Department of Bioinformatics, Telemedicine Jagiellonian University - Collegium Medicum, Lazarza 16, 31-530, Krakow, Poland.
J Mol Model. 2010 Jul;16(7):1269-82. doi: 10.1007/s00894-009-0639-2. Epub 2010 Jan 19.
The proteins composed of short polypeptides (about 70 amino acid residues) representing the following functional groups (according to PDB notation): growth hormones, serine protease inhibitors, antifreeze proteins, chaperones and proteins of unknown function, were selected for structural and functional analysis. Classification based on the distribution of hydrophobicity in terms of deficiency/excess as the measure of structural and functional specificity is presented. The experimentally observed distribution of hydrophobicity in the protein body is compared to the idealized one expressed by a three-dimensional Gauss function. The differences between these two distributions reveal the specificity of structural/functional characteristics of the protein. The residues of hydrophobicity deficiency versus the idealized distribution are assumed to indicate cavities with the potential to bind ligands, while the residues of hydrophobicity excess are interpreted as potentially participating in protein-protein complexation. The distribution of hydrophobicity irregularity seems to be specific for particular structures and functions of proteins. A comparative analysis of such profiles is carried out to identify the potential biological activity of proteins of unknown function.
选择了由短肽（约 70 个氨基酸残基）组成的蛋白质进行结构和功能分析，这些短肽代表了以下功能组（根据 PDB 符号）：生长激素、丝氨酸蛋白酶抑制剂、抗冻蛋白、伴侣蛋白和未知功能的蛋白。基于疏水性分布的分类，以不足/过剩作为结构和功能特异性的度量标准。将实验观察到的蛋白体内疏水性分布与由三维高斯函数表达的理想化分布进行比较。这两种分布之间的差异揭示了蛋白质结构/功能特征的特异性。与理想化分布相比，疏水性不足的残基被认为指示具有结合配体潜力的空穴，而疏水性过剩的残基被解释为可能参与蛋白质-蛋白质复合物形成。疏水性不规则性的分布似乎对特定的蛋白质结构和功能具有特异性。对这些分布进行比较分析，以确定未知功能蛋白的潜在生物学活性。
