Effects of the cowpea chlorotic mottle bromovirus beta-hexamer structure on virion assembly

A minimal coarse-grained model for the low-frequency normal mode analysis of icosahedral viral capsids

The main goal of this work is the design of a coarse-grained theoretical model of minimal resolution for the study of the physical properties of icosahedral virus capsids within the linear-response regime. In this model the capsid is represented as an interacting many-body system whose composing elements are capsid subunits (capsomers), which are treated as three-dimensional rigid bodies. The total interaction potential energy is written as a sum of pairwise capsomer-capsomer interactions. Based on previous work [Gomez Llorente et al., Soft Matter, 2014, 10, 3560], a minimal and complete anisotropic binary interaction that includes a full Hessian matrix of independent force constants is proposed. In this interaction model, capsomers have rotational symmetry around an axis of order n > 2. The full coarse-grained model is applied to analyse the low-frequency normal-mode spectrum of icosahedral T = 1 capsids. The model performance is evaluated by fitting its predicted spectrum to the full-atom results for the Satellite Tobacco Necrosis Virus (STNV) capsid [Dykeman and Sankey, Phys. Rev. Lett., 2008, 100, 028101]. Two capsomer choices that are compatible with the capsid icosahedral symmetry are checked, namely pentamers (n = 5) and trimers (n = 3). Both subunit types provide fair fits, from which the magnitude of the coarse-grained force constants for a real virus is obtained. The model is able to uncover latent instabilities whose analysis is fully consistent with the current knowledge about the STNV capsid, which does not self-assemble in the absence of RNA and is thermally unstable. The straightforward generalisability of the model beyond the linear regime and its completeness make it a promising tool to theoretically interpret many experimental data such as those provided by the atomic force microscopy or even to better understand processes far from equilibrium such as the capsid self-assembly.

Curating viscoelastic properties of icosahedral viruses, virus-based nanomaterials, and protein cages

The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity. In this study, we employed Quartz Crystal Microbalance with Dissipation technology (QCM-D) to characterize and compare the mechanical rigidity of different protein cages and viruses. We attempted to unveil the relationships between rigidity, radius, shell thickness, and triangulation number. We show that the rigidity and triangulation numbers are inversely related to each other and the comparison of rigidity and radius also follows the same trend. Our results suggest that subunit orientation, protein-protein interactions, and protein-nucleic acid interactions are important for the resistance to deformation of these complexes, however, the relationships are complex and need to be explored further. The QCM-D based viscoelastic measurements presented here help us elucidate these relationships and show the future prospect of this technique in the field of physical virology and nano-biotechnology.

A minimal representation of the self-assembly of virus capsids

Viruses are biological nanosystems with a capsid of protein-made capsomer units that encloses and protects the genetic material responsible for their replication. Here we show how the geometrical constraints of the capsomer-capsomer interaction in icosahedral capsids and the requirement of low frustration fix the form of the shortest and universal truncated multipolar expansion of the two-body interaction between capsomers. The structures of many of the icosahedral and related virus capsids are located as single lowest energy states of a potential energy surface built from this interaction. Our minimalist representation is consistent with other models known to produce a controllable and efficient self-assembly, and unveils relevant features of the natural design of the capsids. It promises to be very useful in physical virology and may also be of interest in fields of nanoscience and nanotechnology where similar hollow convex structures are relevant.

Challenging the state of the art in protein structure prediction: Highlights of experimental target structures for the 10th Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10

For the last two decades, CASP has assessed the state of the art in techniques for protein structure prediction and identified areas which required further development. CASP would not have been possible without the prediction targets provided by the experimental structural biology community. In the latest experiment, CASP10, more than 100 structures were suggested as prediction targets, some of which appeared to be extraordinarily difficult for modeling. In this article, authors of some of the most challenging targets discuss which specific scientific question motivated the experimental structure determination of the target protein, which structural features were especially interesting from a structural or functional perspective, and to what extent these features were correctly reproduced in the predictions submitted to CASP10. Specifically, the following targets will be presented: the acid-gated urea channel, a difficult to predict transmembrane protein from the important human pathogen Helicobacter pylori; the structure of human interleukin (IL)-34, a recently discovered helical cytokine; the structure of a functionally uncharacterized enzyme OrfY from Thermoproteus tenax formed by a gene duplication and a novel fold; an ORFan domain of mimivirus sulfhydryl oxidase R596; the fiber protein gene product 17 from bacteriophage T7; the bacteriophage CBA-120 tailspike protein; a virus coat protein from metagenomic samples of the marine environment; and finally, an unprecedented class of structure prediction targets based on engineered disulfide-rich small proteins.

Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly

BACKGROUND

In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly).

RESULTS

In order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results.

CONCLUSIONS

Our analysis shows for which molecular parameters hierarchical assembly schemes can outperform direct ones and suggests that viruses with high bond stability might prefer hierarchical assembly schemes. These insights increase our physical understanding of an essential biological process, with many interesting potential applications in medicine and materials science.

Molecular characterization of the complete genomes of two new field isolates of Cowpea chlorotic mottle virus, and their phylogenetic analysis

Cowpea chlorotic mottle virus (CCMV, family Bromoviridae) is found worldwide and has been used as a model virus for a long time, but no data is available about the genetic diversity of field isolates. Recently, two new field isolates (Car1 and Car2) of CCMV obtained from cowpea showed distinct phenotypic symptoms when inoculated to cowpea. CCMV-Car1 induced severe mosaic and interveinal chlorosis, while CCMV-Car2 produced mild mottling and leaf rolling. Both isolates produced asymptomatic infection in Nicotiana benthamiana. The complete genome of both isolates was amplified by reverse transcription-polymerase chain reaction using specific primers against the CCMV sequences available in the GenBank database, cloned and sequenced. Both nucleotide and amino acid sequences were compared between the newly sequenced CCMV isolates and the three previously characterized CCMV strains (T, M1, and R). Phylogenetic analysis of the RNA 1 sequence showed that CCMV-Car1 was in a separate branch from the rest of the CCMV isolates while CCMV-Car2 grouped together with CCMV-R. On the basis of RNA 2 and RNA 3 sequences, two major groupings were obtained. One group included CCMV-Car1 and CCMV-Car2 isolates while the other contained CCMV-T, CCMV-M1, and CCMV-R strains. Recombination programs detected a potential recombination event in the RNA 1 sequence of CCMV-Car2 isolate but not in RNA 2 and RNA 3 sequences. The results showed that both mutations and recombination have played an important role in the genetic diversity of these two new isolates of CCMV.

The structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4

Avian polyomavirus (APV) causes a fatal, multi-organ disease among several bird species. Using cryogenic electron microscopy and other biochemical techniques, we investigated the structure of APV and compared it to that of mammalian polyomaviruses, particularly JC polyomavirus and simian virus 40. The structure of the pentameric major capsid protein (VP1) is mostly conserved; however, APV VP1 has a unique, truncated C-terminus that eliminates an intercapsomere-connecting β-hairpin observed in other polyomaviruses. We postulate that the terminal β-hairpin locks other polyomavirus capsids in a stable conformation and that absence of the hairpin leads to the observed capsid size variation in APV. Plug-like density features were observed at the base of the VP1 pentamers, consistent with the known location of minor capsid proteins VP2 and VP3. However, the plug density is more prominent in APV and may include VP4, a minor capsid protein unique to bird polyomaviruses.

Modelling the self-assembly of virus capsids

We use computer simulations to study a model, first proposed by Wales (2005 Phil. Trans. R. Soc. A 363 357), for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of thermodynamic and geometric factors can be qualitatively related to the potential energy landscape structure of the assembling system. Even though the model is strongly coarse-grained, it exhibits a number of features also observed in experiments, such as sigmoidal assembly dynamics, hysteresis in capsid formation and numerous kinetic traps. We also investigate the effect of macromolecular crowding on the assembly dynamics. Crowding agents generally reduce capsid yields at optimal conditions for non-crowded assembly, but may increase yields for parameter regimes away from the optimum. Finally, we generalize the model to a larger triangulation number T = 3, and observe assembly dynamics more complex than that seen for the original T = 1 model.

Synergistic effects of mutations and nanoparticle templating in the self-assembly of cowpea chlorotic mottle virus capsids

A study of the in vitro nanoparticle-templated assembly of a mutant of cowpea chlorotic mottle virus lacking most of the N-terminal domain (residues 4-37), NDelta34, is presented. Mutant empty proteins assemble into empty capsids with a much broader distribution of sizes than the wild-type virus. This increased flexibility in the assembly outcomes is known to be detrimental for the assembly process in the presence of molecular polyanions. However, when rigid polyanionic cores are used, such as nanoparticles, the assembly process is restored and virus-like particles form. Moreover, the breadth of the nanoparticle-templated capsid size distribution becomes comparable with the wild-type virus size distribution.

