Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Laboratory of Algorithms and Computational Geometry, Department of Mathematics and Computer Science, Amirkabir University of Technology, Tehran, Iran.
Comput Biol Chem. 2013 Dec;47:16-23. doi: 10.1016/j.compbiolchem.2013.06.003. Epub 2013 Jun 25.
The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model.
分析和比较蛋白质-核酸和蛋白质-蛋白质相互作用界面的能力对于理解细胞中发生的生物功能和基本过程具有至关重要的意义。由于具有生物大分子复合物的高分辨率三维（3D）结构，计算界面几何形状成为分子生物学领域的一个重要研究课题。在这项研究中，计算了一组 180 个蛋白质-核酸和蛋白质-蛋白质复合物的界面，以了解它们相互作用的原理。原子和 Alpha 复合物的加权 Voronoi 图为界面原子提供了准确的描述。我们的方法在有水分子和没有水分子的情况下都得到了实现。三种相互作用界面的比较表明，RNA-蛋白质复合物的界面尺寸最大。结果表明，在 Voronoi 模型中和传统基于溶剂可及性的模型中，我们的方法与 PISA 服务器在有水分子和没有水分子的情况下具有高度相关性，并且与经典模型相比，验证参数也很高。
