Cryo-EM structure of a bacteriophage T4 gp24 bypass mutant: the evolution of pentameric vertex proteins in icosahedral viruses

Many large viral capsids require special pentameric proteins at their fivefold vertices. Nevertheless, deletion of the special vertex protein gene product 24 (gp24) in bacteriophage T4 can be compensated by mutations in the homologous major capsid protein gp23. The structure of such a mutant virus, determined by cryo-electron microscopy to 26 angstroms, shows that the gp24 pentamers are replaced by mutant major capsid protein (gp23) pentamers at the vertices, thus re-creating a viral capsid prior to the evolution of specialized major capsid proteins and vertex proteins. The mutant gp23* pentamer is structurally similar to the wild-type gp24* pentamer but the insertion domain is slightly more distant from the gp23* pentamer center. There are additional SOC molecules around the gp23* pentamers in the mutant virus that were not present around the gp24* pentamers in the wild-type virus.     

Suppressors of RNA silencing encoded by plant viruses and their role in viral infections

RNA silencing as a robust host defense mechanism against plant viruses is generally countered by virus-encoded silencing suppressors. This strategy is now increasingly recognized to be used by animal viruses as well. We present here an overview of the common features shared by some of the better studied plant viral silencing suppressors. We then briefly describe the characteristics of the few reported animal viral suppressors, notably their extraordinary ability of cross-kingdom suppression. We next discuss the basis for biased protection of viral RNA and subviral parasites by silencing suppressors, the link between movement and silencing suppression, the influence of temperature on the outcome of viral infection and the effect of viral silencing suppressors on the microRNA pathway.     

Interaction of metal ions with neurotransmitter receptors and potential role in neurodiseases

There is increasing evidence that toxic metals play a role in diseases of unknown etiology. Their action is often mediated by membrane proteins, and in particular neurotransmitter receptors. This brief review will describe recent findings on the direct interaction of metal ions with ionotropic γ-aminobutyric acid (GABA_A) and glutamate receptors, the main inhibitory and excitatory neurotransmitter receptors in the mammalian central nervous system, respectively. Both hyper and hypo function of these receptors are involved in neurological and psychotic syndromes and modulation by metal ions is an important pharmacological issue. The focus will be on three xenobiotic metals, lead (Pb), cadmium (Cd) and nickel (Ni) that have no biological function and whose presence in living organisms is only detrimental, and two trace metals, zinc (Zn) and copper (Cu), which are essential for several enzymatic functions, but can mediate toxic actions if deregulated. Despite limited access to the brain and tight control by metalloproteins, exogenous metals interfere with receptor performances by mimicking physiological ions and occupying one or more modulatory sites on the protein. These interactions will be discussed as a potential cause of neuronal dysfunction.     

Viral metagenomics reveals diverse viruses in the fecal samples of children with diarrhea

Diarrhea is the third leading cause of death in developing countries in children under the age of five. About half a million children die of diarrhea every year, most of which in developing countries. Viruses are the main pathogen of diarrhea. In China, the fecal virome of children with diarrhea has been rarely studied. Using an unbiased viral metagenomics approach, we analyzed the fecal virome in children with diarrhea. Many DNA or RNA viruses associated with diarrhea identified in those fecal samples were mainly from six families of Adenoviridae, Astroviridae, Caliciviridae, Parvoviridae, Picornaviridae, and Reoviridae. Among them, the family of Caliciviridae accounts for the largest proportion of 78.42%, following with Adenoviridae (8.94%) and Picornaviridae (8.36%). In addition to those diarrhea-related viruses that have already been confirmed to cause human diarrhea, the viruses not associated with diarrhea were also identified including anellovirus and picobirnavirus. This study increased our understanding of diarrheic children fecal virome and provided valuable information for the prevention and treatment of viral diarrhea in this area.     

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.     

Isothermal titration calorimetry of metal ions binding to proteins: An overview of recent studies

Isothermal titration calorimetry (ITC) is a technique that is capable of quantifying the stoichiometry, equilibrium constants and thermodynamics of molecular binding events. Thus, important information about the interaction of metal ions with biological macromolecules can be obtained with ITC measurements. This review highlights many of the recent studies of metal ions binding to proteins that have used ITC to quantify the thermodynamics of metal-protein interactions.     

