| 19139490 |
A strategy for precise and large scale identification of core fucosylated glycoproteins. |
10.1074/mcp.m800504-mcp200 |
Mol. Cell. |
A strategy for precise and large scale identification of core fucosylated glycoproteins.
Abstract
- Core fucosylation (CF) patterns of some glycoproteins are more sensitive and specific than evaluation of their total respective protein levels for diagnosis of many diseases, such as cancers. Global profiling and quantitative characterization of CF glycoproteins may reveal potent biomarkers for clinical applications. However, current techniques are unable to reveal CF glycoproteins precisely on a large scale. Here we developed a robust strategy that integrates molecular weight cutoff, neutral loss-dependent MS(3), database-independent candidate spectrum filtering, and optimization to effectively identify CF glycoproteins. The rationale for spectrum treatment was innovatively based on computation of the mass distribution in spectra of CF glycopeptides. The efficacy of this strategy was demonstrated by implementation for plasma from healthy subjects and subjects with hepatocellular carcinoma. Over 100 CF glycoproteins and CF sites were identified, and over 10,000 mass spectra of CF glycopeptide were found. The scale of identification
Results indicates great progress for finding biomarkers with a particular and attractive prospect, and the candidate spectra will be a useful resource for the improvement of database searching
Methods for glycopeptides.
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| 19146970 |
The 2008 update of the Aspergillus nidulans genome annotation: a community effort |
10.1016/j.fgb.2008.12.003. |
Fungal Genet Biol |
The 2008 update of the Aspergillus nidulans genome annotation: a community effort
Abstract
- The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional applications. Nevertheless, the comprehensive annotation of eukaryotic genomes remains a considerable challenge. Many genomes submitted to public databases, including those of major model organisms, contain significant numbers of wrong and incomplete gene predictions. We present a community-based reannotation of the Aspergillus nidulans genome with the primary goal of increasing the number and quality of protein functional assignments through the careful review of experts in the field of fungal biology.
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| 19148511 |
Somatostatin analogues inhibit cancer cell proliferation in an SSTR2-dependent manner via both cytostatic and cytotoxic pathways |
None |
Oncol Rep |
Somatostatin analogues inhibit cancer cell proliferation in an SSTR2-dependent manner via both cytostatic and cytotoxic pathways
Abstract
- Somatostatin receptors (SSTRs) are inhibitory G-protein coupled receptors that are ubiquitously expressed in normal and cancer cells. Somatostatins (SST) are the natural ligands for SSTRs and act as inhibitory regulators of hormone secretion and proliferation. Octreotide and RC-160 (vapreotide) are two well tolerated SSTR2/SSTR5 selective somatostatin analogues (SSA) that have been used in the treatment of cancers with mixed outcomes. Loss-of-expression of SSTR2 in tumor tissues has been suggested to correlate to tumor progressions and to the poor outcomes of somatostatin analogue treatment in certain clinical trials. In this study, exogenous human SSTR2 was overexpressed in two cancer cell lines, capan-2 cells and A549 cells, which had different profiles of endogenous SSTR expression. It was shown that overexpression of SSTR2 dramatically inhibited the proliferation of SSTR2-positive and SSTR2-negative cancer cells. Further growth inhibition of these cancer cells overexpressing SSTR2 was observed by application of octreotide/RC-160 in a dose-dependent fashion. In addition, immunoassay demonstrated that SSA/SSTR2 inhibited proliferation via both cell cycle arresting and promoting apoptosis. The results suggested that SSTR2 could be a promising candidate for gene therapy for SSTR2-positive and SSTR2-negative tumors. The cellular level of SSTR2 might be a critical factor that could affect both tumor progression and the outcomes of somatostatin analogue treatment.
