Orientador: Prof. Dr. Luis Paulo Barbour Scott / Tese (doutorado) - Universidade Federal do ABC, Programa de Pós-Graduação em Biossistemas, 2015. / Mecanismos biologicos envolvidos nas fibras amiloides e sua agregacao ainda sao um dos topicos mais investigados cientificamente. As prions estao entre estas proteinas que agregam-se sob certas condicoes. Estas proteinas adotam duas diferentes formas: i) a forma celular (PrPC) e ii) a forma infecciosa denominada scrapie (PrPSc) que possui propensao a agregacao. Na forma infecciosa, essa proteina pode causar diversas doencas tais como a encefalopatia espongi-forme bovina, doenca de Creutzfeldt-Jakob e doenca de Gerstmann-Straussler-Scheinker. As PrPC e PrPSc sao diferentes com relacao as estruturas secundarias e terciarias. A PrPC contem um numero menor de folha-¿À quando comparada a PrPSc. Nenhuma estrutura da PrPSc foi resolvida ate o presente momento e, alem disso, o mecanismo molecular da transicao entre a PrPC e PrPSc e o processo de agregacao da forma scrapie nao sao bem compreendidos apesar dos numerosos estudos realizados nesta area. Neste trabalho, foi aplicada uma nova metodologia de simulacao recentemente desenvolvida que permite promover grandes mudancas estruturais, nomeada como MDeNM (Molecular Dynamics with excited Normal Modes), com o objetivo de investigar e compreender a transicao conformacional entre a PrPC e PrPSc. Este metodo combina modos normais e dinamica molecular, a partir de movimentos coletivos ativados cineticamente que devem contribuir para um novo rearranjo estrutural dificilmente alcancado por simulacoes de dinamica molecular tradicional. Alem disso, estudos termodinamicos foram realizados com o modelo baseado em estrutura (SBM), que caracteriza as transicoes energeticas. Os resultados do SBM mostraram que as estruturas geradas por MDeNM podem corresponder a via de transicao entre a conformacao nao-infecciosa e a desnovelada. A combinacao de MDeNM e SBM mostrou-se util para extrair informacoes estruturais e energeticas relacionadas a conversao da prion para as formas infecciosas. Os resultados mostraram um aumento significativo na formacao da folha-¿À sob condicoes de baixo pH e considerando a PrP na forma trimerica e tambem em agregados. Estas simulacoes permitiram a caracterizacao de estados intermediarios na transicao da PrPC para a PrPSc, e a proposicao um mecanismo de conversao da PrPC para PrPSc. Estudos iniciais relacionados aos mutantes da prion e o modelo Coarse-Grained tambem foram realizados neste trabalho. / Biological mechanisms involved in the amyloid fibrils and aggregation belong yet to very hot topics of scientific investigation. Prions are among proteins that aggregate under certain conditions. They adopt two different forms: i) the cellular form (PrPC) and ii) infectious form called scrapie (PrPSc) having the propensity to aggregate. In the infectious form, the prion may cause many diseases such as bovine spongiform encephalopathy (commonly known as mad cow disease), Creutzfeldt-Jakob disease and Gerstmann-Straussler-Scheinker disease. The PrPSc and PrPC are widely different regarding secondary and tertiary structures. PrPC contains a much smaller number of ¿À-strands compared to PrPSc. No structures of PrPSc have been solved until nowadays, and furthermore the molecular mechanism of the transition between PrPC and PrPSc, and the aggregation process of the scrapie form are not well understood besides numerous studies achieved in this field. In this work, we applied a recently developed simulation method allowing to promote large structural changes, namely the MDeNM (Molecular Dynamics with excited Normal Modes) in order to better investigate and understand the conformational transition between PrPC and PrPSc. This method makes a combined use of normal modes and molecular dynamics, consisting to kinetically activate collective motions that might contribute to new structural rearrangements difficult to achieve by simple standard MD simulations. Furthermore, a thermodynamical study was achieved with the well know ¿¿-carbon structure-based model (SBM), which characterizes the energetic transitions. SBM results showed that the PrPSc structures that were generated with MDeNM must correspond to the transition pathways between the non-infectious native PrPC and the fully unfolded conformations. The combination of MDeNM and SBM was useful to extract structural to energetical information related to the prion conversion to the frustrated infections forms. The results showed a significant increase in ¿À-sheet formation under low pH condition and when PrPC was in trimeric form, and also when larger assemblies. These simulations allowed us to characterize intermediate states in the transition from the cellular prion to PrPSc, and a model of conversion from PrPC to PrPSc. Also, studies with mutants of prion and Coarse-Grained were performed in this work.
| Identifer | oai:union.ndltd.org:IBICT/oai:BDTD:100855 |
| Date | January 2015 |
| Creators | Lima, Angélica Nakagawa |
| Contributors | Scott, Luis Paulo Barbour, Cordeiro, Rodrigo Maghdissian, Cerchiaro, Giselle, Chahine, Jorge, Oliveira, Paulo Sérgio Lopes de |
| Source Sets | IBICT Brazilian ETDs |
| Language | Portuguese |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, info:eu-repo/semantics/doctoralThesis |
| Format | application/pdf, 188 f. : il. |
| Source | reponame:Repositório Institucional da UFABC, instname:Universidade Federal do ABC, instacron:UFABC |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | http://biblioteca.ufabc.edu.br/index.php?codigo_sophia=100855&midiaext=72203, http://biblioteca.ufabc.edu.br/index.php?codigo_sophia=100855&midiaext=72204, Cover: http://biblioteca.ufabc.edu.brphp/capa.php?obra=100855 |
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