The characterization of intermediates formed during the disassembly of tobacco mosaic virus at alkaline pH

Protein Nanotubes: From Bionanotech towards Medical Applications

Nanobiotechnology involves the study of structures found in nature to construct nanodevices for biological and medical applications with the ultimate goal of commercialization. Within a cell most biochemical processes are driven by proteins and associated macromolecular complexes. Evolution has optimized these protein-based nanosystems within living organisms over millions of years. Among these are flagellin and pilin-based systems from bacteria, viral-based capsids, and eukaryotic microtubules and amyloids. While carbon nanotubes (CNTs), and protein/peptide-CNT composites, remain one of the most researched nanosystems due to their electrical and mechanical properties, there are many concerns regarding CNT toxicity and biodegradability. Therefore, proteins have emerged as useful biotemplates for nanomaterials due to their assembly under physiologically relevant conditions and ease of manipulation via protein engineering. This review aims to highlight some of the current research employing protein nanotubes (PNTs) for the development of molecular imaging biosensors, conducting wires for microelectronics, fuel cells, and drug delivery systems. The translational potential of PNTs is highlighted.

TMV Particles: The Journey From Fundamental Studies to Bionanotechnology Applications

Ever since its initial characterization in the 19th century, tobacco mosaic virus (TMV) has played a prominent role in the development of modern virology and molecular biology. In particular, research on the three-dimensional structure of the virus particles and the mechanism by which these assemble from their constituent protein and RNA components has made TMV a paradigm for our current view of the morphogenesis of self-assembling structures, including viral particles. More recently, this knowledge has been applied to the development of novel reagents and structures for applications in biomedicine and bionanotechnology. In this article, we review how fundamental science has led to TMV being at the vanguard of these new technologies.

Self-assembly of rodlike virus to superlattices

Rodlike tobacco mosaic virus (TMV) has been found to assemble into superlattices in aqueous solution using the polymer methylcellulose to induce depletion and free volume entropy-based attractive forces. Both transmission electron microscopy and small-angle X-ray scattering show that the superlattices form in both semidilute and concentrated regimes of polymer, where the free volume entropy and the depletion interaction are the dominant driving force, respectively. The superlattices are NaCl and temperature responsive. The rigidity of the rodlike nanoparticles also plays an important role for the formation of superlattices through the free volume entropy mechanism. Compared to the rigid TMV particle, flexible bacteriophage M13 particles are only responsive to the depletion force and thus only assemble in highly concentrated polymer solution, where depletion interaction is dominant.

pH control of the electrostatic binding of gold and iron oxide nanoparticles to tobacco mosaic virus

We report the binding of nanoparticles (NPs) to wild type (unmodified) tobacco mosaic virus (TMV). The viruses are simply mixed with citrate-coated, negatively charged gold and iron oxide nanoparticles (IONPs) in acidic solution. This results in TMV decorated along its whole length by the respective particles. Such a decoration usually requires chemical modification or mutation of TMV (e.g., cysteine residues), but here we simply reduce TMV's natural negative charge by protonation. The particles are protonated to a much smaller extent. This charge-based mechanism does not operate for neutral particles.

Au nanocrystals grown on a better-defined one-dimensional tobacco mosaic virus coated protein template genetically modified by a hexahistidine tag

In this paper, tobacco mosaic virus (TMV) coated protein (CP) was genetically modified by introducing a hexahistidine tag into it for a well-defined one-dimensional template, on which Au nanocrystals (NCs) were grown. The results showed that genetic modification could not only ameliorate the one-dimensional structure of the template, but also improve the growth density of Au NCs on the template. This indicated that genetic modification could be an effective method to modulate the structure of the TMVCP template-based nanocomposites allowing for a broader application of them.

