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1.  Structure and Assembly of a T=1 Virus-Like Particle in BK Polyomavirus 
Journal of Virology  2005;79(9):5337-5345.
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.
doi:10.1128/JVI.79.9.5337-5345.2005
PMCID: PMC1082729  PMID: 15827148
2.  Structure of Epsilon15 Phage Reveals Organization of Genome and DNA Packaging/Injection Apparatus 
Nature  2006;439(7076):612-616.
Using single particle electron cryomicroscopy that does not impose icosahedral averaging, we determined the structure of the entire infectious Salmonella phage Epsilon151, including both icosahedral and non-icosahedral components. At least three layers of condensed viral DNA were observed to pack in coaxial coils with local 25 Å hexagonal inter-strand spacing. At one of the five-fold vertices, a portal complex with twelve subunits replaces a capsid pentamer. A tail hub with six projecting trimeric tailspikes sits on the external face of the portal. Below the portal is a cylindrical protein core. An extended shaft of density fills the central channel of the protein core and the portal complex and appears to consist of about 90 nucleotides at the terminus of the packaged DNA poised for injection. Using an icosahedral symmetry imposed reconstruction, the fold of the capsid shell protein is seen to resemble the capsid protein fold of other tailed double-stranded DNA phages2–5 and human herpesvirus6. These common structural features suggest a common evolutionary origin among these viruses.
doi:10.1038/nature04487
PMCID: PMC1559657  PMID: 16452981
3.  Nitrogen-incorporated ultrananocrystalline diamond and multi-layer-graphene-like hybrid carbon films 
Scientific Reports  2014;4:4531.
Nitrogen-incorporated ultrananocrystalline diamond (N-UNCD) and multi-layer-graphene-like hybrid carbon films have been synthesized by microwave plasma enhanced chemical vapor deposition (MPECVD) on oxidized silicon which is pre-seeded with diamond nanoparticles. MPECVD of N-UNCD on nanodiamond seeds produces a base layer, from which carbon structures nucleate and grow perpendicularly to form standing carbon platelets. High-resolution transmission electron microscopy and Raman scattering measurements reveal that these carbon platelets are comprised of ultrananocrystalline diamond embedded in multilayer-graphene-like carbon structures. The hybrid carbon films are of low electrical resistivity. UNCD grains in the N-UNCD base layer and the hybrid carbon platelets serve as high-density diamond nuclei for the deposition of an electrically insulating UNCD film on it. Biocompatible carbon-based heaters made of low-resistivity hybrid carbon heaters encapsulated by insulating UNCD for possible electrosurgical applications have been demonstrated.
doi:10.1038/srep04531
PMCID: PMC3970192  PMID: 24681781
4.  Structures of Hepatitis B Virus Cores Presenting a Model Epitope and Their Complexes with Antibodies 
Journal of Molecular Biology  2012;423(1):63-78.
The core shell of hepatitis B virus is a potent immune stimulator, giving a strong neutralizing immune response to foreign epitopes inserted at the immunodominant region, located at the tips of spikes on the exterior of the shell. Here, we analyze structures of core shells with a model epitope inserted at two alternative positions in the immunodominant region. Recombinantly expressed core protein assembles into T = 3 and T = 4 icosahedral shells, and atomic coordinates are available for the T = 4 shell. Since the modified protein assembles predominantly into T = 3 shells, a quasi-atomic model of the native T = 3 shell was made. The spikes in this T = 3 structure resemble those in T = 4 shells crystallized from expressed protein. However, the spikes in the modified shells exhibit an altered conformation, similar to the DNA containing shells in virions. Both constructs allow full access of antibodies to the foreign epitope, DPAFR from the preS1 region of hepatitis B virus surface antigen. However, one induces a 10-fold weaker immune response when injected into mice. In this construct, the epitope is less constrained by the flanking linker regions and is positioned so that the symmetry of the shell causes pairs of epitopes to come close enough to interfere with one another. In the other construct, the epitope mimics the native epitope conformation and position. The interaction of native core shells with an antibody specific to the immunodominant epitope is compared to the constructs with an antibody against the foreign epitope. Our findings have implications for the design of vaccines based on virus-like particles.
