Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data
Validating Solution Ensembles from Molecular Dynamics Simulation by Wide-Angle X-ray Scattering Data
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DOI：
10.1016/j.bpj.2014.06.006
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发表时间：
2014-07-15
影响因子：
3.4
通讯作者：
Hub, Jochen S.
中科院分区：
文献类型：
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作者：
Chen, Po-chia;Hub, Jochen S.
由于光源和探测器的技术进步，溶液中生物分子的广角 X 射线散射 (WAXS) 实验变得越来越流行。然而，WAXS 剖面的结构解释存在问题，部分原因是根据结构模型准确计算 WAXS 剖面仍然具有挑战性。在这项工作中，我们通过五种不同蛋白质的显式溶剂分子动力学 (MD) 模拟计算了 WAXS 谱。仅使用单个拟合参数来解释由于缓冲减法和暗电流而导致的实验不确定性，我们发现小角度和广角下的实验轮廓都非常一致。由于显式溶剂化消除了与溶剂化层或排除溶剂相关的自由参数，这需要拟合实验数据，因此我们最大限度地减少了过度拟合的风险。我们进一步发现，水模型和蛋白质力场对计算剖面的影响在 q 接近 15 nm(-1) 时微不足道。通过一系列可提高蛋白质灵活性的模拟，我们表明将热波动纳入计算可显着提高与实验数据的一致性，证明蛋白质动力学在解释 WAXS 图谱中的重要性。此外，高达一微秒的自由 MD 模拟表明，计算出的轮廓对于蛋白质的微小构象重排高度敏感，例如环的灵活性增加或回转半径增加 < 1%。本研究表明，MD 模拟与实验 WAXS 剖面之间的定量比较成为验证生物分子解整体的准确工具。
Wide-angle x-ray scattering (WAXS) experiments of biomolecules in solution have become increasingly popular because of technical advances in light sources and detectors. However, the structural interpretation of WAXS profiles is problematic, partly because accurate calculations of WAXS profiles from structural models have remained challenging. In this work, we present the calculation of WAXS profiles from explicit-solvent molecular dynamics (MD) simulations of five different proteins. Using only a single fitting parameter that accounts for experimental uncertainties because of the buffer subtraction and dark currents, we find excellent agreement to experimental profiles both at small and wide angles. Because explicit solvation eliminates free parameters associated with the solvation layer or the excluded solvent, which would require fitting to experimental data, we minimize the risk of overfitting. We further find that the influence from water models and protein force fields on calculated profiles are insignificant up to q approximate to 15 nm(-1). Using a series of simulations that allow increasing flexibility of the proteins, we show that incorporating thermal fluctuations into the calculations significantly improves agreement with experimental data, demonstrating the importance of protein dynamics in the interpretation of WAXS profiles. In addition, free MD simulations up to one microsecond suggest that the calculated profiles are highly sensitive with respect to minor conformational rearrangements of proteins, such as an increased flexibility of a loop or an increase of the radius of gyration by < 1%. The present study suggests that quantitative comparison between MD simulations and experimental WAXS profiles emerges as an accurate tool to validate solution ensembles of biomolecules.