Center for Bioinformatics and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047, USA.
Protein Sci. 2013 Aug;22(8):1141-5. doi: 10.1002/pro.2295. Epub 2013 Jul 3.
Proteins often bind other proteins in more than one way. Thus alternative binding modes is an essential feature of protein interactions. Such binding modes may be detected by X-ray crystallography and thus reflected in Protein Data Bank. The alternative binding is often observed not for the protein itself but for its structural homolog. The results of this study based on the analysis of a comprehensive set of co-crystallized protein-protein complexes show that the alternative binding modes generally do not overlap, but are spatially separated. This effect is based on molecular recognition characteristics of the protein structures. The results are also in excellent agreement with the intermolecular energy funnel size estimates obtained previously by an independent methodology. The results provide an important insight into the principles of protein association, as well as potential guidelines for modeling of protein complexes and the design of protein interfaces.
蛋白质通常以不止一种方式结合其他蛋白质。因此，替代结合模式是蛋白质相互作用的一个基本特征。这种结合模式可以通过 X 射线晶体学检测到，因此反映在蛋白质数据库中。替代结合模式通常不是针对蛋白质本身，而是针对其结构同源物。本研究基于对一套综合共结晶的蛋白质-蛋白质复合物的分析，结果表明，替代结合模式通常不重叠，而是空间分离的。这种效应是基于蛋白质结构的分子识别特征。结果也与以前通过独立方法获得的分子间能量漏斗大小估计值非常吻合。研究结果为蛋白质结合的原理提供了重要的见解，也为蛋白质复合物的建模和蛋白质界面的设计提供了潜在的指导方针。
