scholarly journals New Insights into Viral Architecture via Affine Extended Symmetry Groups

2008 ◽  
Vol 9 (3-4) ◽  
pp. 221-229 ◽  
Author(s):  
T. Keef ◽  
R. Twarock
Keyword(s):  
Viral Genome ◽  
3D Structure ◽  
Icosahedral Symmetry ◽  
Mathematical Framework ◽  
Tertiary Structures ◽  
Virus Structure ◽  
Viral Capsids ◽  
Virus Particles ◽  
Viral Particles ◽  
The Family

Since the seminal work of Caspar and Klug on the structure of the protein containers that encapsulate and hence protect the viral genome, it has been recognized that icosahedral symmetry is crucial for the structural organization of viruses. In particular, icosahedral symmetry has been invoked in order to predict the surface structures of viral capsids in terms of tessellations or tilings that schematically encode the locations of the protein subunits in the capsids. Whilst this approach is capable of predicting the relative locations of the proteins in the capsids, a prediction on the relative sizes of different virus particles in a family cannot be made. Moreover, information on the full 3D structure of viral particles, including the tertiary structures of the capsid proteins and the organization of the viral genome within the capsid are inaccessible with their approach. We develop here a mathematical framework based on affine extensions of the icosahedral group that allows us to address these issues. In particular, we show that the relative radii of viruses in the family of Polyomaviridae and the material boundaries in simple RNA viruses can be determined with our approach. The results complement Caspar and Klug's theory of quasi-equivalence and provide details on virus structure that have not been accessible with previous methods, implying that icosahedral symmetry is more important for virus architecture than previously appreciated.

scholarly journals Assembly and Disassembly of Viral Capsids

2005 ◽  
Vol 6 (2) ◽  
pp. 69-72 ◽  
Author(s):  
Roya Zandi ◽  
David Reguera ◽  
Robijn Bruinsma ◽  
William Gelbart ◽  
Joseph Rudnick
Keyword(s):  
Viral Genome ◽  
Release Mechanism ◽  
Icosahedral Symmetry ◽  
Hamiltonian Approach ◽  
Conformational Switching ◽  
Viral Capsids ◽  
Protein Subunits ◽  
Single Protein ◽  
Shed Light

We address here a theoretical basis for the icosahedral symmetry that is observed so commonly for viral capsids, i.e., the single-protein-thick rigid shells that protect the viral genome. In particular, we outline the phenomenological hamiltonian approach developed recently (see Zandi, R., Reguera, D., Bruinsma, R., Gelbart, W.M. and Rudnick, J. (2004), Original of icosahedral symmetry in viruses,Proc. Natl. Acad. Sci., 101, 15556–15560) to account for the overwhelming prevalence of the Caspar-Klug “T-number” structures that are found for “spherical” viruses. We feature the role of “conformational switching energies” defining the competing multimeric states of the protein subunits. The results of Monte Carlo simulation of this model are argued to shed light as well on the mechanical properties and genome release mechanism for these viruses.

Freisetzung von 51Chrom aus markierten HeLa-Zellen nach Poliovirus-Infektion / Release of 51Chromium from Labeled HeLa-Cells after Infection by Poliovirus

1971 ◽  
Vol 26 (9) ◽  
pp. 929-933 ◽  
Author(s):  
Klaus Koschel
Keyword(s):  
Hela Cells ◽  
Viral Genome ◽  
Time Course ◽  
Rna Synthesis ◽  
Surrounding Medium ◽  
Cellular Proteins ◽  
Virus Particles ◽  
Chromium Release ◽  
Viral Particles ◽  
Intact Virus

HeLa-cells labelled with 51Chromium start to release 51Cr into the medium 5-6 hours after infection with poliovirus. 51Cr-release is only observed when the viral genome is intact. Virus particles previously irradiated by UV do not cause chromium-release. Furthermore, protein synthesis must be allowed to proceed for 3-4 hours, p.i. for the effect to take place. Viral RNA synthesis is not required. Chromium release, release of viral particles and leakage of cellular proteins into the surrounding medium follow the same time course and have identical requirements. They are therefore considered to reflect a single phenomenon, a leakiness of the cell due to virus infection.