Graphical Abstract
Highlights
► The HBV core shell is highly immunogenic and is being used as a vaccine carrier. ► Insertion of model epitopes into the immunodominant region changes the structure. ► Alternative positions of an epitope give different structures and immunogenicity. ► The structural differences lead to different labeling with antibody fragments. ► We conclude that three‐dimensional structural analysis will be important in vaccine design.
doi:10.1016/j.jmb.2012.06.032
PMCID: PMC3465560  PMID: 22750730
EM, electron microscopy; Fab, fragment of antibody; Fv, fragment of antibody variable region; HBV, hepatitis B virus; L1, linker 1; L2, linker 2; MIR, major immunodominant region; PBS, phosphate-buffered saline; 3D, three‐dimensional; cryomicroscopy; image processing; vaccine carriers; virus-like particles; improved immunogenicity
5.  Structure-based engineering of papillomavirus major capsid L1: controlling particle assembly 
Virology Journal  2007;4:3.
The outer shell of the papillomavirus particle is comprised of 72 pentamers of the major capsid L1 protein arranged on a T = 7 icosahedral lattice. The recombinant L1 can form T = 7 virus-like particles in vitro. The crystal structure of a T = 7 papilloma virion has not yet been determined; however, the crystal structure of a T = 1 particle containing 12 pentamers is known. The T = 1 structure reveals that helix-helix interactions, through three helices–h2, h3, and h4–near the C-terminus of L1, mediate the inter-pentameric bonding that is responsible for T = 1 assembly. Based on the T = 1 crystal structure, we have generated a set of internal deletions to test the role of the three C-terminal helices in T = 7 assembly. We have demonstrated that the h2, h3, and h4 near the C-terminal end of L1 are important for the L1 structure and particle assembly. In particular, we found that h2 and h3 are essential for L1 folding and pentamer formation, whereas h4 is indispensable for the assembly of not only T1, but also of the T7 virus-like particle.
doi:10.1186/1743-422X-4-3
PMCID: PMC1781933  PMID: 17210082
6.  African Swine Fever Virus Is Enveloped by a Two-Membraned Collapsed Cisterna Derived from the Endoplasmic Reticulum 
Journal of Virology  1998;72(11):8988-9001.
During the cytoplasmic maturation of African swine fever virus (ASFV) within the viral factories, the DNA-containing core becomes wrapped by two shells, an inner lipid envelope and an outer icosahedral capsid. We have previously shown that the inner envelope is derived from precursor membrane-like structures on which the capsid layer is progressively assembled. In the present work, we analyzed the origin of these viral membranes and the mechanism of envelopment of ASFV. Electron microscopy studies on permeabilized infected cells revealed the presence of two tightly apposed membranes within the precursor membranous structures as well as polyhedral assembling particles. Both membranes could be detached after digestion of intracellular virions with proteinase K. Importantly, membrane loop structures were observed at the ends of open intermediates, which suggests that the inner envelope is derived from a membrane cisterna. Ultraestructural and immunocytochemical analyses showed a close association and even direct continuities between the endoplasmic reticulum (ER) and assembling virus particles at the bordering areas of the viral factories. Such interactions become evident with an ASFV recombinant that inducibly expresses the major capsid protein p72. In the absence of the inducer, viral morphogenesis was arrested at a stage at which partially and fully collapsed ER cisternae enwrapped the core material. Together, these results indicate that ASFV, like the poxviruses, becomes engulfed by a two-membraned collapsed cisterna derived from the ER.
PMCID: PMC110316  PMID: 9765444
7.  In Vitro-Assembled Alphavirus Core-Like Particles Maintain a Structure Similar to That of Nucleocapsid Cores in Mature Virus 
Journal of Virology  2002;76(21):11128-11132.
