Crystal and mol-ecular structures of di-chlorido-palladium(II) containing 2-methyl- or 2-phenyl-8-(diphenyphosphan-yl)quinoline.

The crystal structures of di-chlorido-palladium(II) complexes bearing 2-methyl- and 2-phenyl-8-(di-phenyl-phosphan-yl)quinoline, namely, di-chlorido-[8-(di-phenyl-phosphan-yl)-2-methyl-quinoline-κ2 N,P]palladium(II), [PdCl2(C22H18NP)] (1) and di-chlorido-[8-(di-phenyl-phosphan-yl)-2-phenyl-quinoline-κ2 N,P]palladium(II), [PdCl2(C27H20NP)] (2), were analyzed and compared to that of the 8-(di-phenyl-phosphan-yl)quinoline (PQH) analogue (3). In all three complexes, the phosphanyl-quinoline moiety acts as a bidentate P,N-donating chelate ligand. In the PQH complex (3), the PdII center has a typical planar coordination environment; however, both the methyl- and phenyl-substituted phosphanyl-quinoline (PQMe and PQPh, respectively) complexes (1) and (2) exhibit a considerable tetra-hedral distortion around the PdII center, as parameterized by the τ4 values of 0.1555 (4) and 0.1438 (4) for (1) and (2), respectively. The steric inter-action from the substituted group introduced at the 2-position of the quinoline ring enforces the cis-positioned Cl ligand to be displaced from the ideal coordination plane. Also, the ideally planar phosphanyl-quinoline five-membered chelate ring shows a large bending deformation by the displacement of the PdII center from the quinoline plane. In addition, in the phenyl-substituted complex (3), the coordinating quinolyl and the substituted phenyl rings are not co-planar to each other, having a dihedral angle of 33.08 (7)°. This twist conformation prohibits any inter-molecular π-π stacking inter-action between the quinoline planes, which is observed in the crystals of complexes (1) and (2).

Sterically Demanding 8-(Diphenylphosphino)quinoline Complexes of Group 10 Metal(II): Synthesis, Crystal Structures, and Properties in Solution.

Several series of platinum(II), palladium(II), and nickel(II) complexes bearing 8-(diphenylphosphino)quinoline (PQH) or its 2-methyl or 2-phenyl derivatives (PQMe or PQPh) were synthesized, and their crystal structures and behaviors in solution were investigated. Most of the complexes [M(PQR)2]X2 (MII = PtII, PdII, or NiII; R = H, Me or Ph; X = monoanionic ions) characterized in this study have an approximately square-planar coordination geometry with two bidentate P,N-chelating or monodentate P-donating quinolylphosphine ligands in the cis(P,P) configuration. A large steric requirement from the Me or Ph substituent introduced at the 2-position of the quinoline ring gives the resulting complexes severe distortion. The PtII and PdII complex cations maintained the square-planar coordination geometry, but the MII center was displaced from the chelating ligand plane. This bending of the chelate coordination makes the M-N(quinoline) bond weaker, as demonstrated by the longer M-N bonds. In accord with the bond weakening, the partial dissociation of the PQH or PQMe chelates by substitution with halide anions were observed using UV-vis spectroscopy and X-ray crystallography. In contrast, the PQPh complexes were stable in solution toward the addition of halide anions; the intramolecular π-π stacking interaction between the coordinating quinolyl and the 2-substituted phenyl rings protects the MII center from nucleophilic attack. In the corresponding NiII complexes, the steric congestion arising from the mutually cis-positioned PQR ligands resulted in a large tetrahedral distortion around the NiII center. However, the intramolecular π-π stacking interaction was still effective in the PQPh complex, and this interaction can explain some unusual robustness and electrochemical properties of the NiII-PQPh complex.

Comparison of mol-ecular structures of cis-bis-[8-(di-methyl-phosphan-yl)quinoline]-nickel(II) and -platinum(II) complex cations.

