Classification of Protein Modules

内含子位于球状蛋白质中的小结构单位模块的边界附近。这一事实意味着，模块是由外显子编码的原始构建块，它们在分子进化过程中被融合或洗牌。本研究的目的是对蛋白质的模块进行分类，并通过融合或洗牌来鉴定不同蛋白质中的共同模块。1.分类方法的发展：通过分子动力学计算发现，根据模块在三维结构上的相似性，可以将这些模块划分为不同的组。2.模块的分类：将77个序列同源性小于40%的蛋白质分解为950个模块。其中约2/3的模块被分成66个组，其余的模块没有聚在一起。3.蛋白质中发现的共同模块：这些模块具有共同的生物学功能。这一结果为不同蛋白质之间的外显子/模块改组提供了很好的证据。螺旋-转角-螺旋模块似乎有三种不同的作用：第一种是特异性DNA序列识别，第二种是通过与磷酸盐的相互作用与非特异性DNA结合，第三种是稳定球状蛋白的支架。

Introns are located close to boundaries of modules, small structural units in globular proteins. This fact implies that modules are the original building blocks encoded by exons and they were fused or shuffled during molecular evolution. The purpose of this research project is to classify the modules of proteins and to indentify the common modules recruited into different proteins by fusion or shuffling.1.Development of classification method : We found by molecular dynamics calculation that the modules were able to be classified into groups on the basis of the similarity in their three-dimensional (3D) structures.2.Classification of modules : Seventy-seven proteins with sequence identity less than 40% among one another were decomposed into 950 modules. About 2/3 of them were classified into 66 groups, however, the other modules were remained without making groups together.3.Common modules observed in proteins : These modules had common biological functions. this result gives good evidence for exon/module shuffling among different proteins. The helix-turn-helix module seems to have diverged into three types with different roles ; the first is specific DNA sequence recognition, the second is non-specific DNA binding through the interactions with phosphates, and the third is scaffold stabilizing globular proteins.