In the past decade, there was increased research interest in studying internal motions of flexible proteins in solution using Neutron Spin Echo (NSE) as NSE can simultaneously probe the dynamics at the length and time scales comparable to protein domain motions. However, the collective intermediate scattering function (ISF) measured by NSE has the contributions from translational, rotational, and internal motions, which are rather complicated to be separated. Widely used NSE theories to interpret experimental data usually assume that the translational and rotational motions of a rigid particle are decoupled and independent to each other. To evaluate the accuracy of this approximation for monoclonal antibody (mAb) proteins in solution, dissipative particle dynamic computer simulation is used here to simulate a rigid-body mAb for up to about 200 ns. The total ISF together with the ISFs due to only the translational and rotational motions as well as their corresponding effective diffusion coefficients is calculated. The aforementioned approximation introduces appreciable errors to the calculated effective diffusion coefficients and the ISFs. For the effective diffusion coefficient, the error introduced by this approximation can be as large as about 10% even though the overall agreement is considered reasonable. Thus, we need to be cautious when interpreting the data with a small signal change. In addition, the accuracy of the calculated ISFs due to the finite computer simulation time is also discussed.

中文翻译：

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耗散粒子动力学模拟研究溶液中刚体单克隆抗体蛋白的中间散射函数


在过去的十年中，人们对使用中子自旋回波 (NSE) 研究溶液中柔性蛋白质的内部运动越来越感兴趣，因为 NSE 可以同时探测与蛋白质结构域运动相当的长度和时间尺度的动力学。然而，NSE测量的集体中间散射函数（ISF）有平动、旋转和内部运动的贡献，分离起来相当复杂。广泛使用的 NSE 理论来解释实验数据通常假设刚性粒子的平移和旋转运动是解耦且彼此独立的。为了评估溶液中单克隆抗体 (mAb) 蛋白质的这种近似的准确性，此处使用耗散粒子动态计算机模拟来模拟刚体 mAb 长达约 200 ns。计算总 ISF 以及仅由平移和旋转运动引起的 ISF 及其相应的有效扩散系数。上述近似给计算的有效扩散系数和 ISF 带来了明显的误差。对于有效扩散系数，尽管整体一致性被认为是合理的，但这种近似引入的误差可能高达约 10%。因此，我们在解释信号变化较小的数据时需要谨慎。此外，还讨论了由于计算机模拟时间有限而导致计算的 ISF 的准确性。