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Evaluation of serologic and antigenic relationships between middle eastern respiratory syndrome coronavirus and other coronaviruses to develop vaccine platforms for the rapid response to emerging coronaviruses.
Agnihothram S, Gopal R, Yount BL, Donaldson EF, Menachery VD, Graham RL, Scobey TD, Gralinski LE, Denison MR, Zambon M, Baric RS
(2014) J Infect Dis 209: 995-1006
MeSH Terms: Animals, Antibodies, Viral, Antigens, Viral, Blotting, Western, Chiroptera, Coronaviridae, Cross Reactions, Enzyme-Linked Immunosorbent Assay, Humans, Mice, Mice, Inbred BALB C, Middle Aged, Neutralization Tests, Nucleocapsid Proteins, Spike Glycoprotein, Coronavirus
Show Abstract · Added February 19, 2015
BACKGROUND - Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012, causing severe acute respiratory disease and pneumonia, with 44% mortality among 136 cases to date. Design of vaccines to limit the virus spread or diagnostic tests to track newly emerging strains requires knowledge of antigenic and serologic relationships between MERS-CoV and other CoVs.
METHODS -  Using synthetic genomics and Venezuelan equine encephalitis virus replicons (VRPs) expressing spike and nucleocapsid proteins from MERS-CoV and other human and bat CoVs, we characterize the antigenic responses (using Western blot and enzyme-linked immunosorbent assay) and serologic responses (using neutralization assays) against 2 MERS-CoV isolates in comparison with those of other human and bat CoVs.
RESULTS -  Serologic and neutralization responses against the spike glycoprotein were primarily strain specific, with a very low level of cross-reactivity within or across subgroups. CoV N proteins within but not across subgroups share cross-reactive epitopes with MERS-CoV isolates. Our findings were validated using a convalescent-phase serum specimen from a patient infected with MERS-CoV (NA 01) and human antiserum against SARS-CoV, human CoV NL63, and human CoV OC43.
CONCLUSIONS -  Vaccine design for emerging CoVs should involve chimeric spike protein containing neutralizing epitopes from multiple virus strains across subgroups to reduce immune pathology, and a diagnostic platform should include a panel of nucleocapsid and spike proteins from phylogenetically distinct CoVs.
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15 MeSH Terms
The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry.
Adams NM, Olmsted IR, Haselton FR, Bornhop DJ, Wright DW
(2013) Nucleic Acids Res 41: e103
MeSH Terms: Interferometry, Nucleic Acid Conformation, Nucleic Acid Hybridization, Nucleocapsid Proteins, Oligonucleotide Probes, Oligonucleotides, RNA, RNA Folding, RNA, Viral
Show Abstract · Added March 7, 2014
Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼10(5) target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits.
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9 MeSH Terms
The coiled-coil domain structure of the Sin Nombre virus nucleocapsid protein.
Boudko SP, Kuhn RJ, Rossmann MG
(2007) J Mol Biol 366: 1538-44
MeSH Terms: Amino Acid Sequence, Crystallography, X-Ray, Escherichia coli, Humans, Light, Models, Biological, Models, Molecular, Molecular Sequence Data, Nucleocapsid Proteins, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant Fusion Proteins, Scattering, Radiation, Sequence Homology, Amino Acid, Sin Nombre virus
Show Abstract · Added November 2, 2017
Hantaviruses can cause hemorrhagic fever with a renal syndrome and hantavirus pulmonary syndrome when transmitted to humans. The nucleocapsid protein of hantaviruses encapsidates viral genomic RNA and associates with transcription and replication complexes. Both the amino and carboxy termini of the nucleocapsid protein had been predicted to form trimers prior to the formation of the ribonucleoprotein. Crystal structures of amino-terminal fragments of the nucleocapsid protein showed the formation of intramolecular antiparallel coiled coils, but not intermolecular trimers. Thus, the amino-terminal part of the nucleocapsid protein is probably insufficient to initiate the trimerization of the full-length molecule.
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16 MeSH Terms
Structure of the N-terminal RNA-binding domain of the SARS CoV nucleocapsid protein.