Exposure of protein VP7 on the surface of bluetongue virus

1990 ◽  
Vol 48 (3) ◽  
pp. 600-601
Author(s):  
A.D. Hyatt
Keyword(s):  
Bluetongue Virus ◽  
Structural Proteins ◽  
Major Constituent ◽  
Outer Coat ◽  
Virus Particles ◽  
Antibody Recognition ◽  
The Core ◽  
The Family ◽  
Electron Microscopical ◽  
Physical Accessibility

Bluetongue virus (BTV) is the type species os the genus orbivirus in the family Reoviridae. The virus has a fibrillar outer coat containing two major structural proteins VP2 and VP5 which surround an icosahedral core. The core contains two major proteins VP3 and VP7 and three minor proteins VP1, VP4 and VP6. Recent evidence has indicated that the core comprises a neucleoprotein center which is surrounded by two protein layers; VP7, a major constituent of capsomeres comprises the outer and VP3 the inner layer of the core . Antibodies to VP7 are currently used in enzyme-linked immunosorbant assays and immuno-electron microscopical (JEM) tests for the detection of BTV. The tests involve the antibody recognition of VP7 on virus particles. In an attempt to understand how complete viruses can interact with antibodies to VP7 various antibody types and methodologies were utilized to determine the physical accessibility of the core to the external environment.

scholarly journals Identification and Characterization of a Poliovirus Capsid Mutant with Enhanced Thermal Stability

2018 ◽  
Vol 93 (6) ◽  
Author(s):  
Y Nguyen ◽  
Palmy R. Jesudhasan ◽  
Elizabeth R. Aguilera ◽  
Julie K. Pfeiffer
Keyword(s):  
Thermal Stability ◽  
High Temperatures ◽  
Oral Route ◽  
Mutant Virus ◽  
Single Amino Acid ◽  
Bacterial Surface ◽  
Virus Particles ◽  
Heat Resistant ◽  
Viral Particles ◽  
Very High

ABSTRACTEnteric viruses, including poliovirus, are spread by the fecal-oral route. In order to persist and transmit to a new host, enteric virus particles must remain stable once they are in the environment. Environmental stressors such as heat and disinfectants can inactivate virus particles and prevent viral transmission. It has been previously demonstrated that bacteria or bacterial surface glycans can enhance poliovirus virion stability and limit inactivation from heat or bleach. While investigating the mechanisms underlying bacterially enhanced virion thermal stability, we identified and characterized a poliovirus (PV) mutant with increased resistance to heat inactivation. The M132V mutant harbors a single amino acid change in the VP1 capsid coding that is sufficient to confer heat resistance but not bleach resistance. Although the M132V virus was stable in the absence of bacteria or feces at most temperatures, M132V virus was stabilized by feces at very high temperatures. M132V PV had reduced specific infectivity and RNA uncoating compared with those of wild-type (WT) PV, but viral yields in HeLa cells were similar. In orally inoculated mice, M132V had a slight fitness cost since fecal titers were lower and 12.5% of fecal viruses reverted to the WT. Overall, this work sheds light on factors that influence virion stability and fitness.IMPORTANCEViruses spread by the fecal-oral route need to maintain viability in the environment to ensure transmission. Previous work indicated that bacteria and bacterial surface polysaccharides can stabilize viral particles and enhance transmission. To explore factors that influence viral particle stability, we isolated a mutant poliovirus that is heat resistant. This mutant virus does not require feces for stability at most temperatures but can be stabilized by feces at very high temperatures. Even though the mutant virus is heat resistant, it is susceptible to inactivation by treatment with bleach. This work provides insight into how viral particles maintain infectivity in the environment.

scholarly journals Abundant Defective Viral Particles Budding from Microglia in the Course of Retroviral Spongiform Encephalopathy

