College of Electrical and Computer Engineering, Chungbuk National University, Chungbuk, Korea.
Proteomics. 2011 Oct;11(19):3793-801. doi: 10.1002/pmic.201100189. Epub 2011 Aug 18.
Solvent exposure of amino acids measures how deep residues are buried in tertiary structure of proteins, and hence it provides important information for analyzing and predicting protein structure and functions. Existing methods of calculating solvent exposure such as accessible surface area, relative accessible surface area, residue depth, contact number, and half-sphere exposure still have some limitations. In this article, we propose a novel solvent exposure measure named quadrant-sphere exposure (QSE) based on eight quadrants derived from spherical neighborhood. The proposed measure forms a microenvironment around Cα atom as a sphere with a radius of 13 Å, and subdivides it into eight quadrants according to a rectangular coordinate system constructed based on geometric relationships of backbone atoms. The number of neighboring Cα atoms whose labels are the same is given as the QSE value of the center Cα atom at hand. As evidenced by histograms that show very different distributions for different structure configurations, the proposed measure captures local properties that are characteristic for a residue's eight-directional neighborhood within a sphere. Compared with other measures, QSE provides a different view of solvent exposure, and provides information that is specific for different tertiary structure. As the experimental results show, QSE measure can potentially be used in protein structure analysis and predictions.
氨基酸的溶剂暴露度衡量残基在蛋白质三级结构中的埋藏深度，因此为分析和预测蛋白质结构和功能提供了重要信息。现有的溶剂暴露度计算方法，如可及表面积、相对可及表面积、残基深度、接触数和半球暴露度，仍然存在一些局限性。在本文中，我们提出了一种新的溶剂暴露度度量方法，称为象限球暴露度（QSE），它基于从球型邻域中衍生出的八个象限。所提出的方法以 13Å 的半径围绕 Cα 原子形成一个球体，并根据基于骨架原子几何关系构建的直角坐标系将其细分为八个象限。具有相同标签的相邻 Cα 原子的数量被赋予手头中心 Cα 原子的 QSE 值。从显示不同结构构型具有非常不同分布的直方图可以看出，该度量方法捕获了残基在球体内八个方向邻域的局部特性。与其他度量方法相比，QSE 提供了溶剂暴露度的不同视角，并提供了针对不同三级结构的特定信息。正如实验结果所示，QSE 度量方法有可能用于蛋白质结构分析和预测。