Mechanisms of size control and polymorphism in viral capsid assembly

We simulate the assembly dynamics of icosahedral capsids from subunits that interconvert between different conformations (or quasi-equivalent states). The simulations identify mechanisms by which subunits form empty capsids with only one morphology but adaptively assemble into different icosahedral morphologies around nanoparticle cargoes with varying sizes, as seen in recent experiments with brome mosaic virus (BMV) capsid proteins. Adaptive cargo encapsidation requires moderate cargo-subunit interaction strengths; stronger interactions frustrate assembly by stabilizing intermediates with incommensurate curvature. We compare simulation results to experiments with cowpea chlorotic mottle virus empty capsids and BMV capsids assembled on functionalized nanoparticles and suggest new cargo encapsidation experiments. Finally, we find that both empty and templated capsids maintain the precise spatial ordering of subunit conformations seen in the crystal structure even if interactions that preserve this arrangement are favored by as little as the thermal energy, consistent with experimental observations that different subunit conformations are highly similar.

Self-assembly of brome mosaic virus capsids: insights from shorter time-scale experiments

An amended kinetic model for the self-assembly of empty capsids of brome mosaic virus is proposed. The model has been modified to account for a new feature in the assembly kinetics revealed by time-course light scattering experiments at higher temporal resolution than previously attempted. To be able to simulate the sharp takeoff from the initial lag phase to the growth phase in the kinetic curves, a monomer activation step was proposed.

Controlling viral capsid assembly with templating

We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can dramatically enhance rates and robustness of assembly, as compared to the spontaneous assembly of subunits into empty capsids. For large core-subunit interactions, subunits adsorb onto core surfaces en masse in a disordered manner, and then undergo a cooperative rearrangement into an ordered capsid structure. These assembly pathways are unlike any identified for empty capsid formation. Our models can be directly applied to recent experiments in which viral capsid proteins assemble around functionalized inorganic nanoparticles [Sun, Proc. Natl. Acad. Sci. U.S.A. 104, 1354 (2007)]. In addition, we discuss broader implications for understanding the dynamic encapsidation of single-stranded genomic molecules during viral replication and for developing multicomponent nanostructured materials.

Structure of recombinant capsids formed by the beta-annulus deletion mutant -- rCP (Delta48-59) of Sesbania mosaic virus

A unique feature of several T=3 icosahedral viruses is the presence of a structure called the beta-annulus formed by extensive hydrogen bonding between protein subunits related by icosahedral three-fold axis of symmetry. This unique structure has been suggested as a molecular switch that determines the T=3 capsid assembly. In order to examine the importance of the beta-annulus, a deletion mutant of Sesbania mosaic virus coat protein in which residues 48-59 involved in the formation of the beta-annulus were deleted retaining the rest of the residues in the amino terminal segment (rCP (Delta48-59)) was constructed. When expressed in Escherichia coli, the mutant protein assembled into virus like particles of sizes close to that of the wild type virus particles. The purified capsids were crystallized and their three dimensional structure was determined at 3.6 A resolution by X-ray crystallography. The mutant capsid structure closely resembled that of the native virus particles. However, surprisingly, the structure revealed that the assembly of the particles has proceeded without the formation of the beta-annulus. Therefore, the beta-annulus is not essential for T=3 capsid assembly as speculated earlier and may be formed as a consequence of the particle assembly. This is the first structural demonstration that the virus particle morphology with and without the beta-annulus could be closely similar.

Replication-coupled packaging mechanism in positive-strand RNA viruses: synchronized coexpression of functional multigenome RNA components of an animal and a plant virus in Nicotiana benthamiana cells by agroinfiltration

Flock house virus (FHV), a bipartite RNA virus of insects and a member of the Nodaviridae family, shares viral replication features with the tripartite brome mosaic virus (BMV), an RNA virus that infects plants and is a member of the Bromoviridae family. In BMV and FHV, genome packaging is coupled to replication, a widely conserved mechanism among positive-strand RNA viruses of diverse origin. To unravel the events that modulate the mechanism of replication-coupled packaging, in this study, we have extended the transfer DNA (T-DNA)-based agroinfiltration system to express functional genome components of FHV in plant cells (Nicotiana benthamiana). Replication, intracellular membrane localization, and packaging characteristics in agroinfiltrated plant cells revealed that T-DNA plasmids of FHV were biologically active and faithfully mimicked complete replication and packaging behavior similar to that observed for insect cells. Synchronized coexpression of wild-type BMV and FHV genome components in plant cells resulted in the assembly of virions packaging the respective viral progeny RNA. To further elucidate the link between replication and packaging, coat protein (CP) open reading frames were precisely exchanged between BMV RNA 3 (B3) and FHV RNA 2 (F2), creating chimeric RNAs expressing heterologous CP genes (B3/FCP and F2/BCP). Coinfiltration of each chimera with its corresponding genome counterpart to provide viral replicase (B1+B2+B3/FCP and F1+F2/BCP) resulted in the expected progeny profiles, but virions exhibited a nonspecific packaging phenotype. Complementation with homologous replicase (with respect to CP) failed to enhance packaging specificity. Taken together, we propose that the transcription of CP mRNA from homologous replication and its translation must be synchronized to confer packaging specificity.

