Morphology and Physical Properties of Staphylococcus Bacteriophage P11-M15

The Group B Staphylococcus phage P11-M15 is shown to be 51% protein and 49% deoxyribonucleic acid (DNA). The intact virion has a molecular weight of 66.7 x 10(6) daltons. The purified viral DNA has a molecular weight of 32.7 x 10(6) daltons. The intact virion is shown to be composed of a polyhedral head which is attached at one of its vertices to a flexible tail having helical symmetry. The tail structure is terminated by a complex baseplate which has sixfold symmetry. The virion contains a single molecule of double-stranded DNA which has no apparent single-strand nicks or single-stranded terminal redundancies.     

Molecular weight of adenovirus serotype 2 capsomers a new characterization

We have determined the molecular weight of some of the adenovirus serotype 2 structural proteins: penton, penton base and fibre. Physical techniques, namely neutron scattering and hydrodynamical measurements, indicate that the penton base is a trimer. This is confirmed by analysis of the virion composition based on quantitative gel scanning. This finding implies either that other proteins (e.g. protein IIIa) are essential in the architecture of the fivefold vertex of the virion, or that the usual assumption that icosahedral symmetry involves identical interactions related to the symmetry of the virion does not hold.     

Structural organization of authentic,mature HIV-1 virions and cores

Mature, infectious HIV-1 particles contain a characteristic cone-shaped core that encases the viral RNA and replication proteins. The architectures of mature virions and isolated cores were studied using cryo-electron microscopy. The average size ( approximately 145 nm) of the virion was unchanged during maturation. Most virions contained a single core but roughly one-third contained two or more cores. Consideration of the capsid protein concentration during core assembly indicated that core formation in vivo is template-mediated rather than concentration-driven. Although most cores were conical, 7% were tubular. These displayed a stacked-disc arrangement with 7-, 8-, 9- or 10-fold axial symmetry. Layer line filtration of these images showed that the capsid subunit arrangement is consistent with a 9.6 nm hexamer resembling that previously seen in the helical tubes assembled from purified capsid protein. A common reflection (1/3.2 nm) shared between the tubular and conical cores suggested they share a similar organization. The extraordinary flexibility observed in the assembly of the mature core appears to be well suited to accommodating variation and hence there may be no single structure for the infectious virion.     

Protein and DNA residue orientations in the filamentous virus Pf1 determined by polarized Raman and polarized FTIR spectroscopy

The Pseudomonas bacteriophage Pf1 is a long ( approximately 2000 nm) and thin ( approximately 6.5 nm) filament consisting of a covalently closed, single-stranded DNA genome of 7349 nucleotides coated by 7350 copies of a 46-residue alpha-helical subunit. The coat subunits are arranged as a superhelix of C(1)()S(5.4)() symmetry (class II). Polarized Raman and polarized FTIR spectroscopy of oriented Pf1 fibers show that the packaged single-stranded DNA genome is ordered specifically with respect to the capsid superhelix. Bases are nonrandomly arranged along the capsid interior, deoxynucleosides are uniformly in the C2'-endo/anti conformation, and the average DNA phosphodioxy group (PO(2)(-)) is oriented so that the line connecting the oxygen atoms (O.O) forms an angle of 71 degrees +/- 5 degrees with the virion axis. Raman and infrared amide band polarizations show that the subunit alpha-helix axis is inclined at an average angle of 16 degrees +/- 4 degrees with respect to the virion axis. The alpha-helical symmetry of the capsid subunit is remarkably rigorous, resulting in splitting of Raman-active helix vibrational modes at 351, 445 and 1026 cm(-)(1) into apparent A-type and E(2)()-type symmetry pairs. The subunit tyrosines (Tyr 25 and Tyr 40) are oriented with phenoxyl rings packed relatively close to parallel to the virion axis. The Tyr 25 and Tyr 40 orientations of Pf1 are surprisingly close to those observed for Tyr 21 and Tyr 24 of the Ff virion (C(5)()S(2)() symmetry, class I), suggesting a preferred tyrosyl side chain conformation in packed alpha-helical subunits, irrespective of capsid symmetry. The polarized Raman spectra also provide information on the orientations of subunit alanine, valine, leucine and isoleucine side chains of the Pf1 virion.     

