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Ma Y, He T, Tan Y, Jiang X. Seq-BEL: Sequence-Based Ensemble Learning for Predicting Virus-Human Protein-Protein Interaction. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2022; 19:1322-1333. [PMID: 32750886 DOI: 10.1109/tcbb.2020.3008157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Infectious diseases are currently the most important and widespread health problem, and identifying viral infection mechanisms is critical for controlling diseases caused by highly infectious viruses. Because of the lack of non-interactive protein pairs and serious imbalance between positive and negative sample ratios, the supervised learning algorithm is not suitable for prediction. At the same time, due to the lack of information on viral proteins and significant dissimilarity in sequence, some ensemble learning models have poor generalization ability. In this paper, we propose a Sequence-Based Ensemble Learning (Seq-BEL) method to predict the potential virus-human PPIs. Specifically, based on the amino acid sequence of proteins and the currently known virus-human PPI network, Seq-BEL calculates various features and similarities of human proteins and viral proteins, and then combines these similarities and features to score the potential of virus-human PPIs. The computational results show that Seq-BEL achieves success in predicting potential virus-human PPIs and outperforms other state-of-the-art methods. More importantly, Seq-BEL also has good predictive performance for new human proteins and new viral proteins. In addition, the model has the advantages of strong robustness and good generalization ability, and can be used as an effective tool for virus-human PPI prediction.
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Khodadadi E, Zeinalzadeh E, Taghizadeh S, Mehramouz B, Kamounah FS, Khodadadi E, Ganbarov K, Yousefi B, Bastami M, Kafil HS. Proteomic Applications in Antimicrobial Resistance and Clinical Microbiology Studies. Infect Drug Resist 2020; 13:1785-1806. [PMID: 32606829 PMCID: PMC7305820 DOI: 10.2147/idr.s238446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 05/23/2020] [Indexed: 12/11/2022] Open
Abstract
Sequences of the genomes of all-important bacterial pathogens of man, plants, and animals have been completed. Still, it is not enough to achieve complete information of all the mechanisms controlling the biological processes of an organism. Along with all advances in different proteomics technologies, proteomics has completed our knowledge of biological processes all around the world. Proteomics is a valuable technique to explain the complement of proteins in any organism. One of the fields that has been notably benefited from other systems approaches is bacterial pathogenesis. An emerging field is to use proteomics to examine the infectious agents in terms of, among many, the response the host and pathogen to the infection process, which leads to a deeper knowledge of the mechanisms of bacterial virulence. This trend also enables us to identify quantitative measurements for proteins extracted from microorganisms. The present review study is an attempt to summarize a variety of different proteomic techniques and advances. The significant applications in bacterial pathogenesis studies are also covered. Moreover, the areas where proteomics may lead the future studies are introduced.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Elham Zeinalzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepehr Taghizadeh
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bahareh Mehramouz
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Copenhagen, DK 2100, Denmark
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran
| | | | - Bahman Yousefi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Bastami
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Nathan KG, Lal SK. The Multifarious Role of 14-3-3 Family of Proteins in Viral Replication. Viruses 2020; 12:E436. [PMID: 32294919 PMCID: PMC7232403 DOI: 10.3390/v12040436] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 02/06/2023] Open
Abstract
The 14-3-3 proteins are a family of ubiquitous and exclusively eukaryotic proteins with an astoundingly significant number of binding partners. Their binding alters the activity, stability, localization, and phosphorylation state of a target protein. The association of 14-3-3 proteins with the regulation of a wide range of general and specific signaling pathways suggests their crucial role in health and disease. Recent studies have linked 14-3-3 to several RNA and DNA viruses that may contribute to the pathogenesis and progression of infections. Therefore, comprehensive knowledge of host-virus interactions is vital for understanding the viral life cycle and developing effective therapeutic strategies. Moreover, pharmaceutical research is already moving towards targeting host proteins in the control of virus pathogenesis. As such, targeting the right host protein to interrupt host-virus interactions could be an effective therapeutic strategy. In this review, we generated a 14-3-3 protein interactions roadmap in viruses, using the freely available Virusmentha network, an online virus-virus or virus-host interaction tool. Furthermore, we summarize the role of the 14-3-3 family in RNA and DNA viruses. The participation of 14-3-3 in viral infections underlines its significance as a key regulator for the expression of host and viral proteins.
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Affiliation(s)
- Kavitha Ganesan Nathan
- School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia;
| | - Sunil K. Lal
- School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia;
- Tropical Medicine & Biology Platform, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
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Gillen J, Nita-Lazar A. Experimental Analysis of Viral-Host Interactions. Front Physiol 2019; 10:425. [PMID: 31031644 PMCID: PMC6470254 DOI: 10.3389/fphys.2019.00425] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 03/27/2019] [Indexed: 12/16/2022] Open
Abstract
Viral and pathogen protein complexity is often limited by their relatively small genomes, thus critical functions are often accomplished by complexes of host and pathogen proteins. This requirement makes the study of host-pathogen interactions critical for the understanding of pathogenicity and virology. This review article discusses proteomic methods that offer an opportunity to experimentally identify and analyze the binding partners of a target protein and presents the representative studies performed with these methods. These methods divide into two classes: ex situ and in situ. Ex situ assays depend on bindings that occur outside of the normal cellular environment and include yeast two hybrids, pull-downs, and nucleic acid-programmable protein arrays (NAPPA). In situ assays depend on bindings that occur inside of host cells and include affinity purification (AP) and proximity dependent labeling (PDL). Either ex or in situ methods can be reliably used for generating protein-protein interactions networks but it is important to understand and recognize the limitations of the chosen methods when developing an interactomic network. In summary, proteomic methods can be extremely useful for interactomics but it is important to recognize the nature of the method when designing and analyzing an experiment.
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Affiliation(s)
| | - Aleksandra Nita-Lazar
- Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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