Mudanças conformacionais e modificações pós-traducionais: um estudo estrutural de mecanismos e comportamentos de sistemas proteico
Carregando...
Data
2023-01-27
Autores
Dias, Raphael Vinicius Rodrigues
Título da Revista
ISSN da Revista
Título de Volume
Editor
Universidade Estadual Paulista (Unesp)
Resumo
O estudo de mecanismos no enovelamento de proteínas permite extrair importantes informações sobre o funcionamento de sistemas biológicos, assim como prospectar condições anômalas devido modificações como mutações e glicosilações. Neste trabalho, utilizamos modelos simplificados para estudar dois problemas diferentes envolvendo o enovelamento de proteínas: (I) a indicação de estados metaestáveis da proteína GRB2, apontados por meio de avaliações experimentais e (II) a influência das modificações pós-traducionais (glicosilações) no perfil de enovelamento. A GRB2 é uma proteína multidomínios relacionada com interações e regulação de vias dentro da célula, estruturalmente é formada por dois domínios SH3s flanqueados por um domínio SH2. Os estudos computacionais permitem descrever possíveis caminhos para o enovelamento, inclusive com a diferenciação na ordem de formação dos domínios. Complementarmente, mostramos a relação entre deleção do domínio SH3 N-terminal para com o seu relevo e funil de energia, validando e linkando com resultados de estabilidade térmica já estabelecidos previamente. Ao analisar as diferenças entre o enovelamento de cada domínio separadamente e constituindo a proteína completa, foi verificado pequenas diferenças no processo onde os efeitos da comunicação entre domínios fica evidenciada. No estudo da influência das modificações pós-traducionais (glicosilações) no perfil de enovelamento para proteínas depositadas no PDB, modelamos as glicosilações de acordo com nossos parâmetros de ajuste, simulamos o processo de enovelamento e calculamos aspectos termodinâmicos estatísticos como Calor Específico e Perfil de Energia Livre para cada sistema. Dentre seus resultados, notamos que a presença da glicosilação pode influenciar diretamente no enovelamento em alguns casos específicos, alterando graus de flexibilidade, estabilidade térmica e a importância de alguns resíduos para construção do “ensemble” de transição. Descrever esses mecanismos é um ponto de partida para diversos outros estudos e metodologias que interfiram diretamente nos problemas relacionados com essas proteínas, como por exemplo transporte e desenho racional de fármacos, mutações para especificidade de interação e estabilidade.
The study of mechanisms of protein folding allows us to extract important information about functions of biological systems, as well as to prospect anomalous conditions due to modifications such as mutations and glycosylations. In this work, we used simplified models to study two different problems involving protein folding: (I) evidences of metastable states of the GRB2 protein, indicated by means of experimental evaluations and (II) the influence on the energetic profile of folding in post-translational modifications (glycosylations). Growth factor receptor bound protein 2 (GRB2) is a multidomain protein related to interactions and regulation of pathways within the cell, structurally it is formed by two SH3s domains flanked by an SH2 domain. Computational studies allow us to describe possible paths for folding, including differentiation in the order of formation of domains. In addition, we show the relationship between deletion of the N-terminal SH3 domain and energy funnel, validating and linking it with previously established thermal stability results. When analyzing the differences between the folding of each domain separately and constituting the complete protein, it was verified small differences in the process where the effects of communication between domains is evidenced. In the study of the influence of post-translational modifications (glycosylations) on the folding profile for proteins deposited in the PDB, we modeled the glycosylations according to our adjustment parameters, simulated the folding process and calculated statistical thermodynamic aspects such as specific heat at constant volume and Energy Profile Free for each system. Among their results, we noticed that the presence of glycosylation can directly influence the folding in some specific cases, changing degrees of flexibility, thermal stability and the importance of some residues for the construction of the transition ensemble. Describing these mechanisms is a starting point for several other studies and methodologies that directly interfere with problems related to these proteins, such as transport and rational drug design, mutations for interaction specificity and stability.
The study of mechanisms of protein folding allows us to extract important information about functions of biological systems, as well as to prospect anomalous conditions due to modifications such as mutations and glycosylations. In this work, we used simplified models to study two different problems involving protein folding: (I) evidences of metastable states of the GRB2 protein, indicated by means of experimental evaluations and (II) the influence on the energetic profile of folding in post-translational modifications (glycosylations). Growth factor receptor bound protein 2 (GRB2) is a multidomain protein related to interactions and regulation of pathways within the cell, structurally it is formed by two SH3s domains flanked by an SH2 domain. Computational studies allow us to describe possible paths for folding, including differentiation in the order of formation of domains. In addition, we show the relationship between deletion of the N-terminal SH3 domain and energy funnel, validating and linking it with previously established thermal stability results. When analyzing the differences between the folding of each domain separately and constituting the complete protein, it was verified small differences in the process where the effects of communication between domains is evidenced. In the study of the influence of post-translational modifications (glycosylations) on the folding profile for proteins deposited in the PDB, we modeled the glycosylations according to our adjustment parameters, simulated the folding process and calculated statistical thermodynamic aspects such as specific heat at constant volume and Energy Profile Free for each system. Among their results, we noticed that the presence of glycosylation can directly influence the folding in some specific cases, changing degrees of flexibility, thermal stability and the importance of some residues for the construction of the transition ensemble. Describing these mechanisms is a starting point for several other studies and methodologies that directly interfere with problems related to these proteins, such as transport and rational drug design, mutations for interaction specificity and stability.
Descrição
Palavras-chave
Enovelamento de proteínas, Growth Factor Receptor Bound 2 (GRB2), Mudanças conformacionais, Glicosilações, Dinâmica molecular, Protein folding, Conformational changes, Glycosylation