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.

内含子位于模块的边界，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件，它们在分子进化过程中被融合或洗牌。该研究项目的目的是对蛋白质的模块进行分类，并通过融合或改组将募集到不同蛋白质的共同模块归结为分类方法的开发方法：我们通过分子动力学计算发现，这些模块可以根据其三层（3D）结构的相似性将模块分类为组。彼此之间的序列身份小于40％被分解为950个模块。其中约有2/3分为66组，但是，其他模块保留在没有组合在一起的情况下。3。蛋白质中观察到的常见模块：这些模块具有共同的生物学功能。该结果可以很好地证明外显子/模块在不同蛋白质之间取代。螺旋 - 旋转螺旋模块似乎已经分解为三种具有不同角色的类型。第一个是特定的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，第三个是脚手架稳定的球状蛋白。

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。

T.Nakashima: "Structure of the hurman CCGI gene:relationship between the exons/introns and functional domain/modules of the protein" Gene. 141. 193-200 (1994)

T.Nakashima：“hurman CCGI 基因的结构：蛋白质的外显子/内含子和功能域/模块之间的关系”基因。

Elsevier Science, 197-203 (1995)

爱思唯尔科学，197-203（1995）