The atomic structure of Mengo virus at 3.0 A resolution

Similarity between the picornavirus VP3 capsid polypeptide and the Saccharomyces cerevisiae virus capsid polypeptide

We have compared the sequence of the capsid polypeptide of the Saccharomyces cerevisiae double-stranded RNA virus, ScV, with those of the picornaviruses. A central region of 245 amino acids in the ScV capsid polypeptide of 680 amino acids has significant similarity to the picornavirus VP3. This similarity is more extensive than that already noted for the alphavirus capsid polypeptide and the picornavirus VP3 (Fuller, S.D. and Argos, P, EMBO J. 6, 1099, 1987). Together with the similarity between the ScV RNA polymerase and the picornavirus RNA polymerases, this result implies an evolutionary relationship between a simple double-stranded RNA virus of fungi and the small plus strand RNA animal viruses.

Structure-function relationships of icosahedral plant viruses

X-ray diffraction studies on single crystals of a few viruses have led to the elucidation of their three dimensional structure at near atomic resolution. Both the tertiary structure of the coat protein subunit and the quaternary organization of the icosahedral capsid in these viruses are remarkably similar. These studies have led to a critical re-examination of the structural principles in the architecture of isometric viruses and suggestions of alternative mechanisms of assembly. Apart from their role in the assembly of the virus particle, the coat proteins of certian viruses have been shown to inhibit the replication of the cognate RNA leading to cross-protection. The coat protein amino acid sequence and the genomic sequence of several spherical plant RNA viruses have been determined in the last decade. Experimental data on the mechanisms of uncoating, gene expression and replication of several classes of viruses have also become available. The function of the non-structural proteins of some viruses have been determined. This rapid progress has provided a wealth of information on several key steps in the life cycle of RNA viruses. The function of the viral coat protein, capsid architecture, assembly and disassembly and replication of isometric RNA plant viruses are discussed in the light of this accumulated knowledge.

Trypsin sensitivity of several human rhinovirus serotypes in their low pH-induced conformation

Five serotypes of human rhinovirus (HRV) were examined for sensitivity to trypsin at physiological pH, HRV1A, HRV2, and HRV14 were found to be resistant whereas in serotypes HRV49 and HRV89 degradation of VP2 was observed. However, exposure to low pH followed by neutralization, a treatment which causes irreversible conformational changes in the capsid, led to rapid cleavage by trypsin of VP1 in HRV1A, HRV2, and HRV49 at defined sites followed by degradation of VP2. In the case of HRV2, the cleavage site in VP1 was determined by direct protein sequencing and was shown to occur between Arg260 and Thr261, close to the C-terminus. HRV49 behaves similarly to HRV2 as expected from extensive sequence similarity in this region, whereas VP1 in HRV1A is most probably cleaved at a site closer to the C-terminus than that in HRV2. Although HRV14 contains the same amino acid pair present in HRV2 and HRV49, it was not cleaved under these conditions. HRV89, which lacks a basic residue at the corresponding position, was also insensitive. Examination of the cleavage site on the three-dimensional structural map of native HRV2 reveals that it is most probably buried inside the capsid and thus not accessible. Structural rearrangements of the viral capsid are thus necessary to account for the cleavage observed after low pH treatment.

Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction

The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71 water molecules, and two calcium-binding sites. Viral disassembly is driven by electrostatic repulsions between the charges in two carboxyl-carboxylate pairs and a phosphate-carboxylate pair. The phosphate-carboxylate pair and at least one of the carboxyl-carboxylate pairs appear to be calcium-binding sites. Nucleotide specificity, enabling TMV to recognize its own RNA by a repeating pattern of guanine residues, is provided by two guanine-specific hydrogen bonds in one of the three base-binding sites.

Protein-RNA interactions in an icosahedral virus at 3.0 A resolution

Nearly 20 percent of the packaged RNA in bean-pod mottle virus (BPMV) binds to the capsid interior in a symmetric fashion and is clearly visible in the electron density map. The RNA displaying icosahedral symmetry is single-stranded with well-defined polarity and stereochemical properties. Interactions with protein are dominated by nonbonding forces with few specific contacts. The tertiary and quaternary structures of the BPMV capsid proteins are similar to those observed in animal picornaviruses, supporting the close relation between plant comoviruses and animal picornaviruses established by previous biological studies.

The antigenic structure of poliovirus

We have solved the structure of the Mahoney strain of type 1 and the Sabin (attenuated vaccine) strain of type 3 poliovirus by X-ray crystallographic methods. By providing a three-dimensional framework for the interpretation of a wealth of experimental data, the structures have yielded insight into the architecture and assembly of the virus particle, have provided information regarding the entry of virus into susceptible cells, and defined the sites on the virus particle that are recognized by neutralizing monoclonal antibodies. Thus locating mutations in variants selected for resistance to neutralizing monoclonal antibodies has defined three antigenic sites of the surface of the virion, and provided clues as to the mechanisms by which viruses escape neutralization. Finally, comparison of the structures of the two strains, together with analysis of sequences of many poliovirus strains, have begun to define the structural changes associated with serotypic differences between polioviruses.

