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Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods |
Xianyi Lian1, Xiaodi Yang1, Jiqi Shao2, Fujun Hou3, Shiping Yang4( ), Dongli Pan3, Ziding Zhang1( ) |
1. State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China 2. National Demonstration Center for Experimental Biological Sciences Education, College of Biological Sciences, China Agricultural University, Beijing 100193, China 3. Department of Medical Microbiology and Parasitology, and Department of Infectious Diseases of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China 4. State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China |
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Abstract Background: Herpes simplex virus type 1 (HSV-1) is a ubiquitous infectious pathogen that widely affects human health. To decipher the complicated human-HSV-1 interactions, a comprehensive protein-protein interaction (PPI) network between human and HSV-1 is highly demanded. Methods: To complement the experimental identification of human-HSV-1 PPIs, an integrative strategy to predict proteome-wide PPIs between human and HSV-1 was developed. For each human-HSV-1 protein pair, four popular PPI inference methods, including interolog mapping, the domain-domain interaction-based method, the domain-motif interaction-based method, and the machine learning-based method, were optimally implemented to generate four interaction probability scores, which were further integrated into a final probability score. Results: As a result, a comprehensive high-confidence PPI network between human and HSV-1 was established, covering 10,432 interactions between 4,546 human proteins and 72 HSV-1 proteins. Functional and network analyses of the HSV-1 targeting proteins in the context of human interactome can recapitulate the known knowledge regarding the HSV-1 replication cycle, supporting the overall reliability of the predicted PPI network. Considering that HSV-1 infections are implicated in encephalitis and neurodegenerative diseases, we focused on exploring the biological significance of the brain-specific human-HSV-1 PPIs. In particular, the predicted interactions between HSV-1 proteins and Alzheimer’s-disease-related proteins were intensively investigated. Conclusion: The current work can provide testable hypotheses to assist in the mechanistic understanding of the human-HSV-1 relationship and the anti-HSV-1 pharmaceutical target discovery. To make the predicted PPI network and the datasets freely accessible to the scientific community, a user-friendly database browser was released at http://www.zzdlab.com/HintHSV/index.php.
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Keywords
human-virus interaction
protein-protein interaction
prediction
herpes simplex virus type 1
Alzheimer’s disease
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Corresponding Author(s):
Shiping Yang,Ziding Zhang
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Just Accepted Date: 30 September 2020
Online First Date: 07 December 2020
Issue Date: 24 December 2020
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