Superlattice of rodlike virus particles formed in aqueous solution through like-charge attraction

Rodlike tobacco mosaic virus (TMV) has been found to assemble into a 2D superlattice in aqueous solution with hexagonally packed structures in the presence of Ba(2+) through like-charge attraction whereas lower-Z divalent ions such as Zn(2+), Cd(2+), Mg(2+), and Ca(2+) induce only liquidlike ordering. The molar ratio between Ba(2+) and TMV is a crucial parameter in the formation of the superlattice. There is a critical molar ratio of Ba(2+) to TMV at which TMV exhibits a transition from a nonordered colloidal state to an ordered crystalline state. It is also found that the superlattice is formed regardless of the pH and TMV concentration within the range studied.

Engineered Tobacco mosaic virus mutants with distinct physical characteristics in planta and enhanced metallization properties

Tobacco mosaic virus mutants were engineered to alter either the stability or surface chemistry of the virion: within the coat protein, glutamic acid was exchanged for glutamine in a buried portion to enhance the inter-subunit binding stability (E50Q), or a hexahistidine tract was fused to the surface-exposed carboxy terminus of the coat protein (6xHis). Both mutant viruses were expected to possess specific metal ion affinities. They accumulated to high titers in plants, induced distinct phenotypes, and their physical properties during purification differed from each other and from wild type (wt) virus. Whereas 6xHis and wt virions contained RNA, the majority of E50Q protein assembled essentially without RNA into rods which frequently exceeded 2 μm in length. Electroless deposition of nickel metallized the outer surface of 6xHis virions, but the central channel of E50Q rods, with significantly more nanowires of increased length in comparison to those formed in wtTMV.

Enhancing the magnetoviscosity of ferrofluids by the addition of biological nanotubes

Applying a magnetic field to many ferrofluids leads to a significant increase in viscosity, but the phenomenon has yet to find technological exploitation because of the thinning caused by even weak shear flows. We have discovered that the addition of plant-virus-derived nanotubes to a commercial ferrofluid can give rise to a dramatic enhancement in magnetoviscosity and a suppression of shear thinning. The dependence of this effect on nanotube aspect ratio and surface charge, both of which were varied biotechnologically, is consistent with a "scaffolding" of magnetic particles into quasi-linear arrays. Direct support for this explanation is derived from transmission electron micrographs, which reveal a marked tendency for the magnetic nanoparticles to decorate the outside surface of the virus nanotubes.

Controlled assembly of rodlike viruses with polymers

A practical method to assemble rodlike tobacco mosaic virus and bateriophage M13 with polymers was developed, which afforded a 3D core-shell composite with morphological control.

Plant viruses as biotemplates for materials and their use in nanotechnology

In recent years, plant virus capsids, the protein shells that form the surface of a typical plant virus particle, have emerged as useful biotemplates for material synthesis. All virus capsids are assembled from virus-coded protein subunits. Many plant viruses assemble capsids with precise 3D structures providing nanoscale architectures that are highly homogeneous and can be produced in large quantities. Capsids are amenable to both genetic and chemical modifications allowing new functions to be incorporated into their structure by design. The three capsid surfaces, the interior surface, the exterior surface, or the interface between coat protein subunits, can be independently functionalized to produce multifunctional biotemplates. In this review, we examine the recent advances in using plant virus capsids as biotemplates for nanomaterials and their potential for applications in nanotechnology, especially medicine.

Effect of interfacial interaction on the cross-sectional morphology of tobacco mosaic virus using GISAXS

We have investigated the effect of the interfacial interaction on the cross-sectional morphology of the tobacco mosaic virus (TMV) in solution and on two types of solid substrates, SiOx (polar) on Si(100) and polystyrene film (nonpolar) on Si(100), using small-angle X-ray scattering (SAXS) and grazing incidence small-angle X-ray scattering (GISAXS), respectively. Results reveal that the flexible chains at the outer surface of TMV either expand or contract depending on the nature of the substrate. Although the unfavorable interaction between the TMV and the PS causes a minimal effect, the stronger attractive interaction between the outer protein surface of TMV and the SiOx substrate induces pronounced deformation of its cross-sectional morphology.

pH dependence of the dissociation of multimeric hemoglobin probed by high hydrostatic pressure

