Calcium ion binding by isolated tobacco mosaic virus coat protein

Elucidation of the viral disassembly switch of tobacco mosaic virus

Stable capsid structures of viruses protect viral RNA while they also require controlled disassembly for releasing the viral genome in the host cell. A detailed understanding of viral disassembly processes and the involved structural switches is still lacking. This process has been extensively studied using tobacco mosaic virus (TMV), and carboxylate interactions are assumed to play a critical part in this process. Here, we present two cryo‐EM structures of the helical TMV assembly at 2.0 and 1.9 Å resolution in conditions of high Ca²⁺ concentration at low pH and in water. Based on our atomic models, we identify the conformational details of the disassembly switch mechanism: In high Ca²⁺/acidic pH environment, the virion is stabilized between neighboring subunits through carboxyl groups E95 and E97 in close proximity to a Ca²⁺ binding site that is shared between two subunits. Upon increase in pH and lower Ca²⁺ levels, mutual repulsion of the E95/E97 pair and Ca²⁺ removal destabilize the network of interactions between adjacent subunits at lower radius and release the switch for viral disassembly.

Porous alginate hydrogel functionalized with virus as three-dimensional scaffolds for bone differentiation

In regenerative medicine, a synthetic extracellular matrix is crucial for supporting stem cells during its differentiation process to integrate into surrounding tissues. Hydrogels are used extensively in biomaterials as synthetic matrices to support the cells. However, to mimic the biological niche of a functional tissue, various chemical functionalities are necessary. We present here, a method of functionalizing a highly porous hydrogel with functional groups by mixing the hydrogel with a plant virus, tobacco mosaic virus (TMV), and its mutant. The implication of this process resides with the three important features of TMV: its well-defined genetic/chemical modularity, its multivalency (TMV capsid is composed of 2130 copies of identical subunits), and its well-defined structural features. Previous studies utilizing the native TMV on two-dimensional supports accelerated mesenchymal stem cell differentiation, and surfaces modified with genetically modified viral particles further enhanced cell attachment and differentiation. Herein we demonstrate that functionalization of a porous alginate scaffold can be achieved by the addition of viral particles with minimal processing and downstream purifications, and the cell attachment and differentiation within the macroporous scaffold can be effectively manipulated by altering the peptide or small molecule displayed on the viral particles.

Ordered association of tobacco mosaic virus in the presence of divalent metal ions

The formation of ordered aggregates of tobacco mosaic virus (TMV) in the presence of divalent metal ions has been studied in concentrated (1-25 mg/ml) solutions of the virus. The divalent metal cations Cd2+, Zn2+, Pb2+, Cu2+, and Ni2+ have been found to promote TMV precipitation from solution at a critical concentration Ccrit, which for a given metal depends on the pH and the ionic strength of the solution, but is largely independent of the virus concentration. The TMV precipitate behaves as a nematic liquid crystal and on drying at a glass surface produces highly ordered, optically birefringent films. However, precipitation is not observed with alkali-earth metals such as Ca2+ and Mg2+. The experimental data suggest that, apart from two 'internal' metal-binding sites in each TMV subunit, the virus contains metal-binding sites of a lower affinity which promote cross-linking of TMV rods via metal bridges. The latter seem to be responsible for the precipitation of TMV in the presence of divalent cations at neutral pH. We propose that the metal-induced cross-linking may be the predominant mechanism to account for the limited solubility of a variety of proteins in solution containing metal cations with valence 2 and higher.

Virus-induced permeability transition in mitochondria

Isolated rat liver mitochondria undergo permeability transition after supplementation with a suspension of tobacco mosaic virus. Four mitochondrial parameters proved the opening of the permeability transition pore in the inner mitochondrial membrane: increased oxygen consumption, collapse of the membrane potential, release of calcium ions from mitochondria, and high amplitude mitochondrial swelling. All virus-induced changes in mitochondria were prevented by cyclosporin A. These effects were not observed if the virus was treated with EGTA or disrupted by heating. Protein component of the virus particle in the form of 20S aggregate A-protein, or helical polymer, as well as supernatant of the heat-disrupted virus sample, had no effect on mitochondrial functioning. Electron microscopy revealed the direct interaction of the virus particles with isolated mitochondria. The possible role of the mitochondrial permeability transition pore in virus-induced apoptosis is discussed.

Caspar carboxylates: the structural basis of tobamovirus disassembly

Carboxylate groups have been known for many years to drive the disassembly of simple viruses, including tobacco mosaic virus (TMV). The identities of the carboxylate groups involved and the mechanism by which they initiate disassembly have not, however, been clear. Structures have been determined at resolutions between 2.9 and 3.5 A for five tobamoviruses by fiber diffraction methods. Site-directed mutagenesis has also been used to change numerous carboxylate side chains in TMV to the corresponding amides. Comparison of the stabilities of the various mutant viruses shows that disassembly is driven by a much more complex set of carboxylate interactions than had previously been postulated. Despite the importance of the carboxylate interactions, they are not conserved during viral evolution. Instead, it appears that during evolution, patches of electrostatic interaction drift across viral subunit interfaces. The flexibility of these interactions confers a considerable advantage on the virus, enabling it to change its surface structure rapidly and thus evade host defenses.

Structure of tobraviral particles: a model suggested from sequence conservation in tobraviral and tobamoviral coat proteins

Comparisons of the coat protein sequences of four tobraviruses with those of seven tobamoviruses indicate that these proteins share a common evolutionary origin. Numerous amino acids for which specific functions have been identified in the molecular structure of the tobacco mosaic virus vulgare protein have identical or closely similar counterparts among the tobraviral proteins. These include those with roles in the hydrophobic core of the protein, those that contribute to the RNA binding site and those involved in the control of virus assembly. We suggest a model for the structure of the tobraviral particle that not only offers an explanation for the greater diameter of the tobraviral particle but also confirms an early suggestion for RNA placement within this particle.

