Vijay S. Reddy

VIPERdb2: an enhanced and web API enabled relational database for structural virology.

VIPERdb (http://viperdb.scripps.edu) is a relational database and a web portal for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the virology community, with an emphasis on the description and comparison of derived data from structural and computational analyses of the virus capsids. In the current release, VIPERdb2, we implemented a useful and novel method to represent capsid protein residues in the icosahedral asymmetric unit (IAU) using azimuthal polar orthographic projections, otherwise known as Φ–Ψ (Phi–Psi) diagrams. In conjunction with a new Application Programming Interface (API), these diagrams can be used as a dynamic interface to the database to map residues (categorized as surface, interface and core residues) and identify family wide conserved residues including hotspots at the interfaces. Additionally, we enhanced the interactivity with the database by interfacing with web-based tools. In particular, the applications Jmol and STRAP were implemented to visualize and interact with the virus molecular structures and provide sequence–structure alignment capabilities. Together with extended curation practices that maintain data uniformity, a relational database implementation based on a schema for macromolecular structures and the APIs provided will greatly enhance the ability to do structural bioinformatics analysis of virus capsids.

Crystal Structure of Human Adenovirus at 3.5 Å Resolution

Human Adenovirus Structures Human adenoviruses may be a common cause of acute infections in humans, but they can also be used as vectors for vaccine and therapeutic gene transfer. Rational engineering of safe adenovirus vectors has been hampered by a lack of high-resolution structural information. Two papers now describe the structure of human adenovirus using complementary techniques. Reddy et al. (p. 1071; see the Perspective by Harrison) have determined the crystal structure at 3.5 angstrom resolution, while Liu et al. (p. 1038; see the Perspective by Harrison) solved the structure to 3.6 angstrom resolution by electron microscopy. Together the structures provide insights into viral assembly, stabilization, and cell entry mechanisms. High-resolution structures provide a basis for optimizing adenovirus as a vaccine and gene-therapy vector. Rational development of adenovirus vectors for therapeutic gene transfer is hampered by the lack of accurate structural information. Here, we report the x-ray structure at 3.5 angstrom resolution of the 150-megadalton adenovirus capsid containing nearly 1 million amino acids. We describe interactions between the major capsid protein (hexon) and several accessory molecules that stabilize the capsid. The virus structure also reveals an altered association between the penton base and the trimeric fiber protein, perhaps reflecting an early event in cell entry. The high-resolution structure provides a substantial advance toward understanding the assembly and cell entry mechanisms of a large double-stranded DNA virus and provides new opportunities for improving adenovirus-mediated gene transfer.

Virus Particle Explorer (VIPER), a Website for Virus Capsid Structures and Their Computational Analyses

The number of icosahedral-capsid structures determined at a near-atomic level of resolution is growing rapidly as advances in synchrotron radiation sources, fast-readout detectors, and computer hardware and software are made. Hence, there is an increasing need to organize these mega-assemblies into a uniform and easy-to-use database. The coordinates of the icosahedral-capsid structures deposited in the Protein Data Bank (PDB) (2) follow a variety of conventions in which the icosahedral symmetry axes are oriented differently in the orthogonal coordinate system. While trying to analyze the various capsid structures en masse, we became aware of the need for a database in which all capsid structures (coordinates) are stored in a standard icosahedral orientation. Such a structural database of viral capsids would indeed facilitate the development of tools for high-throughput analyses of the virus structures. We report here the creation of a web-base (website and database) of virus structures, the Virus Particle Explorer (VIPER), which can be accessed through the World Wide Web (WWW) at the uniform resource locator (URL) http://mmtsb.scripps.edu /viper/. The organization of the VIPER database is shown in Fig. ​Fig.1.1. FIG. 1 Flow chart showing the organization of the contents of the VIPER site. The VIPER database contains the structures of viral capsids determined at a nearly atomic-level resolution. Coordinates of the capsid structures are stored in the z(2)-3-5-x(2) convention. ...

