Brylinski Michal, Kochanczyk Marek, Konieczny Leszek, Roterman Irena
Department of Bioinformatics and Telemedicine, Collegium Medicum - Jagiellonian University, Kopernika, Krakow, Poland.
In Silico Biol. 2006;6(6):589-600.
Methods for biological function recognition in silico appeared to be useful also for identifying characteristics of structure-to-function relations. The introduction of a three-dimensional Gauss function was assumed to represent the hydrophobic core in a protein molecule. The discrepancy between idealized "fuzzy oil-drop" and the observed one in real proteins appeared to be localized in the ligation site or in the area of biological function related part of protein molecule. The examples of proteins presented in this paper reveal that the structure-function relation can be evaluated and characterized also using the profile of the difference in value between idealized and real hydrophobicity distribution along the polypeptide chain. The specificity of particular polypeptide chain fragments in respect to their biological function and their specific participation in active site creation is discussed in this paper. The scale allowing comparison of different proteins in respect to their ligand-binding sites characteristics is introduced.
计算机模拟的生物功能识别方法似乎也有助于识别结构与功能关系的特征。引入三维高斯函数被认为可以代表蛋白质分子中的疏水核心。理想化的“模糊油滴”与实际蛋白质中观察到的情况之间的差异似乎定位在连接位点或蛋白质分子生物功能相关部分的区域。本文给出的蛋白质实例表明，也可以利用沿多肽链的理想化和实际疏水性分布之间的差值轮廓来评估和表征结构 - 功能关系。本文讨论了特定多肽链片段在其生物功能方面的特异性及其在活性位点形成中的特定参与情况。引入了一种尺度，用于比较不同蛋白质在其配体结合位点特征方面的情况。