In vitro-assembled core-like particles produced from alphavirus capsid protein and nucleic acid were studied by cryoelectron microscopy. These particles were found to have a diameter of 420 Å with 240 copies of the capsid protein arranged in a T=4 icosahedral surface lattice, similar to the nucleocapsid core in mature virions. However, when the particles were subjected to gentle purification procedures, they were damaged, preventing generation of reliable structural information. Similarly, purified nucleocapsid cores isolated from virus-infected cells or from mature virus particles were also of poor quality. This suggested that in the absence of membrane and glycoproteins, nucleocapsid core particles are fragile, lacking accurate icosahedral symmetry.
doi:10.1128/JVI.76.21.11128-11132.2002
PMCID: PMC136650  PMID: 12368355
8.  Intermolecular Interactions in a Two-Layered Viral Capsid That Requires a Complex Symmetry Mismatch 
Journal of Virology  2003;77(20):11114-11124.
The surface of the bluetongue virus core forms a T=13 quasiequivalent icosahedral protein shell with 260 trimers of a single gene product: VP7 protein. Underneath is a smooth layer, made up of VP3 protein, which appears to guide and nucleate the assembly of VP7 trimers. The contacts between the two shells are extensive but nonspecific, and construction of the T=13 icosahedral shell requires polymorphism in the association of the VP7 subunits, each of which has two domains that contribute to trimer formation. We used structural and relative sequence information to guide an investigation of how such a complex structure is achieved during virus assembly and what residues are required to form a stable capsid. Fifteen single or multiple site-specific substitution mutations were introduced into the helical domain of VP7, which is closely associated with the VP3 layer, and the effects on capsid assembly were analyzed. Our data show that both the position and the nature of single residues are critical for the attachment of VP7 to VP3 and that formation of a stable VP7 lattice is not the automatic consequence of trimer formation.
doi:10.1128/JVI.77.20.11114-11124.2003
PMCID: PMC224973  PMID: 14512559
9.  Cryo-electron microscopy structure of yeast Ty retrotransposon virus-like particles. 
Journal of Virology  1997;71(9):6863-6868.
The virus-like particles (VLPs) produced by the yeast retrotransposon Ty1 are functionally related to retroviral cores. These particles are unusual in that they have variable radif. A paired mass-radius analysis of VLPs by scanning transmission electron microscopy showed that many of these particles form an icosahedral T-number series. Three-dimensional reconstruction to 38-A resolution from cryo-electron micrographs of T = 3 and T = 4 shells revealed that the single structural protein encoded by the TYA gene assembles into spiky shells from trimeric units.
PMCID: PMC191967  PMID: 9261411
10.  Lysine-functionalized nanodiamonds: synthesis, physiochemical characterization, and nucleic acid binding studies 
Purpose:
Detonation nanodiamonds (NDs) are carbon-based nanomaterials that, because of their size (4–5 nm), stable inert core, alterable surface chemistry, fluorescence, and biocompatibility, are emerging as bioimaging agents and promising tools for the delivery of biochemical molecules into cellular systems. However, diamond particles possess a strong propensity to aggregate in liquid formulation media, restricting their applicability in biomedical sciences. Here, the authors describe the covalent functionalization of NDs with lysine in an attempt to develop nanoparticles able to act as suitable nonviral vectors for transferring genetic materials across cellular membranes.
Methods:
NDs were oxidized and functionalized by binding lysine moieties attached to a three-carbon-length linker (1,3-diaminopropane) to their surfaces through amide bonds. Raman and Fourier transform infrared spectroscopy, zeta potential measurement, dynamic light scattering, atomic force microscopic imaging, and thermogravimetric analysis were used to characterize the lysine-functionalized NDs. Finally, the ability of the functionalized diamonds to bind plasmid DNA and small interfering RNA was investigated by gel electrophoresis assay and through size and zeta potential measurements.
Results:
NDs were successfully functionalized with the lysine linker, producing surface loading of 1.7 mmol g−1 of ND. These modified NDs formed highly stable aqueous dispersions with a zeta potential of 49 mV and particle size of approximately 20 nm. The functionalized NDs were found to be able to bind plasmid DNA and small interfering RNA by forming nanosized “diamoplexes”.
