Divalent ion-dependent reversible swelling of tomato bushy stunt virus and organization of the expanded virion

Infectivity of Dengue Virus Serotypes 1 and 2 Is Correlated with E-Protein Intrinsic Dynamics but Not to Envelope Conformations

Dengue is a mosquito-borne virus with dire health and economic impacts. Dengue is responsible for an estimated 390 million infections per year, with dengue 2 (DENV2) being the most virulent strain among the four serotypes. Interestingly, it is also in strains of this serotype that temperature-dependent large-scale morphological changes, termed "breathing," have been observed. Although the structure of these morphologies has been solved to 3.5-Å resolution, the dynamics of the viral envelope are unknown. Here, we combine fluorescence and mass spectrometry with molecular dynamics simulations to provide insights into DENV2 (NGC strain) structural dynamics in comparison with DENV1 (PVP 159). We observe hitherto unseen conformational changes and structural dynamics of the DENV2 envelope that are influenced by both temperature and divalent cations. Our results show that for DENV2 and DENV1 the intrinsic dynamics, but not the specific morphologies, are correlated with viral infectivity.

Calcium ions modulate the mechanics of tomato bushy stunt virus

Viral particles are endowed with physicochemical properties whose modulation confers certain metastability to their structures to fulfill each task of the viral cycle. Here, we investigate the effects of swelling and ion depletion on the mechanical stability of individual tomato bushy stunt virus nanoparticles (TBSV-NPs). Our experiments show that calcium ions modulate the mechanics of the capsid: the sequestration of calcium ions from the intracapsid binding sites reduces rigidity and resilience in ∼24% and 40%, respectively. Interestingly, mechanical deformations performed on native TBSV-NPs induce an analogous result. In addition, TBSV-NPs do not show capsomeric vacancies after surpassing the elastic limit. We hypothesize that even though there are breakages among neighboring capsomers, RNA-capsid protein interaction prevents the release of capsid subunits. This work shows the mechanical role of calcium ions in viral shell stability and identifies TBSV-NPs as malleable platforms based on protein cages for cargo transportation at the nanoscale.

Veritas per structuram

When I entered graduate school in 1963, the golden age of molecular biology had just begun, and myoglobin was the only protein with a known high-resolution structure. The romance of working out the structure of a virus by X-ray crystallography nonetheless captured both my imagination and the ensuing 15 years of my scientific life, during which "protein crystallography" began to morph into "structural biology." The course of the research recounted here follows the broader, 50-year trajectory of structural biology, as I could rarely resist opportunities to capitalize on new technologies when they opened some interesting part of biology to three-dimensional rigor. That fascination shows no sign of subsiding.

A plant derived multifunctional tool for nanobiotechnology based on Tomato bushy stunt virus

Structure, size, physicochemical properties and production strategies make many plant viruses ideal protein based nanoscaffolds, nanocontainers and nano-building blocks expected to deliver a multitude of applications in different fields such as biomedicine, pharmaceutical chemistry, separation science, catalytic chemistry, crop pest control and biomaterials science. Functionalization of viral nanoparticles through modification by design of their external and internal surfaces is essential to fully exploit the potentiality of these objects. In the present paper we describe the development of a plant derived multifunctional tool for nanobiotechnology based on Tomato bushy stunt virus. We demonstrate the ability of this system to remarkably sustain genetic modifications and in vitro chemical derivatizations of its outer surface, which resulted in the successful display of large chimeric peptides fusions and small chemical molecules, respectively. Moreover, we have defined physicochemical conditions for viral swelling and reversible viral pore gating that we have successfully employed for foreign molecules loading and retention in the inner cavity of this plant virus nanoparticles system. Finally, a production and purification strategy from Nicotiana benthamiana plants has been addressed and optimized.

