Site-directed mutation affecting polyomavirus capsid self-assembly in vitro

Nonequivalent bonding of identical protein subunits occurs in the polyomavirus capsid were identical pentameric capsomeres occupy both hexavalent and pentavalent positions in the icosahedral surface lattice. The polyomavirus major capsid protein VP1, purified after expression of the recombinant gene in Escherichia coli, has been isolated as capsomeres that self-assemble into capsid-like structures in vitro. The ability to switch bonding specificity in different symmetry environments therefore must be intrinsic to the VP1 molecule. In vitro self-assembly provides an assay for VP1 mutations affecting capsomere and capsid formation. We report here that a directed mutation in the VP1 expression vector, leading to a protein truncated at the carboxy terminus, results in a mutant VP1 that forms capsomeres, but not capsids, in the in vitro assembly assay. The carboxy terminus of VP1 therefore appears to be involved in the specific bonding responsible for the non-equivalent association of capsomeres.     

Polyoma virus capsid structure at 22.5 A resolution

X-ray diffraction data from polyoma capsid crystals were phased by refinement of low-resolution starting models to obtain a self-consistent structural solution. The unexpected result that the hexavalent morphological unit is a pentamer shows that specificity of bonding is not conserved among the protein subunits in the icosahedrally symmetric capsid.     

Inside polyomavirus at 25-A resolution.

Empty capsids and complete virions of polyomavirus crystallize isomorphously. Here we use difference Fourier analysis of X-ray diffraction data at 25-A resolution from these crystals to obtain an electron-density map of the inside of the virion. The polyomavirus capsid is built from 72 pentamers of VP1 that form three different types of connections in the T = 7d icosahedral surface lattice. Self-assembly of purified recombinant VP1 into capsid-like aggregates has shown that switching of the bonding specificity to form the unanticipated non-equivalent connections is an inherent property of the VP1 pentamers. Our map of the inside of the virion displays 72 prongs of electron density extending from the core into the axial cavities of the VP1 pentamers. We identify these prongs with the VP2 and VP3 molecules, which may function to guide the assembly of the highly ordered capsid on the nucleohistone core. The atomic structure of the closely related simian virus-40 capsid has been determined from the high-resolution diffraction data. Our polyomavirus map, calculated using all the low-resolution diffraction data, shows no indication of regular order inside the spherical core.     

Three-dimensional structure of the wild-type RHDV

The three-dimensional (3D) structure of the wild-type rabbit hemorrhagic disease virus (RHDV) has been determined to a resolution of 3.2 nm by electron cryomicroscopy and computer image reconstruction techniques. The 3D density map exhibits characteristic structural features of a calicivirus: a T=3 icosahedral capsid with 90 arch-like capsomeres at the icosahedral and local 2-fold axes and 32 large surface hollows at the icosahedral 5- and 3-fold axes. This result confirms that the RHDV isolated in China is a member of the Caliciviridae family. A rather continuous capsid shell was found without channels. However, our RHDV structure also reveals some distinct structural characteristics not observed in other caliciviruses, including interconnected capsomeres and the lack of protuberance on the base of each of the surface hollows. Two types of particles were identified with similar outer capsid structure but different density distributions inside the capsid shells, which could not be distinguished by conventional negative staining electron microscopy. As the genomic and subgenomic RNAs are both packaged into particles for RHDV, we suggest that the two types of particles identified correspond to those containing either the genomic or subgenomic RNAs, respectively.     

蛋白亚基局部相互作用模拟构筑二十面体病毒衣壳

二十面体病毒衣壳结构蛋白具有不同的构象。装配过程中,正在附着的蛋白亚基构象与位置在先前蛋白亚基构象的指令下,发生相应的调整后装配到衣壳骨架上。局部相互作用指导下的装配反复进行,最终形成规整的二十面体病毒衣壳的立体结构。对T=1、3、4、7的病毒衣壳,分别建立了蛋白亚基构象局部相互作用的连接方式与增长方式,并构筑了T=4、7的立体模型。     

多瘤病毒的培养特性及血清抗体的检查

多瘤病毒最适宜的培养条件为接种病毒吸附1.5h,培养第4天换液1次,用无牛血清维持液培养12天,其血凝素达高峰。当培养物出现血凝素时,即有细胞内抗原的存在。应用血凝抑制试验(HI)和酶免疫法(EIA)两种方法进行对比性试验,检查实验感染多瘤病毒的10只SPF小鼠和192只普通小鼠血清多瘤病毒抗体的出现,实验结果表明HI较EIA敏感。多瘤病毒存在于我国普通饲养的实验小鼠群中。     