Huang Q, Yu L, Petros AM, Gunasekera A, Liu Z, Xu N, Hajduk P, Mack J, Fesik SW, Olejniczak ET
(2004) Biochemistry 43: 6059-63
MeSH Terms: Animals, Binding Sites, Humans, Ligands, Models, Molecular, Molecular Sequence Data, Molecular Structure, Nuclear Magnetic Resonance, Biomolecular, Nucleocapsid Proteins, Protein Folding, Protein Structure, Tertiary, RNA, SARS Virus
Show Abstract · Added March 5, 2014
The severe acute respiratory syndrome (SARS) virus belongs to the Coronaviridea family of viruses. Its virion encodes several proteins including a replicase and four structural proteins. Here we describe the three-dimensional structure of the N-terminal domain of the SARS coronavirus (CoV) nucleocapsid protein. The protein consists of a five-stranded beta sheet with a folding topology distinct from other RNA-binding proteins. Single-stranded RNAs bind to the protein surface at the junction between a flexible, positively charged beta hairpin and the core structure. NMR-based screening was used to identify low molecular weight compounds that bind to this site.
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13 MeSH Terms
Mouse hepatitis virus replicase protein complexes are translocated to sites of M protein accumulation in the ERGIC at late times of infection.
Bost AG, Prentice E, Denison MR
(2001) Virology 285: 21-9
MeSH Terms: Animals, Calcium-Binding Proteins, Cell Membrane, Endoplasmic Reticulum, Fluorescent Antibody Technique, Golgi Apparatus, Membrane Glycoproteins, Mice, Microscopy, Confocal, Murine hepatitis virus, Myeloma Proteins, Nerve Tissue Proteins, Nucleocapsid, Nucleocapsid Proteins, RNA Helicases, RNA Replicase, Synaptotagmin I, Synaptotagmins, Time Factors, Tumor Cells, Cultured, Viral Proteins, Virus Replication
Show Abstract · Added February 19, 2015
The coronavirus mouse hepatitis virus (MHV) directs the synthesis of viral RNA on discrete membranous complexes that are distributed throughout the cell cytoplasm. These putative replication complexes are composed of intimately associated but biochemically distinct membrane populations, each of which contains proteins processed from the replicase (gene 1) polyprotein. Specifically, one membrane population contains the gene 1 proteins p65 and p1a-22, while the other contains the gene 1 proteins p28 and helicase, as well as the structural nucleocapsid (N) protein and newly synthesized viral RNA. In this study, immunofluorescence confocal microscopy was used to define the relationship of the membrane populations comprising the putative replication complexes at different times of infection in MHV-A59-infected delayed brain tumor cells. At 5.5 h postinfection (p.i.) the membranes containing N and helicase colocalized with the membranes containing p1a-22/p65 at foci distinct from sites of M accumulation. By 8 to 12 h p.i., however, the membranes containing helicase and N had a predominantly perinuclear distribution and colocalized with M. In contrast, the p1a-22/p65-containing membranes retained a peripheral, punctate distribution at all times of infection and did not colocalize with M. By late times of infection, helicase, N, and M each also colocalized with ERGIC p53, a specific marker for the endoplasmic reticulum-Golgi-intermediate compartment. These data demonstrated that the putative replication complexes separated into component membranes that relocalized during the course of infection. These results suggest that the membrane populations within the MHV replication complex serve distinct functions both in RNA synthesis and in delivery of replication products to sites of virus assembly.
Copyright 2001 Academic Press.
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22 MeSH Terms
Mouse hepatitis virus replicase proteins associate with two distinct populations of intracellular membranes.