Genetic and molecular analyses of spontaneous mutants of human rhinovirus 14 that are resistant to an antiviral compound

Spontaneous mutants of human rhinovirus 14 resistant to WIN 52084, an antiviral compound that inhibits attachment to cells, were isolated by selecting plaques that developed when wild-type virus was plated in the presence of high (2 micrograms/ml) or low (0.1 to 0.4 micrograms/ml) concentrations of the compound. Two classes of drug resistance were observed: a high-resistance (HR) class with a frequency of about 4 x 10(-5), and a low-resistance (LR) class with a 10- to 30-fold-higher frequency. The RNA genomes of 56 HR mutants and 13 LR mutants were sequenced in regions encoding the drug-binding site. The HR mutations mapped to only 2 of the 16 amino acid residues that form the walls of the drug-binding pocket. The side chains of these two residues point directly into the pocket and were invariably replaced by bulkier groups. These findings, and patterns of resistance to related WIN compounds, support the concept that HR mutations may hinder the entry or seating of drug within the binding pocket. In contrast, all of the LR mutations mapped to portions of the polypeptide chain near the canyon floor that move when the drug is inserted. Because several LR mutations partially reverse the attachment-inhibiting effect of WIN compounds, these mutants provide useful tools for studying the regions of the capsid structure involved in attachment. This paper shows that the method of escape mutant analysis, previously used to identify antibody binding sites on human rhinovirus 14, is also applicable to analysis of antiviral drug activity.

Genomic differences between the diabetogenic and nondiabetogenic variants of encephalomyocarditis virus

Plaque purification of the M variant of encephalomyocarditis (EMC-M) virus resulted in the isolation of two stable variants. One is a highly diabetogenic D variant (EMC-D) and the other is a nondiabetogenic B variant (EMC-B). The cDNA of EMC-D and EMC-B genomes were cloned and seven overlapping cDNA clones were selected to cover the entire genome except the 5'-end 310 bases which were determined by RNA-dependent DNA sequencing and enzymatic RNA sequencing. Each clone was restriction-mapped, subcloned, and sequenced. The genomes of EMC-D and EMC-B are composed of 7829 and 7825 bases, respectively. Both genomes contain a long open reading frame of 6876 nucleotides starting at position 830 on the consensus sequence, which encodes a polyprotein of 2292 amino acids. The sequences of EMC-D and EMC-B differ by two deletions, one insertion, and eight point mutations. The first deletion of 3 nucleotides is located in the 5' poly(C) tract where EMC-B has 127 nucleotides compared with 130 nucleotides in EMC-D. The second deletion in EMC-B involves 2 nucleotides at the 3'-end polyadenylation site. A single base insertion of U occurs at the 5' noncoding region of EMC-B. The eight point mutations are located in the polyprotein coding region. Two are silent and are each located in the structural gene 1B and in the nonstructural gene 2B. The remaining six mutations, one on the L gene and the other five on the 1D gene, introduce respective amino acid changes. It is concluded that the diabetogenic EMC-D viral genome (7829 bases) differs from the nondiabetogenic EMC-B viral genome (7825 bases) by 14 nucleotides out of 7829.

The cell attachment proteins of type 1 and type 3 reovirus are differentially susceptible to trypsin and chymotrypsin

Purified native sigma 1 proteins from [35S]methionine-labeled reovirions [serotypes 1 (T1) and 3 (T3)] were subjected to limited trypsin and chymotrypsin digestion. It was found that T1 sigma 1 was resistant to both trypsin and chymotrypsin, whereas T3 sigma 1 (49K molecular weight) was cleaved by trypsin to yield a 24K and a 25K fragment, and by chymotrypsin to yield a 42K fragment. The 24K tryptic fragment, but not the 25K tryptic fragment, was shown to possess L-cell binding capacity, and represents the carboxy-terminal half of T3 sigma 1 since it contains the single cysteine residue (amino acid 351) as revealed by tryptic analysis of [35S]cysteine-labeled sigma 1. Neither tryptic fragment was able to bind to glycophorin, the reovirus receptor on human erythrocytes. Thus, the mechanism of reovirus host cell attachment is distinct from that of reovirus hemagglutination. The two tryptic fragments were recognized by different neutralizing monoclonal anti-sigma 1 antibodies, indicating that neutralizing and cell attachment sites are not necessarily equivalent. The 42K chymotryptic fragment of T3 sigma 1 was shown to be generated by a cleavage proximal to the carboxy-terminus. Like intact T3 sigma 1, the 42K protein retained its capacity to bind to both L cells and glycophorin, and was recognized by all the neutralizing monoclonal anti-sigma 1 antibodies tested. Thus, the host cell receptor binding site on T3 sigma 1 is located between the trypsin-sensitive and the chymotrypsin-sensitive sites.