Synergistic Interaction of Sweet potato chlorotic stunt virus (Crinivirus) with Carla-, Cucumo-, Ipomo-, and Potyviruses Infecting Sweet Potato

Co-infection of Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus) with Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) results in sweet potato virus disease (SPVD), a synergistic disease that is widely distributed in the sweet potato (Ipomoea batatas) growing regions of the world. Since both SPCSV and SPFMV are common and often detected as part of multiple co-infections of severely diseased plants, the occurrence of synergistic interactions with other viruses was investigated. Data from this study show that SPCSV, but not SPFMV, can cause synergistic diseases in sweet potato with all viruses tested, including members of the genus Potyvirus (Sweet potato latent virus, Sweet potato mild speckling virus), Ipomovirus (Sweet potato mild mottle virus), Cucumovirus (Cucumber mosaic virus), and putative members of the genus Carlavirus (Sweet potato chlorotic fleck virus and C-6 virus). The synergism was expressed as an increase in the severity of symptoms, virus accumulation, viral movement in plants, and as an effect on yield of storage roots. The presence of a third different virus in plants affected with SPVD increased the severity of symptoms even further compared with SPVD alone. There was a positive correlation between increase in virus accumulation and symptom expression in double and triple SPCSV-associated co-infections. The epidemiological implications of the results are discussed.

Core-controlled polymorphism in virus-like particles

This study concerns the self-assembly of virus-like particles (VLPs) composed of an icosahedral virus protein coat encapsulating a functionalized spherical nanoparticle core. The recent development of efficient methods for VLP self-assembly has opened the way to structural studies. Using electron microscopy with image reconstruction, the structures of several VLPs obtained from brome mosaic virus capsid proteins and gold nanoparticles were elucidated. Varying the gold core diameter provides control over the capsid structure. The number of subunits required for a complete capsid increases with the core diameter. The packaging efficiency is a function of the number of capsid protein subunits per gold nanoparticle. VLPs of varying diameters were found to resemble to three classes of viral particles found in cells (T=1, 2, and 3). As a consequence of their regularity, VLPs form three-dimensional crystals under the same conditions as the wild-type virus. The crystals represent a form of metallodielectric material that exhibits optical properties influenced by multipolar plasmonic coupling.

Evaluation of the roles of specific regions of the Cucumber necrosis virus coat protein arm in particle accumulation and fungus transmission

The Cucumber necrosis virus (CNV) particle is a T=3 icosahedron composed of 180 identical coat protein (CP) subunits. Each CP subunit includes a 34-amino-acid (aa) arm which connects the RNA binding and shell domains. The arm is comprised of an 18-aa "beta" region and a 16-aa "epsilon" region, with the former contributing to a beta-annular structure involved in particle stability and the latter contributing to quasiequivalence and virion RNA binding. Previous work has shown that specific regions of the CNV capsid play important roles in transmission by zoospores of the fungal vector Olpidium bornovanus and that particle expansion is essential for this process. To assess the importance of the two arm regions in particle accumulation, stability, and virus transmission, five CP arm deletion mutants were constructed. Our findings indicate that beta(-) mutants are capable of producing particles in plants; however, the arm(-) and epsilon(-) mutants are not. In addition, beta(-) particles bind zoospores less efficiently than wild-type CNV and are not fungally transmissible. Beta(-) particles are also less thermally stable and disassemble under swelling conditions. Our finding that beta(-) mutants can accumulate in plants suggests that other features of the virion, such as RNA/CP interactions, may also be important for particle stability.