Picornaviruses

The picornavirus family consists of a large number of small RNA viruses, many of which are significant pathogens of humans and livestock. They are amongst the simplest of vertebrate viruses comprising a single stranded positive sense RNA genome within a T = 1 (quasi T = 3) icosahedral protein capsid of approximately 30 nm diameter. The structures of a number of picornaviruses have been determined at close to atomic resolution by X-ray crystallography. The structures of cell entry intermediate particles and complexes of virus particles with receptor molecules or antibodies have also been obtained by X-ray crystallography or at a lower resolution by cryo-electron microscopy. Many of the receptors used by different picornaviruses have been identified, and it is becoming increasingly apparent that many use co-receptors and alternative receptors to bind to and infect cells. However, the mechanisms by which these viruses release their genomes and transport them across a cellular membrane to gain access to the cytoplasm are still poorly understood. Indeed, detailed studies of cell entry mechanisms have been made only on a few members of the family, and it is yet to be established how broadly the results of these are applicable across the full spectrum of picornaviruses. Working models of the cell entry process are being developed for the best studied picornaviruses, the enteroviruses. These viruses maintain particle integrity throughout the infection process and function as genome delivery modules. However, there is currently no model to explain how viruses such as cardio- and aphthoviruses that appear to simply dissociate into subunits during uncoating deliver their genomes into the cytoplasm.

The kinetics of swelling of southern bean mosaic virus: a study using photon correlation spectroscopy

Southern bean mosaic virus swells upon removal of Ca2+ at pH 8.25. Virions do not seem to aggregate significantly; the z-average hydrodynamic diameter increases from 29.9 nm to 44.0 nm. Swelling is virtually complete within 3 min, and swollen virions have a z-average hydrodynamic diameter similar to that of virions swollen by dialysis overnight.

The EDTA-treated expanded satellite tobacco necrosis virus: biochemical properties and crystallization

The calcium ions normally present in the protein shell of the satellite tobacco necrosis virus (STNV) have been removed by EDTA. The radius of the EDTA-treated virion was found to be dependent upon pH. The radial increase was 2% at pH 5.0,4.5% at pH 6.5, and 7% at pH 7.0 as determined by analytical ultracentrifugation and X-ray crystallography. The virion could be recontracted by lowering the pH or by the addition of divalent cations, calcium ions being the most efficient. At pH 7.0 and above, the EDTA-treated virion was sensitive to ribonucleases and to trypsin. The cleavage site for trypsin is at Arg 28, which is near the N terminus of the shell domain of the subunit, but at a point which is well buried in the native structure. Crystals of the expanded STNV particles at pH 5.0 and 6.5 have been produced.

Disassembly of African cassava mosaic virus

The plant-infecting geminiviruses encapsidate their single-stranded DNA genome in characteristic twinned particles that are unique among viruses. These particles are formed by joining two incomplete T=1 icosahedra. African cassava mosaic virions were purified by density-gradient centrifugation from infected Nicotiana benthamiana plants and analysed for their stability with respect to pH changes and heat treatment by using electron microscopy. Negative staining and rotary shadowing revealed stable virions as well as isolated capsomeres between pH 4.0 and 8.5. At pH 9.0 and above, particles disintegrated, whereas they mainly aggregated at a pH below 6.0. Heating the preparations to 55 degrees C and above resulted in the complete loss of any discernible structure. A low proportion (approx. 10 %) of particles ejected their DNA within the pH range of 6.0-8.5. Most virions released their DNA at the top (15.9 %) or the shoulder (71.4 %) of the twin particles and only 12.7 % at the waist. Compared with the expected numbers of pentameric capsomeres at the top (9 %), the shoulder (45.5 %) or the waist (45.5 %), the results revealed a preferential DNA release from the top and shoulder of the geminate particle.

Divalent ion-dependent swelling of Tomato Bushy Stunt Virus: A multi-approach study

Time-resolved small-angle X-ray and neutron scattering (SAXS and SANS) in solution were used to study the swelling reaction of TBSV upon chelation of its constituent calcium at mildly basic pH. SAXS intensities comprise contribution from the protein capsid and the RNA moiety, while neutron scattering, recorded in 72% D2O, is essentially due to the protein capsid. Cryo-electron micrographs of compact and swollen virus were used to produce 3D reconstructions of the initial and final conformations of the virus at a resolution of 13 A and 19 A, respectively. While compact particles appear to be very homogeneous in size, solutions of swollen particles exhibit some size heterogeneity. A procedure has been developed to compute the SAXS pattern from the 3D reconstruction for comparison with experimental data. Cryo-electron microscopy thereby provides an invaluable starting (and ending) point for the analysis of the time-resolved swelling process using the scattering data.

