Simian virus 40 VP1 capsid protein forms polymorphic assemblies in vitro

Protein cages, rings and tubes: useful components of future nanodevices?

There is a great deal of interest in the possibility that complex nanoscale devices can be designed and engineered. Such devices will lead to the development of new materials, electronics and smart drugs. Producing complex nanoscale devices, however will present many challenges and the components of such devices will require a number of special features. Devices will be engineered to incorporate desired functionalities but, because of the difficulties of controlling matter precisely at the nanoscale with current technology, the nanodevice components must self-assemble. In addition, nanocomponents that are to have wide applicability in various devices must have enough flexibility to integrate into a large number of potentially very different environments. These challenges are daunting and complex, and artificial nanodevices have not yet been constructed. However, the existence of nanomachines in nature in the form of proteins (eg, enzymes) suggests that they will be possible to produce. As the material from which nature's nanomachines are made, proteins seem ideal to form the basis of engineered components of such nanodevices. Initially, engineering projects may focus on building blocks such as rings, cages and tubes, examples of which exist in nature and may act as a useful start point for modification and further development. This review focuses on the recent research and possible future development of such protein building blocks.

Blueprints for viral capsids in the family of polyomaviridae

In a seminal paper, Caspar and Klug [1962. Physical principles in the construction of regular viruses. Cold Spring Harbor Symp. Quant. Biol. 27, 1-24] derived a family of surface lattices as blueprints for the structural organisation of the protein shells, called viral capsids, which encapsulate and hence protect the viral genome. These lattices schematically encode, and hence predict, the locations of the proteins in the viral capsids. Despite the huge success and numerous applications of this theory in virology, experimental results have provided evidence for the fact that it is too restrictive to describe all known viruses [Casjens, S., 1985. Virus Structure and Assembly. Jones and Bartlett, Boston, MA]. Especially, the family of Polyomaviridae, which contains cancer-causing viruses, falls out of the scope of this theory. In [Twarock, R., 2004. A tiling approach to virus capsid assembly explaining a structural puzzle in virology. J. Theor. Biol. 226, 477], we have shown that a member of the family of Polyomaviridae can be described via an icosahedrally symmetric tiling. We show here that all viruses in this family can be described by tilings with vertices corresponding to subsets of a quasi-lattice that is constructed based on an affine extended Coxeter group, and we use this methodology to derive their coordinates explicitly. Since the particles appear as different subsets of the same quasi-lattice, their relative sizes are predicted by this approach, and there hence exists only one scaling factor that relates the sizes of all particles collectively to their biological counterparts. It is the first mathematical result that provides a common organisational principle for different types of viral particles in the family of Polyomaviridae, and paves the way for modelling Polyomaviridae polymorphism.

Evidence that SV40 VP1-DNA interactions contribute to the assembly of 40-nm spherical viral particles

The simian virus 40 (SV40) particle is mainly composed of the major capsid protein termed VP1. VP1 self-assembles into virus-like particles (VLPs) of approximately 40 nm in diameter when over-expressed in bacteria or in insect cells, but purified VP1 does not form such a structure under physiological conditions, and thus, the mechanism of VP1 assembly is not well understood. Using a highly purified VP1 assembly/disassembly system in vitro, here we provide evidence that DNA is a factor that contributes to VP1 assembly into 40-nm spherical particles. At pH 5, for example, VP1 preferentially assembles into 40-nm particles in the presence of DNA, whereas VP1 assembles into tubular structures in the absence of DNA. Electron microscopic observations revealed that the concentration of DNA and its length are important for the formation of 40-nm particles. In addition, sucrose gradient sedimentation analysis and DNase I-sensitivity assays indicated that DNA of up to 2,000 bp is packaged into the 40-nm particles under the conditions examined. We propose that DNA may facilitate the formation of 40-nm spherical particles by acting as a scaffold that increases the local concentration of VP1 and/or by acting as an allosteric effector that alters the structure of VP1.

