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Prakash DL, Gosavi S. The diversity of protein-protein interaction interfaces within T=3 icosahedral viral capsids. Front Mol Biosci 2022; 9:967877. [PMID: 36339706 PMCID: PMC9631432 DOI: 10.3389/fmolb.2022.967877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 09/08/2022] [Indexed: 11/20/2022] Open
Abstract
Some non-enveloped virus capsids assemble from multiple copies of a single type of coat-protein (CP). The comparative energetics of the diverse CP-CP interfaces present in such capsids likely govern virus assembly-disassembly mechanisms. The T = 3 icosahedral capsids comprise 180 CP copies arranged about two-, three-, five- and six-fold axes of (quasi-)rotation symmetry. Structurally diverse CPs can assemble into T = 3 capsids. Specifically, the Leviviridae CPs are structurally distinct from the Bromoviridae, Tombusviridae and Tymoviridae CPs which fold into the classic “jelly-roll” fold. However, capsids from across the four families are known to disassemble into dimers. To understand whether the overall symmetry of the capsid or the structural details of the CP determine virus assembly-disassembly mechanisms, we analyze the different CP-CP interfaces that occur in the four virus families. Previous work studied protein homodimer interfaces using interface size (relative to the monomer) and hydrophobicity. Here, we analyze all CP-CP interfaces using these two parameters and find that the dimerization interface (present between two CPs congruent through a two-fold axis of rotation) has a larger relative size in the Leviviridae than in the other viruses. The relative sizes of the other Leviviridae interfaces and all the jelly-roll interfaces are similar. However, the dimerization interfaces across families have slightly higher hydrophobicity, potentially making them stronger than other interfaces. Finally, although the CP-monomers of the jelly-roll viruses are structurally similar, differences in their dimerization interfaces leads to varied dimer flexibility. Overall, differences in CP-structures may induce different modes of swelling and assembly-disassembly in the T = 3 viruses.
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Abstract
Virus-like particle (VLP) technologies are based on virus-inspired artificial structures and the intrinsic ability of viral proteins to self-assemble at controlled conditions. Therefore, the basic knowledge about the mechanisms of viral particle formation is highly important for designing of industrial applications. As an alternative to genetic and chemical processes, different physical methods are frequently used for VLP construction, including well characterized protein complexes for introduction of foreign molecules in VLP structures.This chapter shortly discusses the mechanisms how the viruses form their perfectly ordered structures as well as the principles and most interesting application examples, how to exploit the structural and assembly/disassembly properties of viral structures for creation of new nanomaterials.
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Affiliation(s)
- Andris Zeltins
- Latvian Biomedical Research and Study Centre, Riga, Latvia.
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Liu H, Tian Y, Ji B, Lu H, Xin Q, Jiang Y, Ding L, Zhang J, Chen J, Bai B. Heterodimerization of the kappa opioid receptor and neurotensin receptor 1 contributes to a novel β-arrestin-2-biased pathway. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2719-2738. [PMID: 27523794 DOI: 10.1016/j.bbamcr.2016.07.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 07/28/2016] [Accepted: 07/29/2016] [Indexed: 12/17/2022]
Abstract
Together with its endogenous ligands (dynorphin), the kappa opioid receptor (KOR) plays an important role in modulating various physiological and pharmacological responses, with a classical G protein-coupled pathway mediating analgesia and non-G protein-dependent pathway, especially the β-arrestin-dependent pathway, eliciting side effects of dysphoria, aversion, drug-seeking in addicts, or even relapse to addiction. Although mounting evidence has verified a functional overlap between dynorphin/KOR and neurotensin/neurotensin receptor 1 (NTSR1) systems, little is known about direct interaction between the two receptors. Here, we showed that KOR and NTSR1 form a heterodimer that functions as a novel pharmacological entity, and this heterodimer, in turn, brings about a switch in KOR-mediated signal transduction, from G protein-dependent to β-arrestin-2-dependent. This was simultaneously verified by analyzing a KOR mutant (196th residue) that lost the ability to dimerize with NTSR1. We also found that dual occupancy of the heterodimer forced the β-arrestin-2-dependent pathway back into Gi protein-dependent signaling, according to KOR activation. These data provide new insights into the interaction between KOR and NTSR1, and the newly discovered role of NTSR1 acting as a switch between G protein- and β-arrestin-dependent pathways of KOR also suggests a new approach for utilizing pathologically elevated dynorphin/KOR system into full play for its analgesic effect with limited side effects.
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Affiliation(s)
- Haiqing Liu
- School of Life Science, Shandong Agricultural University, Taian, Shandong 271018, PR China; Department of Physiology, Taishan Medical College, Taian, Shandong 271000, PR China.
| | - Yanjun Tian
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Bingyuan Ji
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Hai Lu
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Qing Xin
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Yunlu Jiang
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Liangcai Ding
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Jingmei Zhang
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
| | - Jing Chen
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China; Division of Translational and Systems, Warwick Medical School, University of Warwick, Coventry, UK.
| | - Bo Bai
- Neurobiology Institute, Jining Medical University, Jining, Shandong 272067, PR China.