The Escherichia coli outer membrane cobalamin transporter BtuB: structural analysis of calcium and substrate binding, and identification of orthologous transporters by sequence/structure conservation

Gram-negative bacteria possess specialized active transport systems that function to transport organometallic cofactors or carriers, such as cobalamins, siderophores, and porphyrins, across their outer membranes. The primary components of each transport system are an outer membrane transporter and the energy-coupling protein TonB. In Escherichiacoli, the TonB-dependent outer membrane transporter BtuB carries out active transport of cobalamin (Cbl) substrates across its outer membrane. Cobalamins bind to BtuB with nanomolar affinity. Previous studies implicated calcium in high-affinity binding of cyanocobalamin (CN-Cbl) to BtuB. We previously solved four structures of BtuB or BtuB complexes: an apo-structure of a methionine-substitution mutant (used to obtain experimental phases by selenomethionine single-wavelength anomalous diffraction studies); an apo-structure of wild-type BtuB; a binary complex of calcium and wild-type BtuB; and a ternary complex of calcium, CN-Cbl and wild-type BtuB. We present an analysis of the binding of calcium in the binary and ternary complexes, and show that calcium coordination changes upon substrate binding. High-affinity CN-Cbl binding and calcium coordination are coupled. We also analyze the binding mode of CN-Cbl to BtuB, and compare and contrast this binding to that observed in other proteins that bind Cbl. BtuB binds CN-Cbl in a manner very different from Cbl-utilizing enzymes and the periplasmic Cbl binding protein BtuF. Homology searches of bacterial genomes, structural annotation based on the presence of conserved Cbl-binding residues identified by analysis of our BtuB structure, and detection of homologs of the periplasmic Cbl-binding binding protein BtuF enable identification of putative BtuB orthologs in enteric and non-enteric bacterial species.

Importance of Vp1 calcium-binding residues in assembly, cell entry, and nuclear entry of simian virus 40

For polyomaviruses, calcium ions are known to be essential for virion integrity and for the assembly of capsid structures. To define the role of calcium ions in the life cycle of the virus, we analyzed simian virus 40 (SV40) mutants in which structurally deduced calcium-binding amino acids of Vp1 were mutated singly and in combination. Our study provides evidence that calcium ions mediate not only virion assembly but also the initial infection processes of cell entry and nuclear entry. Mutations at Glu48, Glu157, Glu160, Glu216, and/or Glu330 are correlated with different extents of packaging defects. The low packaging ability of mutant E216R suggests the need to position the Glu216 side chain for proper virion formation. All other mutants selected for further analysis produced virus-like particles (VLPs) but were poorly infectious. The VLPs of mutant E330K could not attach to or enter the cell, and mutant E157A-E160A and E216K VLPs entered the cell but failed to enter the nucleus, apparently as a result of premature VLP dissociation. Our results show that five of the seven acidic side chains at the two calcium-binding sites-Glu48 and Glu330 (site 1), Glu157 and Glu160 (site 2), and Glu216 (both sites)-are important for SV40 infection. We propose that calcium coordination imparts not only stability but also structural flexibility to the virion, allowing the acquisition or loss of the ion at the two sites to control virion formation in the nucleus, as well as virion structural alterations at the cell surface and in the cytoplasm early during infection.

