Virus Capsid Structures Research Articles

The atomic structures of shrimp nodaviruses reveal new dimeric spike structures and particle polymorphism

Shrimp nodaviruses, including Penaeus vannamei (PvNV) and Macrobrachium rosenbergii nodaviruses (MrNV), cause white-tail disease in shrimps, with high mortality. The viral capsid structure determines viral assembly and host specificity during infections. Here, we show cryo-EM structures of T = 3 and T = 1 PvNV-like particles (PvNV-LPs), crystal structures of the protrusion-domains (P-domains) of PvNV and MrNV, and the crystal structure of the ∆N-ARM-PvNV shell-domain (S-domain) in T = 1 subviral particles. The capsid protein of PvNV reveals five domains: the P-domain with a new jelly-roll structure forming cuboid-like spikes; the jelly-roll S-domain with two calcium ions; the linker between the S- and P-domains exhibiting new cross and parallel conformations; the N-arm interacting with nucleotides organized along icosahedral two-fold axes; and a disordered region comprising the basic N-terminal arginine-rich motif (N-ARM) interacting with RNA. The N-ARM controls T = 3 and T = 1 assemblies. Increasing the N/C-termini flexibility leads to particle polymorphism. Linker flexibility may influence the dimeric-spike arrangement.

Membrane-Containing Icosahedral Bacteriophage PRD1: The Dawn of Viral Lineages.

Membrane-containing enterobacterial phage PRD1 was isolated from sewage more than 40years ago. At that time none would have expected the impact that unravelling its biology would have on modern virology and on the way we understand virus assembly, evolution and classification today. PRD1 structural analyses have provided a framework for understanding some aspects of virus evolution-introducing the concept of "viral lineages"-where the three-dimensional structures of virus capsids represent the fingerprint for evolutionary relationship which cannot be traced from the sequence data. In this review we summarise those findings that have led to the notion of viral lineages and the multidisciplinary efforts made in elucidating PRD1 life cycle. These studies have rendered PRD1 a model system not only for the family Tectiviridae to which it belongs, but more generally to complex DNA viruses enclosing a membrane vesicle beneath the capsid shell.

Structure and architecture of immature and mature murine leukemia virus capsids

Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein-protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry.

Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids.

Analytical Techniques to Characterize the Structure, Properties, and Assembly of Virus Capsids.

VIPERdb: A Tool for Virus Research

The VIrus Particle ExploreR database (VIPERdb) ( http://viperdb.scripps.edu ) is a database and web portal for primarily icosahedral virus capsid structures that integrates structure-derived information with visualization and analysis tools accessed through a set of web interfaces. Our aim in developing VIPERdb is to provide comprehensive structure-derived information on viruses comprising simple to detailed attributes such as size (diameter), architecture ( T number), genome type, taxonomy, intersubunit association energies, and surface-accessible residues. In addition, a number of web-based tools are provided to enable users to interact with the structures and compare and contrast structure-derived properties between different viruses. Recently, we have constructed a series of data visualizations using modern JavaScript charting libraries such as Google Charts that allow users to explore trends and gain insights based on the various data available in the database. Furthermore, we now include helical viruses and nonicosahedral capsids by implementing modified procedures for data curation and analysis. This article provides an up-to-date overview of VIPERdb, describing various data and tools that are currently available and how to use them to facilitate structure-based bioinformatics analysis of virus capsids.

Neutralization Mechanisms of Two Highly Potent Antibodies against Human Enterovirus 71.

ABSTRACTDespite significant advances in health care, outbreaks of infections by enteroviruses (EVs) continue to plague the Asia-Pacific region every year. Enterovirus 71 (EV71) causes hand-foot-and-mouth disease (HFMD), for which there are currently no therapeutics. Here, we report two new antibodies, A9 and D6, that potently neutralize EV71. A9 exhibited a 50% neutralizing concentration (neut50) value of 0.1 nM against EV71, which was 10-fold lower than that observed for D6. Investigation into the mechanisms of neutralization revealed that binding of A9 to EV71 blocks receptor binding but also destabilizes and damages the virus capsid structure. In contrast, D6 destabilizes the capsid only slightly but interferes more potently with the attachment of the virus to the host cells. Cryo-electron microscopy (cryo-EM) structures of A9 and D6 bound with EV71 shed light on the locations and nature of the epitopes recognized by the two antibodies. Although some regions of the epitopes recognized by the two antibodies overlap, there are differences that give rise to dissimilarities in potency as well as in the mechanisms of neutralization. Interestingly, the overlapping regions of the epitopes encompass the site that the virus uses to bind SCARB2, explaining the reason for the observed blocking of the virus-receptor interaction by the two antibodies. We also identified structural elements that might play roles in modulating the stability of the EV71 particles, including particle integrity. The molecular features of the A9 and D6 epitopes unveiled in this study open up new avenues for rationally designing antiviral drugs.

