Obtaining and characterization of spherical particles—new biogenic platforms

The technique of obtaining spherical particles from rod-like plant virus, tobacco mosaic virus, in a preparative scale was developed. The conditions of tobacco mosaic virus isolation for obtaining spherical particles were selected. Spherical particles were examined by methods of electron microscopy, nanoparticle tracking analysis, and dynamic light scattering. Information about inner structure of spherical particles was obtained. High electron density of spherical particles was demonstrated. The analysis of ultrathin sections showed that spherical particles are homogenous within and do not contain any cavities.     

Tobacco mosaic virus as an AFM tip calibrator

The study of high-resolution topographic surfaces of isolated single molecules is one of the applications of atomic force microscopy (AFM). Since tip-induced distortions are significant in topographic images the exact AFM tip shape must be known in order to correct dilated AFM height images using mathematical morphology operators. In this work, we present a protocol to estimate the AFM tip apex radius using tobacco mosaic virus (TMV) particles. Among the many advantages of TMV, are its non-abrasivity, thermal stability, bio-compatibility with other isolated single molecules and stability when deposited on divalent ion pretreated mica. Compared to previous calibration systems, the advantage of using TMV resides in our detailed knowledge of the atomic structure of the entire rod-shaped particle. This property makes it possible to interpret AFM height images in term of the three-dimensional structure of TMV. Results obtained in this study show that when a low imaging force is used, the tip is sensing viral protein loops whereas at higher imaging force the tip is sensing the TMV particle core. The known size of the TMV particle allowed us to develop a tip-size estimation protocol which permits the successful erosion of tip-convoluted AFM height images. Our data shows that the TMV particle is a well-adapted calibrator for AFM tips for imaging single isolated biomolecules. The procedure developed in this study is easily applicable to any other spherical viral particles.     

Subcellular localization of the coat protein in tobacco cells infected by cucumber mosaic virus isolated from Catharanthus roseus

Electron microscopy and immunolabelling with antiserum specific to cucumber mosaic virus coat protein were used to examine tobacco leaf cells infected by cucumber mosaic virus isolated from Catharanthus roseus (CMV-Cr). Crystalline and amorphous inclusions in the vacuoles were the most obvious cytological modifications seen. Immunogold labelling indicated that the crystalline inclusion was made up of virus particles and amorphous inclusions contained coat protein. Rows of CMV-Cr particles were found between membranes of dictyosomes, but membranous bodies and tonoplast-associated vesicles were not evident. Virus particles and/or free coat protein were easily detected in the cytoplasm by immunolabelling. No gold labelling was found within nuclei, chloroplasts and mitochondria.     

Vertical dimension of hydrated biological samples in tapping mode scanning force microscopy.

The vertical dimensions of the well-characterized test samples tobacco mosaic virus, T4 bacteriophage polyhead, purple membrane, and hexagonally packed intermediate (HPI) layer were investigated by tapping mode scanning force microscopy (SFM) in solution. Purple membrane and HPI layer were imaged in both contact mode and tapping mode SFM for direct comparison. All vertical dimensions match the known heights. The practical implications of the absence of frictional forces in tapping mode are discussed.     

Comparative Study of Thermal Remodeling of Viruses with Icosahedral and Helical Symmetry

Study of the possibilities of virions and viral proteins modifications and structural remodeling is an important problem of the modern molecular virology. A technique of heat treatment of rod-shaped tobacco mosaic virus that allowed producing structurally modified spherical particles consisting of the virus coat protein was previously developed in our laboratory. These particles possessed unique adsorption and immunogenic properties and were successfully used to develop a new candidate vaccine against rubella virus. Later, the possibility of thermal remodeling of the filamentous virions of potato virus X was demonstrated. The present work reports a comparative study of thermal remodeling of viruses with different structure belonging to various taxonomic groups. The generation of structurally modified spherical particles by the heat treatment of rod-shaped virions with helical symmetry (dolichos enation mosaic virus and barley stripe mosaic virus) has been demonstrated. The dependence of the size of spherical particles derived from dolichos enation mosaic virus on the initial virus concentration was revealed. The process of thermal remodeling of the filamentous virions and virus-like particles of alternanthera mosaic virus was studied. Heat treatment of plant viruses with icosahedral symmetry was shown to cause no morphological changes.     