Conclusion:
The lysine-substituted ND particles generated in this study exhibit stable aqueous formulations and show potential for use as carriers for genetic materials.
doi:10.2147/IJN.S32877
PMCID: PMC3418073  PMID: 22904623
disaggregation; spectroscopy; dispersion; electrophoresis; size; zeta potential
11.  Reconstructing virus structures from nanometer to near-atomic resolutions with cryo-electron microscopy and tomography 
The past few decades have seen tremendous advances in single particle electron cryo-microscopy (cryo-EM). The field has matured to the point that near-atomic resolution density maps can be generated for icosahedral viruses without the need for crystallization. In parallel, substantial progress has been made in determining the structures of non-icosahedrally arranged proteins in viruses by employing either single particle cryo-EM or cryo-electron tomography (cryo-ET). Implicit in this course has been the availability of a new generation of electron cryo-microscopes and the development of the computational tools that are essential for generating these maps and models. This methodology has enabled structural biologists to analyze structures in increasing detail for virus particles that are in different morphogenetic and biochemical states. Furthermore, electron imaging of frozen, hydrated cells, in the process of being infected by viruses, has also opened up a new avenue for studying virus structures “in situ”. Here we present the common techniques used to acquire and process cryo-EM and cryo-ET data and discuss their implications for structural virology both now and in the future.
doi:10.1007/978-1-4614-0980-9_4
PMCID: PMC3954858  PMID: 22297510
Microscopy; Cryo-EM; Cryo-ET; Subnanometer Resolution; Near-Atomic Resolution; Modeling; Virus Structure
12.  Backbone Model of an Aquareovirus Virion by Cryo-Electron Microscopy and Bioinformatics 
Journal of molecular biology  2009;397(3):852-863.
Grass carp reovirus (GCRV) is a member of the aquareovirus genus in the Reoviridae family and has a capsid with two shells—a transcription-competent core surrounded by a coat. We report a near-atomic-resolution reconstruction of the GCRV virion by cryo-electron microscopy and single-particle reconstruction. A backbone model of the GCRV virion, including seven conformers of the five capsid proteins making up the 1500 molecules in both the core and the coat, was derived using cryo-electron microscopy density-map-constrained homology modeling and refinement. Our structure clearly showed that the amino-terminal segment of core protein VP3B forms an ~120-Å-long α-helix-rich extension bridging across the icosahedral 2-fold-symmetry-related molecular interface. The presence of this unique structure across this interface and the lack of an external cementing molecule at this location in GCRV suggest a stabilizing role of this extended amino-terminal density. Moreover, part of this amino-terminal extension becomes invisible in the reconstruction of transcription-competent core particles, suggesting its involvement in endogenous viral RNA transcription. Our structure of the VP1 turret represents its open state, and comparison with its related structures at the closed state suggests hinge-like domain movements associated with the mRNA-capping machinery. Overall, this first backbone model of an aquareovirus virion provides a wealth of structural information for understanding the structural basis of GCRV assembly and transcription.
doi:10.1016/j.jmb.2009.12.027
PMCID: PMC2900198  PMID: 20036256
aquareovirus; dsRNA virus; backbone model; Reoviridae; cryo-electron microscopy
13.  Atomic Force Microscopy in Imaging of Viruses and Virus-Infected Cells 
Summary: Atomic force microscopy (AFM) can visualize almost everything pertinent to structural virology and at resolutions that approach those for electron microscopy (EM). Membranes have been identified, RNA and DNA have been visualized, and large protein assemblies have been resolved into component substructures. Capsids of icosahedral viruses and the icosahedral capsids of enveloped viruses have been seen at high resolution, in some cases sufficiently high to deduce the arrangement of proteins in the capsomeres as well as the triangulation number (T). Viruses have been recorded budding from infected cells and suffering the consequences of a variety of stresses. Mutant viruses have been examined and phenotypes described. Unusual structural features have appeared, and the unexpectedly great amount of structural nonconformity within populations of particles has been documented. Samples may be imaged in air or in fluids (including culture medium or buffer), in situ on cell surfaces, or after histological procedures. AFM is nonintrusive and nondestructive, and it can be applied to soft biological samples, particularly when the tapping mode is employed. In principle, only a single cell or virion need be imaged to learn of its structure, though normally images of as many as is practical are collected. While lateral resolution, limited by the width of the cantilever tip, is a few nanometers, height resolution is exceptional, at approximately 0.5 nm. AFM produces three-dimensional, topological images that accurately depict the surface features of the virus or cell under study. The images resemble common light photographic images and require little interpretation. The structures of viruses observed by AFM are consistent with models derived by X-ray crystallography and cryo-EM.
doi:10.1128/MMBR.00041-10
PMCID: PMC3122623  PMID: 21646429
14.  Structural and Electrostatic Characterization of Pariacoto Virus: Implications for Viral Asembly 
Biopolymers  2009;91(7):530-538.
