Genome-wide classification and identification of transmembrane protein structure and function

跨膜蛋白结构和功能的全基因组分类和鉴定

• 批准号: 14580665
• 负责人: SHIMIZU Toshio
• 金额: $ 1.86万
• 依托单位: Hirosaki University
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2002
• 资助国家: 日本
• 起止时间: 2002 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-14580665/
• 关键词: transmembrane protein; transmembrane topology; consensus prediction; proteome-wide; binary topology pattern; transmembrane topology evolution; internal gene duplication; GPCR; 膜貫通トポロジー; 機能分類・同定; 膜貫通トポロジー類似度; シグナルペプチド; Binary Topology Pattern /

We first collected experimentally-characterized transmembrane topology models from literatures and constructed them into a database(TMBDB). By using this, we evaluated the performances of several published transmembrane topology prediction methods, and we developed a consensus prediction method(ConPred) which is a combination of some of the proposed methods. By applying ConPred to TM proteomes from 99 completed genomes(88 prokaryotic and 12 eukaryotic), we obtained 52,686 TM protein sequences with reliable TM topologies and analysed the TM topologies of them in detail with respect to their relation to the function. From this analysis, it was revealed that the function of TM protein is closely related to its TM topology, and each functional group pfTM proteins has its own specific TM topology pattern expressed as a binary topology patter. The genome-scale functional classification and identification of GPCRs were also earned out, by applying the binary topology pattern method, and many novel GPCR genes were found by our study. We also investigated die TM topology evolution by internal gene duplication, through the internal sequence similarity comparison within a single sequences.

我们首先从文献中收集实验表征的跨膜拓扑模型，并将它们构建成数据库（TMBDB）。通过使用这一点，我们评估了几种已发表的跨膜拓扑预测方法的性能，我们开发了一种共识预测方法（ConPred），它是一些所提出的方法的组合。通过将ConPred应用于来自99个完整基因组（88个原核和12个真核）的TM蛋白质组，我们获得了52，686个具有可靠TM拓扑结构的TM蛋白质序列，并详细分析了它们的TM拓扑结构与功能的关系。结果表明，TM蛋白的功能与其TM拓扑结构密切相关，每个功能组的pfTM蛋白都有其特定的TM拓扑结构，表现为二元拓扑结构。应用二元拓扑模式法对GPCR基因进行了基因组水平的功能分类和鉴定，发现了许多新的GPCR基因。我们还研究了TM拓扑结构的进化内部基因复制，通过内部序列的相似性比较在一个单一的序列。

项目成果

Kaoru Azumi, Toshio Shimizu: "Genomic analysis of immunity in a Urochordate and the emergence of the vertebrate immune system : "waiting for Godot""Immunogenetics. 55・8. 570-581 (2003)

安住薰、清水俊夫：“尾索动物免疫的基因组分析和脊椎动物免疫系统的出现：“等待戈多””免疫遗传学55・8（2003）。

M.Arai, M.Ikeda, T.Shimizu: "Comprehensive analysis of transmembrane topologies in prokaryotic genomes"Genes. 303(1). 77-86 (2003)

M.Arai、M.Ikeda、T.Shimizu：“原核基因组跨膜拓扑的综合分析”基因。

Lao, D.M., Arai, M., Ikeda, M., Shimizu, T.: "The presence of signal peptide significantly affects transmembrane topology prediction"Bioinformatics. 18(12). 1562-1566 (2002)

Lao, D.M.、Arai, M.、Ikeda, M.、Shimizu, T.：“信号肽的存在显着影响跨膜拓扑预测”生物信息学。

Ikeda, M., Arai, M., Okuno, T., Shimizu, T.: "TMPDB : a database of experimentally-characterized transmembrane topologies"Nucleic Acids Research. 31. 406-409 (2003)

Ikeda, M.、Arai, M.、Okuno, T.、Shimizu, T.：“TMPDB：实验表征的跨膜拓扑数据库”核酸研究。

Sugiyama, Y., Polulyakh, N., Shimizu, T.: "Identification of transmembrane protein functions by binary topology patterns"Protein Engineering. 16. 479-488 (2003)

Sugiyama, Y.、Polulyakh, N.、Shimizu, T.：“通过二元拓扑模式识别跨膜蛋白功能”蛋白质工程。