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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure
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Isolating Influential Regions of Electrostatic Focusing in Protein and DNA Structure

机译：分离静电集中蛋白质和DNA结构中的影响区域

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摘要

Electrostatic focusing is a general phenomenon that occurs in cavities and grooves on the molecular surface of biomolecules. Narrow surface features can partially shield charged atoms from the high-dielectric solvent, enhancing electrostatic potentials inside the cavity and projecting electric field lines outward into the solvent. This effect has been observed in many instances and is widely considered in the human examination of molecular structure, but it is rarely integrated into the digital representations used in protein structure comparison software. To create a computational representation of electrostatic focusing, that is compatible with structure comparison algorithms, this paper presents an approach that generates three-dimensional solids that approximate regions where focusing occurs. We verify the accuracy of this representation against instances of focusing in proteins and DNA. Noting that this representation also identifies thin focusing regions on the molecular surface that are unlikely to affect binding, we describe a second algorithm that conservatively isolates larger focusing regions. The resulting 3D solids can be compared with Boolean set operations, permitting a new range of analyses on the regions where electrostatic focusing occurs. They also represent a novel integration of molecular shape and electrostatic focusing into the same structure comparison framework.
机译：静电聚焦是一种普遍现象，发生在生物分子分子表面的空腔和凹槽中。狭窄的表面特征可以部分屏蔽带电原子与高介电溶剂的接触，从而增强空腔内部的静电势，并将电场线向外投射到溶剂中。在许多情况下都可以观察到这种效果，并且在人体分子结构检查中被广泛考虑，但是很少将其整合到蛋白质结构比较软件中使用的数字表示中。为了创建与结构比较算法兼容的静电聚焦的计算表示，本文提出了一种生成三维实体的方法，该实体近似于发生聚焦的区域。我们针对针对蛋白质和DNA的实例验证了这种表示的准确性。注意，这种表示法还可以识别分子表面上不太可能影响结合的细聚焦区域，因此我们描述了第二种算法，该算法保守地隔离了较大的聚焦区域。可以将所得的3D实体与布尔设置操作进行比较，从而可以对发生静电聚焦的区域进行新的分析范围。它们还代表了分子形状和静电聚焦在同一结构比较框架中的新颖整合。

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