| Project/Area Number |
14580665
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | Hirosaki University |
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Principal Investigator |
SHIMIZU Toshio Hirosaki University, Facalty of Science and Technology, Professor, 理工学部, 教授 (00110750)
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| Project Period (FY) |
2002 – 2003
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| Project Status |
Completed (Fiscal Year 2003)
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| Budget Amount *help |
¥2,900,000 (Direct Cost: ¥2,900,000)
Fiscal Year 2003: ¥1,200,000 (Direct Cost: ¥1,200,000)
Fiscal Year 2002: ¥1,700,000 (Direct Cost: ¥1,700,000)
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| Keywords | 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 / Gタンパク質共役型受容体 / コンセンサス膜貫通トポロジー予測 / トポロジー予測法 / ゲノムスケール解析 / 原核生物ゲノム / シグナル配列 |
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| Research Abstract |
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.
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