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Large-scale identification of protein–protein interaction of Escherichia coli K-12
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Protein–protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular activities, targeted-drug design, and whole cell engineering. A large-scale comprehensive pull-down assay was performed using a His-tagged Escherichia coli ORF clone library. Of 4339 bait proteins tested, partners were found for 2667, including 779 of unknown function. Proteins copurifying with hexahistidine-tagged baits on a Ni 2+-NTA column were identified by MALDI-TOF MS (matrix-assisted laser desorption ionization time of flight mass spectrometry). An extended analysis of these interacting networks by bioinformatics and experimentation should provide new insights and novel strategies for E. coli systems biology.
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“Several high-throughput experimental techniques have been designed to identify interacting protein partners23–26, but their results are far from complete and are often mutually inconsistent.”
From AF2Complex predicts direct physical interactions in multimeric proteins with deep learning (2022) · cites this paper as [25]
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Metadata
- Authors
- Arifuzzaman, M., Maeda, M., Itoh, A., Nishikata, K., Takita, C., Saito, R., Ara, T., Nakahigashi, K., Huang, H.-C., Hirai, A., Tsuzuki, K., Nakamura, S., Altaf-Ul-Amin, M., Oshima, T., Baba, T., Yamamoto, N., Kawamura, T., Ioka-Nakamichi, T., Kitagawa, M., Tomita, M., Kanaya, S., Wada, C., & Mori, H.
- Affiliations
- Japan Bioindustry Association (JP)
- Japan Science and Technology Agency (JP)
- Institute for Advanced Biosciences, Keio University (JP)
- Nara Institute of Science and Technology (JP)
- National Yang Ming University (TW)
- Kyoto University (JP)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2006-04-10
- Volume
- 16
- Issue
- 5
- Pages
- 686-691
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC1457052
- OpenAlex
- W2137012036
- Cited by
- 403
- References
- 44
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 12 · 2023: 9 · 2022: 11 · 2021: 3 · 2020: 16 · 2019: 15 · 2018: 12 · 2017: 12 · 2016: 16 · 2015: 23 · 2014: 22 · 2013: 21 · 2012: 36
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Core Research for Evolutional Science and Technology
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- protein-protein interaction, Escherichia coli K-12, pull-down assay, protein-protein interaction network, interactome networks, protein function, systems biology, drug target identification
- MeSH terms
- Histidine, Models, Biological, Gene Library, Open Reading Frames, Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization, Proteome, Escherichia coli Proteins, Proteomics, Escherichia coli K12
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