Protein structure, comparison, prediction, and design

自然历史群(GO、Yura、Wako、Nishikawa、Mitaku和Umeyama)从二级结构元素的空间排列分类中，Go发现了“对称规则”，即相似的蛋白质折叠，没有共同的祖先，它们的折叠往往具有内部对称性。Yura发现了两种类型的“模块”，一种是在聚合酶和转录因子中常见的磷酸结合模块，另一种是过氧化物酶的底物特异性决定模块。一种新开发的检测原子水平相似性的方法在完全不同的折叠(GO)中揭示了许多相似的ATP结合结构。WAKO提出了一种用代码表示来表示局部环境的高效算法。西川将穿线法应用于此，提出了一种新的二级结构预测方法。对于膜结合蛋白的结构预测，Mitaku改进了他的方法，使其能够准确地预测细菌视紫红质的结构。设计小组(Yomo和Ishimori)Yomo在过氧化氢酶的随机诱变实验中发现，蛋白质的热稳定性和活性对突变具有极强的健壮性，通过进化工程技术进行功能优化的可能性可以通过延长链长来极大地提高。将“模块”的概念应用到嵌合体血红蛋白的合成中，通过模块间的互换来合成嵌合体血红蛋白。从这些嵌合体蛋白质中，石森证实，结构单元模块不仅是维持蛋白质稳定性的单位，也是实现血红蛋白功能的单位。

Natural history group (Go, Yura, Wako, Nishikawa, Mitaku, and Umeyama)From a classification of the spatial arrangements of the secondary structure elements, Go discovered 'the symmetry rule', whish states that apair of similar protein folds, having no common ancestor, tend to possessan internal symmetry in their fold. Yura found two types of 'modules', a phosphate binding module observed commonly in polymerases and transcription factors, and a substrate-specificity determining module of peroxidases. A newly developed method for detecting similarity in the atomic level revealed a lot of similar ATP binding structures in totally different folds (Go). Wako developed an efficient algorithm of expressing the local environment by a code representation. A new secondary structure prediction method was developed by Nishikawa, who applied the threading method for this purpose. As for the structural prediction for membrane bound proteins, Mitaku improved his method to predict the structure of bacteriorhodopsin correctly. Umeyama established a fully automated algorithm of homology modeling, which is estimated to give a sufficient accuracy.Design group (Yomo and Ishimori)Yomo found in random mutagenesis experiments on catalase that the thermal stability and activity of the protein is extremely robust against mutations, and that a possibility of the functional optimization by the evolutional engineering technique can enormously enhanced by the elongation of the chain length. The concept of 'module' was applied to produce chimera hemoglobin, which was synthesized by exchanging its modules each other. From such chimera proteins, Ishimori confirmed that the structural unit, module, works not only as the unit of maintaining the protein stability, but also as a unit for realizing the function of hemoglobin.