甲型H1N1流感病毒蛋白质序列的预测

目的:用长记忆模型预测未来年份的甲型H1N1流感病毒的蛋白质序列.方法:基于时间序列分析,首先建立CGR混沌游走序列,再进行模型拟合.对所选取的1943年～2012年同源性相对较高的70条流感病毒蛋白质序列,先混沌游走再用ARFIMA(p,d,q)模型对其前10个位置去拟合并且预测.结果:几乎所有原始蛋白质序列的各个位置值都在预报区域内(除极个别之外),表明选择的模型比较科学.结论:可以用来预测未来年份的流感病毒蛋白质序列,对流感病毒的预测和预防有着重要的研究价值.     

Intracellular Cleavage of Human Influenza A Virus Hemagglutinin and Its Inhibition

Replication of human influenza A viruses and proteolytic cleavage of the viral glycoprotein HA0 HA1/2 were studied in passaged cultures of epithelial cells of the serous membrane of human large intestine (CACO-2 line), dog kidney cells (MDCK), and monkey kidney cells (CV-1). Cleavage of the viral glycoprotein HA0, synthesis of activated virions, multicycle virus infection, and effective production of viral foci under an agarose overlayer were found in CACO-2 cells. By pulse–chase labeling of viral glycoproteins, testing the sensitivity to endoglycosidase-H of the viral glycoproteins HA0 and HA1/2 synthesized, and inhibiting the HA0 proteolysis with brefeldin A, the HA0 HA1/2 proteolysis was established to occur in the late stages of intracellular transport in the trans-Golgi and plasma membrane areas of the cells. Proteolysis of the viral glycoprotein HA0 in CACO-2 cells was suppressed by aprotinin, a natural inhibitor of serine proteinases. Unlike MDCK and CV-1 cells resistant to apoptosis induced by influenza virus, CACO-2 cells retained their viability for 2-3 days after infection with human influenza A virus.     

Aggregation of Influenza A Virus Nuclear Export Protein

Influenza A virus nuclear export protein (NEP) plays an important role in the viral life cycle. Recombinant NEP proteins containing (His)₆-tag at either N-or C-terminus were obtained by heterologous expression in Escherichia coli cells and their high propensity for aggregation was demonstrated. Dynamic light scattering technique was used to study the kinetics and properties of NEP aggregation in solutions under different conditions (pH, ionic strength, presence of low-molecular-weight additives and organic solvents). Using atomic force microscopy, the predominance of spherical aggregates in all examined NEP preparations was shown, with some amyloid-like structures being observed in the case of NEP-C protein. A number of structure prediction programs were used to identify aggregation-prone regions in the NEP structure. All-atom molecular dynamics simulations indicate a high rate of NEP molecule aggregation and reveal the regions preferentially involved in the intermolecular contacts that are located at the edges of the rod-like protein molecule. Our results suggest that NEP aggregation is determined by different types of interactions and represents an intrinsic property of the protein that appears to be necessary for its functioning in vivo.     

Impact of VP1-Specific Protein Sequence Motifs on Adeno-Associated Virus Type 2 Intracellular Trafficking and Nuclear Entry

Adeno-associated virus type 2 (AAV2) has gained much interest as a gene delivery vector. A hallmark of AAV2-mediated gene transfer is an intracellular conformational change of the virus capsid, leading to the exposure of infection-relevant protein domains. These protein domains, which are located on the N-terminal portion of the structural proteins VP1 and VP2, include a catalytic phospholipase A(2) domain and three clusters of basic amino acids. We have identified additional protein sequence motifs located on the VP1/2 N terminus that also proved to be obligatory for virus infectivity. These motifs include signals that are known to be involved in protein interaction, endosomal sorting and signal transduction in eukaryotic cells. Among different AAV serotypes they are highly conserved and mutation of critical amino acids of the respective motifs led to a severe infection-deficient phenotype. In particular, mutation of a YXXQ-sequence motif significantly reduced accumulation of virus capsids around the nucleus in comparison to wild-type AAV2. Interestingly, intracellular trafficking of AAV2 was shown to be independent of PLA(2) activity. Moreover, mutation of three PDZ-binding motifs, which are located consecutively at the very tip of the VP1 N terminus, revealed a nuclear transport-defective phenotype, suggesting a role in nuclear uptake of the virus through an as-yet-unknown mechanism.     