Atomic force microscopy analysis of icosahedral virus RNA

Single-stranded genomic RNAs from four icosahedral viruses (poliovirus, turnip yellow mosaic virus (TYMV), brome mosaic virus (BMV), and satellite tobacco mosaic virus (STMV)) along with the RNA from the helical tobacco mosaic virus (TMV) were extracted using phenol/chloroform. The RNAs were imaged using atomic force microscopy (AFM) under dynamic conditions in which the RNA was observed to unfold. RNAs from the four icosahedral viruses initially exhibited highly condensed, uniform spherical shapes with diameters consistent with those expected from the interiors of their respective capsids. Upon incubation at 26 degrees C, poliovirus RNA gradually transformed into chains of globular domains having the appearance of thick, irregularly segmented fibers. These ultimately unwound further to reveal segmented portions of the fibers connected by single strands of RNA of 0.5-1 nm thickness. Virtually the same transformations were shown by TYMV and BMV RNA, and with heating, the RNA from STMV. Upon cooling, the chains of domains of poliovirus RNA and STMV RNA condensed and re-formed their original spherical shapes. TMV RNAs initially appeared as single-stranded threads of 0.5-1.0 nm diameter but took on the structure of the multidomain chains upon further incubation at room temperature. These ultimately condensed into short, thick chains of larger domains. Our observations suggest that classical extraction of RNA from icosahedral virions produces little effect on overall conformation. As tertiary structure is lost however, it is evident that secondary structural elements are arranged in a sequential, linear fashion along the polynucleotide chain. At least in the case of poliovirus and STMV, the process of tertiary structure re-formation from the linear chain of secondary structural domains proceeds in the absence of protein. RNA base sequence, therefore, may be sufficient to encode the conformation of the encapsidated RNA even in the absence of coat proteins.     

Nanoscale topography of hepatitis B antigen particles by atomic force microscopy

Hepatitis B virus envelope is mainly composed of three forms of the same protein expressed from different start codons of the same open reading frame. The smaller form named S protein corresponds to the C-terminal common region and represents about 80% of the envelope proteins. It is mainly referred as hepatitis B virus surface antigen (HBsAg). Over expressed in the host cell, this protein can be produced as spherical and tubular self-organized particles. Highly immunogenic, these particles are used in licensed hepatitis B vaccines. In this study we have combined transmission electron microscopy and atomic force microscopy to determine the shape and size of HBsAg particles produced from the yeast Hansenula polymorpha. Tapping mode atomic force microscopy in liquid allows structural details of the surface to be delineated with a resolution in the nanometer range. Particles were decorated by closely packed spike-like structures protruding from particle surface. Protrusions appeared uniformly distributed at the surface and an average number of 75 protrusions per particle were calculated. Importantly, we demonstrated that proteins mainly contribute to the topography of the protrusions.     

Complexes assembled from TMV-derived spherical particles and entire virions of heterogeneous nature

Previously, we described some structural features of spherical particles (SPs) generated by thermal remodelling of the tobacco mosaic virus. The SPs represent a universal platform that could bind various proteins. Here, we report that entire isometric virions of heterogeneous nature bind non-specifically to the SPs. Formaldehyde (FA) was used for covalent binding of a virus to the SPs surface for stabilizing the SP—virus complexes. Transmission and high resolution scanning electron microscopy showed that the SPs surface was covered with virus particles. The architecture of SP–virion complexes was examined by immunologic methods. Mean diameters of SPs and SP–human enterovirus C and SP–cauliflower mosaic virus (CaMV) compositions were determined by nanoparticle tracking analysis (NTA) in liquid. Significantly, neither free SPs nor individual virions were detected by NTA in either FA-crosslinked or FA-untreated compositions. Entirely, all virions were bound to the SPs surface and the SP sites within the SP–CaMV complexes were inaccessible for anti-SP antibodies. Likewise, the SPs immunogenicity within the FA-treated SPs–CaMV compositions was negligible. Apparently, the SP antigenic sites were hidden and masked by virions within the compositions. Previously, we reported that the SPs exhibited adjuvant activity when foreign proteins/epitopes were mixed with or crosslinked to SPs. We found that immunogenicity of entire CaMV crosslinked to SP was rather low which could be due to the above-mentioned masking of the SPs booster. Contrastingly, immunogenicity of the FA-untreated compositions increased significantly, presumably, due to partial release of virions and unmasking of some SPs-buster sites after animals immunization.     