A highly unusual palindromic transmembrane helical hairpin formed by SARS coronavirus E protein

The agent responsible for the recent severe acute respiratory syndrome (SARS) outbreak is a previously unidentified coronavirus. While there is a wealth of epidemiological studies, little if any molecular characterization of SARS coronavirus (SCoV) proteins has been carried out. Here we describe the molecular characterization of SCoV E protein, a critical component of the virus responsible for virion envelope morphogenesis. We conclusively show that SCoV E protein contains an unusually short, palindromic transmembrane helical hairpin around a previously unidentified pseudo-center of symmetry, a structural feature which seems to be unique to SCoV. The hairpin deforms lipid bilayers by way of increasing their curvature, providing for the first time a molecular explanation of E protein's pivotal role in viral budding. The molecular understanding of this critical component of SCoV may represent the beginning of a concerted effort aimed at inhibiting its function, and consequently, viral infectivity.     

Atomic force microscopy investigation of a chlorella virus, PBCV-1

A virus PBCV-1, which infects certain fresh water algae and has been shown by transmission and cryo-electron microscopy to exist as a triskaidecahedron, was imaged using atomic force microscopy (AFM). From AFM the particles have diameters of about 190nm and the overall structure is in all important respects consistent with existing models. The surface lattice of the virion is composed of trimeric capsid proteins distributed according to p3 symmetry to create a honeycomb arrangement of raised edges forming quasi-hexagonal cells. At the pentagonal vertices are five copies of a different protein forming an exact pentagon, and this has yet another unique protein in its center. The apical protein exhibits some unusual mechanical properties in that it can be made to retract into the virion interior when subjected to AFM tip pressure. When PBCV-1 virions degrade, they give rise to small, uniform, spherical, and virus like particles (VLP) consistent with T=1 or 3 icosahedral products. Also observed upon disintegration are strands of linear dsDNA. Fibers of unknown function are also occasionally seen associated with some virions.     

Intensity of the polarized Raman band at 1340-1345 cm-1 as an indicator of protein alpha-helix orientation: application to Pf1 filamentous virus

Raman spectra of oriented alpha-helical protein molecules exhibit a prominent band near 1340-1345 cm(-)(1), the intensity of which is highly sensitive to molecular orientation. Polarization of the 1340-1345 cm(-)(1) marker is evident in Raman spectra of alpha-helical poly-L-alanine (alphaPLA) and alpha-helical poly-gamma-benzyl-L-glutamate (alphaPBLG). Corresponding polarization is also observed in Raman spectra of the filamentous virus Pf1, which is an assembly of alpha-helical coat protein molecules. In alphaPLA and alphaPBLG, we assign the band to a normal mode of symmetry type E(2) and specifically to a vibration localized in the (O=C)-C(alpha)-H linkages of the main chain peptide group. Although strict helical symmetry does not apply to coat subunits of filamentous viruses, an approximate E(2)-type mode may be presumed to account for a corresponding Raman band of Pf1 and fd filamentous viruses. Spectroscopic studies of N-methylacetamide and isotopically-edited fd viruses support the present assignment of the 1340-1345 cm(-)(1) band. Polarization anisotropy indicates that this band may be exploited as a novel indicator of protein alpha-helix orientation. Application of this approach to the polarized Raman spectrum of Pf1 suggests that, on average, the axis of the alpha-helical coat protein subunit in the native virion structure forms an angle of 20 +/- 10 degrees with respect to the virion axis.     

The hand of the filamentous bacteriophage helix

Filamentous bacteriophage (Inovirus) is a widely studied model system in molecular biophysics. The structure of the virion has been analysed by various methods, but the methods have seldom questioned the hand of the virion helix. The hand of the helix relating the protein subunits in the class II virus strain Pf1 was chosen by calculating an electron-density distribution from X-ray fibre diffraction data, using a maximum-entropy method, but to our knowledge this method has not been used for a similar purpose in any other system. Moreover, this same hand was extended only by analogy, with no direct analysis of the corresponding data, to the class I virus strain Ff (fd, f1, M13), which has a different helix symmetry. Here we use published solid-state NMR data to confirm the validity of the hand of Pf1 chosen by the maximum-entropy method, and to confirm the extension to Ff.     

Genome structure and virion polypeptides of the primate herpesviruses Herpesvirus aotus types 1 and 3: comparison with human cytomegalovirus.