Sequences of capsid protein VP1 of two type A foot-and-mouth disease viruses

We have sequenced the nucleotides of the regions that encode the capsid protein VP1 of the foot-and-mouth disease viruses (FMDV) A5Bernbeuren/1984 and A Iran/1987. Amino acid sequences and secondary protein structures are provided. Both proteins consist of 212 amino acids. The sequences and secondary structures are compared to those of FMDV A22/CCCP/64, a strain previously endemic in the Near East. Nucleotide divergency among the three sequences is highest for FMDV A5Bernbeuren/1984 (18% compared to 13% for each other case). Thirty amino acid divergencies are observed between A22/CCCP/64 and A5 Bernbeuren/1984 or A Iran/1987, whereas the latter two differ by 27 residues. The secondary structures of all three proteins are different. A Iran/1987 is considered to belong to a thus far unknown subtype.

Clinical and experimental aspects of viral myocarditis

Picornaviruses are frequently implicated as the etiological agents of acute myocarditis. This association is based historically on serological evidence of rising antibody titers to specific pathogens and more recently on identification of viral genomic material in endocardial biopsy specimens through in situ hybridization. Only rarely is infectious virus isolated from either the patient or the heart during periods of maximum myocardial inflammation and injury. Thus, despite a probable viral etiology, much interest centers on the role of the immune system in cardiac damage and the likelihood that the infection triggers an autoimmune response to heart-specific antigens. Heart-reactive antibodies and T cells are found in most myocarditis patients, and immunosuppressive therapy has proven beneficial in many, though not all, cases. Furthermore, murine models of coxsackievirus group B type 3-induced myocarditis also demonstrate that virus infection initiates autoimmunity and that these autoimmune effectors are predominately responsible for tissue injury. How virus-host interactions overcome presumed self-tolerance to heart antigens is discussed, and evidence supporting various theories of virus-initiated autoimmunity and disease pathogenesis are delineated.

The major human rhinovirus receptor is ICAM-1

The major human rhinovirus receptor has been identified with monoclonal antibodies that inhibit rhinovirus infection. These monoclonal antibodies recognize a 95 kd cell surface glycoprotein on human cells and on mouse transfectants expressing a rhinovirus binding phenotype. Purified 95 kd protein binds to rhinovirus in vitro. Protein sequence from the 95 kd protein showed an identity with that of intercellular adhesion molecule-1 (ICAM-1); a cDNA clone obtained from mouse transfectants expressing the rhinovirus receptor had essentially the same sequence as ICAM-1. Thus, the major human rhinovirus receptor is ICAM-1. The gene for this receptor maps to human chromosome 19, which also contains the genes for a number of other picornavirus receptors.

A cell adhesion molecule, ICAM-1, is the major surface receptor for rhinoviruses

Rhinoviruses, which cause common colds, possess over 100 serotypes, 90% of which (the major group) share a single receptor. Lymphocyte function associated molecule 1 (LFA-1) mediates leukocyte adhesion to a wide variety of cell types by binding to intercellular adhesion molecule 1 (ICAM-1). We demonstrate identity between the receptor for the major group of rhinoviruses and ICAM-1. A major group rhinovirus binds specifically to purified ICAM-1 and to ICAM-1 expressed on transfected COS cells, and binding is blocked by three ICAM-1 monoclonal antibodies (MAb) that block ICAM-1-LFA-1 interaction, but not by an ICAM-1 MAb that does not block ICAM-1-LFA-1 interaction. This suggests that the ICAM-1 contact site(s) for LFA-1 and rhinoviruses is proximal or identical. In addition, ICAM-1 MAb block the cytopathic effect in HeLa cells mediated by representative major but not minor group rhinoviruses. ICAM-1 is induced by soluble mediators of inflammation, suggesting that the host immune response to rhinovirus may facilitate spread to uninfected cells.

Viral infectious complementary-DNA studies may identify nonviral genes critical to central nervous system disease

A major interest of modern science and medicine is the delineation of genes that cause disease. In the case of cancer, the study of viral oncogenic genes led to the recognition of similar human genes that play an important role in this disease. In an analogous fashion, the identification of viral genes important in central nervous system disease may lead to the recognition of related cellular genes that are important in nonviral central nervous system disease. New molecular techniques now provide tools for identification of pathogenic viral genes and elucidation of mechanisms of disease production. Positive-strand RNA viruses such as picornaviruses provide an especially attractive model system for studies of central nervous system disease-producing genes. A limitation in molecular studies of these viruses has resulted from an inability to use restriction enzymes, since these enzymes are active against DNA and not RNA. This limitation has recently been overcome with the preparation of infectious picornavirus complementary-DNA. This review highlights the importance of infectious complementary-DNA in pathogenesis studies and provides a glimpse of the impact of such studies on neurology.

