient en populations effectrices, s’oligoclonalisent, produisent de l’IFN-γ et lysent spécifiquement leur cible suite à la stimulation. Néanmoins, ces cellules produisent moins d’IFN-γ et sont moins bifonctionnelles que leurs homologues issus du sang périphérique d’adultes. Chez les patients, les lymphocytes T du SCO s’épuisent après la TSCO : ils s’oligoclonalisent dramatiquement, sont principalement en différenciation terminale, et une importante fréquence exprime PD-1 (« programmed death-1 ») dans les 3 à 6 premiers mois post-greffe. Très peu de patients sont capables de développer des réponses antivirales durant cette période et la fréquence de lymphocytes T qui expriment PD-1 semble aussi avoir un impact sur le risque subséquent de faire une rechute de leucémie. La deuxième vague de lymphocytes T émergeant à 6 mois post-TSCO mène à une population fonctionnelle et diversifiée. En conclusion, la fonctionnalité des lymphocytes T présents dans les 3 à 6 premiers mois post-TSCO doit être rétablie pour améliorer les risques d’infections opportunistes et de rechute de leucémie. / Umbilical cord blood (UCB) is increasingly used as a source of hematopoietic progenitor cells to treat a variety of disorders in children. UCB transplantation (UCBT) is associated with a reduced incidence of graft-versus-host disease, a robust graft-versus-leukemia effect, more frequent graft failures and a higher incidence of opportunistic infections (OI) compared to bone marrow transplantation; four processes in which donor-derived T lymphocytes are known to be predominantly involved. UCB T cells are mostly naïve. To examine the differential functionality of UCB T cells, CD8+ T cells specific for the melanoma-associated HLA-A2-restricted Melan-A26-35 A27L peptide were isolated from UCB and UCBT recipients, as it represents an abundant preimmune repertoire in human. Following in vitro stimulation, UCB T cells proliferated, oligoclonalized, acquired cell surface markers reflective of effector/memory differentiation, expressed cytolytic activity and produced IFN-γ. While functional properties of UCB T cells resembled their counterparts in adult peripheral blood, they were more likely to reach terminal differentiation following stimulation, produced less IFN-γ and were less frequently bifunctional (IFN-γ and cytolysis). Following UCBT, T cells became exhausted: they oligoclonalized dramatically, exhibited a terminal differentiation phenotype and a high frequency also expressed PD-1 (“ programmed death 1 ”) in the first 3-6 months post-UCBT. Moreover, very few patients developed an antiviral response during this period. Finally, the frequency of PD-1+ CD8+ T cells was significantly higher in subjects who subsequently experienced leukemic relapse. A second wave of T cells emerging at 6 months post-UCBT was observed and characterized by an increase in the repertoire diversity till 1 year, the development of a naïve population with polyfunctional potential and the progressive reconstitution of antiviral responses. This study reports to the biological properties of UCB-derived CD8+ T cells and provides a rationale for the characteristics of UCBT in terms of immune reconstitution and OI. These results also suggest that the first wave of CD8+ T cells in the first 3-6 months post-UCBT should be targeted in priority to improve both OI and leukemic relapse risks.
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Étude du rôle des lymphocytes T chez les receveurs pédiatriques de greffe de sang de cordon ombilicalMerindol, Natacha 11 1900 (has links)
La transplantation de sang de cordon ombilical (TSCO) est utilisée pour traiter les enfants atteints de maladies hématologiques en l’absence de donneurs apparentés compatibles. Elle est associée avec des risques plus élevés d’échec de greffe et d’infections opportunistes dans les premiers mois qui suivent la transplantation en comparaison avec une greffe de moelle osseuse. Par contre, la TSCO comporte un risque plus faible de maladie du greffon contre l’hôte et une incidence comparable de rechute de leucémie. Ces quatre complications impliquent directement les lymphocytes T. Dans le but de mieux comprendre le schéma particulier des évènements qui suivent la TSCO et d’améliorer le pronostic des patients, nous avons étudié le potentiel fonctionnel, la persistance et la reconstitution antivirale des lymphocytes T au sein d’un groupe d’enfants transplantés de sang de cordon ombilical (SCO). Étant donné que le SCO contient une majorité de lymphocytes T naïfs, nous avons étudié les lymphocytes T spécifiques au HLA-A2:Melan-A26-35 A27L; seul répertoire naïf et abondant caractérisé chez l’homme. Nous avons observé que les lymphocytes T du SCO se différencient en populations effectrices, s’oligoclonalisent, produisent de l’IFN-γ et lysent spécifiquement leur cible suite à la stimulation. Néanmoins, ces cellules produisent moins d’IFN-γ et sont moins bifonctionnelles que leurs homologues issus du sang périphérique d’adultes. Chez les patients, les lymphocytes T du SCO s’épuisent après la TSCO : ils s’oligoclonalisent dramatiquement, sont principalement en