Atomic-Level Characterization of the HIV-1 Capsid and Host-Pathogen Interactions from Molecular Dynamics Simulations

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. Therefore, a detailed knowledge of the HIV-1 capsid, including its dynamic structure, interactions with cellular factors, and the specific roles it plays in the replication cycle, is imperative for the development of antiviral therapeutics. In this poster, I present an emerging area of computational biology that focuses on the structure and dynamics of virus capsids. State-of-the-art computer simulations reveal the role of ions in the stability of the HIV-1 capsid. In addition, molecular dynamics reveal the energetics associated with the permeation of nucleotides through various pores of the HIV-1 capsid thus unveiling the molecular mechanism associated with nucleotide translocation. Finally, emergent properties of the entire HIV-1 capsid like acoustic motions and effective electrostatics reveal large-scale cooperativity between capsomers spanning over large regions of the capsid.

Rapid increase of near atomic resolution virus capsid structures determined by cryo-electron microscopy.

The recent technological advances in electron microscopes, detectors, as well as image processing and reconstruction software have brought single particle cryo-electron microscopy (cryo-EM) into prominence for determining structures of bio-molecules at near atomic resolution. This has been particularly true for virus capsids, ribosomes, and other large assemblies, which have been the ideal specimens for structural studies by cryo-EM approaches. An analysis of time series metadata of virus structures on the methods of structure determination, resolution of the structures, and size of the virus particles revealed a rapid increase in the virus structures determined by cryo-EM at near atomic resolution since 2010. In addition, the data highlight the median resolution (∼3.0 Å) and size (∼310.0 Å in diameter) of the virus particles determined by X-ray crystallography while no such limits exist for cryo-EM structures, which have a median diameter of 508 Å. Notably, cryo-EM virus structures in the last four years have a median resolution of 3.9 Å. Taken together with minimal sample requirements, not needing diffraction quality crystals, and being able to achieve similar resolutions of the crystal structures makes cryo-EM the method of choice for current and future virus capsid structure determinations.

Quasicrystalline and crystalline types of local protein order in capsids of small viruses

Like metal alloys and micellar systems in soft matter, the viral capsid structures can be of crystalline and quasicrystalline types. We reveal the local quasicrystalline order of proteins in small spherical viral capsids using their nets of dodecahedral type. We show that the structure of some of the viral shells is well described in terms of a chiral pentagonal tiling, whose nodes coincide with centers of mass of protein molecules. The chiral protein packing found in these capsids originates from the pentagonal Penrose tiling (PPT), due to a specific phason reconstruction needed to fit the protein order at the adjacent dodecahedron faces. Via examples of small spherical viral shells and geminate capsid of a Maize Streak virus, we discuss the benefits and shortcomings of the usage of a dodecahedral net in comparison to icosahedral one, which is commonly applied for the modeling of viral shells with a crystalline local order.

A comparative analysis of the foamy and ortho virus capsid structures reveals an ancient domain duplication

BackgroundThe Spumaretrovirinae (foamy viruses) and the Orthoretrovirinae (e.g. HIV) share many similarities both in genome structure and the sequences of the core viral encoded proteins, such as the aspartyl protease and reverse transcriptase. Similarity in the gag region of the genome is less obvious at the sequence level but has been illuminated by the recent solution of the foamy virus capsid (CA) structure. This revealed a clear structural similarity to the orthoretrovirus capsids but with marked differences that left uncertainty in the relationship between the two domains that comprise the structure.MethodsWe have applied protein structure comparison methods in order to try and resolve this ambiguous relationship. These included both the DALI method and the SAP method, with rigorous statistical tests applied to the results of both methods. For this, we employed collections of artificial fold ’decoys’ (generated from the pair of native structures being compared) to provide a customised background distribution for each comparison, thus allowing significance levels to be estimated.ResultsWe have shown that the relationship of the two domains conforms to a simple linear correspondence rather than a domain transposition. These similarities suggest that the origin of both viral capsids was a common ancestor with a double domain structure. In addition, we show that there is also a significant structural similarity between the amino and carboxy domains in both the foamy and ortho viruses.ConclusionsThese results indicate that, as well as the duplication of the double domain capsid, there may have been an even more ancient gene-duplication that preceded the double domain structure. In addition, our structure comparison methodology demonstrates a general approach to problems where the components have a high intrinsic level of similarity.