Structure of the hepatitis A virion: identification of potential surface-exposed regions

Iodination of highly purified hepatitis A (HAV) virus results in the selective labeling of two viral polypeptides, which are identified as the the VP 1 and VP 2 capsid polypeptides. Based upon the kinetics of labeling, the exposed region of VP 1 appears to be more accessible to iodination, although the ultimate proportion of label present within VP 1 and VP 2 is approximately equal. By utilizing iodinated whole virions, isolated VP 1, VP 2, and the tryptic digest derived from VP 1 and VP 2, binding by heterologous anti-160 S antibody indicated that a significant portion of the antibodies was directed against an epitope on VP 2 that was not affected by denaturation. Identification of the regions exposed for iodination on these two polypeptides was accomplished by tryptic digestion of the isolated polypeptides followed by characterization of the iodinated tryptic peptide by gel filtration and reverse-phase chromatography. The results indicate that tyrosine 100 on VP 2 and a large tryptic peptide composed of amino acids 222 through 260 on VP 1 which contains four tyrosine residues are two regions that are surface-exposed on these molecules.

Proteolytic cleavage of encephalomyocarditis virus capsid region substrates by precursors to the 3C enzyme

Picornavirus protease 3C is normally released from its P3 precursor by two successive self-cleavage reactions. The free enzyme can then catalyze most of the remaining processing events within the viral polyprotein. To investigate the role of the 3C precursors in the processing cascade, we constructed cDNA clones which expressed genetically altered forms of the encephalomyocarditis P3 region in vitro. Site-specific substitutions were introduced into the Gln-Gly residues at the 3B-3C and 3C-3D junctions, and the resulting proteins were tested for their ability to self-process and to catalyze cleavage of viral capsid precursors in cell-free protease assays. We determined that three P3 region precursor proteins (3ABC, 3CD, and P3), harboring inactive cleavage sites, were as active as the free enzyme (3C) in processing assays with capsid substrates. Further, we found that in addition to the naturally occurring Gln-Gly and Gln-Ser amino acid pairs, the encephalomyocarditis 3C enzyme was able to process Gln-Cys but not Gln-Thr, Gln-Ile, Gln-Tyr, Arg-Gly, or Leu-Gly combinations when these residues were substituted into normal cleavage site contexts.

The three-dimensional structure of foot-and-mouth disease virus at 2.9 A resolution

The structure of foot-and-mouth disease virus has been determined at close to atomic resolution by X-ray diffraction without experimental phase information. The virus shows similarities with other picornaviruses but also several unique features. The canyon or pit found in other picornaviruses is absent; this has important implications for cell attachment. The most immunogenic portion of the capsid, which acts as a potent peptide vaccine, forms a disordered protrusion on the virus surface.

The structure of antiviral agents that inhibit uncoating when complexed with viral capsids

The tertiary structure of most icosahedral viral capsid proteins consists of an eight-stranded antiparallel beta-barrel with a hydrophobic interior. In a group of picornaviruses, this hydrophobic pocket can be filled by suitable organic molecules, which stop viral uncoating after attachment and penetration into the host cell. The antiviral activity of these agents is probably due to increased rigidity of the capsid protein, thereby inhibiting disassembly. The hydrophobic pocket may be an essential functional component of the protein and may have been conserved in the evolution of many viruses from a common precursor. Since eight-stranded anti-parallel beta-barrels, with a topology as in viral capsid proteins, are not generally found in other proteins involved in cell metabolism, antiviral agents that bind in the interior of viral capsid proteins are likely to be more virus-specific and less cytotoxic. Furthermore, the greatest conservation of viral capsid proteins occurs within this pocket, whereas the least conserved part is the antigenic exterior. Thus, compounds that bind to such a pocket are likely to be effective against a broader group of serologically distinct viruses. Discovery of antiviral agents of this type depends on designing compounds that can enter and fit snugly into the hydrophobic pocket of a particular viral capsid protein.

Mengo virus maturation is accompanied by C-terminal modification of capsid protein VP1

We have demonstrated that the C-terminal ends of the VP1 proteins of Mengo virus undergo a postassembly trimming of three amino acid residues. A variable proportion of the VP1 molecules isolated from purified virions terminate at Glu 277, which corresponds to the initial viral protease 3C cleavage site. The remainder of the VP1 molecules terminates at Leu 274. When chymotrypsin treatment is included in the virus purification procedure, Leu 274 is the exclusive C-terminal amino acid of the VP1 molecules. The trimming process was found to influence the pH-mediated dissociability of virions in vitro: this was demonstrated by sucrose gradient analysis and electron microscopy. Since long-term incubation of purified virions did not alter the C-terminal Glu 277/Leu 274 ratio, it appears that the trimming process is not autocatalytic.

