Estudo das interações não-nativas, eletrostáticas e hidrofóbicas, no processo de enovelamento de proteínas utilizando modelos minimalistas
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Data
2021-05-20
Autores
Silva, Fernando Bruno da
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Universidade Estadual Paulista (Unesp)
Resumo
O estudo do enovelamento proteína nesse trabalho tem como base o uso do modelo baseado em estrutura, modelo no qual apenas as interações nativas são consideradas como favoráveis durante o enovelamento. Entretanto, as interações ditas como não favoráveis são consideradas pelo modelo. Dessa forma, o objetivo geral desse trabalho buscou averiguar os efeitos das interações não-nativas durante o processo enovelamento. Os potencias não-nativos adotados são: potencial eletrostático (Elec), hidrofóbico (HP) e de dessolvatação (db ou dsb). Esses potenciais foram combinados de diferentes formas e adicionados no modelo SBM-Cα. Portanto, o trabalho desenvolvido buscou compreender como as interações não-nativas e os estados metaestáveis podem estar correlacionados. O primeiro trabalho desenvolvido envolve a proteina CI2, onde foram analisados diferentes grupos mutacionais para obter uma proteína mais termoestável. O modelo computacional adotado foi o SBM-Cα + Elec + HP. O segundo trabalho foi com os domínios R15, R16 e R16M5 da α-espectrina, esse estudo é continuação dos trabalhos realizadas anteriormente com os domínios R15, R16 e R17. O modelo computacional utilizado foi o mesmo proposto para CI2 e tem como objetivo analisar os fatores mutacionais envolvidos na redução do tempo de enovelamento devido a um grupo mutacional específico. Além disso, por meio do método ELViM, foram averiguados os perfis energéticos dessas proteínas. Por fim, no terceiro trabalho foi investigado os estados intermediários das proteínas Im7 e Im9, pois em diferentes valores de pH, esses estados apresentam diferentes comportamentos. Portanto, o modelo computacional adotado foi o SBM-Cα + Elec + HP + db. Afim de reproduzir o sistema em diferentes valores de pH, foram alterados os valores de carga dos resíduos ionizáveis.
The protein folding studies in this work are based on the structure-based model. Structure-based model are usually used to explore the folding process, but this model consists only the native interactions are favorable to the protein folding. However, unfavorable interactions may also help the process too. The non-native potentials, that incorporate these interactions, it was added to the structure-based Cα model (the electrostatic (Elec), the hydrophobic (HP), and the desolvation potential (db or dsb)). These potentials were combined in different ways into the SBM-Cα model and, as a result, we tried to understand how non-native interactions and the metastable states could be associated. In the present study with the CI2 protein, a group of mutants was selected to obtain a new version of the CI2 protein with a different thermostability. The simulation was performed with the SBM-Cα + Elec + HP. The second project includes two domains from α-spectrin, R15 and R16, and a version of R16 with five mutations, R16M5. This study is part II of our previous work with the domains R15, R16, and R17. The computational model was the same applied for CI2 and the main goal of this study was to understand the mutation effects in the folding time when we have the group of five mutations. The central idea was to explore the presence of a metastable state that may or may not support the folding process when considering the five mutations. In addition, using the ELViM method, the energy profiles of these proteins were analyzed. Finally, in the third project, the Im7 and Im9 intermediate states were investigated. The intermediate states of these proteins stabilized under different pH values. The simulations were carried out with the SBM-Cα + Elec + HP + db model. In order to reproduce the system at different pH values, the charge values of the ionizable residues were changed, according to their theoretical pKa.
The protein folding studies in this work are based on the structure-based model. Structure-based model are usually used to explore the folding process, but this model consists only the native interactions are favorable to the protein folding. However, unfavorable interactions may also help the process too. The non-native potentials, that incorporate these interactions, it was added to the structure-based Cα model (the electrostatic (Elec), the hydrophobic (HP), and the desolvation potential (db or dsb)). These potentials were combined in different ways into the SBM-Cα model and, as a result, we tried to understand how non-native interactions and the metastable states could be associated. In the present study with the CI2 protein, a group of mutants was selected to obtain a new version of the CI2 protein with a different thermostability. The simulation was performed with the SBM-Cα + Elec + HP. The second project includes two domains from α-spectrin, R15 and R16, and a version of R16 with five mutations, R16M5. This study is part II of our previous work with the domains R15, R16, and R17. The computational model was the same applied for CI2 and the main goal of this study was to understand the mutation effects in the folding time when we have the group of five mutations. The central idea was to explore the presence of a metastable state that may or may not support the folding process when considering the five mutations. In addition, using the ELViM method, the energy profiles of these proteins were analyzed. Finally, in the third project, the Im7 and Im9 intermediate states were investigated. The intermediate states of these proteins stabilized under different pH values. The simulations were carried out with the SBM-Cα + Elec + HP + db model. In order to reproduce the system at different pH values, the charge values of the ionizable residues were changed, according to their theoretical pKa.
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Palavras-chave
Modelo baseado em estrutura, Enovelamento de proteína, Dinâmica molecular, Efeito hidrofóbico, Interações eletrostáticas, Potencial de dessolvatação, Estados metaestáveis, Estados intermediários, Strucuture-based model, Protein folding, Molecular dynamics, Hydrophobic effects, Electrostatic interactions, Desolvation potential, Metastable states, Intermidiate states