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Selvaraj C, Pravin MA, Alhoqail WA, Nayarisseri A, Singh SK. Intrinsically disordered proteins in viral pathogenesis and infections. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 132:221-242. [PMID: 36088077 DOI: 10.1016/bs.apcsb.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Disordered proteins serve a crucial part in many biological processes that go beyond the capabilities of ordered proteins. A large number of virus-encoded proteins have extremely condensed proteomes and genomes, which results in highly disordered proteins. The presence of these IDPs allows them to rapidly adapt to changes in their biological environment and play a significant role in viral replication and down-regulation of host defense mechanisms. Since viruses undergo rapid evolution and have a high rate of mutation and accumulation in their proteome, IDPs' insights into viruses are critical for understanding how viruses hijack cells and cause disease. There are many conformational changes that IDPs can adopt in order to interact with different protein partners and thus stabilize the particular fold and withstand high mutation rates. This chapter explains the molecular mechanism behind viral IDPs, as well as the significance of recent research in the field of IDPs, with the goal of gaining a deeper comprehension of the essential roles and functions played by viral proteins.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Wardah A Alhoqail
- Department of Biology, College of Education, Majmaah University, Al Majma'ah, Saudi Arabia
| | - Anuraj Nayarisseri
- In Silico Research Laboratory, Eminent Biosciences, Indore, Madhya Pradesh, India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
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Yasmin AR, Omar AR, Farhanah MI, Hiscox AJ, Yeap SK. Quantitative Proteomics Analysis Revealed Compromised Chicken Dendritic Cells Function at Early Stage of Very Virulent Infectious Bursal Disease Virus Infection. Avian Dis 2020; 63:275-288. [PMID: 31251527 DOI: 10.1637/11936-072418-reg.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/19/2018] [Indexed: 11/05/2022]
Abstract
Chicken dendritic cells (DCs) have been demonstrated to be susceptible to infectious bursal disease virus (IBDV), a causative agent of acute and immunosuppressed disease in young chicks known as infectious bursal disease. Further functional characterization of IBDV-infected DCs of chickens is required to provide a better understanding on the influence of the virus on chicken bone marrow-derived dendritic cells (BM-DCs) following very virulent (vv) IBDV infection. Membrane proteins of BM-DCs were extracted and the proteins were further denatured and reduced before performing labeling with isobaric tags for relative and absolute quantitation. The differential expression protein profiles were identified and quantified using liquid chromatography coupled with tandem mass spectrometry, and later validated using flow cytometry and real-time reverse transcriptase PCR. The analysis has identified 134 differentially regulated proteins from a total of 283 proteins (cutoff values of ≤0.67, ≥1.5, and ProtScore >1.3 at 95% confidence interval), which produced high-yield membrane fractions. The entry of vvIBDV into the plasma membrane of BM-DCs was observed at 3 hr postinfection by the disruption of several important protein molecule functions, namely apoptosis, RNA/DNA/protein synthesis, and transport and cellular organization, without the activation of proteins associated with signaling. At the later stage of infection, vvIBDV induced expression of several proteins, namely CD200 receptor 1-A, integrin alpha-5, HSP-90, cathepsin, lysosomal-associated membrane protein, and Ras-related proteins, which play crucial roles in signaling, apoptosis, stress response, and antigen processing as well as in secretion of danger-associated proteins. These findings collectively indicated that the chicken DCs are expressing various receptors regarded as potential targets for pathogen interaction during viral infection. Therefore, fundamental study of the interaction of DCs and IBDV will provide valuable information in understanding the role of professional antigen-presenting cells in chickens and their molecular interactions during IBDV infection and vaccination.
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Affiliation(s)
- A R Yasmin
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Laboratory Diagnosis, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia,
| | - A R Omar
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.,Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - M I Farhanah
- Laboratory of Vaccines and Immunotherapeutics, Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - A J Hiscox
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, L3 5RF, United Kingdom
| | - S K Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, 43900 Sepang, Selangor, Malaysia
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Banerjee N, Mukhopadhyay S. Viral glycoproteins: biological role and application in diagnosis. Virusdisease 2016; 27:1-11. [PMID: 26925438 PMCID: PMC4758313 DOI: 10.1007/s13337-015-0293-5] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/10/2015] [Indexed: 12/21/2022] Open
Abstract
The viruses that infect humans cause a huge global disease burden and produce immense challenge towards healthcare system. Glycoproteins are one of the major components of human pathogenic viruses. They have been demonstrated to have important role(s) in infection and immunity. Concomitantly high titres of antibodies against these antigenic viral glycoproteins have paved the way for development of novel diagnostics. Availability of appropriate biomarkers is necessary for advance diagnosis of infectious diseases especially in case of outbreaks. As human mobilization has increased manifold nowadays, dissemination of infectious agents became quicker that paves the need of rapid diagnostic system. In case of viral infection it is an emergency as virus spreads and mutates very fast. This review encircles the vast arena of viral glycoproteins, their importance in health and disease and their diagnostic applications.
