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Differences between calcium rich and depleted alpha-lactalbumin investigated by molecular dynamics simulations and incoherent neutron scattering
Physical Review E ( IF 2.4 ) Pub Date : 2020-03-25 , DOI: 10.1103/physreve.101.032415
Dominik Zeller , Pan Tan , Liang Hong , Daniele Di Bari , Victoria Garcia Sakai , Judith Peters

We present a study comparing atomic motional amplitudes in calcium rich and depleted alpha-lactalbumin. The investigations were performed by elastic incoherent neutron scattering (EINS) and molecular dynamics (MD) simulations. As the variations were expected to be very small, three different hydration levels and timescales (instrumental resolutions) were measured. In addition, we used two models to extract the mean square displacements (MSDs) from the EINS data, one taking into account the motional heterogeneity of the MSD. At a timescale of several nanoseconds, small differences in the amplitudes between the calcium enriched and depleted alpha-lactalbumin are visible, whereas at lower timescales no changes can be concluded within the statistics. The results are compared to MD simulations at 280 and 300 K by extracting the MSDs of the trajectories in two separate ways: first by direct calculation, and second by a virtual neutron experiment using the same models as for the experimental data. We show that the simulated data give qualitatively similar results as the experimental data but quantitatively there are differences. Furthermore, the distribution of the MSDs in the simulations suggests that the inclusion of heterogeneity is reasonable for alpha-lactalbumin, but a bi-or trimodal approach may be sufficient.

中文翻译:

通过分子动力学模拟和非相干中子散射研究富钙和贫钙α-乳白蛋白之间的差异

我们提出了一项研究,比较富含钙和贫钙的α-乳白蛋白的原子运动幅度。通过弹性非相干中子散射(EINS)和分子动力学(MD)模拟进行了研究。由于预计变化非常小,因此测量了三种不同的水合作用水平和时间范围(仪器分辨率)。此外,我们使用了两种模型从EINS数据中提取均方位移(MSD),其中一种考虑了MSD的运动异质性。在几纳秒的时间尺度上,可以看到富钙和贫钙的α-乳清蛋白之间振幅的细微差异,而在较低的时间尺度上,统计数据内无法得出任何变化。通过以两种不同的方式提取轨迹的MSD,将结果与280和300 K的MD仿真进行比较:首先是直接计算,其次是使用与实验数据相同的模型通过虚拟中子实验。我们表明,模拟数据在质量上与实验数据相似,但在数量上存在差异。此外,模拟中MSD的分布表明,对于α-乳白蛋白而言,包含异质性是合理的,但双峰或三峰方法可能就足够了。
更新日期:2020-03-26
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