Sims AC, Ostermann J, Denison MR
(2000) J Virol 74: 5647-54
MeSH Terms: Animals, Antigens, CD, Cell Fractionation, Cell Line, Centrifugation, Density Gradient, DNA Helicases, Endoplasmic Reticulum, Endosomes, Fluorescent Antibody Technique, Golgi Apparatus, Intracellular Membranes, Lysosome-Associated Membrane Glycoproteins, Lysosomes, Membrane Glycoproteins, Mice, Microscopy, Confocal, Molecular Weight, Murine hepatitis virus, Nucleocapsid, Nucleocapsid Proteins, RNA Replicase, RNA, Viral, Triiodobenzoic Acids, Viral Matrix Proteins, Viral Proteins
Show Abstract · Added February 19, 2015
The coronavirus replicase gene (gene 1) is translated into two co-amino-terminal polyproteins that are proteolytically processed to yield more than 15 mature proteins. Several gene 1 proteins have been shown to localize at sites of viral RNA synthesis in the infected cell cytoplasm, notably on late endosomes at early times of infection. However, both immunofluorescence and electron microscopic studies have also detected gene 1 proteins at sites distinct from the putative sites of viral RNA synthesis or virus assembly. In this study, mouse hepatitis virus (MHV)-infected cells were fractionated and analyzed to determine if gene 1 proteins segregated to more than one membrane population. Following differential centrifugation of lysates of MHV-infected DBT cells, gene 1 proteins as well as the structural N and M proteins were detected almost exclusively in a high-speed small membrane pellet. Following fractionation of the small membrane pellet on an iodixanol density gradient, the gene 1 proteins p28 and helicase cofractionated with dense membranes (1.12 to 1.13 g/ml) that also contained peak concentrations of N. In contrast, p65 and p1a-22 were detected in a distinct population of less dense membranes (1.05 to 1.09 g/ml). Viral RNA was detected in membrane fractions containing helicase, p28, and N but not in the fractions containing p65 and p1a-22. LAMP-1, a marker for late endosomes and lysosomes, was detected in both membrane populations. These results demonstrate that multiple gene 1 proteins segregate into two biochemically distinct but tightly associated membrane populations and that only one of these populations appears to be a site for viral RNA synthesis. The results further suggest that p28 is a component of the viral replication complex whereas the gene 1 proteins p1a-22 and p65 may serve roles during infection that are distinct from viral RNA transcription or replication.
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25 MeSH Terms
Localization of mouse hepatitis virus nonstructural proteins and RNA synthesis indicates a role for late endosomes in viral replication.
van der Meer Y, Snijder EJ, Dobbe JC, Schleich S, Denison MR, Spaan WJ, Locker JK
(1999) J Virol 73: 7641-57
MeSH Terms: Animals, Antibodies, Viral, Antigens, CD, Endocytosis, Endosomes, Fluorescent Antibody Technique, Indirect, L Cells (Cell Line), Lysosome-Associated Membrane Glycoproteins, Membrane Glycoproteins, Mice, Microscopy, Fluorescence, Murine hepatitis virus, Nucleocapsid Proteins, Open Reading Frames, RNA Helicases, RNA Replicase, RNA, Viral, Subcellular Fractions, Viral Nonstructural Proteins, Viral Proteins, Virus Replication
Show Abstract · Added February 19, 2015
The aim of the present study was to define the site of replication of the coronavirus mouse hepatitis virus (MHV). Antibodies directed against several proteins derived from the gene 1 polyprotein, including the 3C-like protease (3CLpro), the putative polymerase (POL), helicase, and a recently described protein (p22) derived from the C terminus of the open reading frame 1a protein (CT1a), were used to probe MHV-infected cells by indirect immunofluorescence (IF) and electron microscopy (EM). At early times of infection, all of these proteins showed a distinct punctate labeling by IF. Antibodies to the nucleocapsid protein also displayed a punctate labeling that largely colocalized with the replicase proteins. When infected cells were metabolically labeled with 5-bromouridine 5'-triphosphate (BrUTP), the site of viral RNA synthesis was shown by IF to colocalize with CT1a and the 3CLpro. As shown by EM, CT1a localized to LAMP-1 positive late endosomes/lysosomes while POL accumulated predominantly in multilayered structures with the appearance of endocytic carrier vesicles. These latter structures were also labeled to some extent with both anti-CT1a and LAMP-1 antibodies and could be filled with fluid phase endocytic tracers. When EM was used to determine sites of BrUTP incorporation into viral RNA at early times of infection, the viral RNA localized to late endosomal membranes as well. These results demonstrate that MHV replication occurs on late endosomal membranes and that several nonstructural proteins derived from the gene 1 polyprotein may participate in the formation and function of the viral replication complexes.
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21 MeSH Terms
The putative helicase of the coronavirus mouse hepatitis virus is processed from the replicase gene polyprotein and localizes in complexes that are active in viral RNA synthesis.
