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PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms

Takabayashi, Atsushi; Takabayashi, Saeka; Takahashi, Kaori et al.

Plant and Cell Physiology, 2017, 58(1), e10

Permalink : https://hdl.handle.net/2115/68044

このアイテムのアクセス数:1,049件（2026-11-06 08:39 集計）

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Figures pdf 1.70 MB 405
Supplementary Table S1 xlsx 764 KB 272
Supplementary Table S2 xlsx 2.16 MB 245
Supplementary Table S3 xlsx 2.72 MB 215
Supplementary Table S4 xlsx 3.36 MB 309
Supplementary Table S5 xlsx 3.72 MB 256
Supplementary Table S6 xlsx 2.42 MB 247
Supplementary Table S7 xlsx 2.15 MB 185
Supplementary Table S8 xlsx 4.19 MB 244
Supplementary Table S9 docx 54.5 KB 327
PCoM-DB_revised_manuscript_3 pdf 197 KB 430

論文情報

ファイル出力 EndNote Basic出力 Mendeley出力

アクセス権
open access
URI
https://hdl.handle.net/2115/68044
タイトル
PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms
著者
Takabayashi, Atsushi ; Takabayashi, Saeka ; Takahashi, Kaori ; Watanabe, Mai ; Uchida, Hiroko ; Murakami, Akio ; Fujita, Tomomichi ; Ikeuchi, Masahiko ; Tanaka, Ayumi
著者名
Takabayashi, Atsushi
著者名
Takabayashi, Saeka
著者名
Takahashi, Kaori
著者名
Watanabe, Mai
著者名
Uchida, Hiroko
著者名
Murakami, Akio
著者名
Fujita, Tomomichi
著者名
Ikeuchi, Masahiko
著者名
Tanaka, Ayumi
言語
英語
キーワード
Blue-native PAGE
Photosynthetic organisms
Protein complex database
Protein-protein interaction
発行日
2017-01-06
出版者
Oxford University Press
収録物名
Plant and Cell Physiology
巻(号)
58(1)
ページ
e10
抄録
The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandemmass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocya-nobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.
資源タイプ
学術雑誌論文
出版タイプ
Accepted Manuscript
権利情報
This is a pre-copyedited, author-produced PDF of an article accepted for publication in Plant and cell physiology following peer review. The version of record PCoM-DB Update : A Protein Co-Migration Database for Photosynthetic Organisms,　Atsushi Takabayashi,Saeka Takabayashi, Kaori Takahashi,　Mai Watanabe, Hiroko Uchida,　Akio Murakami, Tomomichi Fujita,　Masahiko Ikeuchi, Ayumi Tanaka,　Plant Cell Physiol (2017) 58 (1): e10　is available online at: https://doi.org/10.1093/pcp/pcw219
PISSN
0032-0781
関連情報
PMID
28011869
関連情報 (isVersionOf)
出版社版DOI
https://doi.org/10.1093/pcp/pcw219