Protein structure, comparison, prediction, and design

自然历史组（Go，Yura，和子，Nishikawa，Mitaku和Umeyama）从二级结构元件的空间排列分类中，Go发现了"对称规则"，即没有共同祖先的一组相似蛋白质折叠倾向于在其折叠中具有内部对称性。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盐结合模块，另一种是过氧化物酶的底物特异性决定模块。一种新开发的用于在原子水平上检测相似性的方法揭示了许多完全不同折叠（Go）的相似ATP结合结构。和子开发了一种有效的算法，通过代码表示来表示局部环境。Nishikawa开发了一种新的二级结构预测方法，他为此目的应用了线程方法。在膜结合蛋白的结构预测方面，Mitaku改进了他的方法，正确预测了细菌视紫红质的结构。Umeyama建立了一个全自动的同源性建模算法，估计可以提供足够的准确性。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非常稳健，并且通过延长链长可以极大地提高通过进化工程技术进行功能优化的可能性。应用"模块"概念制备嵌合血红蛋白，通过模块间的互换合成嵌合血红蛋白。从这种嵌合体蛋白质中，Ishimori证实了结构单元，即模块，不仅作为维持蛋白质稳定性的单元，而且作为实现血红蛋白功能的单元。

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.