二十面体病毒衣壳自组装的热力学参数

球状病毒衣壳采用二十面体对称。本文就二十面体病毒蛋白质骨架的自组装提出一个统计热力学模型。统计结果表明病毒衣壳二十面体对称不是自由能最小化的结果，而是衣壳内部蛋白结构参数最优化的结果。     

Image reconstructions of helical assemblies of the HIV-1 CA protein

The type 1 human immunodeficiency virus (HIV-1) contains a conical capsid comprising approximately 1,500 CA protein subunits, which organizes the viral RNA genome for uncoating and replication in a new host cell. In vitro, CA spontaneously assembles into helical tubes and cones that resemble authentic viral capsids. Here we describe electron cryo-microscopy and image reconstructions of CA tubes from six different helical families. In spite of their polymorphism, all tubes are composed of hexameric rings of CA arranged with approximate local p6 lattice symmetry. Crystal structures of the two CA domains were 'docked' into the reconstructed density, which showed that the amino-terminal domains form the hexameric rings and the carboxy-terminal dimerization domains connect each ring to six neighbours. We propose a molecular model for the HIV-1 capsid that follows the principles of a fullerene cone, in which the body of the cone is composed of curved hexagonal arrays of CA rings and the ends are closed by inclusion of 12 pentagonal 'defects'.     

Self-assembly of regular hollow icosahedra in salt-free catanionic solutions

Self-assembled structures having a regular hollow icosahedral form (such as those observed for proteins of virus capsids) can occur as a result of biomineralization processes, but are extremely rare in mineral crystallites. Compact icosahedra made from a boron oxide have been reported, but equivalent structures made of synthetic organic components such as surfactants have not hitherto been observed. It is, however, well known that lipids, as well as mixtures of anionic and cationic single chain surfactants, can readily form bilayers that can adopt a variety of distinct geometric forms: they can fold into soft vesicles or random bilayers (the so-called sponge phase) or form ordered stacks of flat or undulating membranes. Here we show that in salt-free mixtures of anionic and cationic surfactants, such bilayers can self-assemble into hollow aggregates with a regular icosahedral shape. These aggregates are stabilized by the presence of pores located at the vertices of the icosahedra. The resulting structures have a size of about one micrometre and mass of about 1010 daltons, making them larger than any known icosahedral protein assembly or virus capsid. We expect the combination of wall rigidity and holes at vertices of these icosahedral aggregates to be of practical value for controlled drug or DNA release.     

The molecular organization of cypovirus polyhedra

Cypoviruses and baculoviruses are notoriously difficult to eradicate because the virus particles are embedded in micrometre-sized protein crystals called polyhedra. The remarkable stability of polyhedra means that, like bacterial spores, these insect viruses remain infectious for years in soil. The environmental persistence of polyhedra is the cause of significant losses in silkworm cocoon harvests but has also been exploited against pests in biological alternatives to chemical insecticides. Although polyhedra have been extensively characterized since the early 1900s, their atomic organization remains elusive. Here we describe the 2 A crystal structure of both recombinant and infectious silkworm cypovirus polyhedra determined using crystals 5-12 micrometres in diameter purified from insect cells. These are the smallest crystals yet used for de novo X-ray protein structure determination. We found that polyhedra are made of trimers of the viral polyhedrin protein and contain nucleotides. Although the shape of these building blocks is reminiscent of some capsid trimers, polyhedrin has a new fold and has evolved to assemble in vivo into three-dimensional cubic crystals rather than icosahedral shells. The polyhedrin trimers are extensively cross-linked in polyhedra by non-covalent interactions and pack with an exquisite molecular complementarity similar to that of antigen-antibody complexes. The resulting ultrastable and sealed crystals shield the virus particles from environmental damage. The structure suggests that polyhedra can serve as the basis for the development of robust and versatile nanoparticles for biotechnological applications such as microarrays and biopesticides.     

