Zhou Ruhong, Silverman B David, Royyuru Ajay K, Athma Prasanna
IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Proteins. 2003 Sep 1;52(4):561-72. doi: 10.1002/prot.10419.
A recent study of 30 soluble globular protein structures revealed a quasi-invariant called the hydrophobic ratio. This invariant, which is the ratio of the distance at which the second order hydrophobic moment vanished to the distance at which the zero order moment vanished, was found to be 0.75 +/- 0.05 for 30 protein structures. This report first describes the results of the hydrophobic profiling of 5,387 non-redundant globular protein domains of the Protein Data Bank, which yields a hydrophobic ratio of 0.71 +/- 0.08. Then, a new hydrophobic score is defined based on the hydrophobic profiling to discriminate native-like proteins from decoy structures. This is tested on three widely used decoy sets, namely the Holm and Sander decoys, Park and Levitt decoys, and Baker decoys. Since the hydrophobic moment profiling characterizes a global feature and requires reasonably good statistics, this imposes a constraint upon the size of the protein structures in order to yield relatively smooth moment profiles. We show that even subject to the limitations of protein size (both Park & Levitt and Baker sets are small protein decoys), the hydrophobic moment profiling and hydrophobic score can provide useful information that should be complementary to the information provided by force field calculations.
最近一项针对30种可溶性球状蛋白质结构的研究揭示了一种名为疏水比的准不变量。这种不变量是二阶疏水矩消失时的距离与零阶矩消失时的距离之比，研究发现30种蛋白质结构的该值为0.75±0.05。本报告首先描述了蛋白质数据库中5387个非冗余球状蛋白质结构域的疏水分析结果，其疏水比为0.71±0.08。然后，基于疏水分析定义了一种新的疏水分数，以区分天然样蛋白质和诱饵结构。这在三个广泛使用的诱饵集上进行了测试，即霍尔姆和桑德诱饵集、帕克和莱维特诱饵集以及贝克诱饵集。由于疏水矩分析表征的是全局特征且需要相当好的统计数据，这对蛋白质结构的大小施加了限制，以便产生相对平滑的矩分布。我们表明，即使受到蛋白质大小的限制（帕克和莱维特集以及贝克集都是小蛋白质诱饵），疏水矩分析和疏水分数也能提供有用信息，这些信息应与力场计算提供的信息互补。
