依那西普融合蛋白二聚体在真空和水溶液中活性结构稳定性的拉伸模拟方法研究

Investigation of Structural Stability of Etanercept in Vacuum and Aqueous Solution by Steered Molecular Dynamics Simulation

目的研究单克隆抗体依那西普融合蛋白二聚体在不同状态下的动力学稳定性和热力学稳定性,为其活性保护的研究奠定基础。方法利用Gromacs 4.6分子模拟软件和Amber99sb-ildn分子力场以及拉伸模拟和伞状采样的方法,获取依那西普抗体蛋白的解离自由能和解离拉力的变化。结果研究结果表明,依那西普抗体蛋白在真空中的解离自由能是在水溶液中的10.05倍,其在真空中解离的平均作用力是在水溶液中的3.03倍。溶剂化环境对于抗体蛋白的稳定性具有显著的影响,而真空冷冻干燥可以提高其结构的稳定性。结论拉伸模拟过程中,最大拉力简单易得,且影响因素少,可以用最大拉力表征抗体蛋白二聚体的活性结构稳定性。

OBJECTIVE To investigate the stability of etanercept in vacuum and water to lay foundation for study on its bioactiveprotection. METHODS Umbrella sampling and steered molecular dynamics simulation aqueous solution adopted to study the dissociation process of dimer etanercept with Gromacs software and amber99sb-ildn force field. RESULTS Potential of mean forcel（ PMF）free energy of etanercept dissociation in vacuum was approximately three times of that in aqueous solution. And the maximum barrier force of etanercept dissociation in vacuum was approximately ten times of that in aqueous solution. The solvation environment had effect on the stability of antibody protein. Freeze-drying in vacuum could improve the stability of antibody protein. CONCLUSION In the process of steered molecular dynamics simulation,the pulling force can be got easily and is less affected by other factors,which can be used to characterize the stability of active structure of antibody protein dimer.