Yang Yuedong, Zhou Yaoqi
Indiana University School of Informatics, Indianapolis, Indiana 46202, USA.
Proteins. 2008 Aug;72(2):793-803. doi: 10.1002/prot.21968.
Proteins fold into unique three-dimensional structures by specific, orientation-dependent interactions between amino acid residues. Here, we extract orientation-dependent interactions from protein structures by treating each polar atom as a dipole with a direction. The resulting statistical energy function successfully refolds 13 out of 16 fully unfolded secondary-structure terminal regions of 10-23 amino acid residues in 15 small proteins. Dissecting the orientation-dependent energy function reveals that the orientation preference between hydrogen-bonded atoms is not enough to account for the structural specificity of proteins. The result has significant implications on the theoretical and experimental searches for specific interactions involved in protein folding and molecular recognition between proteins and other biologically active molecules.
蛋白质通过氨基酸残基之间特定的、依赖取向的相互作用折叠成独特的三维结构。在此，我们通过将每个极性原子视为具有方向的偶极子，从蛋白质结构中提取依赖取向的相互作用。所得的统计能量函数成功地使15种小蛋白质中16个由10 - 23个氨基酸残基组成的完全展开的二级结构末端区域中的13个重新折叠。剖析依赖取向的能量函数表明，氢键原子之间的取向偏好不足以解释蛋白质的结构特异性。该结果对蛋白质折叠以及蛋白质与其他生物活性分子之间分子识别中涉及的特定相互作用的理论和实验研究具有重要意义。
