Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization
Quantifying the Separation of Positive and Negative Areas in Electrostatic Potential for Predicting Feasibility of Ammonium Sulfate for Protein Crystallization
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DOI：
10.1021/acs.jcim.1c00505
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发表时间：
2021-09
影响因子：
5.6
通讯作者：
Yan Guo;N. Nishida;T. Hoshino
中科院分区：
文献类型：
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作者：
Yan Guo;N. Nishida;T. Hoshino
硫酸铵 (AS) 和聚乙二醇 (PEG) 是蛋白质结晶中最常用的沉淀剂。有些蛋白质优选通过AS结晶，而有些则通过PEG结晶。静电势与沉淀剂的偏好有关。 AS 结晶蛋白的静电势等值面显示出共同的形状以及正负区域之间的明显分离。相反，PEG 结晶蛋白显示出不清晰的正负分离。在这项工作中，我们提出了定量评估分离效果的方案，以预测哪种沉淀剂有利于 AS 或 PEG 之间的晶体生长。尝试了三种方法来量化分离幅度、分离距离、偶极矩和形状规律性。正面积和负面积近似于由点电荷引起的球形电势。第一种方法是测量正负点电荷之间的距离。第二个是评估，包括距离内的电荷量。最后一种是监控正负分离清晰度的方法。三种方法中 25 种 AS 偏好蛋白的平均值均高于 PEG 偏好蛋白。因此，每种方法都可以区分偏好AS晶体生长的蛋白质和偏好PEG的蛋白质。这些方法需要以某个轮廓值描绘的静电势的等值面。等值面的形状取决于轮廓值。通过描绘具有 ±0.8、±0.5 和 ±0.2 kT/e 三个值的静电势等值面来检查对轮廓的依赖性。虽然减小轮廓值会导致间隔距离增加和形状规则性降低，但偶极矩与轮廓值的变化无关。虽然 AS 偏好蛋白在任何轮廓值上都可以与 PEG 偏好蛋白区分开来，但 ±0.5 kT/e 的等值面似乎足以满足常规使用。偶极矩评估对于选择实验中晶体生长的有效沉淀剂是可行的。
Ammonium sulfate (AS) and poly(ethylene glycol) (PEG) are the most popular precipitants in protein crystallization. Some proteins are preferably crystallized by AS, while some are by PEG. The electrostatic potential is related to the preference of the precipitant agents. The iso-surfaces of the electrostatic potentials for the AS-crystallized proteins display a common shape and a distinct separation between the positive and negative areas. In contrast, the PEG-crystallized proteins show unclear positive and negative separation. In this work, we propose schemes to quantitatively evaluate the separation for predicting which precipitant is favorable for crystal growth between AS or PEG. Three methods were attempted to quantify the amplitude of the separation, separation distance, dipole moment, and shape regularity. The positive and negative areas are approximated to the spherical potentials caused by point charges. The first method is a measurement of the distance between the positive and negative point charges. The second one is an assessment including the quantity of electric charge into the distance. The last one is an approach monitoring the clarity of the positive and negative separation. The average value for 25 kinds of AS-preferring proteins was higher than that for the PEG-preferring ones in all three methods. Therefore, every method can distinguish the proteins preferring AS for crystal growth from those preferring PEG. These methods require an iso-surface of the electrostatic potential depicted at a certain contouring value. The shape of the iso-surface depends on the contouring value. The dependency on contour was examined by depicting the iso-surfaces of electrostatic potential with three values at ±0.8, ±0.5, and ±0.2 kT/e. While reducing the contouring value leads to the increase in separation distance and the decrease in shape regularity, dipole moment is independent of the alteration of contouring value. While the AS-preferring proteins are distinguishable from the PEG-preferring ones in any contouring values, the iso-surface at ±0.5 kT/e seems adequate for regular use. The dipole moment assessment is feasible for the choice of potent precipitants for crystal growth in experiments.