A New Procedure for Quantitative Measurements of Virus Particles in Crude Preparations

A new method is described for the quantitative measurement of virus concentration in crude preparations by density gradient centrifugation and electron microscopy. The centrifugation is carried out in a specially designed centrifuge tube which permits separation and sedimentation of virus particles at different levels according to their sedimentation velocity. The gradient of a mixture of heavy and normal water (D(2)O-H(2)O) is designed to sediment the virus particles with constant velocity so that the optimal time of centrifugation can easily be calculated. The virus particles are collected on carbon-coated nickel grids floating on mercury at the bottom of the centrifuge tube and are counted by means of electron microscopy. The efficiency of the method is demonstrated with a crude plant extract of tobacco mosaic virus.     

Manipulation of individual viruses: friction and mechanical properties.

We present our results on the manipulation of individual viruses using an advanced interface for atomic force microscopes (AFMs). We show that the viruses can be dissected, rotated, and translated with great facility. We interpret the behavior of tobacco mosaic virus with a mechanical model that makes explicit the competition between sample-substrate lateral friction and the flexural rigidity of the manipulated object. The manipulation behavior of tobacco mosaic virus on graphite is shown to be consistent with values of lateral friction observed on similar interfaces and the flexural rigidity expected for macromolecular assemblies. The ability to manipulate individual samples broadens the scope of possible studies by providing a means for positioning samples at specific binding sites or predefined measuring devices. The mechanical model provides a framework for interpreting quantitative measurements of virus binding and mechanical properties and for understanding the constraints on the successful, nondestructive AFM manipulation of delicate samples.     

Quantitation of molecular densities by cryo-electron microscopy. Determination of the radial density distribution of tobacco mosaic virus.

We have determined the absolute mass and radial scattering density distribution of tobacco mosaic virus in the frozen-hydrated state by energy-filtered low-dose bright-field transmission electron microscopy. The absolute magnitude of electron scattering from tobacco mosaic virus in 150 nm of ice was within 3.0% of that predicted, with inelastic scattering accounting for approximately 80% of the scattering contrast. In order to test the accuracy of the radial reconstruction, a computer model of tobacco mosaic virus was built from the atomic co-ordinates assuming uniform solvent density. The validity of the model was confirmed by comparison of X-ray scattering and predictions of the model (R factor = 0.05). First-order corrections for the microscope contrast transfer function were necessary and sufficient for conversion of the cryo-electron microscopy images into accurate representations of the mass density. At 1.9 nm resolution the compensated reconstruction and model had density peaks of similar magnitude at 2.4, 4.2, 6.0 and 7.8 nm radius and a central hole of 2 nm radius. Equatorial Fourier transforms of the corrected electron images were in excellent agreement with predictions of the model (R factor = 0.12). Thus, the uniform solvent approximation was adequate at 1.9 nm resolution to describe quantitatively X-ray scattering in liquid water and electron imaging in vitreous ice. This is the first demonstration that cryo-electron microscopy images can be used to quantitate the absolute mass, mass per unit length and internal density distributions of proteins and nucleic acids.     