The crystal structures of the complexes (SP-4-2)-cis-bis-[8-(di-methyl-phosphan-yl)quinoline-κ2 N,P]nickel(II) bis-(perchlorate) nitro-methane monosolvate, [Ni(C11H12NP)2](ClO4)2·CH3NO2 (1), and (SP-4-2)-cis-bis-[8-(di-methyl-phos-phan-yl)quinoline-κ2 N,P]platinum(II) bis-(tetra-fluoro-borate) aceto-nitrile monosolvate, [Pt(C11H12NP)2](BF4)2·C2H3N (2), are reported. In both complex cations, two phosphanyl-quinolines act as bidentate P,N-donating chelate ligands and form the mutually cis configuration in the square-planar coordination geometry. The strong trans influence of the di-methyl-phosphanyl donor group is confirmed by the Ni-N bond lengths in 1, 1.970 (2) and 1.982 (2) Šand, the Pt-N bond lengths of 2, 2.123 (4) and 2.132 (4) Å, which are relatively long as compared to those in the analogous 8-(di-phenyl-phosphan-yl)quinoline complexes. Mutually cis-positioned quinoline donor groups would give a severe steric hindrance between their ortho-H atoms. In order to reduce such a steric congestion, the NiII complex in 1 shows a tetra-hedral distortion of the coordination geometry, as parameterized by τ4 = 0.199 (1)°, while the PtII complex in 2 exhibits a typical square-planar coordination geometry [τ4 = 0.014 (1)°] with a large bending deformation of the ideally planar Me2Pqn chelate planes. In the crystal structure of 2, three F atoms of one of the BF4 - anions are disordered over two sets of positions with refined occupancies of 0.573 (10) and 0.427 (10).

Development of INSOL-tag for proteome-wide protein handling and its application in protein array analysis.

Proteomic analysis requires protein tags that enable high-throughput handling; however, versatile tags that can be used in in vitro expression systems are currently lacking. In this study, we developed an insoluble protein tag, INSOL-tag, derived from human transcription factor MafG. The INSOL-tagged target protein is expressed in a eukaryotic in vitro expression system and recovered as a pellet following centrifugation at 19,000 × g for 20 min. Comparisons of the target protein recovery rates of GST-tag and INSOL-tag using 111 cytoplasmic proteins revealed a fourfold increase in the yield of INSOL-tagged proteins. Using 267 cancer antigens purified with INSOL-tag, we subsequently developed an INSOL-CTA array method, for profiling autoantibodies in sera of cancer patients. The detection limit of the array was approximately 11.1 pg IgG, and the correlation with ELISA was high (R2  = .993, .955). Moreover, when autoantibody profiling of digestive cancer patient sera was performed, antigen spreading was observed. These data suggest that INSOL-tag is a versatile tag that can insolubilize a wide range of target proteins. It is therefore expected to become a powerful tool in comprehensive protein preparation for protein arrays, antibody production, and mass spectrometry.

A large-scale targeted proteomics assay resource based on an in vitro human proteome.

Targeted proteomics approaches are of value for deep and accurate quantification of protein abundance. Extending such methods to quantify large numbers of proteins requires the construction of predefined targeted assays. We developed a targeted proteomics platform-in vitro proteome-assisted multiple reaction monitoring (MRM) for protein absolute quantification (iMPAQT)-by using >18,000 human recombinant proteins, thus enabling protein absolute quantification on a genome-wide scale. Our platform comprises experimentally confirmed MRM assays of mass tag (mTRAQ)-labeled peptides to allow for rapid and straightforward measurement of the absolute abundance of predefined sets of proteins by mass spectrometry. We applied iMPAQT to delineate the quantitative metabolic landscape of normal and transformed human fibroblasts. Oncogenic transformation gave rise to relatively small but global changes in metabolic pathways resulting in aerobic glycolysis (Warburg effect) and increased rates of macromolecule synthesis. iMPAQT should facilitate quantitative biology studies based on protein abundance measurements.

The anti-inflammatory effects of flavanol-rich lychee fruit extract in rat hepatocytes.

Flavanol (flavan-3-ol)-rich lychee fruit extract (FRLFE) is a mixture of oligomerized polyphenols primarily derived from lychee fruit and is rich in flavanol monomers, dimers, and trimers. Supplementation with this functional food has been shown to suppress inflammation and tissue damage caused by high-intensity exercise training. However, it is unclear whether FRLFE has in vitro anti-inflammatory effects, such as suppressing the production of the proinflammatory cytokine tumor necrosis factor α (TNF-α) and the proinflammatory mediator nitric oxide (NO), which is synthesized by inducible nitric oxide synthase (iNOS). Here, we analyzed the effects of FRLFE and its constituents on the expression of inflammatory genes in interleukin 1ß (IL-1ß)-treated rat hepatocytes. FRLFE decreased the mRNA and protein expression of the iNOS gene, leading to the suppression of IL-1ß-induced NO production. FRLFE also decreased the levels of the iNOS antisense transcript, which stabilizes iNOS mRNA. By contrast, unprocessed lychee fruit extract, which is rich in flavanol polymers, and flavanol monomers had little effect on NO production. When a construct harboring the iNOS promoter fused to the firefly luciferase gene was used, FRLFE decreased the luciferase activity in the presence of IL-1ß, suggesting that FRLFE suppresses the promoter activity of the iNOS gene at the transcriptional level. Electrophoretic mobility shift assays indicated that FRLFE reduced the nuclear transport of a key regulator, nuclear factor κB (NF-κB). Furthermore, FRLFE inhibited the phosphorylation of NF-κB inhibitor α (IκB-α). FRLFE also reduced the mRNA levels of NF-κB target genes encoding cytokines and chemokines, such as TNF-α. Therefore, FRLFE inhibited NF-κB activation and nuclear translocation to suppress the expression of these inflammatory genes. Our results suggest that flavanols may be responsible for the anti-inflammatory and hepatoprotective effects of FRLFE and may be used to treat inflammatory diseases.

