Estudo sobre a variação da energia livre de ligação em complexos lectina-peroxidase através da dinâmica molecular
Carregando...
Data
2019-08-06
Autores
Santo, Anderson Aparecido do Espirito
Título da Revista
ISSN da Revista
Título de Volume
Editor
Universidade Estadual Paulista (Unesp)
Resumo
A capacidade de reconhecimento molecular da enzima peroxidase (HRP) tem sido muito estudada para o desenvolvimento de biossensores eletroquímicos através de sua ligação com receptores formados pela lectina (ArtinM) complexada com uma molécula de manotriose. Os biossensores eletroquímicos podem ser usados para estimar o número de sítios de ligação ocupados na superfície de um detector para medir uma constante de afinidade relacionada a energia livre de ligação entre a HRP e ArtinM. A incorporação de moléculas de água na estrutura durante o reconhecimento molecular entre as duas proteínas poderia influenciar o valor da constante de afinidade medida pelo biossensor, sendo um caso de estudo que pode ser esclarecido com uso de dinâmica molecular clássica em conjunto com o método de cálculo de energia livre de ligação MM-PBSA. Foram realizadas dinâmicas moleculares com possíveis conformações do complexo formado por HRP e ArtinM gerados por modelos de docking de corpo rígido. As simulações foram realizadas em diferentes condições iniciais onde os complexos se encontravam livres em solução ou imobilizados em um modelo de superfície representando, de forma simplificada, o ambiente existente no biossensor. Os cálculos para energia livre de ligação obtidos através das simulações de dinâmica molecular confirmam o valor da constante de afinidade medida experimentalmente pelos biossensores eletroquímicos e demonstram que a influência de possíveis moléculas de água estruturais é muito pequena em comparação com a massa total das proteínas do complexo. As análises das trajetórias das simulações demonstram que o reconhecimento molecular é quase inteiramente mediado pela manotriose, com contribuições pequenas de outros resíduos do sítio de reconhecimento.
The molecular recognition capacity of the enzyme peroxidase (HRP) has been extensively studied for the electrochemical biosensors by its binding to receptors formed by lectin (ArtinM) complexed with a mannotriose molecule. Electrochemical biosensors can be used to estimate the number of binding sites occupied on the surface of a detector to measure an affinity constant related to free binding energy between HRP and ArtinM. The incorporation of structural water molecules during molecular recognition between the two proteins could influence the value of the affinity constant measured by the biosensor, being a case study that can be clarified by using classical molecular dynamics in conjunction with the method of MM-PBSA binding free energy calculation. Molecular dynamics were performed with possible conformations of the complex formed by HRP and ArtinM generated by rigid body docking models. The simulations were performed under different initial conditions where the complexes were free in solution or immobilized in a surface model representing, in a simplified way, the existing environment in the biosensor. The calculations for binding free energy obtained through molecular dynamics simulations confirm the value of the affinity constant experimentally measured by electrochemical biosensors and demonstrate that the influence of possible structural water molecules is very small compared to the total protein mass of complex. Analysis of the simulation trajectories show that molecular recognition is almost entirely mediated by the mannotriose, with small contributions from other recognition site residues.
The molecular recognition capacity of the enzyme peroxidase (HRP) has been extensively studied for the electrochemical biosensors by its binding to receptors formed by lectin (ArtinM) complexed with a mannotriose molecule. Electrochemical biosensors can be used to estimate the number of binding sites occupied on the surface of a detector to measure an affinity constant related to free binding energy between HRP and ArtinM. The incorporation of structural water molecules during molecular recognition between the two proteins could influence the value of the affinity constant measured by the biosensor, being a case study that can be clarified by using classical molecular dynamics in conjunction with the method of MM-PBSA binding free energy calculation. Molecular dynamics were performed with possible conformations of the complex formed by HRP and ArtinM generated by rigid body docking models. The simulations were performed under different initial conditions where the complexes were free in solution or immobilized in a surface model representing, in a simplified way, the existing environment in the biosensor. The calculations for binding free energy obtained through molecular dynamics simulations confirm the value of the affinity constant experimentally measured by electrochemical biosensors and demonstrate that the influence of possible structural water molecules is very small compared to the total protein mass of complex. Analysis of the simulation trajectories show that molecular recognition is almost entirely mediated by the mannotriose, with small contributions from other recognition site residues.
Descrição
Palavras-chave
Biomoléculas, Biossensores, Dinâmica molecular, Energia livre, MM-PBSA