Host-dependent recombination of a Tomato bushy stunt virus coat protein mutant yields truncated capsid subunits that form virus-like complexes which benefit systemic spread

This study examined the contribution of the Tomato bushy stunt virus (TBSV) coat protein (CP) and its corresponding RNA to systemic infection of plants. Compared to results obtained with a mutant lacking the 5'-half of the CP gene, the presence of those CP-RNA sequences in another mutant benefited TBSV infection on Nicotiana benthamiana even though wild-type CP expression was eliminated by introduction of a small out-of-frame deletion. RT-PCR of viral RNA associated with rapid infections established by this CP frameshift deletion mutant revealed that in planta recombination had provided the progeny with the ability to express a truncated CP (tCP) with a block of N-proximal 30 residues deleted from the 66 amino acid RNA-binding domain. Subsequent biochemical characterizations revealed the presence of large ribonucleoprotein complexes that were shown to contain viral RNA as well as the approximately 38-kDa tCP. Electron microscopic examination of purified complexes showed particle-like structures that were nonuniform in size and shape compared to wild-type TBSV particles. Inoculation of pepper with the tCP-containing ribonucleoprotein complexes resulted in a rapid systemic infection similar to that caused by wild-type TBSV. In contrast, infections established in pepper by the original CP frameshift deletion mutant transcripts were restricted to inoculated leaves and did not yield recombinants capable of systemically infecting this host. In summary, TBSV possesses the flexibility to form alternative virion-like structures even if a substantial portion of the RNA-binding domain is deleted from the CP; mutants producing the tCP-containing particle-like structures are more effective for virus spread than those devoid of CP expression; and recombination events to produce the alternative tCP-RNA complexes are host-dependent.

Analysis of rapid, large-scale protein quaternary structural changes: time-resolved X-ray solution scattering of Nudaurelia capensis omega virus (NomegaV) maturation

Time-resolved small-angle X-ray scattering (TR-SAXS) was used to study the kinetics of a large conformational change that occurs during the maturation of an icosahedral virus. Virus-like particles (VLPs) of the T=4 non-enveloped RNA virus Nudaurelia capensis omega virus (NomegaV) were shown to undergo a large pH-dependent conformational change. Electron cryo-microscopy (cryoEM) and X-ray solution scattering were used to show that the precursor VLP (procapsid) was 16 % larger in diameter than the resulting capsid, which was shown by the cryoEM study to closely resemble the infectious mature virion. The procapsid form of the VLPs was observed at pH 7.5 and was converted to the capsid form at pH 5.0. Static SAXS measurements of the VLPs in solutions ranging between these pH values determined that the half-titration point of the transition was pH 6.0. Time-resolved SAXS experiments were performed on VLP solutions by initiating a pH change from 7.5 to 5.0 using a stopped-flow device, and the time-scale of the conformational change occurred in the subsecond range. Using a less drastic pH change (lowering the pH to 5.8 or 5.5), the conformational change occurred more slowly, on the subminute or minute time-scale, with the detection of a fast-forming intermediate in the transition. Further characterization using static SAXS measurements showed that the conformational change was initially reversible but became irreversible after autoproteolytic maturation was about 15 % complete. In addition to characterizing the large quaternary conformational change, we have been able for the first time to demonstrate that it takes place on the subsecond time-scale, a regime comparable to that observed in other multisubunit assemblies.

Conformational changes preceding decapsidation of bromegrass mosaic virus under hydrostatic pressure: a small-angle neutron scattering study

The stability of bromegrass mosaic virus (BMV) and empty shells reassembled in vitro from purified BMV coat protein was investigated under hydrostatic pressure, using solution small-angle neutron scattering. This technique allowed us to monitor directly the dissociation of the particles, and to detect conformational changes preceding dissociation. Significant dissociation rates were observed only if virions swelled upon increase of pressure, and pressure effects became irreversible at very high-pressure in such conditions. At pH 5.0, in buffers containing 0.5 M NaCl and 5 mM MgCl(2), BMV remained compact (radius 12.9 nm), dissociation was limited to approximately 10 % at 200 MPa, and pressure effects were totally reversible. At pH 5.9, BMV particles were slightly swollen under normal pressure and swelling increased with pressure. The dissociation was reversible to 90 % for pressures up to 160 MPa, where its rate reached 28 %, but became totally irreversible at 200 MPa. Pressure-induced swelling and dissociation increased further at pH 7.3, but were essentially irreversible. The presence of (2)H(2)O in the buffer strongly stabilized BMV against pressure effects at pH 5.9, but not at pH 7.3. Furthermore, the reversible changes of the scattered intensity observed at pH 5.0 and 5.9 provide evidence that pressure could induce the release of coat protein subunits, or small aggregates of these subunits from the virions, and that the dissociated components reassociated again upon return to low pressure. Empty shells were stable at pH 5.0, at pressures up to 260 MPa. They became ill-shaped at high-pressure, however, and precipitated slowly after return to normal conditions, providing the first example of a pressure-induced conformational drift in an assembled system.

