Unification of the copper(I) binding affinities of the metallo-chaperones Atx1, Atox1, and related proteins : Detection probes and affinity standards

Literature estimates of metal-protein affinities are widely scattered for many systems, as highlighted by the class of metallo-chaperone proteins, which includes human Atox1. The discrepancies may be attributed to unreliable detection probes and/or inconsistent affinity standards. In this study, application of the four CuI ligand probes bicinchoninate, bathocuproine disulfonate, dithiothreitol (Dtt), and glutathione (GSH) is reviewed, and their CuI affinities are re-estimated and unified. Excess bicinchoninate or bathocuproine disulfonate reacts with CuI to yield distinct 1:2 chromatophoric complexes [CuIL2] 3- with formation constants β2 = 1017.2 and 1019.8 M-2, respectively. These constants do not depend on proton concentration for pH ≥7.0. Consequently, they are a pair of complementary and stable probes capable of detecting free Cu+ concentrations from 10-12 to 10-19 M. Dtt binds CuI with KD∼10-15 M at pH 7, but it is air-sensitive, and its CuI affinity varies with pH. The CuI binding properties of Atox1 and related proteins (including the fifth and sixth domains at the N terminus of the Wilson protein ATP7B) were assessed with these probes. The results demonstrate the following: (i) their use permits the stoichiometry of high affinity CuI binding and the individual quantitative affinities (KD values) to be determined reliably via noncompetitive and competitive reactions, respectively; (ii) the scattered literature values are unified by using reliable probes on a unified scale; and (iii) Atox1-type proteins bind CuI with sub-femtomolar affinities, consistent with tight control of labile Cu+ concentrations in living cells.

Analysis of the contribution of reverse transcriptase and integrase proteins to retroviral RNA dimer conformation

All retroviruses contain two copies of genomic RNA that are linked noncovalently. The dimeric RNA of human immunodeficiency virus type 1 (HIV-1) undergoes rearrangement during virion maturation, whereby the dimeric RNA genome assumes a more stable conformation. Previously, we have shown that the packaging of the HIV-1 polymerase (Pol) proteins reverse transcriptase (RT) and integrase (IN) is essential for the generation of the mature RNA dimer conformation. Analysis of HIV-1 mutants that are defective in processing of Pol showed that these mutant virions contained altered dimeric RNA conformation, indicating that the mature RNA dimer conformation in HIV-1 requires the correct proteolytic processing of Pol. The HIV-1 Pol proteins are multimeric in their mature enzymatically active forms; RT forms a heterodimer, and IN appears to form a homotetramer. Using RT and IN multimerization defective mutants, we have found that dimeric RNA from these mutant virions has the same stability and conformation as wild-type RNA dimers, showing that the mature enzymatically active RT and IN proteins are dispensable for the generation of mature RNA dimer conformation. This also indicated that formation of the mature RNA dimer structure occurs prior to RT or IN maturation. We have also investigated the requirement of Pol for RNA dimerization in both Mason-Pfizer monkey virus (M-PMV) and Moloney murine leukemia virus (MoMuLV) and found that in contrast to HIV-1, Pol is dispensable for RNA dimer maturation in M-PMV and MoMuLV, demonstrating that the requirement of Pol in retroviral RNA dimer maturation is not conserved among all retroviruses.

Interactions between fibroin and sericin proteins from antheraea pernyi and bombyx mori silk fibers

Silkworm silk fibers are core-shell composites of fibroin and sericin proteins. Studying the interactions between fibroin and sericin is essential for understanding the properties of these composites. It isobserved that compared to the domestic silk cocoon Bombyx mori (B. mori), the adhesion between fibroin and sericin from the wild silk cocoon, Antheraea pernyi (A. pernyi), is significantly stronger with a higherdegree of heterogeneity. The adsorption of A. pernyi sericin on its fibroin is almost twice the value for B.mori sericin on fibroin, both showing a monolayer Langmuir adsorption. 1H NMR and FTIR studiesdemonstrate on a molecular level the stronger interactions and the more intensive complex formation between A. pernyi fibroin and sericin, facilitated by the hydrogen bonding between glycine and serine.The findings of this study may help the design of composites with superior interfacial adhesion between different components.