Energetics of Quasiequivalence: Computational Analysis of Protein-Protein Interactions in Icosahedral Viruses

Quaternary structure polymorphism found in quasiequivalent virus capsids provides a static framework for studying the dynamics of protein interactions. The same protein subunits are found in different structural environments within these particles, and in some cases, the molecular switching required for the polymorphic quaternary interactions is obvious from high-resolution crystallographic studies. Employing atomic resolution structures, molecular mechanics, and continuum electrostatic methods, we have computed association energies for unique subunit interfaces of three icosahedral viruses, black beetle virus, southern bean virus, and human rhinovirus 14. To quantify the chemical determinants of quasiequivalence, the energetic contributions of individual residues forming quasiequivalent interfaces were calculated and compared. The potential significance of the differences in stabilities at quasiequivalent interfaces was then explored with the combinatorial assembly approach. The analysis shows that the unique association energies computed for each virus serve as a sensitive basis set that may determine distinct intermediates and pathways of virus capsid assembly. The pathways for the quasiequivalent viruses displayed isoenergetic oligomers at specific points, suggesting that these may determine the quaternary structure polymorphism required for the assembly of a quasiequivalent particle.

VIPERdb: a relational database for structural virology

VIPERdb () is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.

The Structure and Function of Nodavirus Particles: A Paradigm for Understanding Chemical Biology

Publisher Summary Genetic and particle complexity vary greatly among different viruses, there are general requirements for the sustenance of the extracellular portion of the virus life cycle that are remarkably similar for all animal viruses. This chapter applies the minimalistic approach to explore the extracellular portion of the virus life cycle and uses the insect nodaviruses as the subject of investigation. Nodavirus life cycle reflects a complex series of highly controlled events that reflect the behavior of animal viruses in general. The information presented is obtained with biophysical methods including crystallography, electron microscopy, and kinetic studies as well as with site-directed mutagenesis and other techniques of molecular biology. The goals are to understand dynamic processes associated with the viral processes including assembly, receptor-mediated interactions, a more detailed description of RNA release, and structural transitions that occur as a particle enters the cell. These studies required new methods of approach including computational chemistry, time-resolved analyses with spectroscopy, mass spectrometry, single crystal and solution X-ray scattering, and electron microscopy.

Invariant Polymorphism in Virus Capsid Assembly

Directed self-assembly of designed viral capsids holds significant potential for applications in materials science and medicine. However, the complexity of preparing these systems for assembly and the difficulty of quantitative experimental measurements on the assembly process have limited access to critical mechanistic questions that dictate the final product yields and isomorphic forms. Molecular simulations provide a means of elucidating self-assembly of viral proteins into icosahedral capsids and are the focus of the present study. Using geometrically realistic coarse-grained models with specialized molecular dynamics methods, we delineate conditions of temperature and coat protein concentration that lead to the spontaneous self-assembly of T = 1 and T = 3 icosahedral capsids. In addition to the primary product of icosahedral capsids, we observe a ubiquitous presence of nonicosahedral yet highly symmetric and enclosed aberrant capsules in both T = 1 and T = 3 systems. This polymorphism in assembly products recapitulates the scope and morphology of particle types that have been observed in mis-assembly experiments of virus capsids. Moreover, we find that this structural polymorphism in the end point structures is an inherent property of the coat proteins and arises from condition-dependent kinetic mechanisms that are independent of the elemental mechanisms of capsid growth (as long as the building blocks of the coat proteins are all monomeric, dimeric, or trimeric) and the capsid T number. The kinetic mechanisms responsible for self-assembly of icosahedral capsids and aberrant capsules are deciphered; the self-assembly of icosahedral capsids requires a high level of assembly fidelity, whereas self-assembly of nonicosahedral capsules is a consequence of an off-pathway mechanism that is prevalent under nonoptimal conditions of temperature or protein concentration during assembly. The latter case involves kinetically trapped dislocations of pentamer-templated proteins with hexameric organization. These findings provide insights into the complex processes that govern viral capsid assembly and suggest some features of the assembly process that can be exploited to control the assembly of icosahedral capsids and nonicosahedral capsules.