Citrus nobiletin suppresses inducible nitric oxide synthase gene expression in interleukin-1ß-treated hepatocytes.

BACKGROUND: Nobiletin is a polymethoxylated flavone that is abundant in the peels of citrus fruits, such as Citrus unshiu (Satsuma mandarin) and Citrus sinensis. The dried peels of C. unshiu (chinpi) have been included in several formulae of Japanese Kampo medicines. Nobiletin may suppress the induction of inducible nitric oxide synthase (iNOS), which synthesizes the inflammatory mediator nitric oxide (NO) in hepatocytes. METHODS: A C. unshiu peel (CUP) extract was prepared. Primary cultured rat hepatocytes were treated with the CUP extract or nobiletin in the presence of interleukin 1ß (IL-1ß), which induces iNOS expression. NO production and iNOS gene expression were analyzed. RESULTS: High-performance liquid chromatography analyses revealed that the nobiletin content in the CUP extract was 0.14%. Nobiletin dose-dependently reduced the NO levels and decreased iNOS expression at the protein, mRNA and antisense transcript levels. Flavone, which does not contain any methoxy groups, also suppressed iNOS induction. Nobiletin reduced the transcriptional activity of iNOS promoter-luciferase constructs and the DNA-binding activity of nuclear factor κB (NF-κB) in the nuclei. CONCLUSIONS: The suppression of iNOS induction by nobiletin suggests that nobiletin may be responsible for the anti-inflammatory effects of citrus peels and have a therapeutic potential for liver diseases.

Specificity of botulinum protease for human VAMP family proteins.

The botulinum neurotoxin light chain (BoNT-LC) is a zinc-dependent metalloprotease that cleaves neuronal SNARE proteins such as SNAP-25, VAMP2, and Syntaxin1. This cleavage interferes with the neurotransmitter release of peripheral neurons and results in flaccid paralysis. SNAP, VAMP, and Syntaxin are representative of large families of proteins that mediate most membrane fusion reactions, as well as both neuronal and non-neuronal exocytotic events in eukaryotic cells. Neuron-specific SNARE proteins, which are target substrates of BoNT, have been well studied; however, it is unclear whether other SNARE proteins are also proteolyzed by BoNT. Herein, we define the substrate specificity of BoNT-LC/B, /D, and /F towards recombinant human VAMP family proteins. We demonstrate that LC/B, /D, and /F are able to cleave VAMP1, 2, and 3, but no other VAMP family proteins. Kinetic analysis revealed that all LC have higher affinity and catalytic activity for the non-neuronal SNARE isoform VAMP3 than for the neuronal VAMP1 and 2 isoforms. LC/D in particular exhibited extremely low catalytic activity towards VAMP1 relative to other interactions, which we determined through point mutation analysis to be a result of the Ile present at residue 48 of VAMP1. We also identified the VAMP3 cleavage sites to be at the Gln 59-Phe 60 (LC/B), Lys 42-Leu 43 (LC/D), and Gln 41-Lys 42 (LC/F) peptide bonds, which correspond to those of VAMP1 or 2. Understanding the substrate specificity and kinetic characteristics of BoNT towards human SNARE proteins may aid in the development of novel therapeutic uses for BoNT.

Development and evaluation of data-driven designed tags (DDTs) for controlling protein solubility.

Production of proteins is an important issue in protein science and pharmaceutical studies. Numerous protein expression systems using living cells and cell-free methods have been developed to date. In these systems, a promising strategy for improving the success rate of obtaining soluble proteins is the attachment of various tags into target proteins based on empirical rules. This paper presents a method for the production of data-driven designed tags (DDTs) based on highly frequent sequence property patterns in an experimentally assessed protein solubility dataset in a wheat germ cell-free system. We constructed seven proteins combined with 12 kinds of DDTs (six for enhancing solubility and six for insolubility) at the N-terminal region as tags. Then we investigated their behavior using SDS-PAGE. Results show that three and four proteins respectively showed a trend toward solubilization and insolubilization, which indicates the possibility that the theoretically designed sequence can control protein solubility.

