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首页> 美国卫生研究院文献>Proceedings of the National Academy of Sciences of the United States of America >Determination of solvent content in cavities in IL-1β using experimentally phased electron density
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Determination of solvent content in cavities in IL-1β using experimentally phased electron density

机译：实验相电子密度法测定IL-1β腔中溶剂的含量

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摘要

The extent to which water is present within apolar cavities in proteins remains unclear. In the case of interleukin-1β (IL-1β), four independent structures solved by x-ray crystallography indicate that water is not present in the central apolar cavity. In contrast, results from NMR spectroscopy suggest that water has high occupancy within the cavity but is positionally disordered, making it undetectable by standard crystallographic methods. A theoretically based crystallographic-phase refinement technique also suggested that there was the equivalent of two fully occupied water molecules within the apolar cavity. To resolve these discrepancies we sought to obtain an experimentally phased electron density map that was free of possible bias caused by mathematical modeling of the protein or the solvent. By combining native diffraction data with multiple wavelength anomalous data from a platinum derivative, accurate phases were obtained. Using these experimental phases, we estimate that occupancy of the apolar cavity in IL-1β by solvent is close or equal to zero. Polar cavities in the protein that contain ordered solvent molecules serve as internal controls.
机译：蛋白质的非极性腔内水的存在程度尚不清楚。在白介素-1β（IL-1β）的情况下，通过X射线晶体学解析的四个独立结构表明在中央非极性腔中不存在水。相比之下，NMR光谱的结果表明，水在腔体内具有很高的占有率，但位置无序，因此无法通过标准晶体学方法检测到。从理论上讲，结晶相细化技术还表明，非极性腔内有两个完全被占据的水分子。为了解决这些差异，我们试图获得一个实验阶段化的电子密度图，该图没有蛋白质或溶剂的数学模型造成的可能偏差。通过将天然衍射数据与来自铂衍生物的多个波长异常数据相结合，可以获得准确的相位。使用这些实验阶段，我们估计溶剂在IL-1β中非极性腔的占有率接近或等于零。包含有序溶剂分子的蛋白质中的极性腔用作内部对照。

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