Two serologically distinguishable primate herpesviruses, Herpesvirus aotus type 1 and type 3, were examined with regard to their genomes and structural polypeptides. The duplex DNA genomes of these two viruses were found to be essentially identical in molecular weight (Mr approximately equal to 145 X 10(6)) and guanine plus cytosine composition (55%). Both contained unique and inverted repeat nucleotide sequences of the same size and arrangement, which, as judged by DNA-DNA hybridization and restriction enzyme analyses, were at least 95% homologous. In addition, no differences were observed in electrophoretic profiles of virion polypeptides. Because of their great similarity with respect to these criteria, the two viruses ought to be considered independent isolates (or strains) of a single virus, which should be designated H. aotus type 1. The elevated molecular weight and presence of two sets of inverted repeat sequences closely resemble the structure of the human cytomegalovirus genome. However, no sequence homology (less than 5%) nor similarity in virion polypeptides was detected between H. aotus type 1 and human cytomegalovirus.     

A second symmetry mismatch at the portal vertex of bacteriophage T7: 8-fold symmetry in the procapsid core

Like other bacteriophages, T7 has a singular vertex that is the site of a symmetry mismatch involving the portal/connector protein, a 12-fold ring at the vertex site which is also a 5-fold axis for the icosahedral capsid. In the mature virion, a 6-fold-symmetric tail extends outwards from the connector. T7 also has a cylindrical "core" that assembles on the inner surface of the connector during procapsid formation, is retained in the mature virion, and is required for infectivity. We have investigated the core structure by cryo-electron microscopy and image analysis of procapsids and find that it observes 8-fold symmetry. Stoichiometry data indicate that its major constituent is an octamer of gp15.     

Assembly and organization of glycoproteins B, C, D, and H in herpes simplex virus type 1 particles lacking individual glycoproteins: No evidence for the formation of a complex of these molecules

Glycoprotein B (gB), gC, gD, and gH:L of herpes simplex virus type 1 (HSV-1) are implicated in virus adsorption and penetration. gB, gD, and gH:L are essential for these processes, and their expression is necessary and sufficient to induce cell fusion. The current view is that these molecules act in concert as a functional complex, and cross-linking studies support this view (C. G. Handler, R. J. Eisenberg, and G. H. Cohen, J. Virol. 70:6067-6075, 1996). We examined the glycoprotein composition, with respect to gB, gC, gD, and gH, of mutant virions lacking individual glycoproteins and the sedimentation characteristics of glycoproteins extracted from these virions. The amounts of gB, gC, gD, or gH detected in virions did not alter when any one of these molecules was absent, and it therefore appears that they are incorporated into the virion independently of each other. The sedimentation characteristics of gB and gD from mutant virions were not different from those of wild-type virions. We confirmed that gB, gC, and gD could be cross-linked to each other on the virion surface but found that the absence of one glycoprotein did not alter the outcome of cross-linking reactions between the remaining molecules. The incorporation and arrangement of these glycoproteins in the virion envelope therefore appear to be independent of the individual molecular species. This is difficult to reconcile with the concept that gB, gC, gD, and gH:L are incorporated as a functional complex into the virion envelope.     

The stoichiometry of antibody-mediated neutralization and enhancement of West Nile virus infection

Antibody binding to the icosahedral arrangement of envelope proteins on the surface of flaviviruses can result in neutralization or enhancement of infection. We evaluated how many antibodies must bind to a given epitope on West Nile virus (WNV) to achieve neutralization. The most potent monoclonal antibodies (mAbs) block infection at concentrations that result in low occupancy of accessible sites on the virion, with neutralization occurring when as few as 30 of 180 envelope proteins are bound. In contrast, weakly neutralizing mAbs recognize fewer sites on the virion and require almost complete occupancy to inhibit WNV infection. For all mAbs studied, enhancement of infection is possible in cells bearing activating Fc-gamma receptors when the number of mAbs docked to the virion is not sufficient for neutralization. Thus, neutralization is best described by a model requiring "multiple hits" with the cumulative functional outcome determined by interplay between antibody affinity and epitope accessibility.     

Molecular symmetry and arrangement of subunits in extracellular hemoglobin from the nematode Ascaris suum

The arrangement of subunits and molecular symmetry of extracellular hemoglobin from the nematode Ascaris suum, an 11.7S molecular of molecular mass 332 kDa and composed of eight identical subunits, was studied. Dissociation of the molecule at alkaline and acid pH yielded 4.6S and 2.7S components, identified as polypeptide-chain dimers and monomers, respectively. Cross-linking with glutardialdehyde followed by SDS/PAGE resulted in a maximum number of eight bands identified in order of decreasing mobility as monomeric and 2-8 cross-linked-polypeptide-chain species. Comparison with values predicted from theory shows that the distribution of protein among the various cross-linked species, obtained after different extents of exposure to cross-linker, is consistent with a two-layered arrangement of subunits involving one type of interaction between subunits from different layers and another between subunits within the same layer. Electron micrographs of the molecule showed two profiles, a square and a rectangle. We propose a model for the molecule which is eight subunits arranged in two layers, stacked in an eclipsed orientation. The proposed model is consistent with the results from sedimentation, cross-linking and electron microscopy. Taken together, our findings indicate D4 symmetry for Ascaris hemoglobin.     

