David M. Belnap

Molecular Tectonic Model of Virus Structural Transitions: the Putative Cell Entry States of Poliovirus

ABSTRACT Upon interacting with its receptor, poliovirus undergoes conformational changes that are implicated in cell entry, including the externalization of the viral protein VP4 and the N terminus of VP1. We have determined the structures of native virions and of two putative cell entry intermediates, the 135S and 80S particles, at ∼22-Å resolution by cryo-electron microscopy. The 135S and 80S particles are both ∼4% larger than the virion. Pseudoatomic models were constructed by adjusting the beta-barrel domains of the three capsid proteins VP1, VP2, and VP3 from their known positions in the virion to fit the 135S and 80S reconstructions. Domain movements of up to 9 Å were detected, analogous to the shifting of tectonic plates. These movements create gaps between adjacent subunits. The gaps at the sites where VP1, VP2, and VP3 subunits meet are plausible candidates for the emergence of VP4 and the N terminus of VP1. The implications of these observations are discussed for models in which the externalized components form a transmembrane pore through which viral RNA enters the infected cell.

The Structure of the Poliovirus 135S Cell Entry Intermediate at 10-Angstrom Resolution Reveals the Location of an Externalized Polypeptide That Binds to Membranes

ABSTRACT Poliovirus provides a well-characterized system for understanding how nonenveloped viruses enter and infect cells. Upon binding its receptor, poliovirus undergoes an irreversible conformational change to the 135S cell entry intermediate. This transition involves shifts of the capsid protein β barrels, accompanied by the externalization of VP4 and the N terminus of VP1. Both polypeptides associate with membranes and are postulated to facilitate entry by forming a translocation pore for the viral RNA. We have calculated cryo-electron microscopic reconstructions of 135S particles that permit accurate placement of the β barrels, loops, and terminal extensions of the capsid proteins. The reconstructions and resulting models indicate that each N terminus of VP1 exits the capsid though an opening in the interface between VP1 and VP3 at the base of the canyon that surrounds the fivefold axis. Comparison with reconstructions of 135S particles in which the first 31 residues of VP1 were proteolytically removed revealed that the externalized N terminus is located near the tips of propeller-like features surrounding the threefold axes rather than at the fivefold axes, as had been proposed in previous models. These observations have forced a reexamination of current models for the role of the 135S particle in transmembrane pore formation and suggest testable alternatives.

Structure, Assembly, and Antigenicity of Hepatitis B Virus Capsid Proteins

Publisher Summary This chapter reviews current information pertaining to the structure and assembly properties of hepatitis B virus (HBV) capsid protein, as well as the insights into its antigenicity and other interactions. HBV has a small (3.2 kb) DNA genome, although this modest genetic endowment is amplified by a variety of strategies, including alternative expression products of the same gene. In the replication cycle of HBV, the genome is initially incorporated into the assembling virus particle as a single-stranded RNA molecule—the pregenome—that is subsequently retrotranscribed in situ by the viral reverse transcriptase (RT). The DNA-containing nucleocapsid subsequently becomes enveloped by a membrane containing the viral glycoprotein—surface antigen (sAg), of which there are three size variants called S, M, and L, respectively—to yield the completely assembled and infectious virion. The capsid protein of HBV has several unexpected properties. It was found to have a novel fold, rich in a helix, and quite distinct from the eight-stranded b barrel that was common to the first dozen or so capsid proteins to be solved (from plant, animal, and bacterial viruses) and the other capsid protein folds that have been determined more recently.

The morphogenic linker peptide of HBV capsid protein forms a mobile array on the interior surface.

Many capsid proteins have peptides that influence their assembly. In hepatitis B virus capsid protein, the peptide STLPETTVV, linking the shell‐forming ‘core’ domain and the nucleic acid‐binding ‘protamine’ domain, has such a role. We have studied its morphogenic properties by permuting its sequence, substituting it with an extraneous peptide, deleting it to directly fuse the core and protamine domains and assembling core domain dimers with added linker peptides. The peptide was found to be necessary for the assembly of protamine domain‐containing capsids, although its size‐determining effect tolerates some modifications. Although largely invisible in a capsid crystal structure, we could visualize linker peptides by cryo‐EM difference imaging: they emerge on the inner surface and extend from the capsid protein dimer interface towards the adjacent symmetry axis. A closely sequence‐similar peptide in cellobiose dehydrogenase, which has an extended conformation, offers a plausible prototype. We propose that linker peptides are attached to the capsid inner surface as hinged struts, forming a mobile array, an arrangement with implications for morphogenesis and the management of encapsidated nucleic acid.

Diversity of core antigen epitopes of hepatitis B virus

Core antigen (cAg), the viral capsid, is one of the three major clinical antigens of hepatitis B virus. cAg has been described as presenting either one or two conformational epitopes involving the “immunodominant loop.” We have investigated cAg antigenicity by cryo-electron microscopy at ≈11-Å resolution of capsids labeled with monoclonal Fabs, combined with molecular modeling, and describe here two conformational epitopes. Both Fabs bind to the dimeric external spikes, and each epitope has contributions from the loops on both subunits, explaining their discontinuous nature: however, their binding aspects and epitopes differ markedly. To date, four cAg epitopes have been characterized: all are distinct. Although only two regions of the capsid surface are accessible to antibodies, local clustering of the limited number of exposed peptide loops generates a potentially extensive set of discontinuous epitopes. This diversity has not been evident from competition experiments because of steric interference effects. These observations suggest an explanation for the distinction between cAg and e-antigen (an unassembled form of capsid protein) and an approach to immunodiagnosis, exploiting the diversity of cAg epitopes.