Nicotiana velutina mosaic virus: purification, properties and affinities with other rod-shaped viruses

Nicotiana velutina mosaic virus (NVMV), found in Australia, was transmitted by inoculation of sap to twenty species in the Solanaceae and Chenopodiaceae, and to Gomphrena globosa; its host range closely resembles that of potato mop-top virus (PMTV). Infectivity was abolished when sap was kept at room temperature between 1 and 4 days, or when heated for 10 min between 60 and 70 °C. NVMV was frequently transmitted through the seed of four Nicotiana spp. NVMV and PMTV were purified by a method that involved redissolving virus particles sedimented by low speed centrifugation of leaf extracts, followed by sedimentation through sucrose cushions. NVMV preparations contain rod-shaped particles about 18 nm wide and with a large range of lengths, the commonest being 125–150 nm. The particles have a helical structure with a pitch of 2–9 nm, break easily, and contain a single protein of apparent mol. wt. 21|400, slightly larger than that of PMTV (19 800). In serological tests assessed by electron microscopy, no relationship was detected between NVMV and PMTV, or barley stripe mosaic, beet necrotic yellow vein, soil-borne wheat mosaic, tobacco mosaic or tobacco rattle viruses. However, antiserum to soil-borne wheat mosaic virus reacted quite strongly with PMTV and weakly with tobacco mosaic virus. NVMV is considered to be a distinct member of the tobamovirus group; its frequent transmission through seed may be an adaptation to the arid environment where it was found. Its cryptogram is */*:*/*:E/E:S/*.     

The mechanism of infection of plant protoplasts by viruses

Summary The process of virus infection of protoplasts isolated from tobacco leaves has been examined by means of electron microscopy. Immediately after inoculation, virus particles appear at two types of site: trapped in complex surface lesions of the plasmalemma, or in peripheral cytoplasmic vesicles. The complex lesions are only visible after treatment of the protoplasts with inocula containing poly-l-ornithine. With infection by tobacco mosaic virus and cowpea chlorotic mottle virus, which require poly-l-ornithine, the majority of virus particles occur at lesion sites. Pea enation mosaic virus, which does not require poly-l-ornithine for infection to become established, is found predominantly and in high numbers in peripheral vesicles. The behaviour of these three viruses is discussed in terms of a probable mechanism for infection of the protoplasts.     

Optical chemical imaging of tobacco mosaic virus in solution at 60-nm resolution.

Scanning near-field optical microscopy can provide images with a resolution less than the wavelength of light, and therefore ought in principle to be of great value in studies of biological structures. In this work we show how for the first time images have been obtained of tobacco mosaic virus particles at 60-nm resolution, combined with chemical imaging using monoclonal antibodies under in vitro conditions.     

Self-repair of biological fibers catalyzed by the surface of a virus crystal.

Helical fibers, presumably proteinaceous and of microbial origin, have been visualized by atomic force microscopy on the surfaces of crystals of satellite tobacco mosaic virus. If the crystals are growing, then the fibers are incorporated intact into the crystal lattice. If broken on the crystal surface, then within a few minutes, the fibers self-reassemble to reestablish continuity. This, we believe, is the first observation of such a crystal surface-catalyzed repair of a biological structure. The surfaces of virus crystals provide ideal workbenches for the visualization and manipulation of nanoscale objects, particularly extended structures such as these fibers.     

Purification,electron microscopy and serology of virus isolated fromEuonymus europaea

“Euonymus mosaic virus”, purified from cucumber cotyledons by the differential and density-gradient centrifugation, shows typical nucleoprotein absorption spectrum. Electron microscopy reveals isometric virus particles of about 37 nm diameter. No reaction of purified “Euonymus mosaic virus” was observed with antisera against a raspberry ringspot virus, tobacco ringspot virus, cherry leaf roll virus, strawberry latent ringspot virus, tomato ringspot virus, elm mosaic virus, arabis mosaic virus, tomato bushy stunt virus and watermelon mosaic virus.     

Surface processes in the crystallization of turnip yellow mosaic virus visualized by atomic force microscopy.

In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV). Growth of the (101) face of TYMV crystals proceeded by two-dimensional nucleation. The molecular structure of the step edges and adsorption of individual virus particles and their aggregates on the crystalline surface were recorded. The surfaces of individual virions within crystals were visualized and seen to be quite distinctive with the hexameric and pentameric capsomers of the T = 3 capsids being clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions. In some cases areas of a single crystal surface were recorded in which were captured successive phases of the transition. We believe this provides the first visual record of a cooperative restructuring of the surface of a supramolecular crystal.     