Structural analysis of antiviral agents that interact with the capsid of human rhinoviruses

X-Ray diffraction data have been obtained for nine related antiviral agents ("WIN compounds") while bound to human rhinovirus 14 (HRV14). These compounds can inhibit both viral attachment to host cells and uncoating. To calculate interpretable electron density maps it was necessary to account for (1) the low (approximately 60%) occupancies of these compounds in the crystal, (2) the large (up to 7.9 A) conformational changes induced at the attachment site, and (3) the incomplete diffraction data. Application of a density difference map technique, which exploits the 20-fold noncrystallographic redundancy in HRV14, resulted in clear images of the HRV14:WIN complexes. A real-space refinement procedure was used to fit atomic models to these maps. The binding site of WIN compounds in HRV14 is a hydrophobic pocket composed mainly from residues that form the beta-barrel of VP1. Among rhinoviruses, the residues associated with the binding pocket are far more conserved than external residues and are mostly contained within regular secondary structural elements. Molecular dynamics simulations of three HRV14:WIN complexes suggest that portions of the WIN compounds and viral protein near the entrance of the binding pocket are more flexible than portions deeper within the beta-barrel.

Characterization of anti-idiotypic antibodies generated against foot-and-mouth disease virus neutralizing monoclonal antibodies

A series of seven neutralizing monoclonal antibodies (nMAbs) against type A12 foot-and-mouth disease virus (FMDV) was used to induce polyclonal anti-idiotypic antibodies (anti-ids) in rabbits. The anti-ids were semi-purified through isotype affinity columns and assayed by solid-phase radioimmunoassay for cross-reactivity. nMAbs which map to the same epitope on the virion appear to contain a common idiotype, and the corresponding anti-ids competitively inhibited the virus-nMAb reaction. Using a modified ELISA assay, it was possible to demonstrate binding of purified anti-ids to FMDV susceptible tissue culture cells. Such antibodies however, did not interfere with the binding of virus to cells, and the binding of anti-ids to FMDV receptor-negative cells could also be demonstrated. Mice were inoculated with purified anti-ids, and two elicited anti-viral antibodies, although these antibodies were non-neutralizing. Thus anti-ids to anti-FMDV nMAbs failed to react with cellular receptors for the virus, but were able to induce anti-viral antibody and thus should be examined as an alternative vaccine strategy for this virus.

The canyon hypothesis

The three-dimensional structure of human rhinovirus 14 has a deep surface depression or "canyon" encircling each of the twelve fivefold vertices. The canyon's surface is inaccessible to the broad antigen binding region of antibodies, permitting conservation of residues that might be required for host cell receptor recognition without danger of attack by the host's immune system. In contrast, the exposed surface features, where neutralizing antibodies are known to bind, change rapidly under pressure from the host's immune system. It was, therefore, hypothesized that this depression was the site of receptor attachment. Similar, but smaller, depressions had been observed previously on both the hemagglutinin and neuraminidase spikes of influenza virus. These have also been shown to be the site of host cell interaction. Although support for the canyon hypothesis was only circumstantial in the first place, there are now extensive confirmatory data. These include site-specific mutations of residues in the canyon and conformational changes induced in the canyon by the binding of small organic molecules, all of which alter receptor attachment. The strategy used in human rhinovirus 14 to protect the viral receptor attachment site from immune surveillance may be utilized not only in other picornaviruses but also in many other types of viruses including human immunodeficiency virus.

3D gene of foot-and-mouth disease virus. Conservation by convergence of average sequences

The nucleotide sequence of the 3D (polymerase) gene of eight epidemiologically related isolates of foot-and-mouth disease virus of serotype C1 is reported. The genetic heterogeneity of 3D RNA is compared with that of the VP1-coding RNA of the same viruses. Regression lines of substitutions per nucleotide that distinguish any pair of viruses as a function of the time interval between the corresponding isolations show: (1) the slope (substitutions/nucleotide per month) is 2.1 times larger for the VP1 RNA than for the 3D RNA region; (2) the intercept with the ordinate (substitutions/nucleotide) for VP1 RNA is indistinguishable from that for 3D RNA. Thus, the average heterogeneity of the VP1-coding region is very similar to that of the 3D-coding region only among co-circulating viruses. Nine mutations and points of heterogeneity occurred within nucleotide residues 883 to 1026, which encode an amino acid segment, extremely conserved among many different RNA viruses. The results suggest that, rather than due to inherently lower mutability, the conservation of 3D genes is caused by a limitation in the fixation of substitutions in viable genomes.

Structure of a phage 434 Cro/DNA complex

Comparison of the crystal structure of a complex of the phage 434 Cro protein and a synthetic DNA operator with the complex of the same operator and the 434 repressor DNA-binding domain shows different DNA conformations in the two structures. Binding of the protein determines the precise conformation of the DNA in each case.

Heavy riboflavin synthase from Bacillus subtilis. Crystal structure analysis of the icosahedral beta 60 capsid at 3.3 A resolution

Geometric features as well as possible functional properties of the substrate binding sites at the pentamer interfaces are described. Ligand binding at the pentamer interface regions increases the stability of the beta 60 capsid considerably and influences the reassembly of isolated beta-subunits.

Prediction of three-dimensional models for foot-and-mouth disease virus and hepatitis A virus

Atomic models of foot-and-mouth disease virus and hepatitis A virus have been predicted using amino acid sequence alignments with the known structures of Mengo virus and human rhinovirus 14. The structural models are consistent with results of biochemical and immunological studies. The two viruses appear to have surface features exceedingly different than those of other picornaviruses. They also have large hydrophobic cavities within VP1 suggesting that it may be possible to inhibit their infectivity with suitably designed antiviral agents that block uncoating.

Comparison of the nucleotide sequences of diabetogenic and nondiabetogenic encephalomyocarditis virus

The nucleotide sequences of a diabetogenic variant of encephalomyocarditis (EMC) virus (D variant, ifp- phenotype) and a nondiabetogenic variant of EMC virus (B variant, ifp+ phenotype) have been compared. These variants differ at eight sites. The poly(C) tract of EMC-B is three bases shorter than that of EMC-D. Of the seven sites at which nucleotide substitutions were confirmed using RNA templates, four resulted in amino acid changes in three different proteins, the leader peptide, 1B (VP2), and 1D (VP1). The biological significance of these differences can now be investigated.

Antigenic sites on foot-and-mouth disease virus type A10

A set of monoclonal antibodies was used to isolate nonneutralizable foot-and-mouth disease virus variants, and the RNAs of the variants were sequenced. Cross-neutralization studies and mapping of the amino acid changes indicated two major antigenic sites. The first site was trypsin sensitive and included the VP1 140 to 160 sequence. The second site was trypsin insensitive and included mainly VP3 residues. Two minor sites were located near VP1 169 and on the C terminus of VP1. Comparison with poliovirus type 1 and human rhinovirus 14 showed a similarity in the immunogenicity of comparable sites on the viruses.

Antiviral agents targeted to interact with viral capsid proteins and a possible application to human immunodeficiency virus

The tertiary structure of most icosahedral viral capsid proteins consists of an eight-stranded antiparallel beta-barrel with a hydrophobic interior. In a group of picornaviruses, this hydrophobic pocket can be filled by suitable organic molecules, which thereby stop viral uncoating after attachment and penetration into the host cell. The antiviral activity of these agents is probably due to increased rigidity of the capsid protein, which inhibits disassembly. The hydrophobic pocket may be an essential functional component of the protein and, therefore, may have been conserved in the evolution of many viruses from a common precursor. Since eight-stranded anti-parallel beta-barrels, with a topology as in viral capsid proteins, are not generally found for other proteins involved in cell metabolism, this class of antiviral agents is likely to be more virus-specific and less cytotoxic. Furthermore, the greatest conservation of viral capsid proteins occurs within this pocket, whereas the least conserved part is the antigenic exterior. Thus, compounds that bind to such a pocket are likely to be effective against a broader group of serologically distinct viruses. Discovery of antiviral agents of this type will, therefore, depend on designing compounds that can enter and fit snugly into the hydrophobic pocket of a particular viral capsid protein. The major capsid protein, p24, of human immunodeficiency virus would be a likely suitable target.

Three-dimensional model of the capsid proteins of two biologically different Theiler virus strains: clustering of amino acid difference identifies possible locations of immunogenic sites on the virion

To explore structural features of the Theiler murine encephalomyelitis virion, we have constructed a three-dimensional model of the capsid proteins (VP1, VP2, and VP3) of the BeAn strain based on the atomic coordinates of the closely related Mengo virus. By superimposition of amino acid differences between BeAn virus and another Theiler virus strain, GDVII, on the three-dimensional model, clusters of differences were found in four distinct sites; the VP1 third corner, the VP2 "puff," and the VP3 first corner and "knob." These clusters, which are found on the surface of the virion, may represent neutralizing immunogenic sites that have come under selective pressure from neutralizing antibodies. Furthermore, the putative viral receptor binding site ("pit") of the two Theiler virus strains was found to be markedly conserved.

Conservation of the putative receptor attachment site in picornaviruses

A deep canyon or pit on the surfaces of human rhinovirus 14 and Mengo virus, respectively, has been proposed as a putative receptor binding site. Amino acids lining the surface of the canyon or pit have been identified and show greater conservation than other surface residues.

Structural analysis of a series of antiviral agents complexed with human rhinovirus 14

The binding to human rhinovirus 14 of a series of eight antiviral agents that inhibit picornaviral uncoating after entry into host cells has been characterized crystallographically. All of these bind into the same hydrophobic pocket within the viral protein VP1 beta-barrel structure, although the orientation and position of each compound within the pocket was found to differ. The compounds cause the protein shell to be less flexible, thereby inhibiting disassembly. Although the antiviral potency of these compounds varies by 120-fold, they all induce the same conformational changes on the virion. The interactions of these compounds with the viral capsid are consistent with their observed antiviral activities against human rhinovirus 14 drug-resistant mutants and other rhinovirus serotypes. Crystallographic studies of one of these mutants confirm the partial sequencing data and support the finding that this is a single mutation that occurs within the binding pocket.

Antiviral agents

Potent effective antiviral drugs recently have been licensed for several viral diseases, ushering in a new era in the treatment of viral diseases. Several unique features in the process of a viral infection have been identified as target points for inhibition. The unique steps and the interfering compounds are the subject of this review.

Three-dimensional structure of poliovirus serotype 1 neutralizing determinants

Antigenic mutants of poliovirus (Sabin strain, serotype 1) were isolated by the resistance of the virus to anti-Sabin neutralizing monoclonal antibodies. The amino acid replacements within the capsid protein sequence causing the altered antigenicity were identified for each of 63 isolates. The mutations cluster into distinct nonoverlapping peptide segments that group into three general immunological phenotypes on the basis of cross-neutralization analyses with 15 neutralizing anti-Sabin monoclonal antibodies. Location of the mutated amino acid residues within the three-dimensional structure of the virion indicates that the majority of these amino acid residues are highly exposed and located within prominent structural features of the viral surface. Those mutated amino acid residues that are less accessible to antibody interaction are often involved in hydrogen bonds or salt bridges that would stabilize the local tertiary structure of the antigenic site. The interactions of the peptide segments that form these neutralizing sites suggest specific models for the generation of neutralization-resistant variants and for the interaction between the viral surface and antibody.

Molecular cloning and sequence determination of DA strain of Theiler's murine encephalomyelitis viruses

Theiler's murine encephalomyelitis viruses (TMEV) belong to the Picornaviridae, and are divided into two subgroups. TO subgroup strains produce a persistent demyelinating central nervous system infection in mice, while GDVII subgroup strains cause acute polioencephalomyelitis. We generated three overlapping clones of the genome of DA strain, a member of TO subgroup. Sequence analysis revealed that the genome is 8093 nucleotides long with a poly(A) tail. The 5' noncoding region stretches from nucleotides 1 to 1065 and lacks a poly(C) tract. The open reading frame stretches from 1066 to 7968 and encodes 2301 amino acids. DA strain sequence is more closely related to members of the Cardiovirus genus than to members of other Picornavirus genera. Comparison with sequence of BeAn strain, another TO subgroup strain, showed that the P1 area has the greatest number of differences, while the noncoding regions are more well-conserved. The three overlapping clones will be important in recombinant infectious cDNA studies between strains of both subgroups.

Amino acid differences in capsid protein, VP1, between diabetogenic and nondiabetogenic variants of encephalomyocarditis virus

The genes for the major capsid protein, VP1(1D), of both diabetogenic D variant (EMC-D) and nondiabetogenic B variant (EMC-B) of encephalomyocarditis virus were cloned by using two synthetic primers which are common to both EMC-D and EMC-B. The cloned genes were mapped for major restriction enzyme sites including AccI, BamHI, EcoRI, HincII, KpnI, PvuII, SstI, TaqI, and XbaI. Among those nine restriction enzyme sites, only the TaqI site distinguished EMC-D genome from the counterpart of EMC-B genome. The complete nucleotide sequences (831 bases) of the VP1 genes revealed five amino acid differences between the two variants. Three of the changes, at positions 41, 58, and 152, were Thr (EMC-B) to Ala (EMC-D). The additional two changes occurred at positions 63 [Gln (EMC-B) to Glu (EMC-D)] and 181 [Thr (EMC-B) to Ser (EMC-D)]. All of these amino acid changes were due to point mutations at the first base of each codon.

