Cyclosporin A Associated Helicase-Like Protein Facilitates the Association of Hepatitis C Virus RNA Polymerase with Its Cellular Cyclophilin B

BACKGROUND: Cyclosporin A (CsA) is well known as an immunosuppressive drug useful for allogeneic transplantation. It has been reported that CsA inhibits hepatitis C virus (HCV) genome replication, which indicates that cellular targets of CsA regulate the viral replication. However, the regulation mechanisms of HCV replication governed by CsA target proteins have not been fully understood. PRINCIPAL FINDINGS: Here we show a chemical biology approach that elucidates a novel mechanism of HCV replication. We developed a phage display screening to investigate compound-peptide interaction and identified a novel cellular target molecule of CsA. This protein, named CsA associated helicase-like protein (CAHL), possessed RNA-dependent ATPase activity that was negated by treatment with CsA. The downregulation of CAHL in the cells resulted in a decrease of HCV genome replication. CAHL formed a complex with HCV-derived RNA polymerase NS5B and host-derived cyclophilin B (CyPB), known as a cellular cofactor for HCV replication, to regulate NS5B-CyPB interaction. CONCLUSIONS: We found a cellular factor, CAHL, as CsA associated helicase-like protein, which would form trimer complex with CyPB and NS5B of HCV. The strategy using a chemical compound and identifying its target molecule by our phage display analysis is useful to reveal a novel mechanism underlying cellular and viral physiology

Heterogeneous Nucleation of Protein Crystals on Fluorinated Layered Silicate

Here, we describe an improved system for protein crystallization based on heterogeneous nucleation using fluorinated layered silicate. In addition, we also investigated the mechanism of nucleation on the silicate surface. Crystallization of lysozyme using silicates with different chemical compositions indicated that fluorosilicates promoted nucleation whereas the silicates without fluorine did not. The use of synthesized saponites for lysozyme crystallization confirmed that the substitution of hydroxyl groups contained in the lamellae structure for fluorine atoms is responsible for the nucleation-inducing property of the nucleant. Crystallization of twelve proteins with a wide range of pI values revealed that the nucleation promoting effect of the saponites tended to increase with increased substitution rate. Furthermore, the saponite with the highest fluorine content promoted nucleation in all the test proteins regardless of their overall net charge. Adsorption experiments of proteins on the saponites confirmed that the density of adsorbed molecules increased according to the substitution rate, thereby explaining the heterogeneous nucleation on the silicate surface

Simvastatin Sodium Salt and Fluvastatin Interact with Human Gap Junction Gamma-3 Protein

Finding pleiomorphic targets for drugs allows new indications or warnings for treatment to be identified. As test of concept, we applied a new chemical genomics approach to uncover additional targets for the widely prescribed lipid-lowering pro-drug simvastatin. We used mRNA extracted from internal mammary artery from patients undergoing coronary artery surgery to prepare a viral cardiovascular protein library, using T7 bacteriophage. We then studied interactions of clones of the bacteriophage, each expressing a different cardiovascular polypeptide, with surface-bound simvastatin in 96-well plates. To maximise likelihood of identifying meaningful interactions between simvastatin and vascular peptides, we used a validated photo-immobilisation method to apply a series of different chemical linkers to bind simvastatin so as to present multiple orientations of its constituent components to potential targets. Three rounds of biopanning identified consistent interaction with the clone expressing part of the gene GJC3, which maps to Homo sapiens chromosome 7, and codes for gap junction gamma-3 protein, also known as connexin 30.2/31.3 (mouse connexin Cx29). Further analysis indicated the binding site to be for the N-terminal domain putatively ‘regulating’ connexin hemichannel and gap junction pores. Using immunohistochemistry we found connexin 30.2/31.3 to be present in samples of artery similar to those used to prepare the bacteriophage library. Surface plasmon resonance revealed that a 25 amino acid synthetic peptide representing the discovered N-terminus did not interact with simvastatin lactone, but did bind to the hydrolysed HMG CoA inhibitor, simvastatin acid. This interaction was also seen for fluvastatin. The gap junction blockers carbenoxolone and flufenamic acid also interacted with the same peptide providing insight into potential site of binding. These findings raise key questions about the functional significance of GJC3 transcripts in the vasculature and other tissues, and this connexin’s role in therapeutic and adverse effects of statins in a range of disease states

Exploring the catalytic properties of supported palladium catalysts in the transfer hydrogenolysis of glycerol

The transfer hydrogenolysis of glycerol promoted by supported palladium catalysts is reported. The reactions were carried out under mild conditions (453K and 5 bar of N-2) in absence of added hydrogen by using the reaction solvent, 2-propanol, as hydrogen source. The catalytic results are interpreted in terms of metal (Pd)-metal (Co or Fe) interaction that modifies the electronic properties of palladium and affords bimetallic PdM sites (M= Co or Fe), thus enhancing the catalytic properties of the systems in the conversion of glycerol as well as in the selectivity to 1,2-propanediol and 1-propanol. The transfer hydrogenolysis mechanism is here elucidated and involves the glycerol dehydration to 1-hydroxyacetone and the subsequent hydrogenation of 1-hydroxyacetone to propylene glycol