We investigated the thermodynamic features of the classic alkaline dissociation of multimeric hemoglobin (3.1 MDa) from Glossoscolex paulistus (Annelidea) using high hydrostatic pressure. Light scattering measurements up to microscopic thermodynamic equilibrium indicated a high pH dependency of dissociation and association. Electron microscopy and gel filtration corroborated these findings. The volume change of dissociation decreased in absolute values from -48.0 mL/mol of subunit at pH 6.0 to -19.2 mL/mol at pH 9.0, suggesting a lack of protein interactions under alkaline conditions. Concomitantly, an increase in pH reduced the Gibbs free energy of dissociation from 37.7 to 27.5 kJ/mol of subunit. The stoichiometry of proton release calculated from the pressure-induced dissociation curves was +0.602 mol of H(+)/mol of subunit. These results provide a direct quantification of proton participation in stabilizing the aggregated state of the hemoglobin, and contribute to our understanding of protein-protein interactions and of the surrounding conditions that modulate the process of aggregation.

Proton dependence of tobacco mosaic virus dissociation by pressure

Tobacco mosaic virus (TMV) is an intensely studied model of viruses. This paper reports an investigation into the dissociation of TMV by pH and pressure up to 220 MPa. The viral solution (0.25 mg/ml) incubated at 277 K showed a significant decrease in light scattering with increasing pH, suggesting dissociation. This observation was confirmed by HPLC gel filtration and electron microscopy. The calculated volume change of dissociation (DeltaV) decreased (absolute value) from -49.7 ml/mol of subunit at pH 3.8 to -21.7 ml/mol of subunit at pH 9.0. The decrease from pH 9.0 to 3.8 caused a stabilization of 14.1 kJ/mol of TMV subunit. The estimated proton release calculated from pressure-induced dissociation curves was 0.584 mol H(+)/mol of TMV subunit. These results suggest that the degree of virus inactivation by pressure and the immunogenicity of the inactivated structures can be optimized by modulating the surrounding pH.

Binding the tobacco mosaic virus to inorganic surfaces

We studied the adsorption behavior and surface chemistry of the tobacco mosaic virus (TMV) on well-defined metal and insulator surfaces. TMV serves as a tubular supramolecular model system with precisely known surface termination. We show that if the surface chemistry of the substrate and the pH-dependent chemistry of the molecular surface match, for example, by hydrogen bonding, a strong adsorption occurs, and lateral movement is impeded. Due to the immobilization, the virion can be imaged by atomic force microscopy (AFM) in contact mode. We also used self-assembled monolayers with an acyl chloride group to induce covalent bonding via ester formation. Noncontact AFM proved that TMV keeps its cylindrical cross section only under weak adsorption conditions, that is, on hydrophobic surfaces, while on hydrophilic substrates a deformation occurs to maximize the number of interacting chemical groups.

Virus particles of cucumber green mottle mosaic tobamovirus move systemically in the phloem of infected cucumber plants

Systemic movement through the phloem of infected host plants is a key process in the life cycle of plant viruses, knowledge of which is scant. A main point to be elucidated is the structural form in which virus infection moves within the phloem. Indirect evidence suggests that virions might be the viral structure that moves in the phloem, but data from direct analysis in phloem sap have not been reported. We have done such analysis in the system cucumber (from which phloem exudate can be collected)/cucumber green mottle mosaic tobamovirus (CGMMV). CGMMV has structurally well-characterized particles. Both CGMMV coat protein and RNA were found in phloem exudate from infected cucumbers. Analysis of the accessibility of CGMMV RNA in phloem exudate to RNase A indicates that it is protected within a ribonucleoprotein structure. The accessibility to RNase A of the RNA in these structures was as in virus particles. Centrifugation analyses showed that the ribonucleoprotein structures in the phloem exudate have the same mass and isopycnic density as virions. Virus particles indistinguishable from purified virions were detected by electron microscopy in phloem exudate. No evidence of free RNA or other CGMMV-related structure was found in phloem exudate of infected plants. These results indicate that CGMMV movement in the phloem occurs mainly, if not exclusively, in the form of virus particles.