Polymorphism of turnip yellow mosaic virus empty shells and evidence for conformational changes occurring after release of the viral RNA. A differential scanning calorimetric study

Turnip yellow mosaic virus (TYMV) is a small isometric plant virus which decapsidates by releasing its RNA through a hole in the capsid, leaving behind an empty shell [R. E. F. Matthews and J. Witz, (1985) Virology 144, 318-327]. Similar empty shells (artificial top component, ATC) can be obtained by submitting the virions to various treatments in vitro. We have used differential scanning calorimetry, analytical sedimentation, and electron microscopy to investigate the thermodenaturation of natural empty shells (NTC, natural top component) present in purified virus suspensions, and of several types of ATCs. ATCs divided in two major classes. Those obtained by alkaline titration, by the action of urea or butanol behaved as NTC: their thermograms contained only one peak corresponding to the irreversible dissociation of the shells and the denaturation of the coat protein. The temperature of this unique transition varied significantly with pH, from 71 degrees C at pH 4.5 to 84 degrees C at pH 8.5. The thermograms of ATCs obtained by freezing and thawing, or by the action of high pressure, contained two peaks: shells dissociated first into smaller protein aggregates at 57 degrees C (at pH 5.0) to 61 degrees C (at pH 8.5), which denatured at the temperature of the unique transition of NTC. Shells obtained by heating virions to 55 degrees C at pH 7.6, changed conformation after the release of the viral RNA, as upon continuous heating to 95 degrees C, their thermograms were similar to those of the shells obtained by freezing and thawing, whereas after purification they behaved like NTC. Structural implications of these observations are discussed.

Expression of the human papillomavirus type 11 L1 capsid protein in Escherichia coli: characterization of protein domains involved in DNA binding and capsid assembly

The L1 major capsid protein of human papillomavirus type 11 (HPV-11) was expressed in Escherichia coli, and the soluble recombinant protein was purified to near homogeneity. The recombinant L1 protein bound DNA as determined by the Southwestern assay method, and recombinant mutant L1 proteins localized the DNA-binding domain to the carboxy-terminal 11 amino acids of L1. Trypsin digestion of the full-length L1 protein yielded a discrete 42-kDa product (trpL1), determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, resulting from cleavage at R415, 86 amino acids from the L1 carboxy terminus. Sucrose gradient sedimentation analysis demonstrated that trpL1 sedimented at 11S, while L1 proteins with amino-terminal deletions of 29 and 61 residues sedimented at 4S. Electron microscopy showed that the full-length L1 protein appeared as pentameric capsomeres which self-assembled into capsid-like particles. The trpL1 protein also had a pentameric morphology but was unable to assemble further. In an enzyme-linked immunosorbent assay, the trpL1 and L1 capsids reacted indistinguishably from virus-like particles purified after expression of HPV-11 L1 in insect cells. The carboxy terminus of L1 therefore constitutes the interpentamer linker arm responsible for HPV-11 capsid formation, much like the carboxy-terminal domain of the polyomavirus VP1 protein. The trypsin susceptibility of HPV-11 L1 capsids suggests a possible mechanism for virion disassembly.

Organization of turnip yellow mosaic virus investigated by neutron small angle scattering at 80 K: an intermediate state preceding decapsidation of the virion?

