Structural transitions in Cowpea chlorotic mottle virus (CCMV)

Viral capsids act as molecular containers for the encapsulation of genomic nucleic acid. These protein cages can also be used as constrained reaction vessels for packaging and entrapment of synthetic cargos. The icosahedral Cowpea chlorotic mottle virus (CCMV) is an excellent model for understanding the encapsulation and packaging of both genomic and synthetic materials. High-resolution structural information of the CCMV capsid has been invaluable for evaluating structure-function relationships in the assembled capsid but does not allow insight into the capsid dynamics. The dynamic nature of the CCMV capsid might play an important role in the biological function of the virus. The CCMV capsid undergoes a pH and metal ion dependent reversible structural transition where 60 separate pores in the capsid open or close, exposing the interior of the protein cage to the bulk medium. In addition, the highly basic N-terminal domain of the capsid, which is disordered in the crystal structure, plays a significant role in packaging the viral cargo. Interestingly, in limited proteolysis and mass spectrometry experiments the N-terminal domain is the first part of the subunit to be cleaved, confirming its dynamic nature. Based on our fundamental understanding of the capsid dynamics in CCMV, we have utilized these aspects to direct packaging of a range of synthetic materials including drugs and inorganic nanoparticles.     

Crystallization of cowpea chlorotic mottle virus

Cowpea chlorotic mottle virus belongs to the brome mosaic virus group of the small spherical plant viruses. It contains 180 protein subunits, which are arranged on a T = 3 icosahedral surface lattice. The virus crystallizes in orthorhombic space group P2₁2₁2 ($\text{a = 394}\text{A}\text{?}\text{, b = 382}\text{A}\text{?}\text{,}\text{and}\text{c = 397}\text{A}\text{?}$). The unit cell contains four virus particles, while the crystallographic asymmetric unit consists of one complete virion. X-ray diffraction data from the crystals extend to nearly 3.0 Å resolution.     

Metal binding to cowpea chlorotic mottle virus using terbium(III) fluorescence

Metals are thought to play a role in the structure of many viruses. The crystal structure of the T=3 icosahedral cowpea chlorotic mottle virus (CCMV) suggests the presence of 180 unique metal-binding sites in the assembled protein cage. Each of these sites is thought to involve the coordination of the metal by five amino acids contributed from two adjacent coat protein subunits. We have used fluorescence resonance energy transfer (FRET), from tryptophan residues proximal to the putative metal-binding sites, to probe Tb(III) binding to the virus. Binding of Tb(III) was investigated on the wild-type virus and a mutant where the RNA binding ability of the virus was removed. Tb(III) binding was observed both in the wild-type virus (K_d=19 M) and the mutant (K_d=17 M), as monitored by the increase in Tb(III) fluorescence (545 nm) and concomitant decrease in tryptophan fluorescence (342 nm). Competitive binding experiments showed Ca(II) to have about 100-fold less affinity for the binding sites (K_d=1.97 mM). This is the first direct evidence of metal binding to the putative metal-binding sites, originally suggested from the crystal structure of CCMV.     

Mitotic protoplasts and their infection with tobacco mosaic virus RNA encapsulated in liposomes

M-phase and S-phase protoplasts were prepared from tobacco cells in suspension culture after a high degree of synchronization using aphidicolin, a specific inhibitor for eukaryotic DNA polymerase. When TMV-RNA was introduced into these protoplasts mediated by REV liposomes, 37% of M-phase and 26% of S-phase protoplasts were infected as determined by the fluorescent antibody technique. After the 24 hr interval between the introduction of TMV-RNA into protoplasts and the determination of infection, half of the infected mitotic protoplasts formed dumbell-shaped daughter cells. The significance of synchronized protoplasts in genetic engineering of plant cells is discussed in reference to the delivery of DNA into the nucleus.Abbreviation LS medium, Linsmaier and Skoog medium - PEG polyethylene glycol - REV reversephase evaporation vesicles - TMV tobacco mosaic virus     

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Electrostatic properties of cowpea chlorotic mottle virus (CCMV) and cucumber mosaic virus (CMV) were investigated using numerical solutions to the Poisson-Boltzmann equation. Experimentally, it has been shown that CCMV particles swell in the absence of divalent cations when the pH is raised from 5 to 7. CMV, although structurally homologous, does not undergo this transition. An analysis of the calculated electrostatic potential confirms that a strong electrostatic repulsion at the calcium-binding sites in the CCMV capsid is most likely the driving force for the capsid swelling process during the release of calcium. The binding interaction between the encapsulated genome material (RNA) inside of the capsid and the inner capsid shell is weakened during the swelling transition. This probably aids in the RNA release process, but it is unlikely that the RNA is released through capsid openings due to unfavorable electrostatic interaction between the RNA and capsid inner shell residues at these openings. Calculations of the calcium binding energies show that Ca(2+) can bind both to the native and swollen forms of the CCMV virion. Favorable binding to the swollen form suggests that Ca(2+) ions can induce the capsid contraction and stabilize the native form.     