Physicochemical Studies on L-Cell Virions

The L-cell virion (LCV) has been purified from supernatant fluids of mouse L cells grown in suspension culture. The virion is similar to other RNA tumor viruses by several criteria: (i) the density of the virion is 1.16 g/cm(3); (ii) the virion appears as a rounded membranous particle with an outer diameter of 146.7 +/- 11.8 nm, and contains knobs (7-nm diameter) over its surface; (iii) 15 polypeptides (ranging in molecular weight from 7,000 to 110,000) are detectable after electrophoresis of virion protein in sodium dodecyl sulfate-polyacrylamide gels; (iv) three species of RNA can be isolated-high molecular weight (80 to 88s) (50%), 7s (35%) and 4s (15%); (v) heat denaturation of the high-molecular-weight RNA yields a heterogeneous population of molecules (20 to 35s) as well as a 7s and 4s species. Despite the general similarity to infectious RNA tumor viruses, LCV is apparently defective as evidenced by the fact that it does not induce tumors in animals or transform normal mouse cells in vitro (Kindig and Kirsten [17]). The defective nature of the LCV might be related to the fact that assays for DNA polymerase in the virion showed only a negligible activity when compared to Rous sarcoma virus.     

Three-dimensional reconstruction of hibiscus chlorotic ringspot virus

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense, single-stranded RNA virus, which belongs to the Tombusviridae family and infects plants of the Hibiscus genus, including kenaf, a woody plant of agricultural importance. These icosahedral viruses have a capsid consisting of 180 copies of coat protein (CP) arranged with T=3 symmetry. The CP consists of an internal RNA-binding domain, a shell-forming domain and a protruding domain. The HCRSV virion was reconstructed to about 12A resolution from cryo-EM images using the program EMAN. The structure had the arrangement of 90 dimers of protruding domains characteristic of the Tombusviridae. Reconstructions were also made from negatively stained samples, and showed essentially the same features. In addition, a particle of a different, "smooth" appearance was also identified in the negatively stained samples. These particles were slightly smaller and lacked protruding domains. Biochemical analysis confirmed the presence of two protein products: a 37 kDa protein identified as HCRSV CP and a 54 kDa protein that appeared to be of non-HCRSV origin.     

Crystal structure of the pyridoxal 5'-phosphate dependent L-methionine gamma-lyase from Pseudomonas putida

L-Methionine gamma-lyase (MGL) catalyzes the pyridoxal 5'-phosphate (PLP) dependent alpha,gamma-elimination of L-methionine. We have determined two crystal structures of MGL from Pseudomonas putida using MAD (multiwavelength anomalous diffraction) and molecular replacement methods. The structures have been refined to an R-factor of 21.1% at 2.0 and 1.7 A resolution using synchrotron radiation diffraction data. A homotetramer with 222 symmetry is built up by non-crystallographic symmetry. Two monomers associate to build the active dimer. The spatial fold of subunits, with three functionally distinct domains and their quarternary arrangement, is similar to those of L-cystathionine beta-lyase and L-cystathionine gamma-synthase from Escherichia coli.     

pH-dependent conformational transformation in mung bean glyceraldehyde-3-phosphate dehydrogenase

In thermal inactivation at pH 7.3 and below, the tetrameric apo-glyceraldehyde-3-phosphate dehydrogenase of mung beans lost half of its activity more rapidly than the rest, suggesting a pairwise arrangement of subunits (or a C2 symmetry). At pH 8.6, the activity was lost in a single exponential decay, characteristic of functional identity of sites as in a tetrahedral arrangement of subunits (or a D2-type symmetry). At intermittent pH values, the kinetics of thermal inactivation were consistent with the presence of a mixture of C2- and D2-symmetry conformations. In "sudden pH change" experiments, the observed thermal inactivation kinetics were characteristic of the final pH at which the enzyme was heated. Thus, the interconversion of the two conformations is facile and very fast. There is no gross change in molecular weight of the enzyme between pH 7.3 and 8.6.     