Importance of calcium-binding site 2 in simian virus 40 infection

The exposure of molecular signals for simian virus 40 (SV40) cell entry and nuclear entry has been postulated to involve calcium coordination at two sites on the capsid made of Vp1. The role of calcium-binding site 2 in SV40 infection was examined by analyzing four single mutants of site 2, the Glu160Lys, Glu160Arg, Glu157Lys (E157K), and Glu157Arg mutants, and an E157K-E330K combination mutant. The last three mutants were nonviable. All mutants replicated viral DNA normally, and all except the last two produced particles containing all three capsid proteins and viral DNA. The defect of the site 1-site 2 E157K-E330K double mutant implies that at least one of the sites is required for particle assembly in vivo. The nonviable E157K particles, about 10% larger in diameter than the wild type, were able to enter cells but did not lead to T-antigen expression. Cell-internalized E157K DNA effectively coimmunoprecipitated with anti-Vp1 antibody, but little of the DNA did so with anti-Vp3 antibody, and none was detected in anti-importin immunoprecipitate. Yet, a substantial amount of Vp3 was present in anti-Vp1 immune complexes, suggesting that internalized E157K particles are ineffective at exposing Vp3. Our data show that E157K mutant infection is blocked at a stage prior to the interaction of the Vp3 nuclear localization signal with importins, consistent with a role for calcium-binding site 2 in postentry steps leading to the nuclear import of the infecting SV40.

Molecular dissection of ø29 scaffolding protein function in an in vitro assembly system

An in vitro assembly system was developed to study prolate capsid assembly of phage ø29 biochemically, and to identify regions of scaffolding protein required for its functions. The crowding agent polyethylene glycol can induce bacteriophage ø29 monomeric capsid protein and dimeric scaffolding protein to co-assemble to form particles which have the same geometry as either prolate T=3 Q=5 procapsids formed in vivo or previously observed isometric particles. The formation of particles is a scaffolding-dependent reaction. The balance between the fidelity and efficiency of assembly is controlled by the concentration of crowding agent and temperature. The assembly process is salt sensitive, suggesting that the interactions between the scaffolding and coat proteins are electrostatic. Three N-terminal ø29 scaffolding protein deletion mutants, Delta 1-9, Delta 1-15 and Delta 1-22, abolish the assembly activity. Circular dichroism spectra indicate that these N-terminal deletions are accompanied by a loss of helicity. The inability of these proteins to dimerize suggests that the N-terminal region of the scaffolding protein contributes to the dimer interface and maintains the structural integrity of the dimeric protein. Two C-terminal scaffolding protein deletion mutants, Delta 79-97 and Delta 62-97, also fail to promote assembly. However, the secondary structure and the dimerization ability of these mutants are unchanged relative to wild-type, which suggests that the C terminus is the likely site of interaction with the capsid protein.

JC virus minor capsid proteins Vp2 and Vp3 are essential for virus propagation

Virus-encoded capsid proteins play a major role in the life cycles of all viruses. The JC virus capsid is composed of 72 pentamers of the major capsid protein Vp1, with one of the minor coat proteins Vp2 or Vp3 in the center of each pentamer. Vp3 is identical to two-thirds of Vp2, and these proteins share a DNA binding domain, a nuclear localization signal, and a Vp1-interacting domain. We demonstrate here that both the minor proteins and the myristylation site on Vp2 are essential for the viral life cycle, including the proper packaging of its genome.

Generation of virus-like particles consisting of the major capsid protein VP1 of goose hemorrhagic polyomavirus and their application in serological tests

Goose hemorrhagic polyomavirus (GHPV) is the causative agent of hemorrhagic nephritis and enteritis of geese (HNEG), a fatal disease of young geese with high mortality rates. GHPV cannot be efficiently propagated in tissue culture. To provide antigens for diagnostic tests and vaccines, its major structural protein VP1 was recombinantly expressed in Sf9 insect cells and in the yeast Saccharomyces cerevisiae. As demonstrated by density gradient centrifugation and electron microscopy, GHPV-VP1 expressed in insect cells formed virus-like particles (VLPs) with a diameter of 45 nm indistinguishable from infectious polyomavirus particles. However, efficiency of VLP formation was low as compared to the monkey polyomavirus SV-40-VP1. In yeast cells, GHPV-VP1 alone formed smaller VLPs, 20 nm in diameter. Remarkably, co-expression of GHPV-VP2 resulted in VLPs with a diameter of 45 nm. All three types of GHPV-VLPs were shown to hemagglutinate chicken erythrocytes. ELISA and hemagglutination inhibition tests using the VLPs as antigen detected GHPV-specific antibodies in up to 85.7% of sera derived from flocks with HNEG but in none of the sera of a clinically healthy flock. However, GHPV-specific antibodies were also detected in sera from two other flocks without HNEG indicating a broad distribution of GHPV due to subclinical or unrecognised infections.