Tethered lipid bilayers on electrolessly deposited gold for bioelectronic applications

This paper presents the formation of a novel biomimetic interface consisting of an electrolessly deposited gold film overlaid with a tethered bilayer lipid membrane (tBLM). Self-assembly of colloidal gold particles was used to create an electrolessly deposited gold film on a glass slide. The properties of the film were characterized using field-effect scanning electron microscopy, energy dispersive spectroscopy, and atomic force microscopy. Bilayer lipid membranes were then tethered to the gold film by first depositing an inner molecular leaflet using a mixture of 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[3-(2-pyridyldithio)propionate], 1,2-di-O-phytanyl-sn-glycero-3-phosphoethanolamine (DPGP), and cystamine in ethanol onto a freshly prepared electrolessly deposited gold surface. The outer leaflet was then formed by the fusion of liposomes made from DPGP or 1,2-dioleoyl-sn-glycero-3-phosphocholine on the inner leaflet. To provide functionality, two membrane biomolecules were also incorporated into the tBLMs: the ionophore valinomycin and a segment of neuropathy target esterase containing the esterase domain. Electrochemical impedance spectroscopy, UV/visible spectroscopy, and fluorescence recovery after pattern photobleaching were used to characterize the resulting biomimetic interfaces and confirm the biomolecule activity of the membrane. Microcontact printing was used to form arrays of electrolessly deposited gold patterns on glass slides. Subsequent deposition of lipids yielded arrays of tBLMs. This approach can be extended to form functional biomimetic interfaces on a wide range of inexpensive materials, including plastics. Potential applications include high-throughput screening of drugs and chemicals that interact with cell membranes and for probing, and possibly controlling, interactions between living cells and synthetic membranes. In addition, the gold electrode provides the possibility of electrochemical applications, including biocatalysis, bio-fuel cells, and biosensors.     

Interrod forces in aqueous gels of tobacco mosaic virus.

The lateral separation of virus rod particles of tobacco mosaic virus has been studied as a function of externally applied osmotic pressure using an osmotic stress technique. The results have been used to test the assumption that lattice equilibrium in such gels results from a balance between repulsive (electrostatic) and attractive (van der Waals and osmotic) forces. Results have been obtained at different ionic strengths (0.001 to 1.0 M) and pH's (5.0 to 7.2) and compared with calculated curves for electrostatic nad van der Waals pressure. Under all conditions studied, interrod spacing decreased with increasing applied pressure, the spacings being smaller at higher ionic strengths. Only small differences were seen when the pH was changed. At ionic strengths near 0.1 M, agreement between theory and experiment is good, but the theory appears to underestimate electrostatic forces at high ionic strengths and to underestimate attractive forces at large interrod spacings (low ionic strengths). It is concluded that an electrostatic-van der Waals force balance can explain stability in tobacco mosaic virus gels near physiological conditions and can provide a good first approximation elsewhere.     

Biological synthesis of gold nanoparticles using Magnolia kobus and Diopyros kaki leaf extracts

Leaf extracts of two plants, Magnolia kobus and Diopyros kaki, were used for ecofriendly extracellular synthesis of metallic gold nanoparticles. Stable gold nanoparticles were formed by treating an aqueous HAuCl₄ solution using the plant leaf extracts as reducing agents. UV–visible spectroscopy was used for quantification of gold nanoparticle synthesis. Only a few minutes were required for >90% conversion to gold nanoparticles at a reaction temperature of 95 °C, suggesting reaction rates higher or comparable to those of nanoparticle synthesis by chemical methods. The synthesized gold nanoparticles were characterized with inductively coupled plasma spectrometry (ICP), energy-dispersive X-ray spectroscopy (EDS), scanning electron microscopy (SEM), transmission electron microscopy (TEM), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared spectroscopy (FTIR), and particle analysis using a particle analyzer. SEM and TEM images showed that a mixture of plate (triangles, pentagons, and hexagons) and spherical structures (size, 5–300 nm) were formed at lower temperatures and leaf broth concentrations, while smaller spherical shapes were obtained at higher temperatures and leaf broth concentrations.