Membrane structure and interactions with protein and DNA in bacteriophage PRD1

Membranes are essential for selectively controlling the passage of molecules in and out of cells and mediating the response of cells to their environment. Biological membranes and their associated proteins present considerable difficulties for structural analysis. Although enveloped viruses have been imaged at about 9 A resolution by cryo-electron microscopy and image reconstruction, no detailed crystallographic structure of a membrane system has been described. The structure of the bacteriophage PRD1 particle, determined by X-ray crystallography at about 4 A resolution, allows the first detailed analysis of a membrane-containing virus. The architecture of the viral capsid and its implications for virus assembly are presented in the accompanying paper. Here we show that the electron density also reveals the icosahedral lipid bilayer, beneath the protein capsid, enveloping the viral DNA. The viral membrane contains about 26,000 lipid molecules asymmetrically distributed between the membrane leaflets. The inner leaflet is composed predominantly of zwitterionic phosphatidylethanolamine molecules, facilitating a very close interaction with the viral DNA, which we estimate to be packaged to a pressure of about 45 atm, factors that are likely to be important during membrane-mediated DNA translocation into the host cell. In contrast, the outer leaflet is enriched in phosphatidylglycerol and cardiolipin, which show a marked lateral segregation within the icosahedral asymmetric unit. In addition, the lipid headgroups show a surprising degree of order.     

Atomic-level modelling of the HIV capsid

The mature capsids of human immunodeficiency virus type 1 (HIV-1) and other retroviruses are fullerene shells, composed of the viral CA protein, that enclose the viral genome and facilitate its delivery into new host cells. Retroviral CA proteins contain independently folded amino (N)- and carboxy (C)-terminal domains (NTD and CTD) that are connected by a flexible linker. The NTD forms either hexameric or pentameric rings, whereas the CTD forms symmetric homodimers that connect the rings into a hexagonal lattice. We previously used a disulphide crosslinking strategy to enable isolation and crystallization of soluble HIV-1 CA hexamers. Here we use the same approach to solve the X-ray structure of the HIV-1 CA pentamer at 2.5?? resolution. Two mutant CA proteins with engineered disulphides at different positions (P17C/T19C and N21C/A22C) converged onto the same quaternary structure, indicating that the disulphide-crosslinked proteins recapitulate the structure of the native pentamer. Assembly of the quasi-equivalent hexamers and pentamers requires remarkably subtle rearrangements in subunit interactions, and appears to be controlled by an electrostatic switch that favours hexamers over pentamers. This study completes the gallery of substructures describing the components of the HIV-1 capsid and enables atomic-level modelling of the complete capsid. Rigid-body rotations around two assembly interfaces appear sufficient to generate the full range of continuously varying lattice curvature in the fullerene cone.     

Transmission of the polyoma virus middle T gene as the oncogene of a murine retrovirus

Polyoma virus is a papovavirus that productively infects mouse cells. In cells of other species, such as rat cells, polyoma virus is virtually unable to replicate, and a small proportion of infected cells become stably transformed. The ability of polyoma virus to transform infected cells is determined by genes that encode the large, middle and small T antigens and which are found in the early region of the virus genome. We have inserted the transforming region of polyoma virus into a murine leukaemia virus (MLV) vector, to generate a replication-defective transforming retrovirus which for the first time allows efficient transformation of mouse cells by the polyoma virus middle T gene. During the life cycle of this recombinant virus the intervening sequence present in the original polyoma virus middle T gene was removed. The recombinant virus that we have constructed is analogous to other acutely transforming retroviruses, and demonstrates that the polyoma middle T gene is a dominant transforming oncogene.     

Experimental measurement of valence electron concentration of icosahedral AlPdMn quasicrystal

The valence charge density distribution for the icosahedral AlPdMn (i-AlPdMn) quasicrystal was obtained with the structure factors of the nine strongest symmetry inequivalent reflections, which were refined by using the quantitative convergent beam electron diffraction (QCBED) technique. It shows that the bonding charge is localized. The enhanced charge density in the middle of the aluminum-transition-metal (Al-TM) bond shown in the valence charge density distribution is the characteristic of covalent bonding. Assuming that the shape of an atom is a sphere with covalent radius, the number of electrons that each atom gains or loses in 55 different pseudo-Mackay clusters (PMCs) was calculated based on the obtained valence charge density distribution. It indicates that almost all the atoms lose electrons except a few Pd atoms that are in some particular shells. It also shows that the atoms of an identified element could have different valences because of chemically and/or structurally different local environments in which the atoms situate. Regardless of the topology and chemical occupancy, the number of valence electrons per atom in a cluster is close to 1.69. This strongly suggests that the pseudo-Mackay clusters are stabilized at a certain electron concentration. Biography: YU Fengmei (1965–), female, Professor, Ph.D., research direction: quasicrystal physics.     