Some effects of metal ions on DNA structure and genetic information transfer

The reaction of metal ions with nucleic acids can lead to a variety of dramatic effects on nucleic acid structure, e.g., crosslinking of the polymer strands, degradation to oligomers and monomers, stabilization or destabilization, and the mispairing of bases. These effects have important implications for genetic information transfer. Metal ions are involved in many aspects of this transfer; we are presently concerned with the effect of metal ions on the orientation of the active site of RNA polymerase. Many of the effects of metal ions on nucleic acid structure involve changes in the conformation of the macromolecules. We have found that conditions that have been used to convert B DNA to Z DNA lead to at least two other conformational changes, and phase diagrams delineate the realms of stability of each of the forms. We have carried out a number of studies that demonstrate that the conversion of B to Z DNA is very closely correlated with a substantial decrease in the ability of the DNA to act as a template for RNA synthesis. A portion of this paper has been taken from another paper on “Changes of Biological Significance Induced by Metal Ions in the Structure of Nucleic Acids,” published in Annali dell' lstituto Superiore di Sanita.     

Studies on the effect of divalent metal ions on exfoliative toxins from Staphylococcus hyicus: indications of ExhA and ExhB being metalloproteins

The exfoliative toxins ExhA and ExhB produced by Staphylococcus hyicus strains NCTC10350 and 1289D-88, respectively, were investigated with regard to the effect of divalent metal ions on toxin production as measured in indirect enzyme-linked immunosorbent assay (ELISA) using monoclonal antibodies. Data were obtained as endpoint titer values and used as semiquantitative measures for the amount of exfoliative toxin detected in culture supernatants. It was shown that the endpoint titers of ExhA in supernatants from cultures of strain NCTC10350 grown in the presence of 0.5 mM CaCl2, Cu(NO3)2 or ZnSO4 were higher compared to titers obtained by growth in medium supplemented with a number of other divalent metal salts. The titer of ExhB as determined in the indirect ELISA was increased by addition of 0.5 mM CoCl2, Cu(NO3)2 or CuSO4 to the growth medium. When ExhA or ExhB, prepared without addition of metal salt to the liquid growth medium, was subsequently incubated with 25 mM of Co2+, Cu2+ or Zn2+, the endpoint titers of the toxins were increased. Dialysis of ExhA and ExhB prepared with Zn2+ and Co2+, respectively, against certain metal chelators, resulted in a reduction of the titer determined in ELISA. Other metal chelators had varied effect in the detection of the toxins in ELISA. It was, however, not possible to restore the recognition of toxins by the monoclonal antibodies by incubation of EDDHA-dialyzed toxin preparations with Co2+, Cu2+ or Zn2+. The results of this study suggest that ExhA and ExhB are metalloproteins.     

Direct Interaction of the Bacteriophage SPP1 Packaging ATPase with the Portal Protein

DNA packaging in tailed bacteriophages and other viruses requires assembly of a complex molecular machine at a specific vertex of the procapsid. This machine is composed of the portal protein that provides a tunnel for DNA entry, an ATPase that fuels DNA translocation (large terminase subunit), and most frequently, a small terminase subunit. Here we characterized the interaction between the terminase ATPase subunit of bacteriophage SPP1 (gp2) and the procapsid portal vertex. We found, by affinity pulldown assays with purified proteins, that gp2 interacts with the portal protein, gp6, independently of the terminase small subunit gp1, DNA, or ATP. The gp2-procapsid interaction via the portal protein depends on gp2 concentration and requires the presence of divalent cations. Competition experiments showed that isolated gp6 can only inhibit gp2-procapsid interactions and DNA packaging at gp6:procapsid molar ratios above 10-fold. Assays with gp6 carrying mutations in distinct regions of its structure that affect the portal-induced stimulation of ATPase and DNA packaging revealed that none of these mutations impedes gp2-gp6 binding. Our results demonstrate that the SPP1 packaging ATPase binds directly to the portal and that the interaction is stronger with the portal embedded in procapsids. Identification of mutations in gp6 that allow for assembly of the ATPase-portal complex but impair DNA packaging support an intricate cross-talk between the two proteins for activity of the DNA translocation motor.     