2000 ◽  
Vol 74 (4) ◽  
pp. 1775-1780 ◽  
Author(s):  
Regine Hansen ◽  
Stefanie Czub ◽  
Evi Werder ◽  
Jens Herold ◽  
Georg Gosztonyi ◽  
...  
Keyword(s):  
Infectious Virus ◽  
Protein Translocation ◽  
Neuronal Damage ◽  
Ex Vivo ◽  
Spongiform Encephalopathy ◽  
Microglia Cell ◽  
Virus Particles ◽  
Viral Particles ◽  
Type C ◽  
Retroviral Infections

ABSTRACT A pathogenetic hallmark of retroviral neurodegeneration is the affinity of neurovirulent retroviruses for microglia cells, while degenerating neurons are excluded from retroviral infections. Microglia isolated ex vivo from rats peripherally infected with a neurovirulent retrovirus released abundant mature type C virions; however, infectivity associated with microglia was very low. In microglia, viral transcription was unaffected but envelope proteins were insufficiently cleaved into mature viral proteins and were not detected on the microglia cell surface. These microglia-specific defects in envelope protein translocation and processing not only may have prevented formation of infectious virus particles but also may have caused further cellular defects in microglia with the consequence of indirect neuronal damage. It is conceivable that similar events play a role in neuro-AIDS.

scholarly journals What is in a Viral Stock: Perspectives and Current Limitations of Flow Virometry

2020 ◽  
Author(s):  
Timothy K. Soh ◽  
Jens B. Bosse
Keyword(s):  
Flow Cytometry ◽  
Full Potential ◽  
Multiple Objects ◽  
Virus Particles ◽  
Viral Particles ◽  
Viral Stock ◽  
Infected Cells ◽  
A Minor ◽  
Unique Capability

Herpesviruses produce a plethora of pleomorphic and heterogeneous particle populations. The composition and biological role of these is not understood. Detailed analysis has been challenging due to the lack of multidimensional identification and purification methodologies. Fluorescence-activated cell sorting (FACS), originally developed to sort objects with at least ten thousand-fold larger volumes, has recently been applied to cellular exosomes as well as viral particles and has been dubbed nanoscale flow cytometry or “flow virometry”. In comparison to other nanoparticles, herpesvirus concentrations can be measured with high precision using simple culturing methods. Here, we used this unique capability to evaluate a standard FACS sorter. We demonstrate that detection and separation capabilities were insufficient to distinguish infectious fluorescent viral populations from populations lacking fluorescence and infectivity. Moreover, fluorescent populations did not contain single virus particles but mostly aggregates. On top, analysis of viral samples by flow cytometry was confounded by swarm detection, as multiple objects are measured simultaneously and interpreted as a single object. Despite these technical difficulties, comparison of crude supernatant to gradient purified HCMV revealed that infectious virus is a minor proportion of the particles released from infected cells. Our data stress the need for a set of standardized controls and protocols when applying FACS to biological nanoparticles and highlights technical challenges that need to be solved before flow virometry can achieve its full potential.

scholarly journals Consistent global structures of complex RNA states through multidimensional chemical mapping

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Clarence Yu Cheng ◽  
Fang-Chieh Chou ◽  
Wipapat Kladwang ◽  
Siqi Tian ◽  
Pablo Cordero ◽  
...  
Keyword(s):  
Secondary Structure ◽  
3D Structure ◽  
Three Dimensions ◽  
Biological Processes ◽  
Chemical Mapping ◽  
Entry Site ◽  
Tertiary Structures ◽  
Internal Ribosome Entry ◽  
Non Coding Rna ◽  
Paired End Sequencing

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

scholarly journals Nucleocapsid Assembly of Baculoviruses

Viruses ◽  
2019 ◽  
Vol 11 (7) ◽  
pp. 595 ◽  
Author(s):  
Shuling Zhao ◽  
Guanghui He ◽  
Yiheng Yang ◽  
Changyong Liang
Keyword(s):  
Viral Genome ◽  
Viral Dna ◽  
Transport Pathways ◽  
Viral Capsids ◽  
Protein Subunits ◽  
Dna Molecule ◽  
Assembly Mechanism ◽  
Large Oligomer ◽  
Related Proteins ◽  
Selection Of