Helical Nucleocapsid Structure of the Oncogenic Ribonucleic Acid Viruses (Oncornaviruses)

Negative staining of virions and isolated nucleoids from avian myeloblastosis virus, murine leukemia virus, murine mammary tumor virus, and feline leukemia virus reveals common internal structures. The majority of virions that are penetrated by phosphotungstate show spherical nucleoids with no apparent symmetry. In a small percentage of virions, two distinctive structures are found: (i) single strands (3 to 5 nm in diameter) which are presumed to be the nucleoprotein and are found randomly oriented throughout the viral interior and (ii) helical structures (7 to 9 nm in diameter) which contain these nucleoprotein strands and are observed at the periphery of the nucleoid. The finding of helical nucleocapsid segments at the periphery of the nucleoid, as well as the hollow spherical structure observed in thin section of budding virions, has led to the hypothesis that the nucleocapsid of the freshly budded oncornavirus is supercoiled as a hollow sphere. This symmetry, however, is considered transient, as the internal structure of the extracellular virus undergoes a conformational rearrangement; thus, due to structural instability, the nucleocapsid uncoils and the nucleoprotein strands fill the interior of the virion. The extracellular virion is therefore considered degenerate in respect to symmetry, explaining the difficulty in detecting a helical nucleocapsid.     

Linear adenovirus DNA is organized into supercoiled domains in virus particles.

Electron microscopic analysis of bis-psoralen crosslinked adenovirus type 5 virion DNA revealed supercoiled domains in an otherwise linear DNA. The existence of supercoiled arrangement in all the virion DNA was demonstrated by the sensitivity of Ad5 DNA in pentonless virus particles to the supercoiling-dependent endonucleolytic activity of Bal31 and S1 nucleases. These nucleases were found to cleave Ad5 virion DNA at specific sites. The observation of stable cleavage sites in the limit digestion of virion DNA by Bal31 suggests that cleavage sites represent boundaries of core proteins which impede the exonuclease activity of Bal31. These data suggest that specific arrangement of core proteins on Ad5 virion DNA. Based on this analysis we determined positions of core proteins in viral genome using indirect end labeling technique. The size of supercoiled domains of virion DNA was estimated by electron microscopy and also by boundaries of mutually exclusive Bal31 cleavage sites at limit digestion condition. Our data suggest each supercoiled domain is equal to about 12% of Ad5 genome length and about 8 loops can be accommodated in Ad5 virion. However sequences at two extreme ends of the viral genome were found to be outside of supercoiled domains. An interesting correlation between supercoiled domains and gene domains of Ad5 genome was noticed.     

Composition, arrangement and cleavage of the mouse mammary tumor virus polyprotein precursor Pr77gag and p110gag.

The amino acid sequence relationship between the nonglycosylated structural proteins of murine mammary tumor virus and the polyproteins from infected cells immunoprecipitated with an anti-p27 serum were examined using two-dimensional tryptic peptide mapping procedures. The proteins were labeled with ¹⁴C-lysine and ¹⁴C-arginine so that all but one of the tryptic peptides released from a protein could be detected. Previous studies have shown that immunoprecipitation of mammary tumor cells with anti-p27 serum results in the isolation of seven proteins in the molecular weight range of 34,000–160,000 daltons; and that cell-free translation using viral genomic RNA yields three p27-related proteins of 160,000, 110,000 and 77,000 daltons, similar to the three high molecular weight proteins detected in vivo. The proteins of lower molecular weight were thought to be cleavage intermediates of Pr77^gag. As judged from the peptide maps, Pr77^gag contained the complete sequences of the four major internal proteins of the virion (p27, pp21, p14 and p10) and possibly a fifth highly basic protein (p8) also found in virions. The putative cleavage intermediates, as expected, lacked some tryptic peptides that could be assigned to one or more of the major virion proteins and thus allow a scheme for the cleavage events to be constructed. p110^gag contained all the tryptic peptides found in Pr77^gag, plus some additional peptides. A minor virion protein p30 was found to include the peptides of p14 as well as some of the additional peptides present in p110^gag, suggesting a precursor-product relationship between the pr110^gag and p30. The data obtained from these studies lead us to propose that there are three protein precursors which include, at least in part, the gag gene region of the virion—p160 (potentially a gag/pol precursor), p110^gag and Pr77^gag—and that the arrangement of the virion proteins within the gag gene (pr77^gag) is p10-pp21-p27-p14.