Tsai Cheng-Fang, Lee Kuei-Jen
Department of Biotechnology, Asia University, Taichung 413, Taiwan.
Int J Mol Sci. 2011;12(12):8449-65. doi: 10.3390/ijms12128449. Epub 2011 Nov 29.
In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (δ). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the proteins is represented by the mean radius of gyration (R(g) ), which follows the Flory scaling law, R(g) ∝ N(ν). The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, |q(i)| ≥ 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range.
在本文中，对150条非同源蛋白质链中的15种球状蛋白质进行了二阶疏水矩的比较研究，该研究涉及两组疏水性：一组选自一致标度，另一组源自CHARMM部分原子电荷。这些蛋白质根据其残基数量（N）和非球度（δ）分为三组。第一组中的蛋白质是球形的，第二组和第三组中的蛋白质是长形的。蛋白质的大小由回转半径平均值（R(g)）表示，其遵循弗洛里标度定律，即R(g) ∝ N(ν)。ν的平均值为0.35，这与处于不良溶剂中的聚合物链相似。使用皮尔逊相关系数比较了从两组疏水性获得的每种蛋白质二阶矩的空间分布；结果表明，当使用为极性原子指定的CHARMM部分原子电荷|q(i)| ≥ 0.3时，每个蛋白质结构的两组数据之间存在很强的相关性。这些分布消失并接近负值的位置大约在溶剂可及性百分比的50%处，这表明蛋白质中存在从疏水内部到亲水外部的转变点。这可能表明蛋白质在该范围之外存在一个位置来确定暴露位点的残基。
