Classification of Protein Modules

蛋白质模块的分类

• 批准号: 06454664
• 负责人: GO Mitiko
• 金额: $ 4.61万
• 依托单位: Nagoya University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for General Scientific Research (B)
• 财政年份: 1994
• 资助国家: 日本
• 起止时间: 1994 至 1995
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-06454664/
• 关键词: module; intron; exon shuffling; protein tertiary structure; functional unit; molecular dynamics; molecular evolution; helix-turn-helix; 分化進化; タンパク質工学; 立体構造; エキソンシャッフリング

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.

内含子位于靠近模块边界的位置，模块是球状蛋白中的小结构单元。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改组。本研究项目的目的是对蛋白质模块进行分类，并识别通过融合或改组招募到不同蛋白质中的共同模块。1.分类方法的开发：通过分子动力学计算，我们发现模块能够根据其三维（3D）结构的相似性进行分类。2.模块的分类：77种蛋白质 彼此之间序列同一性小于40%的序列被分解成950个模块。其中大约2/3被分为66组，而其他模块则保留下来，没有分组。3.在蛋白质中观察到的共同模块：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/模块改组提供了良好的证据。螺旋-转角-螺旋模块似乎分为三种类型，具有不同的作用；第一个是特异性 DNA 序列识别，第二个是通过与磷酸盐相互作用的非特异性 DNA 结合，第三个是支架稳定球蛋白。

项目成果

Noguti,T.: "Modules of barnase:the physicochemical basis for their structures" In Tracing Biological Evolution in Protein and Gene Structures (Eds.M.Go & P.Schimmel) Elsevier Science. 161-174 (1995)

Noguti,T.：“芽孢杆菌RNA酶的模块：其结构的物理化学基础”，追踪蛋白质和基因结构的生物进化（Eds.M.Go）

Go,M.: "Putative origin of introns deduced from protein anatomy" In Tracing Biological Evolution in Protein and Gene Structures (Eds.M.Go & P.Schimmel) Elsevier Science. 229-235 (1995)

Go,M.：“从蛋白质解剖学中推导出内含子的推定起源”，《追踪蛋白质和基因结构中的生物进化》（Eds.M.Go）

Song,S.: "Cloning and characterzation of the gene encoding Halobacterium halobium adenylate kinase" Gene. (in press).

Song,S.：“盐杆菌腺苷酸激酶编码基因的克隆和表征”基因。

Hojo,H.: "Preparation of S-protected cysteine-containing peptide thioester and its use for the synthesis of the barnase-like domain in DNA-directed RNA polymerase II of Saccharomvces cerevisiae" Bull.Chem.Soc.Japan. 68. 330-336 (1995)

Hojo,H.：“S-保护的含半胱氨酸肽硫酯的制备及其在酿酒酵母 DNA 指导的 RNA 聚合酶 II 中合成芽孢杆菌RNA酶样结构域的用途”Bull.Chem.Soc.Japan。

Tateno,M.: "Module Structure and Function of Glutamyl-tRNA Synthetase" In Tracing Biological Evolution in Protein and Gene Structures (Eds.M.Go & P.Schimmel) Elsevier Science. 53-63 (1995)

Tateno,M.：“谷氨酰-tRNA 合成酶的模块结构和功能”追踪蛋白质和基因结构的生物进化 (Eds.M.Go