The organization of turnip yellow mosaic virus has been investigated by neutron small angle scattering at 300 K and 80 K in buffers containing various amounts of D2O. We confirm that in native virions, no substantial part of the RNA is located at a radius larger than ca. 100-110 A, i.e., that there is very little interpretation of the RNA into the capsid. At 80 K, scattering curves do not depend much upon contrast, from 40% D2O to 100% D2O buffers, but are strongly affected by interparticle interference. We could, however, show that it is not the case for the subsidiary intensity maximum at q approximately 0.06 A-1. From the position of this maximum, we conclude that upon freezing, the radius of the capsid expands by c.a. 3.5% and the RNA penetrates deeply into the protein shell. Biological implications of this conformational change immediately preceding decapsidation are discussed.

Calcium chelation induces a conformational change in recombinant herpes simplex virus-1-expressed rotavirus VP7

Rotavirus, strain SA11, glycoprotein VP7 that was expressed by a recombinant herpes simplex virus-1 or contained in purified rotavirus particles lost reactivity with the neutralizing monoclonal antibody (mAb) 159, but not with nonneutralizing mAbs, upon chelation of calcium by EGTA. Exposing VP7, but not the neutralizing mAbs, to a transient excess of EGTA over calcium eliminated VP7 neutralizing epitopes. Therefore, a calcium chelation-induced conformational change in VP7, not in the neutralizing mAbs, caused the epitope loss. Addition of excess calcium or strontium, but not magnesium or barium, to EGTA-treated VP7 restored its 159 epitope. These results suggest that VP7 binds calcium in the absence of other rotavirus proteins and that the calcium chelation-induced conformational change in VP7 may mediate uncoating of double-shelled rotavirus particles.

Cell-induced conformational change in poliovirus: externalization of the amino terminus of VP1 is responsible for liposome binding

Upon attachment to susceptible cells, poliovirus and a number of other picornaviruses undergo conformational transitions which result in changes in antigenicity, increased protease sensitivity, the loss of the internal capsid protein VP4, and a loss of the ability to attach to cells. These conformationally altered particles have been characterized by using a number of sequence-specific probes, including two proteases, a panel of antiviral monoclonal antibodies, and a panel of antisera against synthetic peptides which correspond to sequences from the capsid protein VP1. With these probes, cell-altered virus is clearly distinguishable from native and heat-inactivated virions. The probes also demonstrate that the cell-induced conformational change alters the accessibility of several regions of the virus. In particular, the amino terminus of VP1, which is entirely internal in the native virion, becomes externalized. Unlike native and heat-inactivated virus, cell-altered virions are able to attach to liposomes. The exposed amino terminus of VP1 is shown to be responsible for liposome attachment. We propose that during infection the amino terminus of VP1 inserts into endosomal membranes and thus plays a role in the mechanism of cell entry.

Sequential removal of Ca2+ from satellite tobacco necrosis virus. Crystal structure of two EDTA-treated forms

Two forms of EDTA-treated satellite tobacco necrosis virus (STNV) have been studied with X-ray crystallography methods. The crystals of both forms were isomorphous with native STNV crystals, and (FEDTA-Fnat) maps as well as (2FEDTA-Fnat) maps were calculated with phases from the native structure. The maps were based on partial data sets to 2.8 A resolution, and averaged using the 60-fold non-crystallographic symmetry. In the first crystal form, calcium ions were absent from one of the three sites in the icosahedral protein shell. The crystals were produced at pH 5.0 from a virus solution treated with EDTA at pH 6.5. The virions were not expanded, and no essential changes were seen in the protein shell. In the second crystal form, all calcium ions in the protein shell were absent. The virus material in these crystals had been subjected to treatment with EDTA at pH 8.0 before crystallization at pH 6.5. The high pH treatment caused degradation of the viral RNA. No expansion of the virion had occurred and all protein--protein contacts were retained. These results are compared with the previously presented low-resolution structure of slightly expanded STNV with intact RNA, where calcium ions from two sites were absent. The relevance of Ca2(+)-depleted virions for infection in vivo is discussed as well as the possibility that the Ca2(+)-binding sites may be parts of ion channels in the viral capsid. One possible RNA-binding site was found in the maps of both crystal types, and the same site could also be localized in the high-resolution map of native STNV.

