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On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations

机译：计算机模拟中折叠和本机蛋白质蛋白淋巴谱的计算

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Solution techniques such as small-angle X-ray scattering (SAXS) play a central role in structural studies of intrinsically disordered proteins (IDPs); yet, due to low resolution, it is generally necessary to combine SAXS with additional experimental sources of data and to use molecular simulations. Computational methods for the calculation of theoretical SAXS intensity profiles can be separated into two groups, depending on whether the solvent is modeled implicitly as continuous electron density or considered explicitly. The former offers reduced computational cost but requires the definition of a number of free parameters to account for, for example, the excess density of the solvation layer. Overfitting can thus be an issue, particularly when the structural ensemble is unknown. Here, we investigate and show how small variations of the contrast of the hydration shell,δρ, severely affect the outcome, analysis and interpretation of computed SAXS profiles for folded and disordered proteins. For both the folded and disordered proteins studied here, using a defaultδρmay, in some cases, result in the calculation of non-representative SAXS profiles, leading to an overestimation of their size and a misinterpretation of their structural nature. The solvation layer of the different IDP simulations also impacts their size estimates differently, depending on the protein force field used. The same is not true for the folded protein simulations, suggesting differences in the solvation of the two classes of proteins, and indicating that different force fields optimized for IDPs may cause expansion of the polypeptide chain through different physical mechanisms.
机译：诸如小角度X射线散射（萨克斯）的解决方案技术在本质无序蛋白质（IDP）的结构研究中起着核心作用;然而，由于分辨率低，通常需要将萨克斯与额外的实验来源组合并使用分子模拟。计算理论萨克斯强度分布的计算方法可以分为两组，这取决于溶剂是否被含蓄地模拟为连续的电子密度或明确考虑。前者提供了减少的计算成本，但需要定义许多空闲参数来解释例如溶剂化层的过度密度。因此，过度装备可以是一个问题，特别是当结构集合未知时。在这里，我们研究并展示了水合壳，Δρ，严重影响折叠和无序蛋白质的计算萨克斯曲线的结果的小变化。对于在这里研究的折叠和无序的蛋白质，在某些情况下，使用DefaultΔP7May导致计算非代表性萨克斯曲线，从而高估其大小和对结构性质的误解。不同IDP模拟的溶剂化层也影响其尺寸的估计数，这取决于所使用的蛋白质力场。对于折叠的蛋白质模拟来说，这是不正确的，这表明两类蛋白质的溶剂化的差异，并且表明针对IDPS优化的不同力场可能通过不同的物理机制引起多肽链的膨胀。

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