The VP2/VP3 Minor Capsid Protein of Simian Virus 40 Promotes the in Vitro Assembly of the Major Capsid Protein VP1 into Particles

The SV40 capsid is composed primarily of 72 pentamers of the VP1 major capsid protein. Although the capsid also contains the minor capsid protein VP2 and its amino-terminally truncated form VP3, their roles in capsid assembly remain unknown. An in vitro assembly system was used to investigate the role of VP2 in the assembly of recombinant VP1 pentamers. Under physiological salt and pH conditions, VP1 alone remained dissociated, and at pH 5.0, it assembled into tubular structures. A stoichiometric amount of VP2 allowed the assembly of VP1 pentamers into spherical particles in a pH range of 7.0 to 4.0. Electron microscopy observation, sucrose gradient sedimentation analysis, and antibody accessibility tests showed that VP2 is incorporated into VP1 particles. The functional domains of VP2 important for VP1 binding and for enhancing VP1 assembly were further explored with a series of VP2 deletion mutants. VP3 also enhanced VP1 assembly, and a region common to VP2 and VP3 (amino acids 119-272) was required to promote VP1 pentamer assembly. These results are relevant for controlling recombinant capsid formation in vitro, which is potentially useful for the in vitro development of SV40 virus vectors.

Size and position of truncations in the carboxy-terminal region of major capsid protein VP1 of hamster polyomavirus expressed in yeast determine its assembly capacity

The hamster polyomavirus major capsid protein VP1 was modified in its carboxy-terminal region by consecutive truncations and single amino acid exchanges. The ability of yeast-expressed VP1 variants to form virus-like particles (VLPs) strongly depended on the size and position of the truncation. VP1 variants lacking 21, 69, and 79 amino acid (aa) residues in their carboxy-terminal region efficiently formed VLPs similar to those formed by the unmodified VP1 (diameter 40-45 nm). In contrast, VP1 derivatives with carboxy-terminal truncations of 35 to 56 aa residues failed to form VLPs. VP1 mutants with a single A336G aa exchange or internal deletions of aa 335 to aa 346 and aa 335 to aa 363 resulted in the formation of VLPs of a smaller size (diameter 20 nm). These data indicate that certain parts of the carboxy-terminal region of VP1 are not essential for pentamer-pentamer interactions in the capsid, at least in the yeast expression system used.

Elasticity theory and shape transitions of viral shells

Recently, continuum elasticity theory has been applied to explain the shape transition of icosahedral viral capsids--single-protein-thick crystalline shells--from spherical to "buckled" or faceted as their radius increases through a critical value determined by the competition between stretching and bending energies of a closed two-dimensional (2D) elastic network. In the present work we generalize this approach to capsids with nonicosahedral symmetries, e.g., spherocylindrical and conical shells. One key additional physical ingredient is the role played by nonzero spontaneous curvature. Another is associated with the special way in which the energy of the 12 topologically required fivefold sites depends on the "background" local curvature of the shell in which they are embedded. Systematic evaluation of these contributions leads to a shape "phase" diagram in which transitions are observed from icosahedral to spherocylindrical capsids as a function of the ratio of stretching to bending energies and of the spontaneous curvature of the 2D protein network. We find that the transition from icosahedral to spherocylindrical symmetry is continuous or weakly first order near the onset of buckling, leading to extensive shape degeneracy. These results are discussed in the context of experimentally observed variations in the shapes of a variety of viral capsids.