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Zhou X, Kataoka M, Liu Z, Takeda N, Wakita T, Li TC. Characterization of self-assembled virus-like particles of dromedary camel hepatitis e virus generated by recombinant baculoviruses. Virus Res 2015; 210:8-17. [PMID: 26160190 PMCID: PMC7114528 DOI: 10.1016/j.virusres.2015.06.022] [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: 04/07/2015] [Revised: 06/26/2015] [Accepted: 06/30/2015] [Indexed: 12/18/2022]
Abstract
Dromedary camel hepatitis E virus (DcHEV), a novel hepatitis E virus, has been identified in dromedary camels in Dubai, United Arab Emirates. The antigenicity, pathogenicity and epidemiology of this virus have been unclear. Here we first used a recombinant baculovirus expression system to express the 13 and 111 N-terminus amino-acid-truncated DcHEV ORF2 protein in insect Tn5 cells, and we obtained two types of virus-like particles (VLPs) with densities of 1.300 g/cm(3) and 1.285 g/cm(3), respectively. The small VLPs (Dc4sVLPs) were estimated to be 24 nm in diameter, and were assembled by a protein with the molecular mass 53 kDa. The large VLPs (Dc3nVLPs and Dc4nVLPs) were 35 nm in diameter, and were assembled by a 64-kDa protein. An antigenic analysis demonstrated that DcHEV was cross-reactive with G1, G3-G6, ferret and rat HEVs, and DcHEV showed a stronger cross-reactivity to G1 G3-G6 HEV than it did to rat and ferret HEV. In addition, the antibody against DcHEV-LPs neutralized G1 and G3 HEV in a cell culture system, suggesting that the serotypes of these HEVs are identical. We also found that the amino acid residue Met-358 affects the small DcHEV-LPs assembly.
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Affiliation(s)
- Xianfeng Zhou
- Department of Microbiology, Nanchang Center for Disease Control and Prevention Nanchang, Jiangxi, China
| | - Michiyo Kataoka
- Departments of Pathology, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Zheng Liu
- Department of Biochemistry and Molecular Biophysics, Columbia University, NY, NY 10032, USA
| | - Naokazu Takeda
- Research Institute for Microbial Diseases, Osaka University, Suita, Osaka 565-0781, Japan
| | - Takaji Wakita
- Departments of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan
| | - Tian-Cheng Li
- Departments of Virology II, National Institute of Infectious Diseases, Gakuen 4-7-1, Musashi-murayama, Tokyo 208-0011, Japan.
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Sõmera M, Sarmiento C, Truve E. Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae. Viruses 2015; 7:3076-115. [PMID: 26083319 PMCID: PMC4488728 DOI: 10.3390/v7062761] [Citation(s) in RCA: 45] [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: 03/20/2015] [Revised: 05/18/2015] [Accepted: 06/02/2015] [Indexed: 12/26/2022] Open
Abstract
The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.
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Affiliation(s)
- Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Cecilia Sarmiento
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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Abstract
Orsay, the first virus discovered to naturally infect Caenorhabditis elegans or any nematode, has a bipartite, positive-sense RNA genome. Sequence analyses show that Orsay is related to nodaviruses, but molecular characterizations of Orsay reveal several unique features, such as the expression of a capsid-δ fusion protein and the use of an ATG-independent mechanism for translation initiation. Here we report the crystal structure of an Orsay virus-like particle assembled from recombinant capsid protein (CP). Orsay capsid has a T = 3 icosahedral symmetry with 60 trimeric surface spikes. Each CP can be divided into three regions: an N-terminal arm that forms an extended protein interaction network at the capsid interior, an S domain with a jelly-roll, β-barrel fold forming the continuous capsid, and a P domain that forms surface spike projections. The structure of the Orsay S domain is best aligned to T = 3 plant RNA viruses but exhibits substantial differences compared with the insect-infecting alphanodaviruses, which also lack the P domain in their CPs. The Orsay P domain is remotely related to the P1 domain in calicivirus and hepatitis E virus, suggesting a possible evolutionary relationship. Removing the N-terminal arm produced a slightly expanded capsid with fewer nucleic acids packaged, suggesting that the arm is important for capsid stability and genome packaging. Because C. elegans-Orsay serves as a highly tractable model for studying viral pathogenesis, our results should provide a valuable structural framework for further studies of Orsay replication and infection.
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Ali H, Urolagin S, Gurarslan Ö, Vihinen M. Performance of Protein Disorder Prediction Programs on Amino Acid Substitutions. Hum Mutat 2014; 35:794-804. [DOI: 10.1002/humu.22564] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/04/2014] [Indexed: 01/04/2023]
Affiliation(s)
- Heidi Ali
- Institute of Biomedical Technology; FI-33014 University of Tampere; Tampere Finland
- BioMediTech; Tampere Finland
| | - Siddhaling Urolagin
- Department of Experimental Medical Science; Lund University; SE-22184 Lund Sweden
| | - Ömer Gurarslan
- Institute of Biomedical Technology; FI-33014 University of Tampere; Tampere Finland
- BioMediTech; Tampere Finland
| | - Mauno Vihinen
- Institute of Biomedical Technology; FI-33014 University of Tampere; Tampere Finland
- BioMediTech; Tampere Finland
- Department of Experimental Medical Science; Lund University; SE-22184 Lund Sweden
- Tampere University Hospital; Tampere Finland
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Turnip yellow mosaic virus forms infectious particles without the native beta-annulus structure and flexible coat protein N-terminus. Virology 2012; 422:165-73. [DOI: 10.1016/j.virol.2011.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 09/20/2011] [Accepted: 10/19/2011] [Indexed: 11/22/2022]
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