Conformational states of cowpea chlorotic mottle virus ribonucleic acid components.

The conditions determining conformational changes in the four ribonucleic acid components of cowpea chlorotic mottle virus have been studied. All four components have at least two electrophoretically separable conformers, the occurrence of which can be regulated by both monovalent and polyvalent cations. This phenomenon also occurs, in a much less striking way, in the ribonucleic acids of the two other members of the bromovirus group, brome mosaic virus and broad bean mottle virus. Although specific in some respects, these changes have much in common with effects which have been observed in tRNAs, 55 RNAs and rRNAs. A provisional interpretation of the conformational behaviour of the viral RNAs is given in terms which have been proposed for certain tRNAs which have been studied in great detail.     

The structure of cucumber mosaic virus and comparison to cowpea chlorotic mottle virus

The structure of cucumber mosaic virus (CMV; strain Fny) has been determined to a 3.2-A resolution using X-ray crystallography. Despite the fact that CMV has only 19% capsid protein sequence identity (34% similarity) to cowpea chlorotic mottle virus (CCMV), the core structures of these two members of the Bromoviridae family are highly homologous. As suggested by a previous low-resolution structural study, the 305-A diameter (maximum) of CMV is approximately 12 A larger than that of CCMV. In CCMV, the structures of the A, B, and C subunits are nearly identical except in their N termini. In contrast, the structures of two loops in subunit A of CMV differ from those in B and C. These loops are 6 and 7 residues longer than the analogous regions in CCMV. Unlike that of CCMV, the capsid of CMV does not undergo swelling at pH 7.0 and is stable at pH 9.0. This may be partly due to the fact that the N termini of the B and C subunits form a unique bundle of six amphipathic helices oriented down into the virion core at the threefold axes. In addition, while CCMV has a cluster of aspartic acid residues at the quasi-threefold axis that are proposed to bind metal in a pH-dependent manner, this cluster is replaced by complementing acids and bases in CMV. Finally, this structure clearly demonstrates that the residues important for aphid transmission lie at the outermost portion of the betaH-betaI loop and yields details of the portions of the virus that are hypothesized to mediate binding to aphid mouthparts.     

Interaction with capsid protein alters RNA structure and the pathway for in vitro assembly of cowpea chlorotic mottle virus

Viruses use sophisticated mechanisms to allow the specific packaging of their genome over that of host nucleic acids. We examined the in vitro assembly of the Cowpea chlorotic mottle virus (CCMV) and observed that assembly with viral RNA follows two different mechanisms. Initially, CCMV capsid protein (CP) dimers bind RNA with low cooperativity and form virus-like particles of 90 CP dimers and one copy of RNA. Longer incubation reveals a different assembly path. At a stoichiometry of about ten CP dimers per RNA, the CP slowly folds the RNA into a compact structure that can be bound with high cooperativity by additional CP dimers. This folding process is exclusively a function of CP quaternary structure and is independent of RNA sequence. CP-induced folding is distinct from RNA folding that depends on base-pairing to stabilize tertiary structure. We hypothesize that specific encapsidation of viral RNA is a three-step process: specific binding by a few copies of CP, RNA folding, and then cooperative binding of CP to the "labeled" nucleoprotein complex. This mechanism, observed in a plant virus, may be applicable to other viruses that do not halt synthesis of host nucleic acid, including HIV.     