Assembly models for Papovaviridae based on tiling theory

A vital constituent of a virus is its protein shell, called the viral capsid, that encapsulates and hence provides protection for the viral genome. Assembly models are developed for viral capsids built from protein building blocks that can assume different local bonding structures in the capsid. This situation occurs, for example, for viruses in the family of Papovaviridae, which are linked to cancer and are hence of particular interest for the health sector. More specifically, the viral capsids of the (pseudo-) T = 7 particles in this family consist of pentamers that exhibit two different types of bonding structures. While this scenario cannot be described mathematically in terms of Caspar-Klug theory (Caspar D L D and Klug A 1962 Cold Spring Harbor Symp. Quant. Biol. 27 1), it can be modelled via tiling theory (Twarock R 2004 J. Theor. Biol. 226 477). The latter is used to encode the local bonding environment of the building blocks in a combinatorial structure, called the assembly tree, which is a basic ingredient in the derivation of assembly models for Papovaviridae along the lines of the equilibrium approach of Zlotnick (Zlotnick A 1994 J. Mol. Biol. 241 59). A phase space formalism is introduced to characterize the changes in the assembly pathways and intermediates triggered by the variations in the association energies characterizing the bonds between the building blocks in the capsid. Furthermore, the assembly pathways and concentrations of the statistically dominant assembly intermediates are determined. The example of Simian virus 40 is discussed in detail.

Structure and assembly of a T=1 virus-like particle in BK polyomavirus

In polyomaviruses the pentameric capsomers are interlinked by the long C-terminal arm of the structural protein VP1. The T=7 icosahedral structure of these viruses is possible due to an intriguing adaptability of this linker arm to the different local environments in the capsid. To explore the assembly process, we have compared the structure of two virus-like particles (VLPs) formed, as we found, in a calcium-dependent manner by the VP1 protein of human polyomavirus BK. The structures were determined using electron cryomicroscopy (cryo-EM), and the three-dimensional reconstructions were interpreted by atomic modeling. In the small VP1 particle, 26.4 nm in diameter, the pentameric capsomers form an icosahedral T=1 surface lattice with meeting densities at the threefold axes that interlinked three capsomers. In the larger particle, 50.6 nm in diameter, the capsomers form a T=7 icosahedral shell with three unique contacts. A folding model of the BKV VP1 protein was obtained by alignment with the VP1 protein of simian virus 40 (SV40). The model fitted well into the cryo-EM density of the T=7 particle. However, residues 297 to 362 of the C-terminal arm had to be remodeled to accommodate the higher curvature of the T=1 particle. The loops, before and after the C-terminal short helix, were shown to provide the hinges that allowed curvature variation in the particle shell. The meeting densities seen at the threefold axes in the T=1 particle were consistent with the triple-helix interlinking contact at the local threefold axes in the T=7 structure.

Simian virus 40 persistent infection in long-term immortalized human fibroblast cell lines

Episomal simian virus 40 (SV40) DNA was detected in various SV40-immortalized human fibroblast cell lines, without rearrangements or mutations. In these cells, SV40 established a persistent infection with the release of a viral progeny. However, electron microscopy analysis showed that virions are morphologically altered, whereas infectivity assay indicated that viral production was hampered. The data suggest that in SV40-infected human fibroblasts, some cells support a complete SV40 productive cycle, whereas other cells resist to the SV40 infection. This sort of "balance" observed within the same human fibroblast population may be responsible for the semipermissiveness of these cells to SV40 infection.

Virus-like particles: models for assembly studies and foreign epitope carriers

Virus‐like particles (VLPs), formed by the structural elements of viruses, have received considerable attention over the past two decades. The number of reports on newly obtained VLPs has grown proportionally with the systems developed for the expression of these particles. The chapter outlines the recent achievements in two important fields of research brought about by the availability of VLPs produced in a foreign host. These are: (1) The requirements for VLP assembly and (2) the use of VLPs as carriers for foreign epitopes. VLP technology is a rapidly advancing domain of molecular and structural biology. Extensive progress in VLP studies was achieved as the insect cell based protein production system was developed. This baculovirus expression system has many advantages for the synthesis of viral structural proteins resulting in the formation of VLPs. It allows production of large amounts of correctly folded proteins while also providing cell membranes that can serve as structural elements for enveloped viruses. These features give us the opportunity to gain insights into the interactions and requirements accompanying VLP formation that are similar to the assembly events occurring in mammalian cells. Other encouraging elements are the ability to easily scale up the system and the simplicity of purification of the assembled VLPs. The growing number of VLPs carrying foreign protein fragments on their surface and studies on the successful assembly of these chimeric molecules is a promising avenue towards the development of a new technology, in which the newly designed VLPs will be directed to particular mammalian cell types by exposing specific binding domains. The progress made in modeling the surface of VLPs makes them to date the best candidates for the design of delivery systems that can efficiently reach their targets.