We present the first all-atom model for the structure of a T=3 virus, pariacoto virus (PaV), which is a non-enveloped, icosahedral RNA virus and a member of the Nodaviridae family. The model is an extension of the crystal structure, which reveals about 88% of the protein structure but only about 35% of the RNA structure. Evaluation of alternative models confirms our earlier observation that the polycationic protein tails must penetrate deeply into the core of the virus, where they stabilize the structure by neutralizing a substantial fraction of the RNA charge. This leads us to propose a model for the assembly of small icosahedral RNA viruses: nonspecific binding of the protein tails to the RNA leads to a collapse of the complex, in a fashion reminiscent of DNA condensation. The globular protein domains are excluded from the condensed phase but are tethered to it, so they accumulate in a shell around the condensed phase, where their concentration is high enough to trigger oligomerization and formation of the mature virus.
doi:10.1002/bip.21168
PMCID: PMC2720792  PMID: 19226622
15.  Structure of Double-Shelled Rice Dwarf Virus 
Journal of Virology  1998;72(11):8541-8549.
Rice dwarf virus (RDV), a member of the Reoviridae family, is a double-stranded RNA virus. Infection of rice plants with RDV reduces crop production significantly and can pose a major economic threat to Southeast Asia. A 25-Å three-dimensional structure of the 700-Å-diameter RDV capsid has been determined by 400-kV electron cryomicroscopy and computer reconstruction. The structure revealed two distinctive icosahedral shells: a T=13l outer icosahedral shell composed of 260 trimeric clusters of P8 (46 kDa) and an inner T=1 icosahedral shell of 60 dimers of P3 (114 kDa). Sequence and structural comparisons were made between the RDV outer shell trimer and the two crystal conformations (REF and HEX) of the VP7 trimer of bluetongue virus, an animal analog of RDV. The low-resolution structural match of the RDV outer shell trimer to the HEX conformation of VP7 trimer has led to the proposal that P8 consists of an upper domain of β-sandwich motif and a lower domain of α helices. The less well fit REF conformation of VP7 to the RDV trimer may be due to the differences between VP7 and P8 in the sequence of the hinge region that connects the two domains. The additional mass density and the absence of a known signaling peptide on the surface of the RDV outer shell trimer may be responsible for the different interactions between plants and animal reoviruses.
PMCID: PMC110264  PMID: 9765392
16.  Conformational equilibria and rates of localized motion within Hepatitis B Virus capsids 
Journal of molecular biology  2007;375(2):581-594.
Functional analysis of Hepatitis B virus (HBV) core particles has associated a number of biological roles with the C-terminus of the capsid protein. One set of functions require the C-terminus to be on the exterior of the capsid, while others place this domain on the interior. According to the crystal structure of the capsid, this segment is strictly internal to the capsid shell and buried at a protein-protein interface. Using kinetic hydrolysis, a form of protease digestion assayed by SDS-PAGE and mass spectrometry, the structurally and biologically important C-terminal region of HBV capsid protein assembly domain (Cp149, residues 1-149) has been shown to be dynamic in both dimer and capsid forms. HBV is an enveloped virus with a T=4 icosahedral core that is composed of 120 copies of a homodimer capsid protein. Free dimer and assembled capsid forms of the protein are readily hydrolyzed by trypsin and thermolysin, around residues 127-128, indicating that this region is dynamic and exposed to the capsid surface. The measured conformational equilibria have an opposite temperature dependence between free dimer and assembled capsid. This work helps to explain the previously described allosteric regulation of assembly and functional properties of a buried domain. These observations make a critical connection between structure, dynamics, and function: made possible by the first quantitative measurements of conformational equilibria and rates of conversion between protein conformers for a megadalton complex.
doi:10.1016/j.jmb.2007.10.044
PMCID: PMC2238684  PMID: 18022640
17.  Heterologous RNA Encapsidated in Pariacoto Virus-Like Particles Forms a Dodecahedral Cage Similar to Genomic RNA in Wild-Type Virions 
Journal of Virology  2004;78(20):11371-11378.
