Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori

Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal–protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori.     

Macromolecular assembly of Helicobacter pylori urease investigated by mass spectrometry

The supramolecular assembly of Helicobacter pylori urease was studied by nanoflow electrospray ionization orthogonal time-of-flight mass spectrometry. The measured molecular mass of the urease complex of 1.06 MDa corresponds to a dodecameric (alphabeta)(12) assembly of urease alpha (26 kDa) and beta (61 kDa) subunits. The dodecamer disassembles readily into (alphabeta)(3) subunits in solution and under controlled collisional-induced dissociation in the gas phase. This is in strong support of an ((alphabeta)(3))(4) architecture consistent with the recently published x-ray structure. In vitro, the alpha and beta subunits are capable of re-assembling to (alphabeta)(3), but not further to the dodecameric complex.     

Investigations on the Synthesis,Structural Characterization,and Crystal Structures of Three Diiron and Tetrairon Azadithiolate Complexes

Three diiron and tetrairon azadithiolate complexes as models for the active site of [FeFe] hydrogenase were prepared. Reaction of complex Fe₂(SCH₂OH)₂(CO)₆ and NH₂CH₂CH₂CH₂OCH₃ resulted in the diiron azadithiolate hexcarbonyl complex Fe₂[(SCH₂)₂NCH₂CH₂CH₂OCH₃](CO)₆ ( 1 ) in moderate yield. Furthermore, treatment of complex 1 with mono phosphine ligand PPh₃ and diphosphine ligand Ph₂PCH₂CH₂PPh₂ in the presence of decarbonylation reagent Me₃NO · 2H₂O yielded the phosphine‐substituted azadithiolate complexes Fe₂[(SCH₂)₂NCH₂CH₂CH₂OCH₃]CO)₅(PPh₃) ( 2 ) and {Fe₂[(SCH₂)₂NCH₂CH₂CH₂OCH₃](CO)₅}₂(Ph₂PCH₂CH₂PPh₂) ( 3 ) respectively. The new complexes 1 – 3 were fully characterized by elemental analysis, IR, ¹H, ¹³C, ³¹P NMR spectroscopy and X‐ray crystallography. It is worthy to note that the crystallographic studies show the unusual difference of the methoxypropanyl substituent on the N atom of complexes 1 and 2 , largely because of the affection of phosphine ligand PPh₃. In addition, complex 1 was found to be a catalyst for H₂ production under electrochemical condition.     

Crystallographic report: Crystal structure of tetra(4‐methyl‐5‐imidazole‐carboxyaldehyde)zinc(II) diperchlorate

The central zinc(II) atom in the title complex is tetrahedrally coordinated by four nitrogen atoms derived from 4‐methyl‐5‐imidazolecarboxyaldehyde ligands with Zn? N in the range 2.007(3) to 2.026(4) Å. Copyright © 2003 John Wiley & Sons, Ltd.     

Diagnosis of Helicobacter pylori infection with the (13)C-urea breath test by means of GC-MS analysis

The diagnosis of Helicobacter pylori (H. pylori) infection by GC-MS detection of the (13)CO(2) enrichment in (13)C-urea breath test ((13)C-UBT) samples is reported. This study aimed to optimize the (13)C-UBT with regards to the diagnostic cut-off value, sampling time, and frequency. The H. pylori status of 103 dyspeptic patients was obtained by histological examination, the rapid urease test as well as with the GC-MS (13)C-UBT. Analytical and diagnostic accuracies were determined by comparison of the GC-MS (13)C-UBT results with that of the analytical and diagnostic gold standards, namely GC-isotope ratio MS (IRMS) and histology. The (13)CO(2) enrichment values obtained with GC-MS analysis, correlated favorably (r(2) = 0.993) with those obtained by GC-IRMS analysis. When compared to histology, the GC-MS (13)C-UBT had a diagnostic sensitivity of 92% and a specificity of 93%. The positive predictive value (PPV), negative predictive value (NPV), and accuracy were 95, 89, and 92%, respectively. It was concluded that SIM GC-MS is capable of analyzing nonradioactive (13)C-UBT samples, with a precision and accuracy sufficient to distinguish between H. pylori positive and negative patients.     

The bacterial flagella and the flagellar protein flagellin

In comparison with the relatively complicated flagella of all nucleated organisms, most of the actively motile bacteria have very much simpler locomotion organelles. These flagella are long thin filaments with a helical superstructure, anchored at one end in the cell membrane. Helical waves pass along the flagella in the distal direction during locomotion. In the flagella, identical structural units of a single protein species, flagellin, are linked to one another by non-covalent bonds. The flagellin subunits can be separated from one another by mild methods, and their biochemistry as well as their structure and morphology can be investigated in the isolated state. Under certain conditions they can reaggregate in vitro to form polymorphous helical filaments, which are practically indistinguishable from intact flagella. In the flagellum, the elongated flagellin molecules have a layered arrangement in about ten parallel strands, which in turn form a hollow cylinder. Since this cylinder is deformed into a large helix, the individual chemically identical flagellin protomers and the protomer strands in the helical flagella are only quasi-equivalent. The conformation and bonding pattern of the individual longitudinal flagellin lines can presumably be controlled in vitro by the basal structures, so that movement within the flagellum could conceivably occur as follows. A cyclically induced change in the length of the individual strands could result in an apparent rotation of the helical flagellum. According to hydrodynamic calculations, the resulting forward thrust is sufficient to propel the bacteria at the observed speeds of up to 50 μm/s.     

Proteomic analysis of Helicobacter pylori cellular proteins fractionated by ammonium sulfate precipitation

Among 1590 ORFs in the Helicobacter pylori genome, >250 have been identified as authentic genes by proteomic analysis. Low-abundance proteins need to be enriched to a minimal amount for MALDI-TOF analysis and salt precipitation has generally been used for protein enrichment. Here, a whole-cell extract of H. pylori strain 26695 was subjected to protein fractionation with stepwise concentrations of ammonium sulfate and the proteins were displayed by 2-DE. The protein spots were quantified using PDQUEST software and identified by peptide fingerprinting. The 2-DE profiles and intensities of individual protein spots differed among the protein fractions. Out of the 98 identified proteins, 61 were found in the stepwise ammonium sulfate fractions but not in the whole-cell extract. Out of these, 37 proteins, including KdsA, were found exclusively in a single fraction. In contrast, GroEL, UreA, UreB, TrxA, NapA, and FldA were ubiquitously present in all fractions. Iron-containing proteins such as NapA, SodB, CeuE, and Pfr were found predominantly in the 100% saturated ammonium sulfate precipitate. Additionally, 29 proteins were newly identified in this study. These data will facilitate the preparation of significant H. pylori proteins, as well as provide information about low-abundance proteins.     

A DNAzyme‐Based Colorimetric Paper Sensor for Helicobacter pylori

The reliable detection of pathogenic bacteria in complex biological samples using simple assays or devices remains a major challenge. Herein, we report a simple colorimetric paper device capable of providing specific and sensitive detection of Helicobacter pylori (H. pylori), a pathogen strongly linked to gastric carcinoma, gastric ulcers, and duodenal ulcers, in stool samples. The sensor molecule, an RNA‐cleaving DNAzyme obtained through in vitro selection, is activated by a protein biomarker from H. pylori. The colorimetric paper sensor, designed on the basis of the RNA‐cleaving property of the DNAzyme, is capable of sensitive detection of H. pylori in human stool samples with minimal sample processing and provides results in minutes. It remains fully functional under storage at ambient temperature for at least 130 days. This work lays a foundation for developing DNAzyme‐enabled paper‐based point‐of‐care diagnostic devices for monitoring pathogens in complex samples.     

Structure elucidation of antiproliferative bisbenzylisoquinoline alkaloids from Anisocycla grandidieri from the Madagascar dry forest

Antiproliferative bioassay‐guided fractionation of the ethanol extract of the stems of Anisocycla grandidieri led to the isolation of the known alkaloids stebisimine (1), (+)‐1,2‐dehydrotelobine (2), (+)‐2'‐norcocsuline (3) and puetogaline B (4). Herein, we report the full NMR assignments of all compounds and the X‐ray crystallography of single crystals of compounds 1 and 3. Compounds 2 and 3 showed moderate antiproliferative activity against the A2780 human ovarian cancer cell line with IC₅₀ values of 4.1 ± 0.3 and 2.7 ± 0.3 μM, respectively, and they also displayed selective activity toward the H460 (large cell lung cancer), MCF‐7 (breast ductal carcinoma), and UACC‐257 (melanoma) cell lines. Copyright © 2013 John Wiley & Sons, Ltd.     

Chiral Crystal Structure of Racemic Binaphthyl Poly(ether ketone) Macrocycles

Summary: The crystal structure of rigid, hollow, racemic binaphthyl poly(ether ketone) macrocycles has been elucidated by single crystal X‐ray analysis. Multitudinal interactions were identified within the chiral space group P2₁2₁2₁. The structural analysis revealed that this macrocyclic compound contains an elliptic chiral cavity with a size of 9.80 × 5.18 Å, which is similar to that of cyclodextrins. The knowledge about the interaction sites and the structure of the binaphthyl‐based macrocycle provides a unique opportunity to understand its molecular or chiral recognition properties.

Space‐filling representation of the single (R)‐macrocycle.     

Facile synthesis of pyridinium aryltetrachlorotellurates: crystal and molecular structure of [C5H6N][RTeCl4] (R = m‐O2NC6H4, p‐NCC6H4)

Arylation of TeCl₄ with arylboroxine–pyridine complexes [(RBO)₃·C₅H₅N, where R = m‐O₂NC₆H₄ ( 1 ), p‐O₂NC₆H₄ ( 2 ), m‐NCC₆H₄ ( 3 ), p‐NCC₆H₄ ( 4 )] and advantageous moisture provided good yields of the pyridinium aryltetrachlorotellurates [C₅H₆N][RTeCl₄] [R = m‐O₂NC₆H₄ ( 5 ), p‐O₂NC₆H₄ ( 6 ), m‐NCC₆H₄ ( 7 ), p‐NCC₆H₄ ( 8 )]. Compounds 5 and 8 have been investigated by X‐ray crystallography. Key features of both crystal structures are intermolecular secondary Te???Cl interactions between the aryltetrachlorotellurate anions and weak association of the cations and anions. Electrospray mass spectra of compound 5 reveal that the associative interactions also play a role in solution. Copyright © 2005 John Wiley & Sons, Ltd.     

Antifreeze Protein‐Induced Selective Crystallization of a New Thermodynamically and Kinetically Less Preferred Molecular Crystal

The formation of a new, dihydrate crystalline form of 5‐methyluridine (m⁵U) was selectively induced by a protein additive, antifreeze protein (AFP) in a highly efficient manner (in 10^?6 molar scale, whereas known kinetic additives need 0.1 molar scale). The hemihydrate form (form I, the only previously known crystalline form of m⁵U) and the dihydrate form of m⁵U (form II) obtained herein were characterized using X‐ray crystallography and differential scanning calorimetry (DSC). Compared to form I, remarkably, form II is thermodynamically and kinetically less preferred. The presence of AFP can selectively inhibit the appearance of form I and hence allows the growth of form II, the pure form of which cannot grow directly from m⁵U supersaturated solutions under the same conditions. An explanation supported by both experimental and theoretical results is provided for the AFP‐induced selection process. Implications on AFP‐induced ice shape changes are also discussed. Control of crystallization from supersaturated solutions is of great interest in both fundamental research and practical applications in fields like chemistry, pharmacology and materials science. These findings suggest that crystallization processes with AFPs could be valuable for selective growth of hydrates and polymorphs of important pharmaceutical compounds.     

Two New Cyclic Tetrapeptides of Streptomyces rutgersensis T009 Isolated from Elaphodus davidianus Excrement

Two new cyclic tetrapeptides, cyclo(l ‐Val‐l ‐Leu‐l ‐Val‐l ‐Ile) ( 1 ) and cyclo(l ‐Leu‐l ‐Leu‐l ‐Ala‐l ‐Ala) ( 2 ), and 15 known compounds, cyclo(Gly‐l ‐Leu‐Gly‐l ‐Leu) ( 3 ), cyclo(l ‐Ser‐l ‐Phe) ( 4 ), cyclo(l ‐Leu‐l ‐Ile) ( 5 ), cyclo(l ‐Tyr‐l ‐Phe) ( 6 ), cyclo(Gly‐l ‐Trp) ( 7 ), cyclo(l ‐Leu‐l ‐Tyr) ( 8 ), cyclo(Gly‐l ‐Phe) ( 9 ), cyclo(l ‐Phe‐trans‐4‐hydroxy‐l ‐Pro) ( 10 ), cyclo(l ‐Leu‐l ‐Leu) ( 11 ), cyclo(l ‐Val‐l ‐Phe) ( 12 ), cyclo(l ‐Val‐l ‐Leu) ( 13 ), cyclo(l ‐Ile‐l ‐Ile) ( 14 ), cyclo(l ‐Tyr‐l ‐Tyr) ( 15 ), turnagainolide A ( 16 ), and bacimethrin ( 17 ) were isolated from the fermentation broth of Streptomyces rutgersensis T009 obtained from Elaphodus davidianus excrement. Their structures were identified on the basis of spectroscopic analysis. Meanwhile, the absolute configurations of the amino acid residues of compounds 1 and 2 were determined by advanced Marfey method. Compound 3 was obtained from a natural source for the first time. The X‐ray single crystal diffraction data of bacimethrin ( 17 ) were also reported for the first time. Compounds 1  –  17 exhibited no antimicrobial activities with the MICs > 100 μg/ml.     

From Single Molecule to Crystal: Mapping Out the Conformations of Tartaric Acids and Their Derivatives

Stereoisomers of one of the most important organic compounds, tartaric acid, optically active and meso as well as the ester or amide derivatives, can show diverse structures related to the rotation around the three carbon–carbon bonds. This study determines the controlling factors for conformational changes of these molecules in vacuo, in solution, and in the crystalline state using DFT calculations, spectroscopic measurements, and X‐ray diffraction. All structural variations can be logically accounted for by the possibility of formation and breaking of hydrogen bonds between the hydroxy or amide donors and oxygen acceptors, among these the hydrogen bonds that close five‐membered rings being the most stable. These findings are useful in designing molecular and crystal structures of highly polar, polyfunctional, chiral compounds.     

Vegetable Extracts and Nutrients Useful in the Recovery from Helicobacter pylori Infection: A Systematic Review on Clinical Trials

Helicobacter pylori (H. pylori) infections affect almost half of the world’s population, with gradually increasing incidence in developed countries. Eradication of H. pylori may provide significant benefits to the affected individual by healing a number of gastrointestinal and extra-digestive disorders. But due to increased microbial resistance and lack of patient adherence to the therapy, the eradication rate of H. pylori is below 80% with current pharmacological therapies. The usage of botanicals for their therapeutic purposes and medicinal properties have been increased in last decades. They can be use as alternative H. pylori treatments, especially against drug-resistant strains. Epidemiological studies have revealed that people with lower vegetable and micronutrient intake may be at increased risk of H. pylori infection. We have undertaken a review of clinical trials to evaluate the efficacy of vegetable extracts and micronutrients in patients with H. pylori. Various databases, such as Google Scholar, PubMed, Scopus, Web of Science, and the Cochrane Library, were searched for the articles published in English. A total of 24 clinical studies (15 for vegetable extracts and 9 for micronutrients) were selected to be reviewed and summarized in this article. Vegetable extracts (Broccoli sprouts, curcumin, Burdock complex, and Nigella sativa) and micronutrients (vitamin C and E) were not found to be as effective as single agents in H. pylori eradication, rather their efficacy synergized with conventional pharmacological therapies. Conversely, GutGard was found to be significantly effective as a single agent when compared to placebo control.     

The Structure of 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine in the Solid State and in Solution; Unprecedented Cocrystallization of Four Stereoisomers

The solid and solution structures of a new optically active aminopyridine compound, 2‐[(1S)‐(+)‐10‐camphorsulfonamino]‐6‐aminopyridine [(S)‐csaap], 1 , are reported. Crystal data: space group P2₁, a = 8.9729 (5), b = 10.9447 (6), c = 36.693 (2) Å, β = 96.435 (1)°, V = 3580.8 (3) ų, Z = 8, R₁ = 0.0673 and wR₂ = 0.1600 with I > 2σ(I). This chiral compound shows an unprecedented cocrystallization of four stereoisomers, which are characterized by X‐ray crystallography and NMR spectroscopy.     

Crystal structure of poly(dithiotriethylene adipate)

The crystal structure of poly(dithiotriethylene adipate) has been determined through the best fitting of calculated and experimental X‐ray diffraction powder profiles. A triclinic cell was found with dimensions a = 4.942 (7) Å, b = 4.702 (2) Å, c = 20.56 (2) Å, α = 88.9 (2)°, β = 61.0 (1)°, γ = 67.8 (1)°, P‐1 space group, and one chain in the unit cell. A full extended trans conformation of the chain fitted satisfactory the experimental data, yielding to a discrepancy factor R_p = 0.073. A comparison between the crystal structures of poly(dithiotriethylene adipate) and poly (thiodiethylene adipate) is proposed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 2677–2682, 2005