The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus

Normal mode analysis based on a simplified energy function was used to study the swelling process of the icosahedral virus, cowpea chlorotic mottle virus (CCMV). Native state virus particles (coat proteins) of this T=3 icosahedral virus have been shown to undergo a large conformational change to a swollen state when metal ions are removed or the pH is raised. A normal mode analysis based on the native state capsid showed one preferential direction, a breathing mode, that explains the majority of the structural rearrangement necessary to bring the native structure close to the swollen state. From the native form of CCMV, the structure can be displaced along the direction of a single breathing mode by different amounts to create several candidate swollen structures and a putative pathway for virus expansion. The R-factor between these predicted swollen capsid structures and experimental electron density from cryoelectron microscopy (cryo-EM) measurements is then calculated to indicate how well each structure satisfies the experimental measurements on the swollen capsid state. A decrease of the crystallographic R-factor value from approximately 72% to approximately 49% was observed for these simple incremental displacements along the breathing mode. The simultaneous displacement of the native structure along other relevant (symmetric, non-degenerate) modes produce a structure with an R-factor of 45%, which is further reduced to 43.9% after minimization: a value in good accord with models based on the EM data at 28 A resolution. Based on the incrementally expanded structures, a pathway for the swelling process has been proposed. Analysis of the intermediate structures along this pathway indicates a significant loss of interactions at the quasi-3-fold interfaces occurs in the initial stages of the swelling process and this serves as a trigger for the compact to swollen transition. Furthermore, the pH dependent swelling appears to be triggered by the titration of a single residue with an anomalous pK(a) value in the unswollen particle.     

Encapsulation and crystallization of Prussian blue nanoparticles by cowpea chlorotic mottle virus capsids

Cowpea chlorotic mottle virus (CCMV) capsids were used to encapsulate Prussian blue (PB) particles based on electrostatic interaction. A negatively-charged metal complex, hexacyanoferrate (III), was entrapped inside the capsids through the disassembly/reassembly process under a pH change from 7.5 to 5.2. The loaded capsids reacted with a second Fe(II) to fabricate PB particles. The synthesis of PB in CCMV capsids was confirmed by a unique colour transition at 710 nm and by size-exclusion FPLC. Transmission electron microscopy images of PB-CCMV biohybrids presented discrete spherical particles with a relatively homogeneous size. Dynamic light scattering of PB-CCMV showed two peaks of 29.2 ± 1.7 nm corresponding to triangulation number T = 3 particles, and 17.5 ± 1.2 nm of pseudo T = 2 particles. The encapsulation and crystallization of PB in CCMV provided an efficient method for the self-organization of bimetallic nanoparticles.     

Molecular modeling of the RNA binding N-terminal part of cowpea chlorotic mottle virus coat protein in solution with phosphate ions.

The RNA-binding N-terminal arm of the coat protein of cowpea chlorotic mottle virus has been studied with five molecular dynamics simulations of 2.0 ns each. This 25-residue peptide (pep25) is highly charged: it contains six Arg and three Lys residues. An alpha-helical fraction of the sequence is stabilized in vitro by salts. The interaction of monophosphate (Pi) ions with pep25 was studied, and it was found that only two Pi ions are bound to pep25 on average, but water-mediated interactions between pep25 and Pi, which provide electrostatic screening for intrapeptide interactions, are abundant. Shielding by the Pi ions of repulsive electrostatic interactions between Arg sidechains increases the alpha-helicity of pep25. A hydrogen bond at the N-terminal end of the alpha-helix renders extension of the alpha-helix in the N-terminal direction impossible, in agreement with evidence from nuclear magnetic resonance experiments.     

Expression of bottom component RNA of cowpea mosaic virus in cowpea protoplasts

Upon inoculation of cowpea protoplasts with the bottom component of cowpea mosaic virus, at least six virus-induced proteins (with sizes of 170, 110, 87, 84, 60, and 32 kilodaltons) are synthesized, but not the capsid proteins (37 and 23 kilodaltons). These bottom-component-induced proteins were studied with respect to their genetic origin and mode of synthesis. The analyses were based on their electrophoretic peptide patterns resulting from partial digestion with Staphylococcus aureus protease V8. Comparison of the peptide patterns of the virus-induced proteins with those of the cowpea mosaic virus RNA-coded polypeptides produced in rabbit reticulocyte lysate showed that the 170- and 32-kilodalton polypeptides, which are the first viral products in cowpea mosaic virus-infected cells, were actually coded by the bottom component RNA of the virus. The 110-, 87-, and 84-kilodalton polypeptides, and possibly the 60-kilodalton polypeptide, appeared to have amino acid sequences in common with the 170-kilodalton polypeptide, demonstrating that they were virus coded as well. The results indicated that cowpea mosaic virus bottom component RNA was translated in vivo into a single 200-kilodalton polyprotein from which probably all bottom-component-specific proteins arose by three successive cleavages.     

