Construction, MD Simulation, and Hydrodynamic Validation of an All-Atom Model of a Monoclonal IgG Antibody
Construction, MD Simulation, and Hydrodynamic Validation of an All-Atom Model of a Monoclonal IgG Antibody
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DOI：
10.1016/j.bpj.2010.05.003
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发表时间：
2010-08-04
影响因子：
3.4
通讯作者：
Aragon, Sergio R.
中科院分区：
文献类型：
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作者：
Brandt, J. Paul;Patapoff, Thomas W.;Aragon, Sergio R.
在150 kDa时，Ig G类抗体太大，其结构无法用目前的核磁共振方法确定。由于铰链区的灵活性，很难从晶体中获得原子级结构信息，而且关于抗体结构和溶液中的动力学的问题仍然没有解决。在这里，我们描述了根据片段的晶体结构构建人IgG1单抗(曲妥珠单抗)的模型。我们使用分子动力学(MD)模拟、连续介质流体动力学模拟和实验扩散测量相结合的方法来探索抗体在水溶液中的行为。流体动力学模型提供了MD模拟的原子级细节与流体动力学测量提供的尺寸和形状相关数据之间的联系。使用AMBER程序套件获得了8个独立的40 ns MD轨迹。计算的所有MD轨迹上的输运性质的系综平均值与在20摄氏度和27摄氏度动态光散射获得的平移扩散系数的值以及在20摄氏度测量的特性粘度非常一致。因此，我们的MD结果可能代表了抗体在水溶液中探索的构象空间的真实样本。
At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution.