Crystal structure at 1.5 Å resolution of the PsbV2 cytochrome from the cyanobacterium Thermosynechococcus elongatus

PsbV2 is a c-type cytochrome present in a very low abundance in the thermophilic cyanobacterium Thermosynechococcus elongatus. We purified this cytochrome and solved its crystal structure at a resolution of 1.5 Å. The protein existed as a dimer in the crystal, and has an overall structure similar to other c-type cytochromes like Cytc₆ and Cytc₅₅₀, for example. However, the 5th and 6th heme iron axial ligands were found to be His51 and Cys101, respectively, in contrast to the more common bis-His or His/Met ligands found in most cytochromes. Although a few other c-type cytochromes were suggested to have this axial coordination, this is the first crystal structure reported for a c-type heme with this unusual His/Cys axial coordination. Previous spectroscopic characterizations of PsbV2 are discussed in relation to its structural properties.     

Expression pattern and substrate specificity of Clonorchis sinensis tyrosinases

Tyrosinase (TYR) is a copper-containing glycoenzyme that mediates hydroxylation of tyrosine into dihydroxyphenylalanine and oxidation of dihydroxyphenylalanine into dihydroxyphenylalanine quinone. TYRs play pivotal roles in eggshell sclerotisation of trematode parasites, while their comprehensive biochemical properties remain elusive. We characterised genes encoding four TYRs (CsTYR1–4) of Clonorchis sinensis, a causative agent of human hepatobiliary disease. These genes shared tightly conserved amino acid residues, two copper binding catalytic motifs and a cysteine-rich epidermal growth factor-like domain. The native and recombinant CsTYRs showed high reactivity against diphenol compounds, especially those with hydroxyl groups in ortho-positions (catechol and l-dihydroxyphenylalanine), but showed minimal activity toward monophenol compounds. Diphenolase activity was enhanced by increased pH of the reaction buffer from 5.0 to 7.0. The temporal induction of CsTYR expression coordinated with the sexual maturation of the worm; enzyme activity was mainly in the vitelline glands and intrauterine immature eggs proximal to the ovary. The primary structures and functional domains of CsTYRs showed significant similarities to those of the vertebrate orthologs, whereas the amino acids shared with the nematode and insect proteins were largely restricted in the bicopper active center. Unlike highly diverged TYR homologs in vertebrates, multiple paralogs have not yet evolved into the separate lineages in trematode genomes, suggesting that duplication of TYR genes might relate to increased genic dosage/redundancy in trematodes. In vitro treatment of copper chelator, diethyldithiocarbamic acid, inhibited generation of phenotypically normal egg. TYR proteins are essential for C. sinensis reproduction, thus might be targeted for therapeutic and vaccine strategies against clonorchiasis, which is prevalent in several Asian countries and is one of the most important predisposing factors for human cholangiocarcinoma. The close phylogenetic relationships between trematode and vertebrate homologs also provide a molecular clue to understand the multifaceted evolutionary pathway of TYR homologs across animal taxa.     

Genetic diversity of the Chinese liver fluke Clonorchis sinensis from Russia and Vietnam

Clonorchiasis is a parasitic disease of high public health importance in many countries in southeastern Asia and is caused by the Chinese liver fluke Clonorchis sinensis. However, the genetic structure and demographic history of its populations has not been sufficiently studied throughout the geographic range of the species and available data are based mainly on partial gene sequencing. In this study, we explored the genetic diversity of the complete 1560 bp cytochrome c oxidase subunit 1 (cox1) gene sequence for geographically isolated C. sinensis populations in Russia and Vietnam, to our knowledge for the first time. The results demonstrated low nucleotide and high haplotype differentiation within and between the two compared regions and a clear geographical vector for the distribution of genetic diversity patterns among the studied populations. These results suggest a deep local adaptation of the parasite to its environment including intermediate hosts and the existence of gene flow across the species’ range. Additionally, we have predicted an amino acid substitution in the functional site of the COX1 protein among the Vietnamese populations, which were reported to be difficult to treat with praziquantel. The haplotype networks consisted of several region-specific phylogenetic lineages, the formation of which could have occurred during the most extensive penultimate glaciations in the Pleistocene Epoch. The patterns of genetic diversity and demographics are consistent with population growth of the liver fluke in the late Pleistocene following the Last Glacial Maximum, indicating the lack of a population bottleneck during the recent past in the species’ history. The data obtained have important implications for understanding the phylogeography of C. sinensis, its host-parasite interactions, the ability of this parasite to evolve drug resistance, and the epidemiology of clonorchiasis under global climate change.     

Synthesis, structures, luminescence/magnetic properties of complexes of the M/1-hydroxybenzotriazole, M = cobalt, nickel, silver, zinc and copper

Five novel complexes, Co(OBt)₂ · 7H₂O (1) (OBt = 1-hydroxybenzotriazole ion), Ni₃(OBt)₆ · 6H₂O (2), [Ag(OBt)(HOBt)]_n (3), [Zn(OBt)₂]_n (4) and [Cu₂(OBt)₄ · 3H₂O]_n (5) were synthesized by hydrothermal method and characterized by elemental analysis, IR spectroscopy, TGA, XRPD, and single-crystal X-ray diffraction. The results from single-crystal X-ray diffraction indicate that 1-5 are zero-dimensional (0D), zero-dimensional, one-dimensional (1D), and three-dimensional (3D) frameworks, respectively. In particular, 3 is twin crystal; 4 possesses of double-stranded chains; 5 crystallizes in orthorhombic space group P2₁2₁2₁ with a helical chain in its structure. The luminescence properties and the magnetic properties of the five complexes were investigated.     

Crystal structure and fluorescence of a europium (III) complex: EuCl3(2,2′-bipyridine N,N dioxide) · 2CH3OH

We report the synthesis and characterization of a seven coordinate europium complex, [EuCl₃(C₁₀H₈N₂O₂) ·  2CH₃OH]. The growing interest in developing efficient light conversion molecular devices (LCMDs) necessitates the need for new fluorescent materials. Ideal physicochemical properties of the materials include ligand absorption, efficient metal to ligand transfer, and strong luminescence with a relatively long decay time. The design of such material requires distinct absorbing (ligand) and emitting (metal ion) components. While Eu³⁺ cation has a non-degenerate emitting level, 2,2′-bipyridine N,N dioxide is a heterocyclic ligand known to exhibit strong luminescence. Additional characterization is also described, including single crystal X-ray diffraction, IR and UV-Vis spectroscopies and elemental analysis.     

Resolution of two native monomeric 90 kDa nitrate reductase active proteins from Shewanella gelidimarina and the sequence of two napA genes

The reduction of nitrate to nitrite in the bacterial periplasm occurs in the 90 kDa NapA subunit of the periplasmic nitrate reductase (NAP) system. Most Shewanella genomes contain two nap operons: napEDABC and napDAGHB, which is an unusual feature of this genus. Two native, monomeric, 90 kDa nitrate reductase active proteins were resolved by hydrophobic interaction chromatography from aerobic cultures of Shewanella gelidimarina replete with reduced nitrogen compounds. The 90 kDa protein obtained in higher yield was characterized as NapA by electronic absorption and electron paramagnetic resonance spectroscopies and was identified by LC/MS/MS and MALDI-TOF/TOF MS as NapA from the napEDABC-type operon. The other 90 kDa protein, which was unstable and produced in low yields, was posited as NapA from the napDAGHB-type operon. Two napA genes have been sequenced from the napEDABC-type and napDAGHB-type operons of S. gelidimarina. Native NAP from S. putrefaciens was resolved as one NapA monomer and one NapAB heterodimer. Two amino acid substitutions in NapA correlated with the isolation of NAP as a NapA monomer or a NapAB heterodimer. The resolution of native, redox-active NapA isoforms in Shewanella provides new insight into the respiratory versatility of this genus, which has implications in bioremediation and the assembly of microbial fuel cells.     

Luminescence enhancement of the catalytic 19 kDa protein (KAZ) of Oplophorus luciferase by three amino acid substitutions

To characterize the luminescence properties of nanoKAZ, a 16 amino acid substituted mutant of the catalytic 19 kDa protein (KAZ) of Oplophorus luciferase, the effects of each mutated amino acid were investigated by site-specific mutagenesis. All 16 single substituted KAZ mutants were expressed in Escherichia coli cells and their secretory expressions in CHO-K1 cells were also examined using the signal peptide sequence of Gaussia luciferase. Luminescence activity of KAZ was significantly enhanced by single amino acid substitutions at V44I, A54I, or Y138I. Further, the triple mutant KAZ-V44I/A54I/Y138I, named eKAZ, was prepared and these substitutions synergistically enhanced luminescence activity, showing 66-fold higher activity than wild-KAZ and also 7-fold higher activity than nanoKAZ using coelenterazine as a substrate. Substrate specificity of eKAZ for C2- and/or C6-modified coelenterazine analogues was different from that of nanoKAZ, indicating that three amino acid substitutions may be responsible for the substrate recognition of coelenterazine to increase luminescence activity. In contrast, these substitutions did not stimulate protein secretion from CHO-K1 cells, suggesting that the folded-protein structure of KAZ might be different from that of nanoKAZ.     

Crystal Structures of A. acidocaldarius Endoglucanase Cel9A in Complex with Cello-Oligosaccharides: Strong − 1 and − 2 Subsites Mimic Cellobiohydrolase Activity

Alicyclobacillus acidocaldarius endoglucanase Cel9A (AaCel9A) is an inverting glycoside hydrolase with β-1,4-glucanase activity on soluble polymeric substrates. Here, we report three X-ray structures of AaCel9A: a ligand-free structure at 1.8 Å resolution and two complexes at 2.66 and 2.1 Å resolution, respectively, with cellobiose obtained by co-crystallization and with cellotetraose obtained by the soaking method. AaCel9A forms an (α/α)₆-barrel like other glycoside hydrolase family 9 enzymes. When cellobiose is used as a ligand, three glucosyl binding subsites are occupied, including two on the glycone side, while with cellotetraose as a ligand, five subsites, including four on the glycone side, are occupied. A structural comparison showed no conformational rearrangement of AaCel9A upon ligand binding. The structural analysis demonstrates that of the four minus subsites identified, subsites − 1 and − 2 show the strongest interaction with bound glucose. In conjunction with the open active-site cleft of AaCel9A, this is able to reconcile the previously observed cleavage of short-chain oligosaccharides with cellobiose as main product with the endo mode of action on larger polysaccharides.     

Syntheses and 1D structures of organic-inorganic hydrid polymers combining M(ClO4)2 (M = Cd, Zn) junctions and the semi-flexible bis-pyridyl ligand 3-pmpmd (N,N′-bis(3-pyridylmethyl)pyromellitic diimide)

Two 1D organic-inorganic coordination polymers, [Cd(3-pmpmd)(CH₃CN)₂(H₂O)₂]_n · 2n(ClO₄)₂ (1) and [Zn(3-pmpmd)_1.5(H₂O)₂]_n · 2n(ClO₄)₂ · nCH₃CN (2), were obtained from M(ClO₄)₂ (M = Cd, Zn) and the semi-flexible 3,3′-N-donor bis-pyridyl ligand 3-pmpmd: 1 has an 1D zigzag framework with 3-pmpmd in the Z_T-mode (anti, trans-) conformation, while 2 has an 1D rod and loop network with 3-pmpmd in both Z_T- and Z_C-mode (anti, cis-) conformations. Results showed that the metal ions could influence the coordination mode of a semi-flexible bis-pyridyl ligand.     

Syntheses, crystal structures and properties of [K(2,2,2-crypt)]3K(HP7)2 · en, [K(18-crown-6)]2HP7 and [K(db18-crown-6)]2HP7 · toluene

The polyphosphide anions in ethylenediamine/2,2,2-crypt, ethylenediamine/18-crown-6 and ethylenediamine/db18-crown-6 solutions are isolated as K[K(2,2,2-crypt)]₃(HP₇)₂ · en (1), [K(18-crown-6)]₂HP₇ (2) and [K(db18-crown-6)]₂HP₇ · toluene (3). The mono-protonation of the P₇ cluster is observed in all three compounds. The (HP₇)²⁻ units are stabilized by naked potassium in 1 and complexing potassium in 2 and 3. The significant C-H?P hydrogen bonding interaction is observed in 3, which is responsible for the 3-D supramolecular structure. The 3-D supramolecular structure is also contributed by the η²-interaction between K⁺ and the phenyl. The ³¹P and ¹H NMR spectra of 1-3 indicate that the polyphosphide anions are very fluxional in solution.     

Preparation, crystal structures and spectroscopic properties of novel [MCl3 − n(P)3 + n] (M = Co, Rh; n = 0, 1, 2 or 3) series of complexes containing tripodal tridentate phosphine, 1,1,1-tris(dimethylphosphinomethyl)ethane

Cobalt(III) and rhodium(III) complexes of the series of [M^IIICl_3 − n(P)_3 + n]ⁿ⁺ (M = Co or Rh; n = 0, 1, 2 or 3) have been prepared with the use of 1,1,1-tris(dimethylphosphinomethyl)ethane (tdmme) and mono- or didentate phosphines. The single-crystal X-ray analyses of both series of complexes revealed that the M-P and M-Cl bond lengths were dependent primarily on the strong trans influence of the phosphines, and secondarily on the steric congestion around the metal center resulting from the coordination of several phosphine groups. In fact, the M-P(tdmme) bonds became longer in the order of [MCl₃(tdmme)] < [MCl₂(tdmme)(PMe₃)]⁺ < [MCl(tdmme)(dmpe)]²⁺ (dmpe = 1,2-bis(dimethylphosphino)ethane) < [M(tdmme)₂]³⁺ for both Co^III and Rh^III series of complexes, while the M-Cl bond lengths were shortened in this order (except for [M(tdmme)₂]³⁺). Such a steric congestion around the metal center can also account for the structural and spectroscopic characteristics of the series of complexes, [MCl(tdmme)(dmpm, dmpe or dmpp)]²⁺ (dmpm = bis(dimethylphosphino)methane, dmpp = 1,3-bis(dimethylphosphino)propane). The X-ray analysis for [CoCl(tdmme)(dmpm or dmpe)](BF₄)₂ showed that all Co-P bonds in the dmpm complex were shorter by 0.03-0.04 Å than those in the dmpe complex. Furthermore, the first d-d transition energy of the Co^III complexes and the ¹J_Rh-P(tdmme) coupling constants observed for the Rh^III complexes indicated an unusual order in the coordination bond strengths of the didentate diphosphines, i.e., dmpm > dmpe > dmpp.     

Fasciola gigantica: Immunolocalization of 28.5 kDa antigen in the tegument of metacercaria and juvenile fluke

Specific monoclonal antibody (MoAb) to 28.5 kDa tegumental antigen (TA) was used to localize this antigen in the tissues of metacercariae, newly excysted juvenile (NEJ), 1, 3, 5, and 7-week-old juveniles of Fasciola gigantica by using indirect immunofluorescence, immunoperoxidase and immunogold techniques. Both indirect immunofluorescence and immunoperoxidase detections showed that this antigen was concentrated in the tegument particularly in its outer rim, tegumental cells and their processes as well as epithelial linings of the oral sucker. Unlike adult F. gigantica, it was not detected in spermatogenic cells in the testes, cells of Mehlis’gland, oocytes within the ovary, and ovum within the egg of parasites. At the ultrastructural level, the immunogold labeling showed deposit of gold particles specifically in G₂ tegumental granules and on the surface membrane. Thus, this 28.5 kDa antigen is expressed in the tegument and associated structures of juvenile parasites, and it could be a major component of the G₂ granules which are shown to fuse with the surface membrane and contribute material to replace the casted-off membrane. This process is the replenishment and turnover of the surface membrane to prevent the attachment of the host immune effector cells.     

Synthesis, structures and DNA binding of ternary transition metal complexes M(II)L with the 2,2-bipyridylamine (L = p-HB, M = Co, Ni, Cu and Zn)

New ternary transition metal complexes of formulations [Co(bpa)(p-HB)₂](bpa = 2,2′-bipyridylamine, p-HB = p-hydroxybenzenecarboxylic acid) (1), [Ni(bpa)(p-HB)(H₂O)₂]⁺(NO₃)⁻ · H₂O (2), , [Cu(bpa)(p-HB)Cl] (4) and [Zn(bpa)(p-HB)₂]₂ · 0.5H₂O (5) are prepared, their structural features are characterized by crystal structural studies, and their DNA binding propensity has been evaluated by fluorescence method. The molecular structure of complex 1 shows the six coordinate octahedral geometry with one bpa and two p-HB ligands, complex 2 is the cationic complex and has the six coordinate octahedral structure with one bpa, one p-HB and two aqua ligands, complex 3 is also the cationic complex of octahedral coordination with two bpa and one p-HB ligands, complex 4 is five coordinate distorted square pyramidal with one bpa, one p-HB and chloride ligands and complex 5 has the distorted octahedral coordination with two p-HB and one bpa ligands. In all of the complexes, both bpa and p-HB act as the bidentate N and O-donor ligands, respectively. The intermolecular H-bond networks, together with π-π interaction in their solid state are also described. The complexes show the competitive inhibition of ethidium binding to DNA, and the DNA binding propensity can be reflected as the relative order: 3 > 2 > 1 > 5 > 4, in which the cationic charged Ni(II) complexes 2 and 3 show the most effective inhibition ability.     

Reversible binding of zinc in Plasmodium falciparum Sir2: Structure and activity of the apoenzyme

Reversible zinc chelation via thiol groups of cysteines leading to modulation of activity in redox regulated proteins forms a basis for switching on–off of various biochemical processes. Silent information regulator 2 (Sir2), a NAD⁺ dependent deacetylase, contains a non-catalytic zinc ion coordinated by thiol groups of cysteines. Using Plasmodium falciparum Sir2 (PfSir2), we have examined the effect of zinc removal on the structure and activity of this enzyme. Our studies show that the enzyme with high affinity for zinc exhibits partial collapse of structure upon removal of the metal ion. Zinc reconstitution of apo PfSir2 led to recovery of both structure and activity highlighting the reversibility of the process.     

Mechanistic role of each metal ion in Streptomyces dinuclear aminopeptidase: Peptide hydrolysis and 7 × 10-fold rate enhancement of phosphodiester hydrolysis

The dinuclear aminopeptidase from Streptomyces griseus (SgAP) and its metal derivatives catalyze the hydrolysis of the phosphoester bis(p-nitrophenyl) phosphate (BNPP) and the phosphonate ester p-nitrophenyl phenylphosphonate with extraordinary rate enhancements at pH 7.0 and 25 °C [A. Ercan, H. I. Park, L.-J. Ming, Biochemistry 45, (2006) 13779-13793.], reaching 6.7 billion-fold in terms of the first-order rate constant of the di-Co(II) derivative with respect to the autohydrolytic rates. Since phosphoesters are transition state-like inhibitors in peptide hydrolysis, their hydrolysis by SgAP is quite novel. Herein, we report the investigation of this proficient alternative catalysis of SgAP and the role of each metal ion in the dinuclear site toward peptide and BNPP hydrolysis. Mn(II) selectively binds to one of the dinuclear metal sites (M1), affording MnE-SgAP with an empty (E) second site for the binding of another metal (M2), including Mn(II), Co(II), Ni(II), Zn(II), and Cd(II). Peptide hydrolysis is controlled by M2, wherein the k_cat values for the derivatives MnM2-SgAP are different yet similar between MnCo- and CoCo-SgAP and pairs of other metal derivatives. On the other hand, BNPP hydrolysis is affected by metals in both sites. Thus, the two hydrolytic catalyses must follow different mechanisms. Based on crystal structures, docking, and the results presented herein, the M1 site is close to the hydrophobic specific site and the M2 site is next to Tyr246 that is H-bonded to a coordinated nucleophilic water molecule in peptide hydrolysis; whereas a coordinated water molecule on M1 becomes available as the nucleophile in phosphodiester hydrolysis.     

Fasciola gigantica: Immunodiagnosis of fasciolosis by detection of circulating 28.5 kDa tegumental antigen

A monoclonal antibody (MoAb)-based sandwich ELISA was developed for the detection of circulating 28.5 kDa tegumental antigen (28.5 kDa TA) in the sera from mice experimentally infected with Fasciola gigantica. The MoAb was immobilized on a microtiter plate, and the antigen in the serum was captured and detected with biotinylated polyclonal rabbit anti TA antibody. The test could detect 28.5 kDa in the extracts of tegument (TA), whole body (WB) and excretory-secretory (ES) fractions at the concentrations of these crude antigens as low as 600 pg/ml, 16 and 60 ng/ml, respectively. This sandwich ELISA assay could detect the infection from day 1 to 35 post infection and showed that circulating level of 28.5 kDa TA peaked at day 1 post infection. In contrast, the antibody detection by indirect ELISA could only demonstrate the antibody level from 35 days post infection. The reliability of the assay method was evaluated using sera from mice infected with F. gigantica or Schistosoma mansoni, and hamsters infected with Opisthorchis viverrini, as well as healthy mice and hamsters. The sandwich ELISA exhibited a sensitivity and specificity at 94.55% and 100%, respectively, and with a positive predictive value of 100%, a negative predictive value of 97.39%, false positive rate of 0%, false negative rate of 5.50% and an accuracy of 98.2%. Thus, this detection method exhibited high specificity and sensitivity as well as could be used for early diagnosis of fasciolosis by F. gigantica.     

Antifungal activity of zinc oxide nanoparticles against Botrytis cinerea and Penicillium expansum

Antifungal activities of zinc oxide nanoparticles (ZnO NPs) and their mode of action against two postharvest pathogenic fungi (Botrytis cinerea and Penicillium expansum) were investigated in this study. ZnO NPs with sizes of 70 ± 15 nm and concentrations of 0, 3, 6 and 12 mmol l⁻¹ were used. Traditional microbiological plating, scanning electron microscopy (SEM), and Raman spectroscopy were used to study antifungal activities of ZnO NPs and to characterize the changes in morphology and cellular compositions of fungal hyphae treated with ZnO NPs. Results show that ZnO NPs at concentrations greater than 3 mmol l⁻¹ can significantly inhibit the growth of B. cinerea and P. expansum. P. expansum was more sensitive to the treatment with ZnO NPs than B. cinerea. SEM images and Raman spectra indicate two different antifungal activities of ZnO NPs against B. cinerea and P. expansum. ZnO NPs inhibited the growth of B. cinerea by affecting cellular functions, which caused deformation in fungal hyphae. In comparison, ZnO NPs prevented the development of conidiophores and conidia of P. expansum, which eventually led to the death of fungal hyphae. These results suggest that ZnO NPs could be used as an effective fungicide in agricultural and food safety applications.     

Structural analysis of a putative SAM-dependent methyltransferase,YtqB, from Bacillus subtilis

S-adenosyl-l-methionine (SAM)-dependent methyltransferases (MTases) methylate diverse biological molecules using a SAM cofactor. The ytqB gene of Bacillus subtilis encodes a putative MTase and its biological function has never been characterized. To reveal the structural features and the cofactor binding mode of YtqB, we have determined the crystal structures of YtqB alone and in complex with its cofactor, SAM, at 1.9 Å and 2.2 Å resolutions, respectively. YtqB folds into a β-sheet sandwiched by two α-helical layers, and assembles into a dimeric form. Each YtqB monomer contains one SAM binding site, which shapes SAM into a slightly curved conformation and exposes the reactive methyl group of SAM potentially to a substrate. Our comparative structural analysis of YtqB and its homologues indicates that YtqB is a SAM-dependent class I MTase, and provides insights into the substrate binding site of YtqB.