The genome of some icosahedral RNA viruses plays an essential role in capsid assembly and structure. In T=3 particles of the nodavirus Pariacoto virus (PaV), a remarkable 35% of the single-stranded RNA genome is icosahedrally ordered. This ordered RNA can be visualized at high resolution by X-ray crystallography as a dodecahedral cage consisting of 30 24-nucleotide A-form RNA duplex segments that each underlie a twofold icosahedral axis of the virus particle and interact extensively with the basic N-terminal region of 60 subunits of the capsid protein. To examine whether the PaV genome is a specific determinant of the RNA structure, we produced virus-like particles (VLPs) by expressing the wild-type capsid protein open reading frame from a recombinant baculovirus. VLPs produced by this system encapsidated similar total amounts of RNA as authentic virus particles, but only about 6% of this RNA was PaV specific, the rest being of cellular or baculovirus origin. Examination of the VLPs by electron cryomicroscopy and image reconstruction at 15.4-Å resolution showed that the encapsidated RNA formed a dodecahedral cage similar to that of wild-type particles. These results demonstrate that the specific nucleotide sequence of the PaV genome is not required to form the dodecahedral cage of ordered RNA.
doi:10.1128/JVI.78.20.11371-11378.2004
PMCID: PMC521806  PMID: 15452258
18.  Particle Polymorphism Caused by Deletion of a Peptide Molecular Switch in a Quasiequivalent Icosahedral Virus† 
Journal of Virology  1998;72(7):6024-6033.
The capsid of flock house virus is composed of 180 copies of a single type of coat protein which forms a T=3 icosahedral shell. High-resolution structural analysis has shown that the protein subunits, although chemically identical, form different contacts across the twofold axes of the virus particle. Subunits that are related by icosahedral twofold symmetry form flat contacts, whereas subunits that are related by quasi-twofold symmetry form bent contacts. The flat contacts are due to the presence of ordered genomic RNA and an ordered peptide arm which is inserted in the groove between the subunits and prevents them from forming the dihedral angle observed at the bent quasi-twofold contacts. We hypothesized that by deleting the residues that constitute the ordered peptide arm, formation of flat contacts should be impossible and therefore result in assembly of particles with only bent contacts. Such particles would have T=1 symmetry. To test this hypothesis we generated two deletion mutants in which either 50 or 31 residues were eliminated from the N terminus of the coat protein. We found that in the absence of residues 1 to 50, assembly was completely inhibited, presumably because the mutation removed a cluster of positively charged amino acids required for neutralization of encapsidated RNA. When the deletion was restricted to residues 1 to 31, assembly occurred, but the products were highly heterogeneous. Small bacilliform-like structures and irregular structures as well as wild-type-like T=3 particles were detected. The anticipated T=1 particles, on the other hand, were not observed. We conclude that residues 20 to 30 are not critical for formation of flat protein contacts and formation of T=3 particles. However, the N terminus of the coat protein appears to play an essential role in regulating assembly such that only one product, T=3 particles, is synthesized.
PMCID: PMC110407  PMID: 9621065
19.  From structure of the complex to understanding of the biology 
The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy single-particle reconstructions. This paper concerns itself with the study of the macromolecular complexes that constitute viruses, using structural hybrid techniques.
The most extensive structural information on viruses relates to apparently icosahedral virions and is based on X-ray crystallography and on cryo-electron microscopy (cryo-EM) single-particle reconstructions. Both techniques lean heavily on imposing icosahedral symmetry, thereby obscuring any deviation from the assumed symmetry. However, tailed bacteriophages have icosahedral or prolate icosahedral heads that have one obvious unique vertex where the genome can enter for DNA packaging and exit when infecting a host cell. The presence of the tail allows cryo-EM reconstructions in which the special vertex is used to orient the head in a unique manner. Some very large dsDNA icosahedral viruses also develop special vertices thought to be required for infecting host cells. Similarly, preliminary cryo-EM data for the small ssDNA canine parvovirus complexed with receptor suggests that these viruses, previously considered to be accurately icosahedral, might have some asymmetric properties that generate one preferred receptor-binding site on the viral surface. Comparisons are made between rhinoviruses that bind receptor molecules uniformly to all 60 equivalent binding sites, canine parvovirus, which appears to have a preferred receptor-binding site, and bacteriophage T4, which gains major biological advantages on account of its unique vertex and tail organelle.