Comparative analysis of human SRC-family kinase substrate specificity in vitro.

Src family kinases (SFKs) are the earliest known family of tyrosine kinases and are widely thought to play essential roles in cellular signal transduction. Although numerous functional analyses have been performed, no study has analyzed the specificity of all SFKs on an equal platform. To gain a better understanding of SFK phosphorylation, we designed a high-throughput in vitro kinase assay on the subproteome scale using surface plasmon resonance. We reacted each of the 11 human SFKs with 519 substrate proteins, and significant phosphorylation was detected in 33.6% (1921) of the total 5709 kinase-substrate combinations. A large number of novel phosphorylations were included among them. Many substrates were shown to be phosphorylated by multiple SFKs, which might reflect functional complementarity of SFKs. Clustering analysis of phosphorylation results grouped substrates into 10 categories, while the similarity of SFK catalytic specificity exhibited no significant correlation with that of amino acid sequences. In silico predictions of SRC-specific phosphorylation sites were not consistent with experimental results, implying some unknown SRC recognition modes. In an attempt to find biologically meaningful novel substrates, phosphorylation data were integrated with annotation data. The extensive in vitro data obtained in this study would provide valuable clues for further understanding SFK-mediated signal transduction.

Solitary fibrous tumors of the pleura presenting satellite tumors.

A 29-year-old man presented with a mass in the left lower lung field on a chest radiograph obtained during a medical checkup. Computed tomography revealed a tumor adjacent to the diaphragm. A sessile tumor measuring 10.5 x 8.5 x 4.5 cm arising from the parietal pleura was resected. The tumor was accompanied by several little tumors on the nearby diaphragm. Pathologically, the major tumor consisted of typical spindle-shaped cells with myxoid degeneration. There was no increased cellularity, cellular pleomorphism, or a high mitotic count. In immunohistochemical studies, the spindle cells showed positive staining for CD34 and were negative for bcl-2. The smaller tumors also consisted of myxoid degeneration. We diagnosed benign solitary fibrous tumor of the pleura with satellite tumors. We must be aware of the possibility of satellite tumors when we treat patients with a benign solitary fibrous tumor.

Human protein factory for converting the transcriptome into an in vitro-expressed proteome,.

Appropriate resources and expression technology necessary for human proteomics on a whole-proteome scale are being developed. We prepared a foundation for simple and efficient production of human proteins using the versatile Gateway vector system. We generated 33,275 human Gateway entry clones for protein synthesis, developed mRNA expression protocols for them and improved the wheat germ cell-free protein synthesis system. We applied this protein expression system to the in vitro expression of 13,364 human proteins and assessed their biological activity in two functional categories. Of the 75 tested phosphatases, 58 (77%) showed biological activity. Several cytokines containing disulfide bonds were produced in an active form in a nonreducing wheat germ cell-free expression system. We also manufactured protein microarrays by direct printing of unpurified in vitro-synthesized proteins and demonstrated their utility. Our 'human protein factory' infrastructure includes the resources and expression technology for in vitro proteome research.

[A case of non-Hodgkin's lymphoma after chemotherapy for cancer of unknown origin].

We present a case of non-Hodgkin's lymphoma after chemotherapy for a cancer of unknown origin. A 68-year-old man was hospitalized for hoarseness. Computed tomography(CT)scans showed a swelling of the superior mediastinal lymph node and a tumor of the right lobe of thyroid gland. Resection of the superior mediastinal lymph node and right hemithyroidectomy were performed. Pathological findings of the lymph node showed adenosquamous cell carcinoma, but no malignant lesion was found in the thyroid gland. Post-operative systemic survey failed to identify the origin of the adenosquamous cell carcinoma. Six courses of chemotherapy consisting of carboplatin and docetaxel were carried out. Seven months later, CT and positron emission tomography revealed swelling of the mediastinal lymph nodes and a tumor in the left abdominal tumor. An open biopsy of the abdominal tumor demonstrated non-Hodgkin's lymphoma, mature B cell type, follicular lymphoma, grade 1. Radiotherapy was done for the malignant lymphoma, and radiochemotherapy for the mediastinal lymph nodes. Seven months later, the patient died of systemic metastases of the adenosquamous cell carcinoma.