Transfer hydrogenolysis of aromatic ethers promoted by the bimetallic Pd/Co catalyst

The transfer hydrogenolysis of lignin derived aromatic ethers (benzyl phenyl ether, phenethyl phenyl ether and diphenyl ethers) have been investigated by using the coprecipitated Pd/Co as heterogeneous catalyst and 2propanol as H-donor/solvent. A quantitative conversion of benzyl phenyl ether into toluene and cyclohexanol was obtained after 180 min at 240 degrees C. The bimetallic Pd/Co catalyst is, by far, more efficient if compared to commercial Pd/C and Co-based catalytic systems showing, at the same time, a good reusability. The enhanced ability in the CeO bond cleavage in aromatic ethers is related to the formation of bimetallic Pd-Co ensembles, arisen from the preparation procedure adopted, as confirmed by a complete physico-chemical characterization that includes XRD, SEM, TEM, H-2-TPR, XPS and EXAFS analysis

Operando Observation of Ni2P Structural Changes during Catalytic Reaction: Effect of H2S Pretreatment

In situ X-ray absorption spectroscopy was used to study the effect of H2S pretreatment on the activation of Ni2P catalysts for the thiophene hydrodesulfurization (HDS) reaction. It was found that H2S treatment produced Ni-S bonds that were slightly longer and that had higher coordination numbers than those formed during reaction. The longer Ni-S bonds formed by H2S treatment were changed to the shorter Ni-S bonds by the catalytic reaction, and these shorter bonds were associated with high activity. The work provides evidence that a NiPS phase is active in the HDS reaction

Operando QEXAFS studies of Ni2P during thiophene hydrodesulfurization: direct observation of Ni-S bond formation under reaction conditions

Structural changes in Ni2P/MCM-41 were followed by quick extended X-ray absorption fine structure (QEXAFS) and were directly related to changes in X-ray absorption near-edge structure (XANES) which had been used earlier for the study of the active catalyst phase. An equation is proposed to correct the transient QEXAFS spectra up to second-order in time to remove spectral distortions induced by structural changes occurring during measurements. A good correlation between the corrected QEXAFS and the XANES spectral changes was found, giving support to the conclusions derived from the XANES in the previous work, namely that the formation of a Ni-S bond in a surface NiPS phase is involved in the active site for the hydrodesulfurization reaction

Dynamical LEED analysis of Ni2P (0001)-1 x 1 : Evidence for P-covered surface structure

Nickel phosphide (Ni2P) is an emerging catalyst for hydrodesulfurization and other important environment- and energy-related catalytic reactions. To understand its high performance, the surface structure of a Ni2P (0 0 0 1) single crystal surface was investigated using dynamical LEED analysis. The obtained surface structure for Ni2P (0 0 0 1)-1 x 1 is a P-covered Ni3P2 structure (Ni3P_P structure) as opposed to the expected bulk terminated surface structures. This Letter discusses the driving force for the formation of the Ni3P_P surface, which involves the minimization of dangling bonds

STM studies on the reconstruction of the Ni2P (101[-]0) surface

The surface structure of Ni2P (101[-]0), a model for highly active hydrodesulfurization catalysts, was studied using scanning tunneling microscopy (STM) and low energy electron diffraction (LEED) in order to understand the reconstruction of the surface layers. Annealing at 573 K revealed a (1 x 1) LEED pattern which changed to a c(2 x 4) arrangement by further heating to 723 K. Atomic scale STM images were obtained for both the (1 x 1) and c(2 x 4) structures. Bright spots observed in the STM images were interpreted to be due to surface phosphorus atoms and this was supported by a density functional theory (DFT) simulation. Several possible models for the c(2 x 4) reconstructed structures were proposed including a P-dimer defect model, a missing-row model and a missing-row + added row model. The last model gave the best explanation for the c(2 x 4) structure. The mechanism for the c(2 x 4) reconstruction on the Ni2P (101[-]0) surface is discussed

A new spectroelectrochemical cell for in situ measurement of Pt and Au K-edge X-ray absorption fine structure

A new spectroelectrochemical cell to investigate the structure of Pt/Au nanoclusters using Pt and Au K-edge X-ray absorption fine structure (XAFS) measurements under the electrochemical conditions is developed. K-edge XAFS measurements for Pt and Au require a sample as thick as 1-2 cm, which prevents homogeneous potential distribution. We can measure in situ Pt and Au K-edge XAFS spectra and determine reasonable electrochemical surface areas using our developed spectroelectrochemical cell. This work provides a new approach to analyze Pt/Au core-shell nanoclusters. The new cell is designed to be applied to both spectra with high absorption-edge energies such as the K-edge of Pt and Au and those with low absorption-edge energy such as Pt L-edge