Mechanisms of cooperativity and allosteric regulation in proteins

AUosteric proteins control and coordinate chemical events in the living cell. When Monod conceived that idea he said that he had discovered the second secret of life. The first was the structure of DNA. The theory as published by Monodet al.(1963) was concerned chiefly with cooperativity and feedback inhibition of enzymes, such as the inhibition of threonine deaminase, the first enzyme in the pathway of the synthesis of isoleucine, by isoleucine, and its activation by valine. Two years later the theory was formalized by Monodet al.(1965).

Structural studies of proteins by high-flux X-ray and neutron solution scattering

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Structure of EDTA-treated satellite tobacco necrosis virus at pH 6.5

The crystal structure of EDTA-treated satellite tobacco necrosis virus (STNV) at pH 6.5 has been determined to 7.5 A resolution (1 A = 0.1 nm) with molecular replacement techniques, using the known structure of the protein subunit. The calcium ions at the 3-fold contacts are absent, whereas the calcium ions on the 5-fold axes still remain. The protein shell is slightly expanded. The expansion does not impose any large conformational changes on the subunits and the subunit contacts are to a large extent retained. The electron density map shows high levels of density in the RNA region. It is found close to the protein shell but well-separated from the protein. This density indicates a preferential ordering of the RNA in certain regions, but does not allow a detailed interpretation of the RNA conformation. A similar density in the RNA region is also found in a low resolution map of native STNV.

Accessibility of three continuous epitopes in tomato bushy stunt virus

Three peptides corresponding to residues 28-40, 138-154 and 380-387 of the coat protein of tomato bushy stunt virus (TBSV) were synthesized by the solid phase method and used to raise specific antibodies. These antibodies were used to follow the conformational changes that occur when TBSV particles swell under slightly alkaline conditions. Peptides 28-40 and 380-387 were found to correspond to continuous epitopes in the dissociated viral protein as well as in both compact and swollen virions. The region 138-154, which is also a continuous epitope of the monomeric protein, became accessible to antibody binding in the virion only when the particles were in the swollen state.

Gel electrophoresis of intact subcellular particles

The review describes the application of gel electrophoresis to the characterization and separation of viruses, ribosomes, vesicles and other subcellular particles. The preparation of the sample, the choice of the buffer, the gel medium, the apparatus and the detection of the particle (staining and scanning) as well as the necessary theory are discussed. This includes the mathematical evaluation of experimental data on the basis of Ferguson plots using the extended Ogston theory. Simple methods and sophisticated computer simulation techniques are described and exemplified in application to the determination of particle size and charge, the pore size of the gel (unpublished data) and the two-dimensional agarose electrophoresis (unpublished). It is shown that the nature of the particle (e.g. spherical or rod-shaped, pliable or rigid texture) determines the shape of the non-linear Ferguson plot. In addition, the review gives a number of practical applications of gel electrophoresis, isoelectric focusing, titration curves and immuno-electrophoresis to subcellular particles. Pros and cons are evaluated. A comparison with other analytical procedures is made. The review is concluded by a futuristic outlook.

Purification, crystallization and preliminary X-ray data of the bacteriophage MS2

Single crystals of the bacteriophage MS2 have been produced by the vapour diffusion technique in the presence of 1.5% polyethylene glycol 6000 and 0.2 M-sodium phosphate buffer (pH 7.4). These are the first bacteriovirus crystals diffracting to high resolution. The crystal space group is C2 with the unit cell parameters a = 467.9 A, b = 289.5 A, c = 275.6 A and beta = 121.8 degrees. The asymmetric unit contains one half of the virion. The maximum resolution limit of the X-ray diffraction data obtained from these crystals was 2.9 A. The purification of the virus material was done by mild procedures exclusively and involved precipitation with polyethylene glycol 6000 and size exclusion chromatography on Sepharose CL-4B.

Divalent cation sites in tomato bushy stunt virus. Difference maps at 2-9 A resolution

Difference electron density maps, using as few as four 1/2 degrees oscillation photographs, have been computed for tomato bushy stunt virus crystals soaked in EDTA. GdCl3 and silicotungstate. The maps define a double divalent cation site, responsible for regulating expansion of the virus particle, as well as sites for binding tungstate anions.