Site-directed mutagenesis confirms the involvement of carboxylate groups in the disassembly of tobacco mosaic virus

Electrostatic repulsion between carboxylate groups across subunit interfaces has for many years been recognized as important in the disassembly of simple plant viruses. In the coat protein of tobacco mosaic virus (TMV), the amino acids Glu50 and Asp77 have been proposed as examples of such carboxylate groups. Site-directed mutagenesis has been used to replace these amino acids by Gln and Asn, respectively. Increased virion stability, together with reduced infectivity and reduced capacity for long-distance transport within the host plant confirms that the negative charges on the side chains of these amino acids are involved in the disassembly of TMV. Mixing purified mutant coat proteins with wild-type virions under appropriate conditions stabilizes the virions to alkaline disassembly and reduces their infectivity. It is suggested that transgenic plants expressing such mutant coat proteins could have enhanced resistance to virus infection.

Variable electrostatic interaction between DNA and coat protein in filamentous bacteriophage assembly

A restriction fragment carrying the major coat protein gene (gene VIII) was excised from the DNA of the class I filamentous bacteriophage fd, which infects Escherichia coli. This fragment was cloned into the expression plasmid pKK223-3, where it came under the control of the tac promoter, generating plasmid pKf8P. Bacteriophage fd gene VIII was similarly cloned into the plasmid pEMBL9+, enabling it to be subjected to site-directed mutagenesis. By this means the positively charged lysine residue at position 48, one of four positively charged residues near the C terminus of the protein, was turned into a negatively charged glutamic acid residue. The mutated fd gene VIII was cloned back from the pEMBL plasmid into the expression plasmid pKK223-3, creating plasmid pKE48. In the presence of the inducer isopropyl-beta-D-thiogalactoside, the wild-type and mutated coat protein genes were strongly expressed in E. coli TG1 cells transformed with plasmids pKf8P and pKE48, respectively, and the product procoat proteins underwent processing and insertion into the E. coli cell inner membrane. A net positive charge of only 2 on the side-chains in the C-terminal region is evidently sufficient for this initial stage of the virus assembly process. However, the mutated coat protein could not encapsidate the DNA of bacteriophage R252, an fd bacteriophage carrying an amber mutation in its own gene VIII, when tested on non-suppressor strains of E. coli. On the other hand, elongated hybrid bacteriophage particles could be generated whose capsids contained mixtures of wild-type (K48) and mutant (E48) subunits. This suggests that the defect in assembly may occur at the initiation rather than the elongation step(s) in virus assembly. Other mutations of lysine-48 that removed or reversed the positive charge at this position in the C-terminal region of the coat protein were also found to lead to the production of commensurately longer bacteriophage particles. Taken together, these results indicate direct electrostatic interaction between the DNA and the coat protein in the capsid and support a model of non-specific binding between DNA and coat protein subunits with a stoicheiometry that can be varied during assembly.

The origin of multiple polypeptides of molecular weight below 110 000 encoded by tobacco mosaic virus RNA in the messenger-dependent rabbit reticulocyte lysate

Multiple polypeptides encoded by tobacco mosaic virus (TMV) RNA in the messenger-dependent rabbit reticulocyte lysate are not attributable to contaminating 3'-coterminal RNA fragments, multiple leaky termination codons or endonuclease activity opening-up legitimate or spurious internal initiation sites. Quantitative analysis of polypeptides encoded over a range of added RNA concentrations from 0.09 microgram X ml-1 to 180 micrograms X ml-1 compared with those synthesized in response to size-fractionated RNAs from a crude virus preparation, or with RNA extracted from the alkali-stable fraction of TMV suggest that apart from four legitimate virus-coded products of apparent Mr approx. 165 000, 110 000, 30 000 and 17 500 all other polypeptides arise from the overlapping 5'-proximal cistrons either by (i) site-selective endonucleolytic cleavage, (ii) sense codon misreading, or (iii) specific regions of secondary structure on TMV RNA which impede ribosome translocation.

