An integrated bioinformatics platform for investigating the human E3 ubiquitin ligase-substrate interaction network

Yang Li, Ping Xie, Liang Lu, Jian Wang, Lihong Diao, Zhongyang Liu, Feifei Guo, Yangzhige He, Yuan Liu, Qin Huang, Han Liang, Dong Li () and Fuchu He ()
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Yang Li: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Ping Xie: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Liang Lu: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Jian Wang: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Lihong Diao: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Zhongyang Liu: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Feifei Guo: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Yangzhige He: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Yuan Liu: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Qin Huang: Guangxi University for Nationalities
Han Liang: The University of Texas MD Anderson Cancer Center
Dong Li: National Center for Protein Sciences (The PHOENIX Center, Beijing)
Fuchu He: National Center for Protein Sciences (The PHOENIX Center, Beijing)

Nature Communications, 2017, vol. 8, issue 1, 1-9

Abstract: Abstract The ubiquitination mediated by ubiquitin activating enzyme (E1), ubiquitin conjugating enzyme (E2), and ubiquitin ligase (E3) cascade is crucial to protein degradation, transcription regulation, and cell signaling in eukaryotic cells. The high specificity of ubiquitination is regulated by the interaction between E3 ubiquitin ligases and their target substrates. Unfortunately, the landscape of human E3-substrate network has not been systematically uncovered. Therefore, there is an urgent need to develop a high-throughput and efficient strategy to identify the E3-substrate interaction. To address this challenge, we develop a computational model based on multiple types of heterogeneous biological evidence to investigate the human E3-substrate interactions. Furthermore, we provide UbiBrowser as an integrated bioinformatics platform to predict and present the proteome-wide human E3-substrate interaction network ( http://ubibrowser.ncpsb.org ).

Date: 2017
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DOI: 10.1038/s41467-017-00299-9

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