RNA-protein interactions and secondary structures of cowpea chlorotic mottle virus for in vitro assembly

Laser Raman spectroscopy of the cowpea chlorotic mottle virus (CCMV) in native (pH 5.0) and partially swollen (pH 7.5) states reveals the presence of small percentages of protonated adenine (less than 15%) and cytosine (less than 7%) bases in the encapsidated RNA molecule of the native virion. The protonated bases are titrated with pH-induced swelling of the virus. Titration of putative COOH groups of aspartic and glutamic side chains of the virion subunit cannot be detected over the same pH range, which suggests that carboxyl anions (CO-2) and protonated bases are both available at pH 5 to stabilize the ribonucleoprotein particles by electrostatic interactions. The highly (95%) ordered secondary structure of encapsidated RNA may undergo a small additional increase (less than 3%) in ordered structure with release from the virion, suggesting at most a marginal structure-distorting influence from protein contacts in the native particle. The Raman spectra of the virion are also compared by difference spectroscopy with spectra of capsids (empty shells devoid of RNA), subunit dimers, and protein-free RNA. The results indicate that the subunit structure is altered by the release of RNA from the virion, as well as by the swelling of the virion. Amino acid residues and protein secondary structures that are affected in these in vitro assembly and disassembly processes are identified from their characteristic Raman lines. Two classes of cysteinyl SH groups, solvent exposed and solvent protected, are revealed for the capsid and virion subunit.(ABSTRACT TRUNCATED AT 250 WORDS)     

The amino acid sequences of the tryptic peptides of cowpea chlorotic mottle virus protein

The amino acid sequences of the major tryptic peptides from the coat protein of wild type cowpea chlorotic mottle virus are presented. The sequences have been determined by a combination of enzyme hydrolysis, mass spectrometry and Edman degradation, and the relative usefulness of mass spectrometry in this peptide sequence determination is discussed.     

Electrostatic interaction between RNA and protein capsid in cowpea chlorotic mottle virus simulated by a coarse-grain RNA model and a Monte Carlo approach

Although many viruses have been crystallized and the protein capsid structures have been determined by x-ray crystallography, the nucleic acids often cannot be resolved. This is especially true for RNA viruses. The lack of information about the conformation of DNA/RNA greatly hinders our understanding of the assembly mechanism of various viruses. Here we combine a coarse-grain model and a Monte Carlo method to simulate the distribution of viral RNA inside the capsid of cowpea chlorotic mottle virus. Our results show that there is very strong interaction between the N-terminal residues of the capsid proteins, which are highly positive charged, and the viral RNA. Without these residues, the binding energy disfavors the binding of RNA by the capsid. The RNA forms a shell close to the capsid with the highest densities associated with the capsid dimers. These high-density regions are connected to each other in the shape of a continuous net of triangles. The overall icosahedral shape of the net overlaps with the capsid subunit icosahedral organization. Medium density of RNA is found under the pentamers of the capsid. These findings are consistent with experimental observations.     

Virion swelling is not required for cotranslational disassembly of cowpea chlorotic mottle virus in vitro.

The mechanism by which virions of cowpea chlorotic mottle virus (CCMV) disassemble and allow for translation of the virion RNA is not well understood. Previous models have suggested that virion swelling is required to expose the virion RNA for translation in a process referred to as cotranslational disassembly (M. Brisco, R. Hull, and T. M. A. Wilson, Virology 148:210-217, 1986; J. W. Roenhorst, J. W. M. van Lent, and B. J. M. Verduin, Virology 164:91-98, 1988; J. W. Roenhorst, J. M. Verduin, and R. W. Goldbach, Virology 168:138-146, 1989). Previous work in our laboratory has identified point mutations in the CCMV coat protein which result in virions with altered swelling characteristics (J. Fox, F. G. Albert, J. Speir, and M. J. Young, Virology 227:229-233, 1997; J. M. Fox, X. Zhao, J. A. Speir, and M. J. Young, Virology 222:115-122, 1996). The wild-type and mutant CCMV virions were used to correlate virion swelling with the ability of virion RNA to be translated in a cell-free wheat germ extract. Mutant virions unable to swell (cpK42R) are as infectious as wild-type virions in vivo, and the levels of translated encapsidated virion RNA are similar to those of wild-type virions in vitro. Mutant virions capable of swelling but not of disassembling in vitro (cpR26C) are noninfectious and have severely reduced levels of translation of the encapsidated virion RNA in vitro. These studies suggest that virion swelling is not required for the cotranslational disassembly of CCMV. Additionally, the results indicate that there is a pH-dependent structural transition in the virion, other than swelling, that results in the RNA's being exposed for translation in vitro. An alternative model suggesting that cotranslational disassembly of CCMV involves presentation of the virion RNA through the virion fivefold axis is proposed.