Basic carboxyl groups of hemoglobin S: influence of oxy-deoxy conformation on the chemical reactivity of Glu-43(beta)

The gamma-carboxyl groups of Glu-43(beta) and Glu-22(beta) of hemoglobin-S (HbS), two intermolecular contact residues of deoxy protein, are activated by carbodiimide at pH 6.0. The selectivity of the modification by the two nucleophiles, glycine ethyl ester (GEE) and glucosamine, is distinct. Influence of N-hydroxysulfosuccinimide, a reagent that rescues carbodiimide-activated carboxyl (O-acyl isourea) as sulfo-NHS ester, on the overall selectivity and efficiency of the coupling of Glu-22(beta) and Glu-43(beta) with nucleophiles has been investigated. Sulfo-NHS increases the extent of coupling of nucleophiles to HbS. The rescuing efficiency of sulfo-NHS(increase in modification) with GEE and galactosamine as nucleophiles is 2.0 and 2.8, respectively. In the presence of sulfo-NHS, the extent of modification of a carboxyl group is a direct reflection of the extent to which it is activated (i.e., the protonation state of the carboxyl group). The modification reaction exhibits very high selectivity for Glu-43(beta) with GEE and galactosamine (GA) in the presence of sulfo-NHS. From the studies of the kinetics of amidation of oxy-HbS at its Glu-43(beta) (i.e., chemical reactivity) as a function of the pH in the region of 5.5-7.5, the apparent pKa of its gamma-carboxyl group has been calculated to be 6.35. Deoxygenation of HbS, nearly doubles the chemical reactivity of Glu-43(beta) of HbS at pH 7.0. It is suggested that the increased hydrophobicity of the microenvironment of Glu-43(beta), which occurs on deoxygenation of the protein, is reflected as the increased chemical reactivity of the gamma-carboxyl group and could be one of the crucial preludes to the polymerization process.

Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction

The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites.

Preliminary X-ray fiber diffraction studies of cucumber green mottle mosaic virus, watermelon strain

Fiber diffraction patterns have been obtained for cucumber green mottle mosaic virus, watermelon strain (a distant relative of tobacco mosaic virus), and two heavy-atom derivatives. These patterns and the similarity between the cucumber and the tobacco virus offer the potential of a full structure determination of the cucumber virus.

Structure of tobacco mosaic virus at 3.6 A resolution: implications for assembly

X-ray fiber diffraction analysis of tobacco mosaic virus (TMV) has led to the building of a molecular model of the intact virus, based on a map at 3.6 A resolution derived from five separated Bessel orders. This has been made possible by advances in the solution of the fiber diffraction phase problem. It is now possible to understand much of the chemical basis of TMV assembly, particularly in terms of intersubunit electrostatic interactions and RNA binding. Consideration of the molecular structure in conjunction with physical chemical studies by several groups of investigators suggests that the nucleating aggregate for initiation of TMV assembly is a short (about two turns) helix of protein subunits, probably inhibited from further polymerization in the absence of RNA by the disordering of peptide loop near the inner surface of the virus.

Calcium and potassium ion binding by tobacco mosaic virus ribonucleic acid

Calcium and potassium ion titration experiments were performed on solutions of tobacco mosaic virus RNA using ion-specific electrodes. The data obtained were analyzed using Scatchard and Klotz plots for the number of binding sites per nucleotide (n), and the apparent stability constant for complex formation, beta Me. The experimental design also allowed for the determination of the number of protons released per metal ion bound, chi. The calcium ion titration in water yielded values of 0.45 for n, 6.03 for log beta Ca and 0.24 for chi. When this titration was repeated in 0.01 M-KCl, the values were found to be 0.11 for n, 5.08 for log beta Ca and zero for chi. An aqueous potassium titration was also performed, with values for n, log beta K and chi of 0.25, 2.96 and less than 0.10, respectively.

Calcium ion binding by tobacco mosaic virus

Calcium ion titrations were performed on solutions of tobacco mosaic virus using a calcium-specific ion-exchange electrode. Scatchard analyses were used to obtain the number of calcium ion binding sites per protein subunit (n) and the apparent stability constant for complex formation (beta' Ca). These experiments were performed on unbuffered solutions, in either water or 0.01 M-KCl, to allow a determination of the number of hydrogen ions released per calcium ion bound (chi). The results indicate that near neutrality, the virus particle possesses two calcium ion binding sites per subunit having apparent stability constants greater than 10(4) M-1. The results are interpreted as if these two sites are non-identical and titrate independently. The higher affinity site for the virus in water has a value of log beta' Ca, which varies from about 8.5 at pH 8.5 to about 3.9 at pH 5.0, and for the virus in 0.01 M-KCl has a value that varies from about 6.2 at pH 8.0 to about 3.7 at pH 5.5. The higher affinity site for the virus in water binds up to two competing hydrogen ions, one with an apparent pKH value greater than 8.5 and the other with a value that varies from 6.0 at pH 5.5 to 7.3 at pH 8.0. For the virus in 0.01 M-KCl, only the competing hydrogen ion binding with an apparent pKH value greater than 8.5 remains. The results could be interpreted as indicating that the electrical charge on the virus particle has a constant value in the pH range 5.5 to 8.0 despite the fact that hydrogen ion titration curves for the intact virus particle indicate that the charge should vary from about -1 per subunit at pH 5.5 to about -4 at pH 8.0.