Structural Analysis of Influenza A Virus Matrix Protein M1 and Its Self-Assemblies at Low pH

Influenza A virus matrix protein M1 is one of the most important and abundant proteins in the virus particles broadly involved in essential processes of the viral life cycle. The absence of high-resolution data on the full-length M1 makes the structural investigation of the intact protein particularly important. We employed synchrotron small-angle X-ray scattering (SAXS), analytical ultracentrifugation and atomic force microscopy (AFM) to study the structure of M1 at acidic pH. The low-resolution structural models built from the SAXS data reveal a structurally anisotropic M1 molecule consisting of a compact NM-fragment and an extended and partially flexible C-terminal domain. The M1 monomers co-exist in solution with a small fraction of large clusters that have a layered architecture similar to that observed in the authentic influenza virions. AFM analysis on a lipid-like negatively charged surface reveals that M1 forms ordered stripes correlating well with the clusters observed by SAXS. The free NM-domain is monomeric in acidic solution with the overall structure similar to that observed in previously determined crystal structures. The NM-domain does not spontaneously self assemble supporting the key role of the C-terminus of M1 in the formation of supramolecular structures. Our results suggest that the flexibility of the C-terminus is an essential feature, which may be responsible for the multi-functionality of the entire protein. In particular, this flexibility could allow M1 to structurally organise the viral membrane to maintain the integrity and the shape of the intact influenza virus.     

Soluble Antigens of Vaccinia-infected Mammalian Cells II. Time Course of Synthesis of Soluble Antigens and Virus Structural Proteins

Virus-induced soluble antigens produced in mammalian cells after infection with vaccinia virus can be divided into two classes on the basis of molecular weight. Synthesis of the low molecular weight antigens begins early in the course of infection (1 to 2 hr), and is switched-off rather abruptly 4 to 5 hr after infection in a manner similar to that reported for the early enzymes characteristic of this same system. It was demonstrated, however, that these antigens do not include virus-induced thymidine kinase, a major virus-induced enzyme, nor is it likely that the low molecular weight antigens described here share identity with any of the virus-induced enzymes. A portion of the low molecular weight antigens appear to be incorporated into the structure of newly synthesized virus, probably as internal proteins. In contrast, synthesis of the high molecular weight antigen class is initiated later in the course of infection (4 to 5 hr), just prior to the appearance of newly synthesized virus. Antiserum directed specifically against virus structural proteins forms precipitin bands with all of the high molecular weight antigens recognizable by immunoelectrophoresis. This evidence, coupled with the observation that the high molecular weight antigen fraction elicits production of specific virus-neutralizing antibody, strongly suggests that this antigen class represents virus structural subunits produced in excess.     

Preferential Phosphorylation of NP-Protein of Influenza A2 Virus by Virion-Associated Protein Kinase

Influenza A₂ virions were found to contain protein kinase activity which was stimulated, like in other virion-associated kinases, with Mg⁺⁺ and Nonidet-P 40 but not with cyclic AMP. The kinase phosphorylated only the NP-protein fraction of the influenza virions in the in vitro reaction. In contrast, none of the influenza virion proteins were phosphorylated significantly during the process of virus production in infected chorioallantoic membranes, The in vitro and in vivo phosphorylations of influenza viral proteins were compared with those of Sendai virus (HVJ).     