Endosomal trafficking of the Menkes copper ATPase ATP7A is mediated by vesicles containing the Rab7 and Rab5 GTPase proteins

The Cu-ATPase ATP7A (MNK) is localized in the trans-Golgi network (TGN) and relocalizes in the plasma membrane via vesicle-mediated traffic following exposure of the cells to high concentrations of copper. Rab proteins are organelle-specific GTPases, markers of different endosomal compartments; their role has been recently reviewed (Trends Cell Biol. 11(2001) 487). In this article we analyze the endosomal pathway of trafficking of the MNK protein in stably transfected clones of CHO cells, expressing chimeric Rab5-myc or Rab7-myc proteins, markers of early or late endosome compartments, respectively. We demonstrate by immunofluorescence and confocal and electron microscopy techniques that the increase in the concentration of copper in the medium (189 μM) rapidly induces a redistribution of the MNK protein from early sorting endosomes, positive for Rab5-myc protein, to late endosomes, containing the Rab7-myc protein. Cell fractionation experiments confirm these results; i.e., the MNK protein is recruited to the endosomal fraction on copper stimulation and colocalizes with Rab5 and Rab7 proteins. These findings allow the first characterization of the vesicles involved in the intracellular routing of the MNK protein from the TGN to the plasma membrane, a key mechanism allowing appropriate efflux of copper in cells grown in high concentrations of the metal.

An analysis of side chain interactions and pair correlations within antiparallel β-sheets : the differences between backbone hydrogen-bonded and non-hydrogen-bonded residue pairs

Cross-strand pair correlations are calculated for residue pairs in antiparallel β-sheet for two cases: pairs whose backbone atoms are hydrogen bonded together (H-bonded site) and pairs which are not (non-H-bonded site). The statistics show that this distinction is important. When glycine is located on the edge of a sheet, it shows a 3:1 preference for the H-bonded site. Thestrongest observed correlations are for pairs of disulfide-bonded cystines, many of which adopt a close-packed conformation with each cystine in a spiral conformation of opposite chirality to its partner. It is likely that these pairs are a signature for the family of small, cystine-rich proteins. Most other strong positive and negative correlations involve charged and polar residues. It appears that electrostatic compatibility is the strongest factor affecting pair correlation. Significant correlations are observed for β- and γ-branched residues inthe non-H-bonded site. An examination of the structures showsa directionality in side chain packing. There is a correlation between (1) the directionality in the packing interactions of non-H-bonded β- and γ-branched residue pairs, (2) the handedness of the observed enantiomers of chiral β-branched side chains, and (3) the handedness of the twist of β-sheet. These findings have implications for the formation of β-sheets during protein folding and the mechanism by which the sheet becomes twisted

Solvent induced changes in the conformational state of β-lactoglobulin and the influence of protic ionic liquids

The protic ionic liquids (pILs), triethylammonium acetate, triethylammonium trifluoroacetate, triethylammonium mesylate and trimethylammonium sulfate were used to induce various native and non-native conformational states of the protein β-lactoglobulin (βLG). Changes in the secondary structure of βLG were observed on moving from a high water content to a high pIL content. We examined the stability of various pIL induced states via thermal unfolding and refolding, where it was found that at a given pIL concentration a highly stable non-native conformation was formed. The βLG non-native conformation was characterized by a high α-helical content. Additionally, pIL conditions that promoted amyloid fibril formation were identified and characterized by CD, a Thioflavin T binding assay and transmission electron microscopy (TEM). This work highlights the use of pILs as solvents in the study of protein folding using βLG as a model system.

Analysis and prediction of major blood proteins based on their amino acid and dipeptide composition

A method has been developed for predicting blood proteins using the SVM based machine learning approach. In this prediction method a two-step strategy was deployed to predict blood proteins and their subclasses. We have developed models of blood proteins and achieved the maximum accuracies of 90.57% and 91.39% with Matthews correlation coefficient (MCC) of 0.89 and 0.90 using single amino acid and dipeptide composition respectively. Furthermore, the method is able to predict major subclasses of blood proteins; developed based on amino acid (AC) and dipeptide composition (DC) with a maximum accuracy 90.38%, 92.83%, 87.41%, 92.52% and 85.27%, 89.07%, 94.82%, 86.31 for albumin, globulin, fibrinogen, and regulatory proteins respectively. All modules were trained, tested, and evaluated using the five-fold cross-validation technique.

Copper in disorders with neurological symptoms: Alzheimer`s, Menkes, and Wilson Diseases

Copper is an essential element for the activity of a number of physiologically important enzymes. Enzyme-related malfunctions may contribute to severe neurological symptoms and neurological diseases: copper is a component of cytochrome c oxidase, which catalyzes the reduction of oxygen to water, the essential step in cellular respiration. Copper is a cofactor of Cu/Zn-superoxide-dismutase which plays a key role in the cellular response to oxidative stress by scavenging reactive oxygen species. Furthermore, copper is a constituent of dopamine-β-hydroxylase, a critical enzyme in the catecholamine biosynthetic pathway. A detailed exploration of the biological importance and functional properties of proteins associated with neurological symptoms will have an important impact on understanding disease mechanisms and may accelerate development and testing of new therapeutic approaches. Copper binding proteins play important roles in the establishment and maintenance of metal-ion homeostasis, in deficiency disorders with neurological symptoms (Menkes disease, Wilson disease) and in neurodegenerative diseases (Alzheimer’s disease). The Menkes and Wilson proteins have been characterized as copper transporters and the amyloid precursor protein (APP) of Alzheimer’s disease has been proposed to work as a Cu(II) and/or Zn(II) transporter. Experimental, clinical and epidemiological observations in neurodegenerative disorders like Alzheimer’s disease and in the genetically inherited copper-dependent disorders Menkes and Wilson disease are summarized. This could provide a rationale for a link between severely dysregulated metal-ion homeostasis and the selective neuronal pathology.

Surface morphologies and internal fine structures of bast fibers

Fiber surface morphologies and associated internal structures are closely related to its properties. Unlike other fibers including cotton, bast fibers possess transverse nodes and fissures in cross-sectional and longitudinal directions. Their morphologies and associated internal structures were anatomically examined under the scanning electron microscope. The results showed that the morphologies of the nodes and the fissures of bast fibers varied depending on the construction of the inner fibril cellular layers. The transverse nodes and fissures were formed by the folding and spiralling of the cellular layers during plant growth. The dimensions of nodes and fissures were determined by the dislocations of the cellular layers. There were also many longitudinal fissures in bast fibers. Some deep longitudinal fissures even opened the fiber lumen for a short way along the fiber. In addition, the lumen channel of the bast fibers could be disturbed or disrupted by the nodes and the spirals of the internal cellular layers. The existence of the transverse nodes and fissures in the bast fibers could degrade the fiber mechanical properties, whereas the longitudinal fissures may contribute to the very rapid moisture absorption and desorption.

Soft-sediment deformation structures in the middle permian Wandrawandian siltstone, southern Sydney basin: implications for depositional environment and basin tectonics

The Middle Permian Wandrawandian Siltstone at Warden Head near Ulladulla in the southern Sydney Basin is dominated by fossiliferous siltstone and mudstone, with a large amount of dropstones (lonestones) and some pebbly sandstone beds. Two general types of deposits are recognised from the cliff succession in view of the timing and mechanism of their formation. One is represented by the background (or primary) deposits of offshore to slope environments with abundant dropstones of glacial marine origin. This facies occurs throughout the cliff sections at Warden Head. The second type is distinguished by secondary, soft-sediment deformational deposits and structures of the primary (background) deposits, and comprises three successive layers of sandy mudstone dikes. In the second type of deposit, metre scale, laterally extensive syn-depositional slump deformation structures occur extensively in the middle part of the Wandrawandian Siltstone. The deformation structures vary in morphology and pattern, including large-scale complex-type folds, flexural stratification, concave-up structures, small-magnitude -faults accompanied by folding and brecciation. The slumps and associated syn-depositional structures are herein attributed to penecontemporaneous deformations of soft sediments (mostly mud and silty mud), formed as a result of mass movement of unconsolidated and/or semi-consolidated substrate following earthquake events. The occurrence of the earthquake event deposits (or seismites) at Warden Head supports the current view that the Sydney Basin was located in a back-arc setting near the New England magmatic arc on an active continental margin during the Middle Permian, and the timing of the earthquake events is here interpreted to indicate the onset of the Hunter Bowen Orogeny in the southern Sydney Basin.

Suppression of bovine viral diarrhea virus replication by small interfering RNA and short hairpin RNA-mediated RNA interference

Bovine viral diarrhea virus (BVDV) is a ubiquitous viral pathogen that affects cattle herds’ worldwide causing significant economic loss. The current strategies to control BVDV infection include vaccination (modified-live or killed) and control of virus spread by enhanced biosecurity management, however, the disease remains prevalent. With the discovery of the sequence-specific method of gene silencing known as RNA interference (RNAi), a new era in antiviral therapies has begun. Here we report the efficient inhibition of BVDV replication by small interfering (siRNA) and short hairpin RNA (shRNA)-mediated gene silencing. siRNAs were generated to target the 5′ non-translated (NTR) region and the regions encoding the C, NS4B and NS5A proteins of the BVDV genome. The siRNAs were first validated using an EGFP/BVDV reporter system and were then shown to suppress BVDV-induced cytopathic effects and viral titers in cell culture with surprisingly different activities compared to the reporter system. Efficient viral suppression was then achieved by bovine 7SK-expressed BVDV-specific shRNAs. Overall, our results demonstrated the use of siRNA and shRNA-mediated gene silencing to achieve efficient inhibition of the  replication of this virus in cell culture.