Dynamic pathways for viral capsid assembly

We develop a class of models with which we simulate the assembly of particles into T1 capsidlike objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive assembly. For some ranges of parameters, assembly is facile; for others, assembly is dynamically frustrated by kinetic traps corresponding to malformed or incompletely formed capsids. Our simulations sample many independent trajectories at various capsomer concentrations, allowing for statistically meaningful conclusions. Depending on subunit (i.e., capsomer) geometries, successful assembly proceeds by several mechanisms involving binding of intermediates of various sizes. We discuss the relationship between these mechanisms and experimental evaluations of capsid assembly processes.

Enhanced local symmetry interactions globally stabilize a mutant virus capsid that maintains infectivity and capsid dynamics

Structural transitions in viral capsids play a critical role in the virus life cycle, including assembly, disassembly, and release of the packaged nucleic acid. Cowpea chlorotic mottle virus (CCMV) undergoes a well-studied reversible structural expansion in vitro in which the capsid expands by 10%. The swollen form of the particle can be completely disassembled by increasing the salt concentration to 1 M. Remarkably, a single-residue mutant of the CCMV N-terminal arm, K42R, is not susceptible to dissociation in high salt (salt-stable CCMV [SS-CCMV]) and retains 70% of wild-type infectivity. We present the combined structural and biophysical basis for the chemical stability and viability of the SS-CCMV particles. A 2.7-A resolution crystal structure of the SS-CCMV capsid shows an addition of 660 new intersubunit interactions per particle at the center of the 20 hexameric capsomeres, which are a direct result of the K42R mutation. Protease-based mapping experiments of intact particles demonstrate that both the swollen and closed forms of the wild-type and SS-CCMV particles have highly dynamic N-terminal regions, yet the SS-CCMV particles are more resistant to degradation. Thus, the increase in SS-CCMV particle stability is a result of concentrated tethering of subunits at a local symmetry interface (i.e., quasi-sixfold axes) that does not interfere with the function of other key symmetry interfaces (i.e., fivefold, twofold, quasi-threefold axes). The result is a particle that is still dynamic but insensitive to high salt due to a new series of bonds that are resistant to high ionic strength and preserve the overall particle structure.

The role of subunit hinges and molecular "switches" in the control of viral capsid polymorphism

The coat protein (CP) of cowpea chlorotic mottle virus assembles exclusively into a T=3 capsid in vivo and, under proper conditions, in vitro. The N-terminal domain of CP has been implicated in proper assembly and was viewed as a required switch for mediating hexamer and pentamer formation in T=3 assembly. We observed that a mutant CP lacking most of the N-terminal domain, NDelta34, assembles, in vitro, into statistically predictable numbers of: native-like T=3 capsids of 90 dimers; "T=2" capsids of 60 dimers; T=1 capsids of 30 dimers. We generated cryo-EM image reconstructions of each form and built pseudo-atomic models based on the subunits from the crystal structure of plant-derived T=3 virus allowing a detailed comparison of stabilizing interactions in the three assemblies. The statistical nature of the distribution of assembly products and the observed structures indicates that the N-terminus of CP is not a switch that is required to form the proper ratio of hexamers and pentamers for T=3 assembly; rather, it biases the direction of assembly to T=3 particles from the possibilities available to NDelta34 through flexible dimer hinges and variations in subunit contacts. Our results are consistent with a pentamer of dimers (PODs) nucleating assembly in all cases but subunit dimers can be added with different trajectories that favor specific T=3 or T=1 global particle geometries. Formation of the "T=2" particles appears to be fundamentally different in that they not only nucleate with PODs, but assembly propagates by the addition of mostly, if not exclusively PODs generating an entirely new subunit interface in the process. These results show that capsid geometry is flexible and may readily adapt to new requirements as the virus evolves.

The Role of Arginine-rich Motif and β-Annulus in the Assembly and Stability of Sesbania Mosaic Virus Capsids

Sesbania mosaic virus (SeMV) capsids are stabilized by protein-protein, protein-RNA and calcium-mediated protein-protein interactions. The N-terminal random domain of SeMV coat protein (CP) controls RNA encapsidation and size of the capsids and has two important motifs, the arginine-rich motif (ARM) and the beta-annulus structure. Here, mutational analysis of the arginine residues present in the ARM to glutamic acid was carried out. Mutation of all the arginine residues in the ARM almost completely abolished RNA encapsidation, although the assembly of T=3 capsids was not affected. A minimum of three arginine residues was found to be essential for RNA encapsidation. The mutant capsids devoid of RNA were less stable to thermal denaturation when compared to wild-type capsids. The results suggest that capsid assembly is entirely mediated by CP-dependent protein-protein inter-subunit interactions and encapsidation of genomic RNA enhances the stability of the capsids. Because of the unique structural ordering of beta-annulus segment at the icosahedral 3-folds, it has been suggested as the switch that determines the pentameric and hexameric clustering of CP subunits essential for T=3 capsid assembly. Surprisingly, mutation of a conserved proline within the segment that forms the beta-annulus to alanine, or deletion of residues 48-53 involved in hydrogen bonding interactions with residues 54-58 of the 3-fold related subunit or deletion of all the residues (48-59) involved in the formation of beta-annulus did not affect capsid assembly. These results suggest that the switch for assembly into T=3 capsids is not the beta-annulus. The ordered beta-annulus observed in the structures of many viruses could be a consequence of assembly to optimize intersubunit interactions.