Complete nucleotide sequence of a cell culture-adapted variant of hepatitis A virus: comparison with wild-type virus with restricted capacity for in vitro replication

To determine the molecular changes associated with adaptation of hepatitis A virus (HAV) to growth in cell culture, the genome of a cell culture-adapted variant of HM175 strain HAV (p16 HM175, 16th in vitro passage level) was molecularly cloned and the complete nucleotide sequence of the virus was determined. Compared with wild-type virus, p16 HM175 replicates efficiently in monkey kidney (BS-C-1) cells (approximately 58 RNA-containing particles per one infectious unit, compared with 2.4 x 10(5) for wild-type HM175). The nucleotide sequence of p16 HM175 revealed a total of 19 mutations from the wild-type genome, including 5 mutations in the 5' nontranslated region, 1 mutation in the 3' nontranslated region, and 13 mutations predicting 8 changes in the amino acid sequences of HAV proteins. Only one amino acid substitution occurred among the capsid proteins (VP2), while others involved proteins 2A, 2B, 2C, VPg, and 3Dpol. When the sequence of p16 virus was compared with that reported previously for an independently isolated, cell culture-adapted variant of HM175 virus (J.I. Cohen et al., (1987). Proc. Natl. Acad. Sci. USA 84, 2497-2501), there were three identical mutations in nontranslated regions of the RNA, and four mutations involving identical amino acids in proteins VP2, 2B, and 3Dpol. The distribution of these mutations within the genome suggests that changes in RNA replication may be of primary importance in adaptation of the virus to growth in vitro. These data are thus helpful in understanding the molecular basis of adaptation of HAV to cell culture and, since attenuation frequently accompanies adaptation of virus to growth in cell culture, may be of benefit in planning for attenuated vaccine development.

Preliminary X-ray crystallographic analysis of canine parvovirus crystals

The first diffraction pattern of a crystalline single-stranded DNA virus has been obtained. Canine parvovirus was crystallized in a monoclinic P21 unit cell with a = 264.4 A, b = 350.3 A, c = 267.8 A and beta = 90.86 degrees (1 A = 0.1 nm). The diffraction pattern extends to at least 2.8 A resolution. Packing of the particles suggests that they have a diameter around 257 A, in excellent agreement with the reported molecular weight of 5.5 x 10(6).

Construction of a chimaeric type 1/type 2 poliovirus by genetic recombination

A chimaeric poliovirus carrying a type-2-specific neutralization epitope on a type 1 capsid was created by site-directed mutagenesis of the Mahoney strain of poliovirus type 1. An EcoRV and a HindIII restriction sites were first constructed in the cDNA of poliovirus type 1 at nucleotide positions 2756 and 2786, respectively, i.e. on either side of the sequence encoding neutralization epitope C3 (VP1 amino acids 93-103), which is part of neutralization site NImI. The cDNA sequence framed by the two sites was next taken out and replaced by custom-made oligonucleotides encoding the equivalent region of VP1 from the Lansing strain of poliovirus type 2. The DNA from the plasmid carrying such a hybrid construct was transfected onto CV1 cells generating a chimaeric virus, v510. Neutralization of v510 with a panel of monoclonal antibodies showed that v510 has lost the poliovirus type 1 C3 epitope but acquired a new, poliovirus type-2-specific neutralization epitope. Preliminary results indicate that v510 also shows neurovirulence for mice, which is a specific trait of the Lansing strain of poliovirus type 2.

Host and viral genetic factors which influence viral neurotropism

This chapter reviews host and viral genetic factors that influence viral neurotropism. It highlights a few recent insights that have been gained into the molecular and genetic basis for viral tropism, with specific emphasis on the factors that appear particularly relevant to understanding the basis for the tropism of viruses for the nervous system. The chapter discusses the way by which host genes, acting through a variety of mechanisms, can influence the susceptibility or resistance of animals to neurotropic viruses. It also reviews investigations concerning the role played by individual viral genes and the proteins they encode in determining specific pathways of viral spread to the central nervous system in the infected host. The chapter presents several examples illustrating the current state of knowledge concerning the nature of viral cell attachment proteins and host cell receptors for neurotropic viruses. It also presents examples of the way by which specific viral genetic elements such as enhancers can act to determine the cell-specificity of certain neurotropic viruses.

Site-specific mutations at a picornavirus VP3/VP1 cleavage site disrupt in vitro processing and assembly of capsid precursors

Most proteolytic cleavages within the picornavirus polyproteins are carried out by viral protease 3C. For encephalomyocarditis virus, the protease 3C-catalyzed processing occurs between Gln-Gly or Gln-Ser amino acid pairs which are flanked by proline residues, but the sequence-specific constraints on recognition and cleavage by the enzyme are not completely understood. To examine alternative cleavage site sequences, we constructed a cDNA plasmid which expresses the viral L-P1-2A capsid precursor in vitro and introduced site-specific mutations into the Gln-Gly pair at the VP3/VP1 junction. The altered protein substrates were tested for cleavage activity in assays with protease 3C. The encephalomyocarditis virus 3C processed Gln-Ala as efficiently as its natural sites but did not cleave Gln-Val, Gln-Glu, Lys-Gly, Lys-Ala, Lys-Val, Lys-Glu, or Pro-Gly combinations. Displacement of the flanking proline residue by an engineered insertion slowed but did not prevent cleavage at this site. Also, a mutant defective in processing at the VP3/VP1 junction was unable to form 14S pentameric assembly intermediates in vitro.