Denison MR, Spaan WJ, van der Meer Y, Gibson CA, Sims AC, Prentice E, Lu XT
(1999) J Virol 73: 6862-71
MeSH Terms: Amino Acid Sequence, Animals, Cell Membrane, Cytoplasm, Mice, Molecular Sequence Data, Murine hepatitis virus, Nucleocapsid, Nucleocapsid Proteins, Protein Processing, Post-Translational, Proteins, RNA Helicases, RNA Replicase, RNA, Viral
Show Abstract · Added February 19, 2015
The coronavirus mouse hepatitis virus (MHV) translates its replicase gene (gene 1) into two co-amino-terminal polyproteins, polyprotein 1a and polyprotein 1ab. The gene 1 polyproteins are processed by viral proteinases to yield at least 15 mature products, including a putative RNA helicase from polyprotein 1ab that is presumed to be involved in viral RNA synthesis. Antibodies directed against polypeptides encoded by open reading frame 1b were used to characterize the expression and processing of the MHV helicase and to define the relationship of helicase to the viral nucleocapsid protein (N) and to sites of viral RNA synthesis in MHV-infected cells. The antihelicase antibodies detected a 67-kDa protein in MHV-infected cells that was translated and processed throughout the virus life cycle. Processing of the 67-kDa helicase from polyprotein 1ab was abolished by E64d, a known inhibitor of the MHV 3C-like proteinase. When infected cells were probed for helicase by immunofluorescence laser confocal microscopy, the protein was detected in patterns that varied from punctate perinuclear complexes to large structures that occupied much of the cell cytoplasm. Dual-labeling studies of infected cells for helicase and bromo-UTP-labeled RNA demonstrated that the vast majority of helicase-containing complexes were active in viral RNA synthesis. Dual-labeling studies for helicase and the MHV N protein showed that the two proteins almost completely colocalized, indicating that N was associated with the helicase-containing complexes. This study demonstrates that the putative RNA helicase is closely associated with MHV RNA synthesis and suggests that complexes containing helicase, N, and new viral RNA are the viral replication complexes.
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14 MeSH Terms
Point mutations in the beta chain CDR3 can alter the T cell receptor recognition pattern on an MHC class I/peptide complex over a broad interface area.
Goyarts EC, Vegh Z, Kalergis AM, Hörig H, Papadopoulos NJ, Young AC, Thomson CT, Chang HC, Joyce S, Nathenson SG
(1998) Mol Immunol 35: 593-607
MeSH Terms: Amino Acid Sequence, Amino Acid Substitution, Animals, Antigen Presentation, Antigens, Viral, H-2 Antigens, Hybridomas, Interleukin-2, Lymphocyte Activation, Macromolecular Substances, Mice, Mice, Inbred C57BL, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Nucleocapsid, Nucleocapsid Proteins, Peptide Fragments, Point Mutation, Protein Conformation, Receptors, Antigen, T-Cell, alpha-beta, Structure-Activity Relationship, T-Lymphocytes, Cytotoxic, Transfection, Vesicular stomatitis Indiana virus
Show Abstract · Added October 2, 2015
To study how the T cell receptor interacts with its cognate ligand, the MHC/peptide complex, we used site directed mutagenesis to generate single point mutants that alter amino acids in the CDR3beta loop of a H-2Kb restricted TCR (N30.7) specific for an immunodominant peptide N52-N59 (VSV8) derived from the vesicular stomatitis virus nucleocapsid. The effect of each mutation on antigen recognition was analyzed using wild type H-2Kb and VSV8 peptide, as well as H-2Kb and VSV8 variants carrying single replacements at residues known to be exposed to the TCR. These analyses revealed that point mutations at some positions in the CDR3beta loop abrogated recognition entirely, while mutations at other CDR3beta positions caused an altered pattern of antigen recognition over a broad area on the MHC/peptide surface. This area included the N-terminus of the peptide, as well as residues of the MHC alpha1 and alpha2 helices flanking this region. Assuming that the N30 TCR docks on the MHC/peptide with an orientation similar to that recently observed in two different TCR-MHC/peptide crystal structures, our findings would suggest that single amino acid alterations within CDR3beta can affect the interaction of the TCR with an MHC surface region distal from the predicted CDR3beta-Kb/VSV8 interface. Such unique recognition capabilities are generated with minimal alterations in the CDR3 loops of the TCR. These observations suggest the hypothesis that extensive changes in the recognition pattern due to small perturbations in the CDR3 structure appears to be a structural strategy for generating a highly diversified TCR repertoire with specificity for a wide variety of antigens.
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25 MeSH Terms