différenciation terminale, et une importante fréquence exprime PD-1 (« programmed death-1 ») dans les 3 à 6 premiers mois post-greffe. Très peu de patients sont capables de développer des réponses antivirales durant cette période et la fréquence de lymphocytes T qui expriment PD-1 semble aussi avoir un impact sur le risque subséquent de faire une rechute de leucémie. La deuxième vague de lymphocytes T émergeant à 6 mois post-TSCO mène à une population fonctionnelle et diversifiée. En conclusion, la fonctionnalité des lymphocytes T présents dans les 3 à 6 premiers mois post-TSCO doit être rétablie pour améliorer les risques d’infections opportunistes et de rechute de leucémie. / Umbilical cord blood (UCB) is increasingly used as a source of hematopoietic progenitor cells to treat a variety of disorders in children. UCB transplantation (UCBT) is associated with a reduced incidence of graft-versus-host disease, a robust graft-versus-leukemia effect, more frequent graft failures and a higher incidence of opportunistic infections (OI) compared to bone marrow transplantation; four processes in which donor-derived T lymphocytes are known to be predominantly involved. UCB T cells are mostly naïve. To examine the differential functionality of UCB T cells, CD8+ T cells specific for the melanoma-associated HLA-A2-restricted Melan-A26-35 A27L peptide were isolated from UCB and UCBT recipients, as it represents an abundant preimmune repertoire in human. Following in vitro stimulation, UCB T cells proliferated, oligoclonalized, acquired cell surface markers reflective of effector/memory differentiation, expressed cytolytic activity and produced IFN-γ. While functional properties of UCB T cells resembled their counterparts in adult peripheral blood, they were more likely to reach terminal differentiation following stimulation, produced less IFN-γ and were less frequently bifunctional (IFN-γ and cytolysis). Following UCBT, T cells became exhausted: they oligoclonalized dramatically, exhibited a terminal differentiation phenotype and a high frequency also expressed PD-1 (“ programmed death 1 ”) in the first 3-6 months post-UCBT. Moreover, very few patients developed an antiviral response during this period. Finally, the frequency of PD-1+ CD8+ T cells was significantly higher in subjects who subsequently experienced leukemic relapse. A second wave of T cells emerging at 6 months post-UCBT was observed and characterized by an increase in the repertoire diversity till 1 year, the development of a naïve population with polyfunctional potential and the progressive reconstitution of antiviral responses. This study reports to the biological properties of UCB-derived CD8+ T cells and provides a rationale for the characteristics of UCBT in terms of immune reconstitution and OI. These results also suggest that the first wave of CD8+ T cells in the first 3-6 months post-UCBT should be targeted in priority to improve both OI and leukemic relapse risks.
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The structural basis of immune receptor signallingHamer, Rebecca K. January 2008 (has links)
This work investigates the mechanisms of binding of T cell receptors (TCRs) to Class I MHC-peptide complexes (pMHC). The structure of a TCR specific for the Melan-A tumour antigen bound to its cognate pMHC was solved to a resolution of 2.5 Å which gives insight into how this TCR could be mutated to optimize binding and subsequently used as a cancer vaccine. Detailed sequence and geometric analyses of all currently available structures of Class I TCR-pMHC complexes revealed that TCRs can bind to pMHC with a range of orientations, yet always focus on the central portion of the peptide and use a specific subset of six residues on the MHC helices for binding. The most striking finding was the use of aromatic residues in the TCR CDR loops to bind to residue Q155 on the MHC α2 helix. Attempts were also made to express and purify Toll-like receptors (TLRs) with the aim of solving one or more of these structures. However, despite testing of over 50 different constructs from 12 different TLRs or associated proteins, insufficient soluble protein expression was obtained for crystallization trials. Finally, a protein disorder prediction tool was developed to aid construct design for structural biology studies and improve the chances of obtaining protein crystals. This tool is based on a novel type of neural network and blind tests comparing it to 8 other disorder prediction tools showed it is one of the best in the field. It is freely available at www.strubi.ox.ac.uk/RONN. Analysis of large datasets revealed that the position of order/disorder transitions is quite precisely defined in amino-acid sequences and that transition regions have an amino acid composition distinct from that of bulk ordered and disordered sequences. There is a steady decrease in order-promoting residues on the ordered side of boundaries as well as a weak sequence signal, both of which signify the approaching disorder and may prove useful for improving existing disorder prediction tools.
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