Beta-Propiolactone Inactivation of Coxsackievirus A16 Induces Structural Alteration and Surface Modification of Viral Capsids.

Beta-propiolactone (BPL) is an inactivating agent that is widely used in the vaccine industry. However, its effects on vaccine protein antigens and its mechanisms of action remain poorly understood. Here we present cryo-electron microscopy (cryo-EM) structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids at resolutions of 3.9 Å and 6.5 Å, respectively. Notably, both particles were found to adopt an expanded conformation resembling the 135S-like uncoating intermediate, with characteristic features including an opened 2-fold channel, the externalization of the N terminus of VP1 capsid protein, and the absence of pocket factor. However, major neutralizing epitopes are very well preserved on these particles. Further biochemical analyses revealed that BPL treatment impairs the abilities of CVA16 particles to bind to the attachment receptor heparan sulfate and to a conformation-dependent monoclonal antibody in a BPL dose-dependent manner, indicating that BPL is able to modify surface-exposed amino acid residues. Taken together, our results demonstrate that BPL treatment may induce alteration of the overall structure and surface properties of a nonenveloped viral capsid, thus revealing a novel mode of action of BPL.IMPORTANCE Beta-propiolactone (BPL) is commonly used as an inactivating reagent to produce viral vaccines. It is recognized that BPL inactivates viral infectivity through modification of viral nucleic acids. However, its effect on viral proteins remains largely unknown. Here, we present high-resolution cryo-EM structures of BPL-treated coxsackievirus A16 (CVA16) mature virions and procapsids, which reveals an expanded overall conformation and characteristic features that are typical for the 135S-like uncoating intermediate. We further show that the BPL concentration affects the binding of inactivated CVA16 particles to their receptor/antibody. Thus, BPL treatment can alter the overall structure and surface properties of viral capsids, which may lead to antigenic and immunogenic variations. Our findings provide important information for future development of BPL-inactivated vaccines.

Stimuli-Responsive Polymersomes for Biomedical Applications.

Polymersomes, the structural analogues of liposomes, are hollow structures enclosed by a bilayer membrane made from amphiphilic copolymers. Polymersomes have been proposed to mimic the structure and properties of cellular membranes and viral capsids. Excellent robustness and stability, chemical versatility for tunable membrane properties and surface functionalization make polymersomes attractive candidates for drug delivery, diagnostic imaging, nanoreactor vessels, and artificial organelles. In further biomimetic strategies, stimuli-responsive polymersomes that can recognize various external physical or internal biological environmental stimuli and conduct "on demand" release in dose-, spatial-, and temporal-controlled fashions have been widely developed. This Perspective focuses on recent advances in stimuli-responsive polymersomes and their potential biomedical applications. Representative examples of each stimulus, the advantages and limitations of different strategies, and the future opportunities and challenges are discussed.

Crystal Structure of the Human Astrovirus Capsid Protein.

ABSTRACTHuman astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominant protein species with molecular masses of ∼34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP9071–415 (amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP9071–415 encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP9071–415 is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP9071–415 structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation.IMPORTANCE Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. As a nonenveloped virus, HAstV exhibits an intriguing feature in that its maturation requires extensive proteolytic processing of the astrovirus capsid protein (CP) both inside and outside the host cell. Mature HAstV contains three predominant protein species, but the mechanism for acquired infectivity upon maturation is unclear. We have solved the crystal structure of VP9071–415 of human astrovirus serotype 8. VP9071–415 encompasses the conserved N-terminal domain of the viral CP. Fitting of the VP9071–415 structure into the cryo-EM maps of HAstV produced an atomic model for the T=3 icosahedral capsid. Our model of the HAstV capsid provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation. Such information has potential applications in the development of a VLP vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation.