T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly

Sesbania mosaic virus particles consist of 180 coat protein subunits of 29kDa organized on a T=3 icosahedral lattice. N-terminal deletion mutants of coat protein that lack 36 (CP-NDelta36) and 65 (CP-NDelta65) residues from the N terminus, when expressed in Escherichia coli, produced similar T=1 capsids of approximate diameter 20nm. In contrast to the wild-type particles, these contain only 60 copies of the truncated protein subunits (T=1). CP-NDelta65 lacks the "beta-annulus" believed to be responsible for the error-free assembly of T=3 particles. Though the CP-NDelta36 mutant has the beta-annulus segment, it does not form a T=3 capsid, presumably because it lacks an arginine-rich motif found close to the amino terminus. Both CP-NDelta36 and CP-NDelta65 T=1 capsids retain many key features of the T=3 quaternary structure. Calcium binding geometries at the coat protein interfaces in these two particles are also nearly identical. When the conserved aspartate residues that coordinate the calcium, D146 and D149 in the CP-NDelta65, were mutated to asparagine (CP-NDelta65-D146N-D149N), the subunits assembled into T=1 particles but failed to bind calcium ions. The structure of this mutant revealed particles that were slightly expanded. The analysis of the structures of these mutant capsids suggests that although calcium binding contributes substantially to the stability of T=1 particles, it is not mandatory for their assembly. In contrast, the presence of a large fraction of the amino-terminal arm including sequences that precede the beta-annulus and the conserved D149 appear to be indispensable for the error-free assembly of T=3 particles.

Evidence that vector transmission of a plant virus requires conformational change in virus particles

Transmission of Cucumber necrosis virus (CNV) by zoospores of its fungal vector, Olpidium bornovanus, involves specific adsorption of virus particles onto the zoospore plasmalemma prior to infestation of cucumber roots by virus-bound zoospores. Previous work has shown that specific components of both CNV and zoospores are required for successful CNV/zoospore recognition. Here, we show that limited trypsin digestion of CNV following in vitro CNV/zoospore binding assays, results in the production of specific proteolytic digestion products under conditions where native CNV is resistant. The proteolytic digestion pattern of zoospore-bound CNV was found to be similar to that of swollen CNV particles produced in vitro, suggesting that zoospore-bound CNV is in an altered conformational state, perhaps similar to that of swollen CNV. We show that an engineered CNV mutant (Pro73Gly) in which a conserved proline residue (Pro73) in the beta-annulus of the CP arm is changed to glycine is resistant to proteolysis following in vitro zoospore binding assays. Moreover, Pro73Gly particles are transmitted only poorly by O.bornovanus. Together, the results of these studies suggest that CNV undergoes conformational change upon zoospore binding and that the conformational change is important for CNV transmissibility.

Genetic and functional analyses of the øX174 DNA binding protein: the effects of substitutions for amino acid residues that spatially organize the two DNA binding domains

The øX174 DNA binding protein contains two DNA binding domains, containing a series of DNA binding basic amino acids, separated by a proline-rich linker region. Within each DNA binding domain, there is a conserved glycine residue. Glycine and proline residues were mutated and the effects on virion structure were examined. Substitutions for glycine residues yield particles with similar properties to previously characterized mutants with substitutions for DNA binding residues. Both sets of mutations share a common extragenic second-site suppressor, suggesting that the defects caused by the mutant proteins are mechanistically similar. Hence, glycine residues may optimize DNA-protein contacts. The defects conferred by substitutions for proline residues appear to be fundamentally different. The properties of the mutant particles along with the atomic structure of the virion suggest that the proline residues may act to guide the packaged DNA to the adjacent fivefold related asymmetric unit, thus preventing a chaotic packaging arrangement.