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Affiliation(s)
- Nilotpal Banerjee
- Department of Laboratory Medicine, School of Tropical Medicine, 108, C.R Avenue, Kolkata, 700073 India
| | - Sumi Mukhopadhyay
- Department of Laboratory Medicine, School of Tropical Medicine, 108, C.R Avenue, Kolkata, 700073 India
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High throughput proteomic analysis and a comparative review identify the nuclear chaperone, Nucleophosmin among the common set of proteins modulated in Chikungunya virus infection. J Proteomics 2015; 120:126-41. [PMID: 25782748 PMCID: PMC7102674 DOI: 10.1016/j.jprot.2015.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 02/14/2015] [Accepted: 03/04/2015] [Indexed: 01/14/2023]
Abstract
Global re-emergence of Chikungunya virus (CHIKV) has renewed the interest in its cellular pathogenesis. We subjected CHIKV-infected Human Embryo Kidney cells (HEK293), a widely used cell-based system for CHIKV infection studies, to a high throughput expression proteomics analysis by Liquid Chromatography–tandem mass spectrometry. A total of 1047 differentially expressed proteins were identified in infected cells, consistently in three biological replicates. Proteins involved in transcription, translation, apoptosis and stress response were the major ones among the 209 proteins that had significant up-regulation. In the set of 45 down-regulated proteins, those involved in carbohydrate and lipid metabolism predominated. A STRING network analysis revealed tight interaction of proteins within the apoptosis, stress response and protein synthesis pathways. We short-listed a common set of 30 proteins that can be implicated in cellular pathology of CHIKV infection by comparing our results and results of earlier CHIKV proteomics studies. Modulation of eight proteins selected from this set was re-confirmed at transcript level. One among them, Nucleophosmin, a nuclear chaperone, showed temporal modulation and cytoplasmic aggregation upon CHIKV infection in double immunofluorescence staining and confocal microscopy. The short-listed cellular proteins will be potential candidates for targeted study of the molecular interactions of CHIKV with host cells. Biological significance Chikungunya remained as a neglected tropical disease till its re-emergence in 2005 in the La RéUnion islands and subsequently, in India and many parts of South East Asia. These and the epidemics that followed in subsequent years ran an explosive course leading to extreme morbidity and attributed mortality to this originally benign virus infection. Apart from classical symptoms of acute fever and debilitating polyarthralgia lasting for several weeks, a number of complications were documented. These included aphthous-like ulcers and vesiculo-bullous eruptions on the skin, hepatic involvement, central nervous system complications such as encephalopathy and encephalitis, and transplacental transmission. The disease has recently spread to the Americas with its initial documentation in the Caribbean islands. The Asian genotype of this positive-stranded RNA virus of the Alphavirus genus has been attributed in these outbreaks. However, the disease ran a similar course as the one caused by the East, Central and South African (ECSA) genotype in the other parts of the world. Studies have documented a number of mutations in the re-emerging strains of the virus that enhances mosquito adaptability and modulates virus infectivity. This might support the occurrence of fiery outbreaks in the absence of herd immunity in affected population. Several research groups work to understand the pathogenesis of chikungunya and the mechanisms of complications using cellular and animal models. A few proteomics approaches have been employed earlier to understand the protein level changes in the infected cells. Our present study, which couples a high throughput proteomic analysis and a comparative review of these earlier studies, identifies a few critical molecules as hypothetical candidates that might be important in this infection and for future study. High throughput expression proteomics analysis in HEK293 cells Identified four major cellular pathways affected in Chikungunya virus infection Short-listed 30 key proteins modulated by a comparative review Confirmed modulation of Nucleophosmin and other selected proteins upon infection
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Nandal UK, Vlietstra WJ, Byrman C, Jeeninga RE, Ringrose JH, van Kampen AHC, Speijer D, Moerland PD. Candidate prioritization for low-abundant differentially expressed proteins in 2D-DIGE datasets. BMC Bioinformatics 2015; 16:25. [PMID: 25627479 PMCID: PMC4384356 DOI: 10.1186/s12859-015-0455-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023] Open
Abstract
Background Two-dimensional differential gel electrophoresis (2D-DIGE) provides a powerful technique to separate proteins on their isoelectric point and apparent molecular mass and quantify changes in protein expression. Abundantly available proteins in spots can be identified using mass spectrometry-based approaches. However, identification is often not possible for low-abundant proteins. Results We present a novel computational approach to prioritize candidate proteins for unidentified spots. Our approach exploits noisy information on the isoelectric point and apparent molecular mass of a protein spot in combination with functional similarities of candidate proteins to already identified proteins to select and rank candidates. We evaluated our method on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. Using leave-one-out cross-validation, we show that the true-positive rate for the top-5 ranked proteins is 43.8%. Conclusions Our approach shows good performance on a 2D-DIGE dataset comparing protein expression in uninfected and HIV-1 infected T-cells. We expect our method to be highly useful in (re-)mining other 2D-DIGE experiments in which especially the low-abundant protein spots remain to be identified. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0455-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Umesh K Nandal
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Wytze J Vlietstra
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Carsten Byrman
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Rienk E Jeeninga
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Jeffrey H Ringrose
- Laboratory of Experimental Virology, Department of Medical Microbiology, Center for Infection and Immunity Amsterdam (CINIMA), Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Antoine H C van Kampen
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands. .,Biosystems Data Analysis Group, University of Amsterdam, Science Park 9041098, XH Amsterdam, The Netherlands.
| | - Dave Speijer
- Department of Medical Biochemistry, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
| | - Perry D Moerland
- Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, DE Amsterdam, 1100, The Netherlands.
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Berkhout B, Coombs KM. Quantitative omics and its application to study virus-host interactions-a new frontier. Front Microbiol 2013; 4:31. [PMID: 23468816 PMCID: PMC3587804 DOI: 10.3389/fmicb.2013.00031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2013] [Accepted: 02/04/2013] [Indexed: 12/27/2022] Open
Affiliation(s)
- Ben Berkhout
- Department of Medical Microbiology, Laboratory of Experimental Virology, University of Amsterdam Amsterdam, Netherlands
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