doi:10.1107/S0907444906047330
PMCID: PMC2483488  PMID: 17164521
Bacteriophage T4; canine parvovirus; cryo-electron microscopy; image reconstruction; large dsDNA icosahedral viruses; special vertex
20.  Understanding ultrafine nanodiamond formation using nanostructured explosives 
Scientific Reports  2013;3:2159.
The detonation process is able to build new materials with a bottom-up approach. Diamond, the hardest material on earth, can be synthesized in this way. This unconventional synthesis route is possible due to the presence of carbon inside the high-explosive molecules: firing high-explosive mixtures with a negative oxygen balance in a non-oxidative environment leads to the formation of nanodiamond particles. Trinitrotoluene (TNT) and hexogen (RDX) are the explosives primarily used to synthesize nanodiamonds. Here we show that the use of nanostructured explosive charges leads to the formation of smaller detonation nanodiamonds, and it also provides new understanding of nanodiamond formation-mechanisms. The discontinuity of the explosive at the nanoscale level plays the key role in modifying the diamond particle size, and therefore varying the size with microstructured charges is impossible.
doi:10.1038/srep02159
PMCID: PMC3703608  PMID: 23831716
21.  Three-dimensional structure of vaccinia virus-produced human papillomavirus type 1 capsids. 
Journal of Virology  1994;68(7):4503-4505.
The capsid proteins of papillomavirus self-assemble to form empty capsids or virus-like particles that appear quite similar to naturally occurring virions by conventional electron microscopy. To characterize such virus-like particles more fully, cryoelectron microscopy and image analysis techniques were used to generate three-dimensional reconstructions of capsids produced by vaccinia virus recombinants (V capsids) that expressed human papillomavirus type 1 L1 protein only or both L1 and L2 proteins. All V capsids had 72 pentameric capsomers arranged on a T = 7 icosahedral lattice. Each particle (approximately 60 nm in diameter) consisted of an approximately 2-nm-thick shell of protein with a radius of 22 nm with capsomers that extend approximately 6 nm from the shell. At a resolution of 3.5 nm, both V capsid structures appear identical to the capsid structure of native human papillomavirus type 1 (T. S. Baker, W. W. Newcomb, N. H. Olson, L. M. Cowsert, C. Olson, and J. C. Brown, Biophys. J. 60:1445-1456, 1991), thus implying that expressed and native capsids are structurally equivalent.
Images
PMCID: PMC236376  PMID: 8207824
22.  Single-particle cryo-electron microscopy of Rift Valley fever virus 
Virology  2009;387(1):11-15.
Rift Valley fever virus (RVFV; Bunyaviridae; Phlebovirus) is an emerging human veterinary pathogen causing acute hepatitis in ruminants and has the potential to Single-particle cryo-EM reconstruction of RVFV MP-12 hemorrhagic fever in humans. We report a three-dimensional reconstruction of RVFV vaccine strain MP-12 (RVFV MP-12) by cryo-electron microcopy using icosahedral symmetry of individual virions. Although the genomic core of RVFV MP-12 is apparently poorly ordered, the glycoproteins on the virus surface are highly symmetric and arranged on a T=12 icosahedral lattice. Our RVFV MP-12 structure allowed clear identification of inter-capsomer contacts and definition of possible glycoprotein arrangements within capsomers. This structure provides a detailed model for phleboviruses, opens new avenues for high-resolution structural studies of the bunyavirus family, and aids the design of antiviral diagnostics and effective subunit-vaccines.
doi:10.1016/j.virol.2009.02.038
PMCID: PMC2673237  PMID: 19304307
Bunyaviridae; Rift Valley fever virus; cryo-electron microscopy; single-particle averaging; inter-capsomer contacts
23.  In-flight gas phase growth of metal/multi layer graphene core shell nanoparticles with controllable sizes 
Scientific Reports  2013;3:2814.