The Permian of Timor : stratigraphy, palaeontology and palaeography

The Permian of Timor in the Lesser Sunda Islands has attracted the attention of palaeontologists since the middle of the nineteenth century because of the richness, diversity and excellent state of preservation of its fauna. These abundant fossil data have been compiled and updated for the present account. The Permian rocks of Timor were deposited on the northern margin of Australia. At the present time the northern margin of Australia, in the region of Timor, is involved in a continent–arc collision, where Australia is colliding with the Banda Arcs. As a result of this collision, Permian rocks of the Australian margin have been disrupted by folding and faulting with the generation of mud-matrix mélange, and uplifted to form part of the island of Timor. Due to this tectonic disruption, it has proved difficult to establish a reliable stratigraphy for the Permian units on Timor, especially as the classic fossil collections were obtained largely from the mélange or purchased from the local people, and do not have adequate stratigraphic control. Detailed systematic, structural, stratigraphic and sedimentological studies since the 1960s have provided a firmer stratigraphic and palaeogeographic background for reconsideration of the significance of the classic fossil collections. Permian rocks on Timor belong either to a volcanic-carbonate sequence (Maubisse Formation), or to a clastic sequence (Atahoc and Cribas formations) in which volcanics are less prominent. The Permian sequences were deposited on Australian continental basement which was undergoing extension with spasmodic volcanic activity. Carbonates of the Maubisse Formation were deposited on horst blocks and volcanic edifices, while clastic sediments of the Atahoc and Cribas formations were deposited in grabens. The clastic sediments are predominantly fine-grained, derived from a distant siliciclastic source, and are interbedded with sediments derived from the volcanics and carbonates of adjacent horst blocks. Bottom conditions in the graben were often anoxic. In the present account, events on Timor during the Permian are related to the regional tectonic context, with the northward movement of Australia leading to the amelioration of the climate from sub-glacial to sub-tropical, together with the separation of crustal blocks from the northern Australian margin to form the Meso-Tethys.

Earthquake-controlled event deposits and its tectonic significance from the Middle Permian Wandrawandian Siltstone in the Sydney Basin, Australia

The Sydney-Bowen basin in eastern Australia is an elongate back arc-converted foreland basin system situated between the Lachlan Fold Belt in the west and the New England Fold Belt in the east. The Middle Permian Wandrawandian Siltstone at Warden Head near Ulladulla in the southern Sydney Basin is dominated by fossiliferous siltstone and mudstone, with a large amount of dropstones and minor pebbly sandstone beds. Two general types of deposits are recognized from the siltstone unit in view of the timing and mechanism of formation. One is represented by the primary deposits from offshore to subtidal environments with abundant dropstones of glacial marine origin. The second type is distinguished by secondary, soft-sediment deformational deposits and structures, and comprises three layers of mudstone dykes of seismic origin. In the latter type, metre scale, laterally extensive syn-depositional slump deformation structures occur in the middle part of the Wandrawandian Siltstone. The deformation structures vary in morphol-ogy and pattern, including large-scale complex-type folds, flexural stratification, concave-up structures, faulting of small displacements accompanied by folding and brecciation. The slumps and associated syn-sedimentary structures are attributed to penecontemporaneous deformations of soft sediments (mostly silty mud) formed as a result of mass movement of unconsolidated and/or semi-consolidated substrate following an earthquake event. The occurrence of the earthquake event deposits supports the current view that the Sydney Basin was located in a back-arc setting near the New England magmatic arc on an active continental margin during the Middle Permian.

Using bioinformatics techniques for gene identification in drug discovery and development

As more and more evidence has become available, the link between gene and emergent disease has been made including cancer, heart disease and parkinsonism. Analyzing the diseases and designing drugs with respect to the gene and protein level obviously help to find the underlying causes of the diseases, and to improve their rate of cure. The development of modern molecular biology, biochemistry, data collection and analysis techniques provides the scientists with a large amount of gene data. To draw a link between genes and their relation to disease outcomes and drug discovery is a big challenge: How to analyze large datasets and extract useful knowledge? Combining bioinformatics with drug discovery is a promising method to tackle this issue. Most techniques of bioinformatics are used in the first two phases of drug discovery to extract interesting information and find important genes and/or proteins for speeding the process of drug discovery, enhancing the accuracy of analysis and reducing the cost. Gene identification is a very fundamental and important technique among them. In this paper, we have reviewed gene identification algorithms and discussed their usage, relationships and challenges in drug discovery and development.