Signal transduction in monocytes: the role of zinc ions

The availability of zinc has a regulatory role in the immune system. It can have either pro- or anti-inflammatory effects, which both seem to be a consequence of a direct interaction of zinc with the cytokine secretion by monocytes. In this review, the molecular basis for this effect, the interaction of zinc with the signal transduction of monocytes, is discussed. In particular, zinc seems to activate or inhibit several signaling pathways that interact with the signal transduction of pathogen sensing receptors, the so-called Toll-like receptors (TLR), which sense pathogen-derived molecular structures and, upon activation, lead to secretion of pro-inflammatory cytokines. The interaction of zinc with protein tyrosine phosphatases and protein kinase C, and a direct modulation of lipopolysaccharide binding to its receptor (TLR-4) all result in enhanced cytokine production. On the other hand, a complex interaction between zinc, NO and cyclic nucleotide signaling, and inhibition of interleukin-1 receptor associated kinase-1, and inhibitor of kappa B kinase all counteract the production of pro-inflammatory cytokines. A role for the zinc binding protein metallothionein as a regulator for intracellular zinc signaling is discussed. By acting on all these signaling molecules, the zinc status of monocytes can have a direct effect on inflammation.     

Properties of microsolvated ions: from the microenvironment of chromophore and alkali metal ions in proteins to negative ions in water clusters

Here we discuss the fascinating chemistry and physics of microsolvated ions that bridge the transition from bare ions in gas phase to ions in solution. Such ions occur in many situations in biochemistry and are crucial for several functions; metal ions, for example, must remove their water shell to pass through ion pumps in membranes. Furthermore, only a few water molecules are buried in the hydrophobic pockets of proteins where they are bound to charged amino acid residues or ionic chromophores. Another aspect is the reactivity of microsolvated ions and the importance in atmospheric, organic and inorganic chemistry. We close by a discussion of the stability of molecular dianions, and how hydration affects the electronic binding energy. There is a vast literature on microsolvated ions, and in this review we are far from being comprehensive, rather we mainly bring examples of our own work.     

Metagenomic analysis of viral community in the Yangtze River expands known eukaryotic and prokaryotic virus diversity in freshwater

Viruses in aquatic ecosystems are characterized by extraordinary abundance and diversity. Thus far, there have been limited studies focused on viral communities in river water systems. Here, we investigated the virome of the Yangtze River Delta using viral metagenomic analysis. The compositions of viral communities from six sampling sites were analyzed and compared. By using library construction and next generation sequencing, contigs and singlet reads similar to viral sequences were classified into 17 viral families, including nine dsDNA viral families, four ssDNA viral families and four RNA viral families. Statistical analysis using Friedman test suggested that there was no significant difference among the six sampling sites (P > 0.05). The viromes in this study were all dominated by the order Caudovirales, and a group of Freshwater phage uvFW species were particularly prevalent among all the samples. The virome from Nanjing presented a unique pattern of viral community composition with a relatively high abundance of family Parvoviridae. Phylogenetic analyses based on virus hallmark genes showed that the Caudovirales order and CRESS-DNA viruses presented high genetic diversity, while viruses in the Microviridae and Parvoviridae families and the Riboviria realm were relatively conservative. Our study provides the first insight into viral community composition in large river ecosystem, revealing the diversity and stability of river water virome, contributing to the proper utilization of freshwater resource.     

Structural exploration of viral matrix protein 40 interaction with the transition metal ions (Ag+ and Cu2+)

Here, a theoretical and comprehensive study of the structural features and interaction properties of viral protein 40 is being briefed out to understand the mechanism of Ebola virus (EV) with structural and orbital analysis. In general, viral protein 40 is the key protein for the oligomerization, the N-terminal loop region in the viral protein 40 and it is essential for the viral replication in Ebola. The electronic structures of native N-terminal loop (His124-Asn134) and metalized (Mⁿ⁺=Ag⁺ and Cu²⁺) complexes are optimized at the M06-2X/LANL2DZ level of theory. Among Mⁿ⁺-interacted N-loop complexes, Cu²⁺-interacted N-terminal loop complex has the highest interaction energy of –973.519?kcal/mol and also it has the stabilization energy in the range of 9.92?kcal/mol. The cation-π interactions between His124, Pro131 and Arg134 residues are the important factor, which enhances the interaction energy of viral protein 40. Due to the chelation behavior of metal ions, the backbone and the side chains of N-terminal loop regions are deviated from the planarity that results in the formation of classical hydrogen bonds between N-terminal loop regions. Molecular dynamics simulation studies also revealed that the structural transformations of Nloop into a stable α-helix and β-sheet folded conformations due to the interaction of Ag⁺ and Cu²⁺ ions in the N-terminal loop region. The hydrogen bond formation and hydrophobic interactions are responsible for the stability and structural changes in N-terminal loop region. Therefore, it is clear that interaction of metal ion with viral protein-40 reduces the replication of the disease by inducing the secondary structural changes.

