Animals ; Arteritis Virus, Equine ; chemistry ; genetics ; Horses ; Open Reading Frames ; Viral Nonstructural Proteins ; chemistry ; physiology ; Viral Structural Proteins ; chemistry ; physiology

Norovirus ; chemistry ; Receptors, Virus ; physiology ; Viral Structural Proteins ; chemistry ; immunology ; Viral Vaccines ; immunology

Animals ; Herpesviridae ; genetics ; metabolism ; Humans ; Viral Proteins ; chemistry ; genetics ; metabolism

Baculoviridae ; genetics ; metabolism ; Phylogeny ; Viral Proteins ; chemistry ; classification ; genetics ; metabolism

The recent explosive outbreak of Zika virus (ZIKV) infection has been reported in South and Central America and the Caribbean. Neonatal microcephaly associated with ZIKV infection has already caused a public health emergency of international concern. No specific vaccines or drugs are currently available to treat ZIKV infection. The ZIKV helicase, which plays a pivotal role in viral RNA replication, is an attractive target for therapy. We determined the crystal structures of ZIKV helicase-ATP-Mn(2+) and ZIKV helicase-RNA. This is the first structure of any flavivirus helicase bound to ATP. Comparisons with related flavivirus helicases have shown that although the critical P-loop in the active site has variable conformations among different species, it adopts an identical mode to recognize ATP/Mn(2+). The structure of ZIKV helicase-RNA has revealed that upon RNA binding, rotations of the motor domains can cause significant conformational changes. Strikingly, although ZIKV and dengue virus (DENV) apo-helicases share conserved residues for RNA binding, their different manners of motor domain rotations result in distinct individual modes for RNA recognition. It suggests that flavivirus helicases could have evolved a conserved engine to convert chemical energy from nucleoside triphosphate to mechanical energy for RNA unwinding, but different motor domain rotations result in variable RNA recognition modes to adapt to individual viral replication.
Crystallography, X-Ray ; Protein Domains ; RNA Helicases ; chemistry ; RNA, Viral ; chemistry ; Viral Proteins ; chemistry ; Zika Virus ; enzymology

Codon ; Dengue Virus ; chemistry ; genetics ; Gene Expression ; Genes, Viral ; Hydrophobic and Hydrophilic Interactions ; Viral Structural Proteins ; genetics

The secondary structures of fusion protein pp150/MDBP, including alpha-helix, beta-sheet, turn regions, were analyzed by Garnier-Robson's and Chou-Fasman's methods; the antigenic epitopes of B cells were analysed by using hydrophilicity plot. The results showed that the fusion protein pp150/MDBP might have less alpha-helix, but be rich in beta-sheet and turn regions. The epitopes recognized by B cells may be at 7-56 amino acid residues or adjacent to 137-192 amino acid residues.
Amino Acid Sequence ; Binding Sites ; Cytomegalovirus ; chemistry ; Epitopes ; Humans ; Molecular Sequence Data ; Phosphoproteins ; chemistry ; immunology ; Protein Structure, Secondary ; Viral Fusion Proteins ; chemistry ; immunology ; Viral Matrix Proteins ; chemistry ; immunology

The Cre recombinase, an integrase from bacteriophage P1, catalyzes site-specific recombination between 34-bp repeats termed loxP sites, in the absence of any additional cofactors and energy. Mediated by Cre recombinase, specific DNA fragments can be excised, inversed or integrated depending on the orientation or position of loxP sites in vitro or in vivo. Because of its simplicity and high efficiency, Cre/loxP site-specific recombination system has been widely used in gene deletion and function identification, gene site-specific integration, gene trapping and chromosome engineering. It has been used as a useful tool for DNA recombination in transgenic yeast, plants, insects and mammals. Here progress in the study of the structure and function of Cre recombinase is discussed.
Integrases ; chemistry ; physiology ; Organisms, Genetically Modified ; Recombination, Genetic ; Viral Proteins ; chemistry ; physiology

Faldaprevir analogue molecule (FAM) has been reported to effectively inhibit the catalytic activity of HCV NS3/4A protease, making it a potential lead compound against HCV. A series of HCV NS3/4A protease crystal structures were analyzed by bioinformatics methods, and the FAM-HCV NS3/4A protease crystal structure was chosen for this study. A 20.4 ns molecular dynamics simulation of the complex consists of HCV NS3/4A protease and FAM was conducted. The key amino acid residues for interaction and the binding driving force for the molecular recognition between the protease and FAM were identified from the hydrogen bonds and binding free energy analyses. With the driving force of hydrogen bonds and van der Waals, FAM specifically bind to the active pocket of HCV NS3/4A protease, including V130-S137, F152-D166, D77-D79 and V55, which agreed with the experimental data. The effect of R155K, D168E/V and V170T site-directed mutagenesis on FAM molecular recognition was analyzed for their effect on drug resistance, which provided the possible molecular explanation of FAM resistance. Finally, the system conformational change was explored by using free energy landscape and conformational cluster. The result showed four kinds of dominant conformation, which provides theoretical basis for subsequent design of Faldaprevir analogue inhibitors based on the structure of HCV NS3/4A protease.
Antiviral Agents ; chemistry ; Carrier Proteins ; chemistry ; Drug Resistance, Viral ; Endopeptidases ; Hepacivirus ; Molecular Dynamics Simulation ; Mutagenesis, Site-Directed ; Oligopeptides ; chemistry ; Protease Inhibitors ; chemistry ; Serine Proteases ; Thiazoles ; chemistry ; Viral Nonstructural Proteins ; chemistry

Hepatitis C virus (HCV) is a positive sense, single-stranded RNA virus in the Flaviviridae family. It causes acute hepatitis with a high propensity for chronic infection. Chronic HCV infection can progress to severe liver disease including cirrhosis and hepatocellular carcinoma. In the last decade, our basic understanding of HCV virology and life cycle has advanced greatly with the development of HCV cell culture and replication systems. Our ability to treat HCV infection has also been improved with the combined use of interferon, ribavirin and small molecule inhibitors of the virally encoded NS3/4A protease, although better therapeutic options are needed with greater antiviral efficacy and less toxicity. In this article, we review various aspects of HCV life cycle including viral attachment, entry, fusion, viral RNA translation, posttranslational processing, HCV replication, viral assembly and release. Each of these steps provides potential targets for novel antiviral therapeutics to cure HCV infection and prevent the adverse consequences of progressive liver disease.
Antigens, CD81/metabolism ; Genome, Viral ; Hepacivirus/genetics/*physiology ; Humans ; RNA, Viral/metabolism ; Scavenger Receptors, Class B/metabolism ; Viral Envelope Proteins/chemistry/metabolism ; Viral Nonstructural Proteins/chemistry/metabolism ; Virus Assembly ; Virus Internalization ; Virus Replication