Characterization of a Conformational Epitope on Hepatitis B Virus Core Antigen and Quasiequivalent Variations in Antibody Binding

ABSTRACT We have characterized a conformational epitope on capsids of hepatitis B virus (HBV) by cryo-electron microscopy and three-dimensional image reconstruction of Fab-labeled capsids to ∼10-Å resolution, combined with molecular modeling. The epitope straddles the interface between two adjacent subunits and is discontinuous, consisting of five peptides—two on one subunit and three on its neighbor. Together, the two icosahedral forms of the HBV capsid—T=3 and T=4 particles—present seven quasiequivalent variants of the epitope. Of these, only three bind this Fab. Occupancy ranges from ∼100 to ∼0%, reflecting conformational variations in the epitope and steric blocking effects. In the former, small shifts of the component peptides have large effects on binding affinity. This approach appears to hold general promise for elucidating conformational epitopes of HBV and other viruses, including those of neutralizing and diagnostic significance.

Ultrasound sensitive eLiposomes containing doxorubicin for drug targeting therapy

UNLABELLED This study describes a novel nanocarrier of emulsion liposomes (eLiposomes) composed of a perfluoropentane nanodroplet within the aqueous interior of a DPPC liposome, along with the anticancer drug doxorubicin (Dox). The eLiposome containing Dox (eLipoDox) displayed good release of Dox upon insonation with low intensity ultrasound at 20-kHz, 1.0-MHz and 3.0-MHz. More release occurs in vitro at 20-kHz than at the higher frequencies. Controlled delivery was demonstrated by applying ultrasound (US) to HeLa tumor cells in vitro. The confocal images of Dox release to cells indicate that eLipoDox is an effective carrier of chemotherapeutic agent, and releases Dox to the cell cytosol upon insonation. This novel drug delivery system promises to provide more effective US therapy and tumor treatment and has the potential to reduce the side effects of cardiotoxicity caused by Dox. FROM THE CLINICAL EDITOR In this paper, an ultrasound-sensitive doxorubicine-carrying nanoliposome delivery system is reported. Doxorubicin release as a result of ultrasound exposure is clearly demonstrated, paving the way to potential clinical applications with the aim of reducing the systemic toxicity and enhanced local delivery of this compound.

Encapsulating Nanoemulsions Inside eLiposomes for Ultrasonic Drug Delivery

An eLiposome is a liposome encapsulating an emulsion nanodroplet and can be used for drug delivery. For example, therapeutic agents are encapsulated inside the eLiposomes, and the application of ultrasound can cause the emulsion droplet to change from liquid to gas, thus increasing the volume inside the vesicle and causing rupture and the release of the drug. In this research, two different methods were used to prepare eLiposomes. In the first method, emulsion droplets were made of perfluorohexane or perfluoropentane and stabilized with 1,2-dipalmitoyl-sn-glycero-3-phosphate. A layer of 1,2-dimyristoyl-sn-glycero-3-phosphocholine was dried in a round-bottomed flask. Then the emulsion suspension was added to the flask. As the suspension hydrated the phospholipids, they formed liposomes around the emulsions. In the second method, emulsions and liposomes were made separately, and then they were mixed using ultrasound. The advantage of this second method compared to the previous one is that eLiposomes can be made with fewer restrictions because of incompatible combinations of surfactants. Dynamic light scattering and transmission electron microscopy were used to measure the size of the emulsions, liposomes, and eLiposomes. The size of eLiposomes is appropriate for extravasation into tumors with malformed capillary beds. We hypothesize that ultrasound breaks open these eLiposomes. Both types of eLiposomes were constructed with folate attached via a poly(ethylene glycol) tether to induce endocytosis of the eLiposome. The latter eLiposomes were successfully used to deliver calcein as a model drug to HeLa cells.

Structure of the Fab-Labeled “Breathing” State of Native Poliovirus

ABSTRACT At 37°C, the structure of poliovirus is dynamic, and internal polypeptides VP4 and N terminus of VP1 (residues 1 to 53) externalize reversibly. An Fab fragment of a monospecific antibody, which binds to residues 39 to 55 of VP1, was utilized to locate the N termini of VP1 in native (160S) particles in this “breathing” state. Fab and virus were mixed and imaged via cryogenic electron microscopy. The resulting reconstruction showed the capsid expands similarly to the irreversibly altered cell entry intermediate (135S) particle, but the N terminus of VP1 is located near the 2-fold axes, instead of the “propeller tip” as in 135S particles.

Formation of eLiposomes as a drug delivery vehicle

This paper discusses the formation of eLiposomes, defined as a liposome with internal emulsion droplets. Liposomes have been investigated as passively targeted drug carriers due to their ability to deliver drugs to a cancerous tumor via the enhanced permeability and retention (EPR) effect. The enclosed emulsion droplets in an eLiposome add the ability to further control the location and time of release from the liposome with ultrasound. Emulsion droplets were formed from perfluorohexane (PFC6) by sonication at 20 kHz and stabilized with dipalmitoyl phosphatidyl choline (DPPC). The size of the resulting droplets was reduced to approximately 100 nm or 50 nm by extrusion through polycarbonate filters of the same size at 50°C. Small unilamellar vesicles (SUVs) were prepared from DPPC by thin film hydration and extrusion through a 50 nm filter. Interdigitated DPPC sheets were prepared from the SUVs by the addition of ethanol to a concentration of 3M. Excess ethanol was removed by centrifugation washing. The sheets were mixed with emulsion and the solution was heated to 50°C, resulting in the refolding of the DPPC sheets into closed vesicles. Emulsion droplets were encapsulated inside of the newly formed eLiposomes. The size of the eLiposomes was reduced by extrusion. Cryogenic transmission electron microscopy (cryoTEM) and negative-staining TEM were used to image the emulsion droplets and the eLiposomes. Encapsulation of emulsion droplets was verified by rotating the microscope stage of cryoTEM samples.