Helical capsids of plant viruses: architecture with structural lability.

Capsids of numerous filamentous and rod-shaped plant viruses possess helical symmetry. In positive-stranded RNA viruses, helical capsids are typically composed of many identical subunits of the viral capsid protein (CP), encapsidating a molecule of viral genomic RNA. Current progress in structural studies of helical plant viruses has revealed differences between filamentous and rod-shaped viruses, both in structural folds of their CPs and in the interactions of CP molecules in their capsids. Many filamentous and rod-shaped viruses have functionally similar lateral inter-subunit contacts on the outer virion surface. Additionally, the extreme N-terminal CP region in filamentous viruses is intrinsically disordered. Taken together, the available data establish a link between the structural features of molecular interactions of CP molecules and the physical properties of helical virions ranging from rigidity to flexibility. Overall, the structure of helical plant viruses is significantly more labile than previously thought, often allowing structural transitions, remodelling and the existence of alternative structural forms of virions. These properties of virions are believed to be functionally significant at certain stages of the viral life cycle, such as during translational activation and cell-to-cell transport. In this review, we discuss structural and functional features of filamentous and rod-shaped virions, highlight their shared features and differences, and lay emphasis on the relationships between the molecular structure of viral capsids and their properties including virion shape, lability and capability of structural remodelling.

Self-Assembly of M30L60 Icosidodecahedron

Summary Self-assembly is invaluable in the construction of giant molecular structures via a bottom-up approach. Although living organisms naturally make the most use of self-assembly and freely handle the mechanism at will, scientists are still far behind the level of nature. Inspired by the elegant structures of virus capsids, we have previously constructed roughly spherical giant metal complexes with the symmetry of an octahedron, cuboctahedron, and rhombicuboctahedron with the compositions M 6 L 12 , M 12 L 24 , and M 24 L 48 , respectively. Here, we report our first successful synthesis of an M 30 L 60 molecular icosidodecahedron that consists of ∼100 components: 30 Pd(II) ions and 60 ligands that assemble into the largest well-defined spherical macromolecule to date (diameter of ∼8.2 nm). Tuning the flexibility of the ligand was the key for successful self-assembly. A highly complex but symmetrically organized structure was identified through X-ray crystallographic analysis. The interior space of the molecular complex is large enough (157,000 A 3 ) to enclose proteins.

Assembly, Engineering and Applications of Virus-Based Protein Nanoparticles.

Viruses and their protein capsids can be regarded as biologically evolved nanomachines able to perform multiple, complex biological functions through coordinated mechano-chemical actions during the infectious cycle. The advent of nanoscience and nanotechnology has opened up, in the last 10 years or so, a vast number of novel possibilities to exploit engineered viral capsids as protein-based nanoparticles for multiple biomedical, biotechnological or nanotechnological applications. This chapter attempts to provide a broad, updated overview on the self-assembly and engineering of virus capsids, and on applications of virus-based nanoparticles. Different sections provide outlines on: (i) the structure, functions and properties of virus capsids; (ii) general approaches for obtaining assembled virus particles; (iii) basic principles and events related to virus capsid self-assembly; (iv) genetic and chemical strategies for engineering virus particles; (v) some applications of engineered virus particles being developed; and (vi) some examples on the engineering of virus particles to modify their physical properties, in order to improve their suitability for different uses.

Structures of spherical viral capsids as quasicrystalline tilings

Spherical viral shells with icosahedral symmetry have been considered as quasicrystalline tilings. Similarly to known Caspar-Klug quasi-equivalence theory, the presented approach also minimizes the number of conformations necessary for the protein molecule bonding with its neighbors in the shell, but is based on different geometrical principles. It is assumed that protein molecule centers are located at vertices of tiles with identical edges, and the number of different tile types is minimal. Idealized coordinates of nonequivalent by symmetry protein positions in six various capsid types are obtained. The approach describes in a uniform way both the structures satisfying the well-known Caspar-Klug geometrical model and the structures contradicting this model.