Communicated by Ramaswamy H. Sarma     

Interaction between viral proteins with the transmission of Potyvirus

Potyviridae is the largest family in plant viruses, in which a group of potyviruses constitutes a very important role in causing diseases in plants. The organisation of the viral genome is positive-sense RNA, ranging in size from 9000 to 12000?bp. The viral genome encodes a large polyprotein that is processed by three virus-encoded proteinases (two proteinases and helper component proteinase) to yield the mature products. This review concentrates on the interaction between viral proteins with the transmission of Potyvirus. Transmission and long-distance movement of Potyvirus is only possible through vector and that time interaction between two viral proteins takes place, named as helper component-proteinase and coat protein. Interaction between NIb, NIa, 6K2 as well as with CI (helicase activity) also involved in the replication of potyviruses. Some researchers developed a yeast two-hybrid system and biomolecular fluorescence complementation system technology which proved the interaction among the viral protein. At last all proteins are correlated with each other and play a very significant role in the transmission of Potyvirus.     

Effect of different metal ions on the oxidative damage and antioxidant capacity of hyaluronic acid

Degradation and the antioxidative effect of Na-, Zn-, Co-, Cu-, and Mn-hyaluronic acid (HA) associates were studied. Our findings revealed the protective effect of certain counterions against ROS-induced HA degradation. We could also separate the antioxidative effect of certain counterions from that of the HA by examining the effect of the counterions in their free ionic forms. The result showed that metal ions with altering oxidative status (Co(2+), Cu(2+), Mn(2+)) proved to be effective in themselves or their effect added to that of HA when HA was also effective. Moreover, the effects of Co-HA against z.rad;O(2)(-) and of Mn-HA against ONOO(-) as well as the synergic effect of Zn-HA associates where Zn(2+) is of fixed oxidative status were attributed to the structure-stabilizing complex formed between certain counterions and HA. Our examination also concerned the influence of HA associates on the indirect antioxidation related to Fe(2+) chelating. The individual effects of Zn(2+), Co(2+), and Cu(2+) were only detectable, which could be explained by the competitive displacement of ferrous from its binding site.     

Spectropotentiometric analysis of metal binding to structural zinc-binding sites: accounting quantitatively for pH and metal ion buffering effects

Studies of the metal-binding affinity of protein sites are ubiquitous in bioinorganic chemistry and are valuable for the information that they can provide about metal speciation and exchange in biological systems. The potential for error in these studies is high, however, since many competing equilibria are present in solution and must be taken into consideration. Here, we report a new spectropotentiometric titration apparatus that allows pH and UV-vis absorption to be monitored simultaneously on small samples under inert atmosphere. In addition, we explain how data obtained from the complex equilibria can be combined with tabulated information about the protonation and metal-binding constants for common buffers to provide detailed, quantitative information about metal-protein interactions. Application of this approach to the investigation of metal binding to structural zinc-binding domains and common pitfalls encountered when performing these experiments are also discussed. We have used this approach to reevaluate the metal-binding constants of the N-terminal zinc-binding peptide from the HIV-1 nucleocapsid protein (10(-8)M相似文献   

Context surrounding processing sites is crucial in determining cleavage rate of a subset of processing sites in HIV-1 Gag and Gag-Pro-Pol polyprotein precursors by viral protease