Insights into adenovirus host cell interactions from structural studies.

Human adenoviruses cause a significant number of acute respiratory, enteric and ocular infections, however they have also served as useful model systems for uncovering fundamental aspects of cell and molecular biology. In addition, replication-defective forms of adenovirus are being used in gene transfer and vaccine clinical trials. Over the past decade, steady advances in structural biology techniques have helped reveal important insights into the earliest events in the adenovirus life cycle as well as virus interactions with components of the host immune system. This review highlights the continuing use of structure-based approaches to uncover the molecular features of adenovirus-host interactions.

A Viral Nanoparticle with Dual Function as an Anthrax Antitoxin and Vaccine

The recent use of Bacillus anthracis as a bioweapon has stimulated the search for novel antitoxins and vaccines that act rapidly and with minimal adverse effects. B. anthracis produces an AB-type toxin composed of the receptor-binding moiety protective antigen (PA) and the enzymatic moieties edema factor and lethal factor. PA is a key target for both antitoxin and vaccine development. We used the icosahedral insect virus Flock House virus as a platform to display 180 copies of the high affinity, PA-binding von Willebrand A domain of the ANTXR2 cellular receptor. The chimeric virus-like particles (VLPs) correctly displayed the receptor von Willebrand A domain on their surface and inhibited lethal toxin action in in vitro and in vivo models of anthrax intoxication. Moreover, VLPs complexed with PA elicited a potent toxin-neutralizing antibody response that protected rats from anthrax lethal toxin challenge after a single immunization without adjuvant. This recombinant VLP platform represents a novel and highly effective, dually-acting reagent for treatment and protection against anthrax.

Structures and organization of adenovirus cement proteins provide insights into the role of capsid maturation in virus entry and infection.

Significance Adenoviruses cause acute respiratory, ocular, and enteric diseases, with significant health concerns for immunocompromised individuals. Replication-deficient adenoviruses are among the most frequently used vectors for human gene therapy. However, the structural details of these large (150-MDa) and complex viral vectors remain obscure. In this study, we determined the crystal structures of all cement proteins in the context of the entire virion and, in the process, revised the existing cement protein structures and their locations. Significantly, our results revealed the structure of protein VI, for the first time to our knowledge, with its cleaved propeptide sequestered within peripentonal hexons. This permits untethering and release of the membrane-lytic segment, thereby providing the molecular basis for maturation cleavage of protein VI in adenovirus-mediated endosome disruption. Adenovirus cement proteins play crucial roles in virion assembly, disassembly, cell entry, and infection. Based on a refined crystal structure of the adenovirus virion at 3.8-Å resolution, we have determined the structures of all of the cement proteins (IIIa, VI, VIII, and IX) and their organization in two distinct layers. We have significantly revised the recent cryoelectron microscopy models for proteins IIIa and IX and show that both are located on the capsid exterior. Together, the cement proteins exclusively stabilize the hexon shell, thus rendering penton vertices the weakest links of the adenovirus capsid. We describe, for the first time to our knowledge, the structure of protein VI, a key membrane-lytic molecule, and unveil its associations with VIII and core protein V, which together glue peripentonal hexons beneath the vertex region and connect them to the rest of the capsid on the interior. Following virion maturation, the cleaved N-terminal propeptide of VI is observed, reaching deep into the peripentonal hexon cavity, detached from the membrane-lytic domain, so that the latter can be released. Our results thus provide the molecular basis for the requirement of maturation cleavage of protein VI. This process is essential for untethering and release of the membrane-lytic region, which is known to mediate endosome rupture and delivery of partially disassembled virions into the host cell cytoplasm.