NS1 Protein of Influenza A Virus Down-Regulates Apoptosis

Wild-type (WT) influenza A/PR/8/34 virus and its variant lacking the NS1 gene (delNS1) have been compared for their ability to mediate apoptosis in cultured cells and chicken embryos. Cell morphology, fragmentation of chromatin DNA, and caspase-dependent cleavage of the viral NP protein have been used as markers for apoptosis. Another marker was caspase cleavage of the viral M2 protein, which was also found to occur in an apoptosis-specific manner. In interferon (IFN)-competent host systems, such as MDCK cells, chicken fibroblasts, and 7-day-old chicken embryos, delNS1 virus induced apoptosis more rapidly and more efficiently than WT virus. As a consequence, delNS1 virus was also more lethal for chicken embryos than WT virus. In IFN-deficient Vero cells, however, apoptosis was delayed and developed with similar intensity after infection with both viruses. Taken together, these data indicate that the IFN antagonistic NS1 protein of influenza A viruses has IFN-dependent antiapoptotic potential.     

流感病毒A非结构蛋白功能的研究进展

流感病毒属正粘病毒科(Orthomyxoviridae),是一种带包膜并且分节段的单负链RNA病毒。根据病毒核衣壳蛋白(Nucleocapsid)和基质蛋白(Matrix,M)抗原性的差异,流感病毒可分为甲、乙、丙3个型。甲型流感病毒呈球形或丝状,其RNA基因组总长度在13.6kb左右,分为8个节段,共编码10个蛋白     

Structural Requirements for the Antiviral Activity of the Human MxA Protein against Thogoto and Influenza A Virus

The interferon-induced dynamin-like MxA protein has broad antiviral activity against many viruses, including orthomyxoviruses such as influenza A and Thogoto virus and bunyaviruses such as La Crosse virus. MxA consists of an N-terminal globular GTPase domain, a connecting bundle signaling element, and the C-terminal stalk that mediates oligomerization and antiviral specificity. We previously reported that the disordered loop L4 that protrudes from the compact stalk is a key determinant of antiviral specificity against influenza A and Thogoto virus. However, the role of individual amino acids for viral target recognition remained largely undefined. By mutational analyses, we identified two regions in the C-terminal part of L4 that contribute to an antiviral interface. Mutations in the proximal motif, at positions 561 and 562, abolished antiviral activity against orthomyxoviruses but not bunyaviruses. In contrast, mutations in the distal motif, around position 577, abolished antiviral activity against both viruses. These results indicate that at least two structural elements in L4 are responsible for antiviral activity and that the proximal motif determines specificity for orthomyxoviruses, whereas the distal sequence serves a conserved structural function.     

Computational Identification of Antigenicity-Associated Sites in the Hemagglutinin Protein of A/H1N1 Seasonal Influenza Virus

The antigenic variability of influenza viruses has always made influenza vaccine development challenging. The punctuated nature of antigenic drift of influenza virus suggests that a relatively small number of genetic changes or combinations of genetic changes may drive changes in antigenic phenotype. The present study aimed to identify antigenicity-associated sites in the hemagglutinin protein of A/H1N1 seasonal influenza virus using computational approaches. Random Forest Regression (RFR) and Support Vector Regression based on Recursive Feature Elimination (SVR-RFE) were applied to H1N1 seasonal influenza viruses and used to analyze the associations between amino acid changes in the HA1 polypeptide and antigenic variation based on hemagglutination-inhibition (HI) assay data. Twenty-three and twenty antigenicity-associated sites were identified by RFR and SVR-RFE, respectively, by considering the joint effects of amino acid residues on antigenic drift. Our proposed approaches were further validated with the H3N2 dataset. The prediction models developed in this study can quantitatively predict antigenic differences with high prediction accuracy based only on HA1 sequences. Application of the study results can increase understanding of H1N1 seasonal influenza virus antigenic evolution and accelerate the selection of vaccine strains.     