Abstract 714: Bioengineering of the adeno-associated virus (AAV) vectors for dendritic cell (DC)-based immunotherapy

Abstract Dendritic cell (DC) based immunotherapy has recently demonstrated great potential for clinical application. However, additional progress in methods of tumor specific antigen delivery to DC is necessary for the further development of the anti-tumor vaccine. In our studies of the adeno-associated virus (AAV) crystal structure combined with data from various mutagenesis experiments on the capsid genes, we have identified specific residues which play a critical role in intracellular trafficking of these vectors. Genetic modifications of these regions increase transduction efficiency of AAV vectors most likely by preventing phosphorylation of serine (S) and threonine (T) residues by cellular kinases and subsequent degradation of vectors by host proteosomes. These studies led to development of several vectors such as AAV6-S663V, AAV6-T492V and AAV6-T492+S663V which can increase transduction efficiency of the monocytes-derived DCs (moDCs) by up to 5-fold compared to AAV6-WT. This significant improvement in infectivity of capsid-optimized over AAV6-WT vectors was associated with advanced nuclear translocation rather than facilitated viral entry into cells, which was confirmed by qPCR analysis on viral genome distribution in cytoplasmic and nuclear fractions. Our data indicate that approximately 85% of viral genomes of mutant AAV vectors accumulated in the nucleus 24 hrs post-infection compared with approximately 50% of AAV6-WT vectors at the same time-point. Considering the relatively short period of time between the initiation of maturation and cytopathic changes in DCs, rapid expression of antigen is critical to provide appropriate signals for T-cell activation. Another important advantage of the employment of such capsid-modified AAV6 vectors for vaccination is that efficient nuclear translocation in DCs will provide less material for potential presentation, and might prevent induction of immuno-competition in immune responses against vector-derived and antigen-derived epitopes. We next evaluated the possibility of whether high transduction efficiency of the new vectors will be associated with better antigen presentation and generating antigen-specific cytotoxic T-cells (CTLs). Our data show that DCs loaded with AAV6-T492+S663V carrying human prostate specific antigen (hPSA) resulted specific T-cell clone proliferation and generation of superior CTLs with higher killing capability of human prostate adenocarcinoma cells, LNCaP, compare CTLs stimulated by AAV6-WT vectors. In summary, our studies lead to the development of effective novel AAV vectors by manipulating viral capsid structure for the potential use in DC-based immunotherapy. Citation Format: Pandya Jheel, Kellee Britt, George Aslanidi. Bioengineering of the adeno-associated virus (AAV) vectors for dendritic cell (DC)-based immunotherapy. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 714. doi:10.1158/1538-7445.AM2014-714

Virus Maturation and the VIPERdb Virus Structural Database

VIPERdb (Carrillo-Tripp, M., Shepherd, C. M., Borelli, I. A., Venkataraman, S., Lander, G., Natarajan, P., Johnson, J. E., Brooks, C. L., 3rd, and Reddy, V. S. 2009. VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Res 37:D436-42) is a database for icosahedral virus capsid structures. The emphasis of the resource is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration. The web site includes powerful search utilities and useful database interface tools. Here we use VIPERdb to address the dynamic character of a virus by relating cryoEM based models of maturation intermediates and associated variance analysis to the high resolution coordinates in VIPERdb for the T=4 Nudaurelia Capensis ω Virus. The outcome is a structure-based description of the maturation energy landscape at near atomic resolution (Tang, J., Kearney, B., Wang, Q., Doerschuk, P. C., Baker, T. S., and Johnson, J. E. 2013. Geometric and Dynamic Analyses of Nudaurelia capensis ω Virus Maturation Reveal the Energy Landscape of Particle Transitions. J. Mol. Recog. Accepted for publication).

Production and applications of engineered viral capsids.

As biological agents, viruses come in an astounding range of sizes, with varied shapes and surface morphologies. The structures of viral capsids are generally assemblies of hundreds of copies of one or a few proteins which can be harnessed for use in a wide variety of applications in biotechnology, nanotechnology, and medicine. Despite their complexity, many capsid types form as homogenous populations of precise geometrical assemblies. This is important in both medicine, where well-defined therapeutics are critical for drug performance and federal approval, and nanotechnology, where precise placement affects the properties of the desired material. Here we review the production of viruses and virus-like particles with methods for selecting and manipulating the size, surface chemistry, assembly state, and interior cargo of capsid. We then discuss many of the applications used in research today and the potential commercial and therapeutic products from engineered viral capsids.