Efficient translation of the coat protein cistron of tobacco mosaic virus in a cell-free system from Escherichia coli

Translation of tobacco mosaic virus (TMV) RNA in a cell-free system derived from Escherichia coli (MRE 600) reveals several discrete polypeptides in the Mr range of 10,000-50,000. The major product is a polypeptide of Mr 17,500 which comigrates with authentic TMV coat protein on sodium dodecyl sulphate/polyacrylamide gel electrophoresis. Structural investigations by peptide-mapping techniques and differential radiolabelling confirm that the major product is TMV coat protein with an N-terminal methionine. The major polypeptide product can be assembled in vitro into virus-like ribonucleoprotein particles. The structural and evolutionary implications of this observation, and the values of TMV in elucidating eukaryotic mRNA interactions with the prokaryotic protein-synthesizing machinery, are discussed.

Mechanism of RNA-protein interactions in tobacco mosaic virus: analysis of the pH stability of virus protein complexes with synthetic polynucleotides

TMV-like RNP complexes were reconstituted from TMV protein and synthetic polynucleotides. Analysis of the pH stability of RNP with polynucleotides containing U, G, or their analogues reveals a correlation between the stability of their structure and the pK values of the bases, and indicates that the -NH-CO-groups of U and G are involved in hydrogen bonding with protein. It is suggested that TMV protein has two U- and one G-specific binding sites which, according to the phase position of the protein subunits relative to the origin of TMV assembly (D. Zimmern (1977), Cell 11, 463) are likely to be organized as UGU. The binding of the A and C residues of RNA with TMV protein is nonspecific. TMV protein groups with pK 6.3, 7.5 and 9.7 were found to be essential in the protein-protein interactions in RNP. A group of the protein with pK 8.2 is also involved in RNP stabilization. Both protein-protein interactions and interactions of protein with RNA phosphate groups were shown to be mediated by a conformational change in the protein induced by base binding. The effect of bases on both types of interactions changes in the order G approximately equal to much greater than A, and incorporation of C in RNP proceeds in a compulsory way at the expense of interaction of the neighbouring nucleotide residues in polynucleotides with protein. The data obtained are used to discuss the principles of the cooperativity of the interactions between TMV components and the mechanism of initiation and elongation in TMV self-assembly.

RNA-protein interactions in the assembly of tobacco mosaic virus

Assembly of tobacco mosaic virus is initiated by the binding of a specific loop of the RNA into the central hole of the disk aggregate of protein subunits. Since the nucleation loop is located about five-sixths along the RNA molecule, subsequent elongation must be bidirectional. We have now measured the rates of elongation in the two directions by determining the lengths of RNA protected from nuclease digestion at different times and using either intact TMV rNA, or RNA with most of the longer tail removed. Comparison of the rates with the protein supplied as either a mixture of disks with A-protein (a mixture of less aggregated states) or just A-protein, shows that different mechanisms and protein aggregates are used for the most rapid growth. When disks are present, they add more rapidly along the longer RNA tail but do not appear to add directly on the shorter tail. In contrast, smaller aggregates (A-protein) can add at both ends of the rod, but do so more slowly. Mechanisms for these processes are discussed. Preliminary results on the binding of the specific hexanucleotide AAGAAG to the disk are given and compared with the known changes on binding nonspecific hexanucleotides or the trinucleotide AAG.

Polar uncoating of tobacco mosaic virus (TMV) with dimethylsulfoxide (DMSO) and subsequent reassembly of partially stripped TMV

Increasing concentrations of dimethylsulfoxide (DMSO) strip tobacco mosaic virus (TMV) stepwise from the 3'end. The RNA tail increases in length up to 2,000 nucleotides (nu) reaching a region of very strong protein-RNA affinity. Thereafter, uncoating occurs from the other end and produces a second RNA tail 500 nu long. Further stripping of TMV proceeds from both ends, the long tail increasing in length up to 4,000 nu and the short one increasing more moderately and remaining below 2,000 nu. The region of strongest protein-RNA affinity is located between 4,000 and 5,000 nu away from the 3' end. Using the same conditions as for in vitro TMV reassembly, it is possible to recoat the RNA tails with viral protein preferentially in the 5' direction. The advantages of DMSO in studies of TMV protein-RNA interactions are discussed.