The baculovirus nucleocapsid is formed through a rod-like capsid encapsulating a genomic DNA molecule of 80~180 kbp. The viral capsid is a large oligomer composed of many copies of various protein subunits. The assembly of viral capsids is a complex oligomerization process. The timing of expression of nucleocapsid-related proteins, transport pathways, and their interactions can affect the assembly process of preformed capsids. In addition, the selection of viral DNA and the injection of the viral genome into empty capsids are the critical steps in nucleocapsid assembly. This paper reviews the replication and recombination of baculovirus DNA, expression and transport of capsid proteins, formation of preformed capsids, DNA encapsulation, and nucleocapsid formation. This review will provide a basis for further study of the nucleocapsid assembly mechanism of baculovirus.

scholarly journals Electron Cryotomography Studies of Maturing HIV-1 Particles Reveal the Assembly Pathway of the Viral Core

2014 ◽  
Vol 89 (2) ◽  
pp. 1267-1277 ◽  
Author(s):  
Cora L. Woodward ◽  
Sarah N. Cheng ◽  
Grant J. Jensen
Keyword(s):  
Viral Genome ◽  
Virus Assembly ◽  
Structural Characteristics ◽  
Hexagonal Lattice ◽  
The Body ◽  
The Core ◽  
Assembly Pathway ◽  
Viral Particles ◽  
Electron Cryotomography ◽  
Hiv 1

ABSTRACTTo better characterize the assembly of the HIV-1 core, we have used electron cryotomography (ECT) to image infected cells and the viral particles cryopreserved next to them. We observed progressive stages of virus assembly and egress, including flower-like flat Gag lattice assemblies, hemispherical budding profiles, and virus buds linked to the plasma membrane via a thin membrane neck. The population of budded viral particles contains immature, maturation-intermediate, and mature core morphologies. Structural characteristics of the maturation intermediates suggest that the core assembly pathway involves the formation of a CA sheet that associates with the condensed ribonucleoprotein (RNP) complex. Our analysis also reveals a correlation between RNP localization within the viral particle and the formation of conical cores, suggesting that the RNP helps drive conical core assembly. Our findings support an assembly pathway for the HIV-1 core that begins with a small CA sheet that associates with the RNP to form the core base, followed by polymerization of the CA sheet along one side of the conical core toward the tip, and then closure around the body of the cone.IMPORTANCEDuring HIV-1 assembly and release, the Gag polyprotein is organized into a signature hexagonal lattice, termed the immature lattice. To become infectious, the newly budded virus must disassemble the immature lattice by proteolyzing Gag and then reassemble the key proteolytic product, the structural protein p24 (CA), into a distinct, mature hexagonal lattice during a process termed maturation. The mature HIV-1 virus contains a conical capsid that encloses the condensed viral genome at its wide base. Mutations or small molecules that interfere with viral maturation also disrupt viral infectivity. Little is known about the assembly pathway that results in the conical core and genome encapsidation. Here, we have used electron cryotomography to structurally characterize HIV-1 particles that are actively maturing. Based on the morphologies of core assembly intermediates, we propose that CA forms a sheet-like structure that associates with the condensed viral genome to produce the mature infectious conical core.

scholarly journals Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication

2018 ◽  
Vol 92 (15) ◽  
Author(s):  
Paula F. Zamora ◽  
Liya Hu ◽  
Jonathan J. Knowlton ◽  
Roni M. Lahr ◽  
Rodolfo A. Moreno ◽  
...  
Keyword(s):  
Virus Replication ◽  
Viral Genome ◽  
Nonstructural Protein ◽  
Dsrna Virus ◽  
Genome Replication ◽  
Nonstructural Proteins ◽  
Content Type ◽  
The Family ◽  
Viral Genome Replication

ABSTRACTViral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, usingin vitroand cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCEFollowing infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the familyReoviridaeencode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the familyReoviridaediverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Usingin vitroand cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the familyReoviridaeassort and replicate their genomes.

Sign in / Sign up

Export Citation Format

Share Document