Compreendendo a cinética de enovelamento da α–espectrina por meio de interações não nativas
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Data
2017-03-22
Autores
Silva, Fernando Bruno da [UNESP]
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Editor
Universidade Estadual Paulista (Unesp)
Resumo
O objetivo deste trabalho foi caracterizar o atrito interno que são evidenciados nos domínios R15, R16 e R17 da chicken brain α–Espectrina. A Espectrina é uma proteína que faz parte do citoesqueleto e foi descoberta primeiramente em eritrócitos, sendo importante para manter a estabilidade, estrutura e forma da membrana celular. Esta proteína é composta de duas subunidades, α e β, sendo que cada um dos domínios presentes nestas subunidades apresentam 106 amino ́acidos. Além disso, estes domínios apresentam alta similaridade estrutural (RMSD < 1 A) e os resultados experimentais indicam que o domínio R15 apresenta um tempo de enovelamento que é três ordens de grandeza menor que seus homólogos (R16 e R17), esta observação foi atribuída aos efeitos do atrito interno na taxa de enovelamento. Portanto, neste trabalho foi estudado o enovelamento do R15, R16 e R17 utilizando o modelo baseado em estrutura Cα . Em nossas simulações, além das interações homogêneas para os contatos nativos (conhecido como modelo vanilla), foi adicionado um potencial atrativo para as interações não nativas hidrofóbicas (conhecido como modelo flavored ) utilizando a tabela do potencial de interação Miyazawa-Jernigan, bem como simulações com carga fixa e a pH constante, onde foram analisadas as interações eletrostáticas no processo de enovelamento. Por fim, realizaram-se simulações com o acoplamento para melhor descrever o sistema estudado.
The main aim of this work is characterized the internal friction evident in the three chicken brain α – spectrin domains, known as R15, R16, and R17. Spectrin is a cytoskeletal protein that was first discovered in erythrocytes and it is important for maintaining the stability, structure, and shape of the cell membrane. The protein is composed of a modular structure of α and β subunits, which typically contain 106 residues amino acid sequence motifs called ”spectrin repeats”. They are very similar in terms of structure and stability (RMSD < 1 A). However, experimental results indicate that R15 folds and unfolds 3 orders of magnitude faster than its homologs. Such baffling observation is usually attributed to the influence of ”internal friction”on protein folding kinetics. However, this effect cannot be satisfactorily corroborated by computer simulation. In the present work, the folding of these three domains is addressed using Cα structure-based models. We carried out simulations using homogeneous interactions on native contacts (known as a vanilla model) and has been added an attractive potential in the non-native hydrophobic interactions with Miyazawa-Jernigan potential (known as flavored model), as well as simulations with fixed charge and at constant pH, where the electrostatic interactions were analyzed in the folding. Finally, simulations were performed with the coupling of the potential (flavored and fixed load) to better describe the system.
The main aim of this work is characterized the internal friction evident in the three chicken brain α – spectrin domains, known as R15, R16, and R17. Spectrin is a cytoskeletal protein that was first discovered in erythrocytes and it is important for maintaining the stability, structure, and shape of the cell membrane. The protein is composed of a modular structure of α and β subunits, which typically contain 106 residues amino acid sequence motifs called ”spectrin repeats”. They are very similar in terms of structure and stability (RMSD < 1 A). However, experimental results indicate that R15 folds and unfolds 3 orders of magnitude faster than its homologs. Such baffling observation is usually attributed to the influence of ”internal friction”on protein folding kinetics. However, this effect cannot be satisfactorily corroborated by computer simulation. In the present work, the folding of these three domains is addressed using Cα structure-based models. We carried out simulations using homogeneous interactions on native contacts (known as a vanilla model) and has been added an attractive potential in the non-native hydrophobic interactions with Miyazawa-Jernigan potential (known as flavored model), as well as simulations with fixed charge and at constant pH, where the electrostatic interactions were analyzed in the folding. Finally, simulations were performed with the coupling of the potential (flavored and fixed load) to better describe the system.
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Palavras-chave
Modelo baseado em estrutura, Enovelamento de proteína, Dinâmica molecular, Método de dinâmica molecular a pH constante, Atrito interno, Interações hidrofóbicas, Interações eletrostáticas, Structure-based models, Protein folding, Molecular dynamics, Constant pH molecular dynamic, Internal friction, Hydrophobic interactions, Eletrostatic interactions