Backbone structure of the infectious epsilon15 virus capsid revealed by electron cryomicroscopy

A half-century after the determination of the first three-dimensional crystal structure of a protein, more than 40,000 structures ranging from single polypeptides to large assemblies have been reported. The challenge for crystallographers, however, remains the growing of a diffracting crystal. Here we report the 4.5-A resolution structure of a 22-MDa macromolecular assembly, the capsid of the infectious epsilon15 (epsilon15) particle, by single-particle electron cryomicroscopy. From this density map we constructed a complete backbone trace of its major capsid protein, gene product 7 (gp7). The structure reveals a similar protein architecture to that of other tailed double-stranded DNA viruses, even in the absence of detectable sequence similarity. However, the connectivity of the secondary structure elements (topology) in gp7 is unique. Protruding densities are observed around the two-fold axes that cannot be accounted for by gp7. A subsequent proteomic analysis of the whole virus identifies these densities as gp10, a 12-kDa protein. Its structure, location and high binding affinity to the capsid indicate that the gp10 dimer functions as a molecular staple between neighbouring capsomeres to ensure the particle's stability. Beyond epsilon15, this method potentially offers a new approach for modelling the backbone conformations of the protein subunits in other macromolecular assemblies at near-native solution states.     

Capsid modification of adeno-associated virus and tumor targeting gene therapy

Targeting is critical for successful tumor gene therapy. The adeno-associated virus （AAV） has aroused wide concern due to its excellent advantages over other viral vectors in gene therapy. AAV has a broad infection spectrum, which also results in poor specificity towards tissues or cells and low transduction efficiency. Therefore, it is imperative to improve target and transduction efficiency in AAV-mediated gene therapy. Up to now, researchers have developed many strategies to modify AAV capsids for im- proving targeting or retargeting only desired cells. These strategies include not only traditional chemical modification, phage display technology, modification of AAV capsid genome, chimeric vectors and so on, but also many novel strategies involved in marker rescue strategy, direct evolution of capsid proteins, direct display random peptides on AAV capsid, AAVP （AAV-Phage）, and etc. This review will summarize the advances of researches on the capsid modification of AAV to target malignant cells.     

采用超声组装与滚压工艺制备铝–碳纳米管复合材料

This study introduced a novel fabrication of aluminum–carbon nanotube (CNT) composites by employing bulk acoustic waves and accumulative roll bonding (ARB). In this method, CNT particles were aligned using ultrasonic standing wave in an aqueous media, and the arrayed particles were precipitated on the aluminum plate substrate. Then, the plates rolled on each other through the ARB process with four passes. Optical and scanning electron micrographs demonstrated the effective aligning of CNTs on the aluminum substrate with a negligible deviation of arrayed CNTs through the ARB process. The X-ray diffraction pattern of the developed composites showed no peaks for carbon and aluminum carbide. In addition, tensile tests showed that the longitudinal strength of the specimens processed with aligned CNTs was significantly greater than that of the specimens with common randomly dispersed particles. The proposed technique is beneficial for the fabrication of Al–CNT composites with directional mechanical strength.     

Structure of epsilon15 bacteriophage reveals genome organization and DNA packaging/injection apparatus

The critical viral components for packaging DNA, recognizing and binding to host cells, and injecting the condensed DNA into the host are organized at a single vertex of many icosahedral viruses. These component structures do not share icosahedral symmetry and cannot be resolved using a conventional icosahedral averaging method. Here we report the structure of the entire infectious Salmonella bacteriophage epsilon15 (ref. 1) determined from single-particle cryo-electron microscopy, without icosahedral averaging. This structure displays not only the icosahedral shell of 60 hexamers and 11 pentamers, but also the non-icosahedral components at one pentameric vertex. The densities at this vertex can be identified as the 12-subunit portal complex sandwiched between an internal cylindrical core and an external tail hub connecting to six projecting trimeric tailspikes. The viral genome is packed as coaxial coils in at least three outer layers with approximately 90 terminal nucleotides extending through the protein core and the portal complex and poised for injection. The shell protein from icosahedral reconstruction at higher resolution exhibits a similar fold to that of other double-stranded DNA viruses including herpesvirus, suggesting a common ancestor among these diverse viruses. The image reconstruction approach should be applicable to studying other biological nanomachines with components of mixed symmetries.