A Novel Influenza Virus Hemagglutinin-Respiratory Syncytial Virus (RSV) Fusion Protein Subunit Vaccine against Influenza and RSV

Influenza A virus and respiratory syncytial virus (RSV) cause substantial morbidity and mortality afflicting the ends of the age spectrum during the autumn through winter months in the United States. The benefit of vaccination against RSV and influenza using a subunit vaccine to enhance immunity and neutralizing antibody was investigated. Influenza virus hemagglutinin (HA) and RSV fusion (F) protein were tested as vaccine components alone and in combination to explore the adjuvant properties of RSV F protein on HA immunity. Mice vaccinated with HA and F exhibited robust immunity that, when challenged, had reduced viral burden for both influenza and RSV. These studies show an enhancing and cross-protective benefit of F protein for anti-HA immunity.     

Proton Channel Activity of Influenza A Virus Matrix Protein 2 Contributes to Autophagy Arrest

Influenza A virus infection can arrest autophagy, as evidenced by autophagosome accumulation in infected cells. Here, we report that this autophagosome accumulation can be inhibited by amantadine, an antiviral proton channel inhibitor, in amantadine-sensitive virus infected cells or cells expressing influenza A virus matrix protein 2 (M2). Thus, M2 proton channel activity plays a role in blocking the fusion of autophagosomes with lysosomes, which might be a key mechanism for arresting autophagy.     

中国流感病毒结构生物学研究——40年回眸

自20世纪70年代以来,中国结构生物学研究日新月异,在多个生命科学领域取得了丰硕成果.近年来,在流感病毒研究领域,也做出了不少出色工作,包括流感病毒的跨种间传播机制和聚合酶复合物结构解析等.本文对国内外流感病毒蛋白的结构生物学进展做一简单总结,为大家提供一个视角,纵观我国病毒结构生物学的发展历程.     

Synthesis and Cleavage of Influenza Virus Proteins

The NWS strain of influenza virus grows rapidly in and kills the MDCK dog kidney cell strain. Within 1 to 2 hr, the virus inhibits host cell protein synthesis and for 3 to 4 hr more it directs the synthesis of influenza virus proteins at a rate about twice that of uninfected cell synthesis. The rates of virus ribonucleic acid (RNA) and protein synthesis reach a maximum within the first few hours after infection and then drop. Plaque assays exhibit a linear dose-response, indicating that only one virion is necessary for productive infection. We have confirmed earlier reports regarding the fragmented nature of the RNA genome of purified influenza virions. However, high resolution gel electrophoresis indicated that each size class of viral RNA is heterogenous, so that there are at least 10 and probably more fragment sizes of RNA in these virions. Repeated attempts to detect infectivity in preparations of extracted viral RNA were completely negative (over a 10(8)-fold loss of infectivity after extraction). Even infection of the "infectious" RNA-treated cells with intact, related, influenza viruses failed to support infectivity of the isolated RNA or to rescue a host range genetic marker of the RNA. Purified influenza virions exhibit only three major protein peaks based on separation according to molecular weights. These three major virion proteins are the only major virion proteins synthesized in infected cells. This is true throughout the infectious cycle from several hours after infection until the cells are dying. However, the molecular weight of these virion proteins differs slightly depending upon the cell type in which the virus is grown. No host membrane proteins are incorporated into the virions as they bud through the cell membrane. Pulse-chase labeling early after infection or prolonged chase experiments indicate that influenza virus proteins are cleaved from one or more precursor polypeptides. In fact, each of the three major peaks seems to be a heterogeneous mixture of polypeptides in various stages of cleavage. Peptide analysis confirms that the three major peaks share common peptides, but the exact precursor product relationships are not clear. There may be one or several precursor proteins. Also there could be overlapping messenger RNA molecules of varying length giving rise to polypeptides of various sizes and overlapping sequences. Late in infection, amino acid labeling shows a preponderance of internal nucleocapsid protein synthesis, indicating that either this protein is much more stable to cleavage in infection or it is made from a more stable messenger. There is no obvious relationship between virion RNA fragments and viral protein sizes, so these fragments may be artifacts.