Processing of the human immunodeficiency virus type 1 (HIV-1) Gag and Gag-Pro-Pol polyproteins by the HIV-1 protease (PR) is essential for the production of infectious particles. However, the determinants governing the rates of processing of these substrates are not clearly understood. We studied the effect of substrate context on processing by utilizing a novel protease assay in which a substrate containing HIV-1 matrix (MA) and the N-terminal domain of capsid (CA) is labeled with a FlAsH (fluorescein arsenical hairpin) reagent. When the seven cleavage sites within the Gag and Gag-Pro-Pol polyproteins were placed at the MA/CA site, the rates of cleavage changed dramatically compared with that of the cognate sites in the natural context reported previously. The rate of processing was affected the most for three sites: CA/spacer peptide 1 (SP1) (≈10-fold increase), SP1/nucleocapsid (NC) (≈10-30-fold decrease), and SP2/p6 (≈30-fold decrease). One of two multidrug-resistant (MDR) PR variants altered the pattern of processing rates significantly. Cleavage sites within the Pro-Pol region were cleaved in a context-independent manner, suggesting for these sites that the sequence itself was the determinant of rate. In addition, a chimera consisting of SP1/NC P4-P1 and MA/CA P1'-P4' residues (ATIM↓PIVQ) abolished processing by wild type and MDR proteases, and the reciprocal chimera consisting of MA/CA P4-P1 and SP1/NC P1'-4' (SQNY↓IQKG) was cleaved only by one of the MDR proteases. These results suggest that complex substrate interactions both beyond the active site of the enzyme and across the scissile bond contribute to defining the rate of processing by the HIV-1 PR.     

Interaction of DNA with heavy metal ions and polybases: cooperative phenomena

The polarographically determined binding constants of Cu⁺⁺ and Cd⁺⁺ to DNA were found to decrease with the degree of binding. The binding causes a reduction in the electrostatic potential ψ on the DNA molecule. The binding constant conforms to the relation K = K₀ exp {-zeψ/kT}. The binding constant at zero potential K₀ depends on the nature of the competing counterfoils to the phosphate group of the DNA; it is apparently smaller when Na⁺ rather than the ethylpyridonium residue of polyvinylpyridine serves as the competing counterfoil. The specific interact ion between the ethylpyridonium residues of the polybase and the DNA is very weak, even though the polyelectrolytic interaction induced by the decrease of the electrostatic free energy is spectacular. The intereaction is reversible and equilibrium is maintained between the different interaction products. A reshuffling of the interacting partners can be effected by spontaneous or induced (by centrifugal forces) precipitation of the least soluble interaction products participating in the equilibrium.     

Interaction of metal ions with D-glucobenzothiazoline: isolation and characterization of the resultant products

Six different metal-ion complexes of D-glucobenzothiazoline were synthesized and characterized by analytical and spectral techniques. Formation of different types of species (ML and ML(2)) were observed with Cu(2+), Ag(+), Cd(2+), Hg(2+), and Zn(2+) ions. Existence of an anomeric mixture in the case of the Cu(2+) complex is identified from the EPR spectra, and the results were further supported by the simulated spectra. The structures were proposed based on different studies.     

Interaction of metal compounds with ‘double-hydrophilic’ block copolymers in aqueous medium and metal colloid formation

The interaction of a ‘double-hydrophilic’ polyethyleneoxide-polyethyleneimine block copolymer (PEO-b-PEI) with AuCl₃, PdCl₂, Na₂PdCl₄, H₂PtCl₆·6H₂O, Na₂PtCl₆·6H₂O, and K₂PtCl₄ in aqueous medium was studied. Micellar structure formation was observed for all metal compounds except Na₂PdCl₄ where additional protonation of the polymer was required to induce micelle formation. The characteristics of the micelles formed depended strongly on the metal type, the molar ratio polymermetal compound, and the type of reducing agent. Micellization in the presence of AuCl₃·H₂O is accompanied with reduction of the salt and the formation of gold colloid without reducing agent induced by oxidation of the PEI block. The interaction with PtCl₆²⁻ ions results in narrowly distributed micelles wi size depending on the metal compound loading. In the case of loading with H₂PtCl₆, it was found that the size and shape of the colloids can be controlled by changing the molar ratio PEI:metal salt. The lower is the metal loading, the smaller are the particles. In addition, differently shaped Pt colloids were observed. This phenomenon can be controlled by the relative ratio of reactants.