In this report, we present a general method for a continuous gas-phase synthesis of size-selected metal/multi layer graphene (MLG) core shell nanoparticles having a narrow size distribution of metal core and MLG shell for direct deposition onto any desired substrate kept under clean vacuum conditions. Evolution of MLG signature is clearly observed as the metal-carbon agglomerates get transformed to well defined metal/MLG core shell nanoparticles during their flight through the sintering zone. The growth takes place via an intermediate state of alloy nanoparticle (Pd-carbon) or composite nanoparticle (Cu-carbon), depending upon the carbon solubility in the metal and relative surface energy values. It has been also shown that metal/MLG nanoparticles can be converted to graphene shells. This study will have a large impact on how graphene or graphene based composite nanostructures can be grown and deposited in applications requiring controllable dimensions, varied substrate choice, large area and large scale depositions.
doi:10.1038/srep02814
PMCID: PMC3792500  PMID: 24100702
24.  Geometric Mismatches within the Concentric Layers of Rotavirus Particles: a Potential Regulatory Switch of Viral Particle Transcription Activity▿  
Journal of Virology  2008;82(6):2844-2852.
Rotaviruses are prototypical double-stranded RNA viruses whose triple-layered icosahedral capsid constitutes transcriptional machinery activated by the release of the external layer. To understand the molecular basis of this activation, we studied the structural interplay between the three capsid layers by electron cryo-microscopy and digital image processing. Two viral particles and four virus-like particles containing various combinations of inner (VP2)-, middle (VP6)-, and outer (VP7)-layer proteins were studied. We observed that the absence of the VP2 layer increases the particle diameter and changes the type of quasi-equivalent icosahedral symmetry, as described by the shift in triangulation number (T) of the VP6 layer (from T = 13 to T = 19 or more). By fitting X-ray models of VP6 into each reconstruction, we determined the quasi-atomic structures of the middle layers. These models showed that the VP6 lattices, i.e., curvature and trimer contacts, are characteristic of the particle composition. The different functional states of VP6 thus appear as being characterized by trimers having similar conformations but establishing different intertrimeric contacts. Remarkably, the external protein VP7 reorients the VP6 trimers located around the fivefold axes of the icosahedral capsid, thereby shrinking the channel through which mRNA exits the transcribing rotavirus particle. We conclude that the constraints arising from the different geometries imposed by the external and internal layers of the rotavirus capsid constitute a potential switch regulating the transcription activity of the viral particles.
doi:10.1128/JVI.02268-07
PMCID: PMC2258973  PMID: 18184711
25.  Impact of Quaternary Organization on the Antigenic Structure of the Tick-Borne Encephalitis Virus Envelope Glycoprotein E▿ †  
Journal of Virology  2009;83(17):8482-8491.
The envelope protein E of flaviviruses mediates both receptor-binding and membrane fusion. At the virion surface, 180 copies of E are tightly packed and organized in a herringbone-like icosahedral structure, whereas in noninfectious subviral particles, 60 copies are arranged in a T=1 icosahedral symmetry. In both cases, the basic building block is an E dimer which exposes the binding sites for neutralizing antibodies at its surface. It was the objective of our study to assess the dependence of the antigenic structure of E on its quaternary arrangement, i.e., as part of virions, recombinant subviral particles, or soluble dimers. For this purpose, we used a panel of 11 E protein-specific neutralizing monoclonal antibodies, mapped to distinct epitopes in each of the three E protein domains, and studied their reactivity with the different soluble and particulate forms of tick-borne encephalitis virus E protein under nondenaturing immunoassay conditions. Significant differences in the reactivities with these forms were observed that could be related to (i) limited access of certain epitopes at the virion surface; (ii) limited occupancy of epitopes in virions due to steric hindrance between antibodies; (iii) differences in the avidity to soluble forms compared to the virion, presumably related to the flexibility of E at its domain junctions; and (iv) modulations of the external E protein surface through interactions with its stem-anchor structure. We have thus identified several important factors that influence the antigenicity of the flavivirus E protein and have an impact on the interaction with neutralizing antibodies.
doi:10.1128/JVI.00660-09
PMCID: PMC2738186  PMID: 19553320

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