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| 19150638 |
Cloning and expression of a hepcidin gene from a marine fish (Pseudosciaena crocea) and the antimicrobial activity of its synthetic peptide |
10.1016/j.peptides.2008.12.014. |
Peptides |
Cloning and expression of a hepcidin gene from a marine fish (Pseudosciaena crocea) and the antimicrobial activity of its synthetic peptide
Abstract
- Hepcidin gene is widely expressed in various fish, suggesting that this antimicrobial peptide is a very important component in the innate immune system. Large yellow croaker (Pseudosciaena crocea) is one of the important economic species of marine-cultured fish but knowledge of its innate immune mechanism is lacking. In this study, we characterize a P. crocea hepcidin gene named as PC-hepc. It consists of an open reading frame of 258 bases encoding 85 amino acids and has a conserved sequence in common with other known hepcidins. The genomic DNA of PC-hepc contains three exons and two introns, the same organization as other reported hepcidins, indicating that PC-hepc is one member of the hepcidin family in fish. The tissue-specific expression of PC-hepc gene in normal fish and the expression pattern in LPS-challenged fish at the time course of stimulation were investigated. The expression of PC-hepc mRNA was significantly increased in the spleen, heart and stomach but not significantly induced in the liver after LPS challenge. An interesting finding is the demonstration of high amounts of PC-hepc transcripts in the kidney in normal fish and their maintenance through 48h exposure to LPS challenge. The synthetic PC-hepc demonstrated a rather wide spectrum of antimicrobial activity in vitro against bacteria and fungi tested, and particularly showed strong activity against the principal fish pathogens, Aeromonas hydrophila, Vibrio parahaemloyticus, Vibrio alginolyticus and Vibrio harvryi. The study indicates that PC-hepc may play a role with a tissue-specific mode in the innate immunity of P. crocea.
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| 19154439 |
A novel diketopiperazine improves functional recovery given after the onset of 6-OHDA-induced motor deficit in rats |
10.1111/j.1476-5381.2008.00064.x. |
Br J Pharmacol |
A novel diketopiperazine improves functional recovery given after the onset of 6-OHDA-induced motor deficit in rats
Abstract
- Cyclo-L-glycyl-L-2-allylproline (NNZ-2591), a modified diketopiperazine, is neuroprotective and improves long-term function after hypoxic-ischaemic brain injury in rats. The present studies were designed to examine both the neuroprotective and neurotrophic actions of NNZ-2591 on neurochemical and behavioural changes in a rat model of Parkinson's disease.
To examine its protective effect, either NNZ-2591 (20 ng.day(-1)) or saline was given intracerebroventricularly for 3 days starting 2 h after 6-hydroxydopamine (6-OHDA) induced unilateral striatal lesion. In a subsequent experiment either NNZ-2591 (0.2, 1 and 5 mg.day(-1), s.c.) or saline was administered daily for 14 days starting 2 weeks after the lesion. Behavioural and neurochemical outcomes were examined using the adjusting step test and immunohistochemical staining.
Cyclo-L-glycyl-L-2-allylproline given 2 h after the lesion reduced the degree of motor deficit compared with the saline-treated group. Delayed treatment with NNZ-2591, initiated after the onset of motor deficit, significantly improved motor function from week 7 onwards compared with the saline-treated group. Neither treatment regime altered nigrostriatal dopamine depletion. NNZ-2591 significantly enhanced the expression of doublecortin-positive neuroblasts in the sub-ventricular zone.
These studies reveal that early treatment with NNZ-2591 protects against the motor deficit induced by 6-OHDA and that treatment initiated after the establishment of motor impairment significantly improves long-term motor function. These effects of NNZ-2591 on functional recovery were independent of dopamine depletion and also appeared not to be symptomatic as the improved motor function was long-lasting. NNZ-2591 has potential as a therapeutic agent for neurodegenerative disorders.
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| 19159218 |
Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry. |
10.1021/pr8008012 |
J. Proteome Res. |
Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.
Abstract
- The study of protein glycosylation has lagged far behind the progress of current proteomics because of the enormous complexity, wide dynamic range distribution and low stoichiometric modification of glycoprotein. Solid phase extraction of tryptic N-glycopeptides by hydrazide chemistry is becoming a popular protocol for the analysis of N-glycoproteome. However, in silico digestion of proteins in human proteome database by trypsin indicates that a significant percentage of tryptic N-glycopeptides is not in the preferred detection mass range of shotgun proteomics approach, that is, from 800 to 3500 Da. And the quite big size of glycan groups may block trypsin to access the K, R residues near N-glycosites for digestion, which will result in generation of big glycopeptides. Thus many N-glycosites could not be localized if only trypsin was used to digest proteins. Herein, we describe a comprehensive way to analyze the N-glycoproteome of human liver tissue by combination of hydrazide chemistry method and multiple enzyme digestion. The lysate of human liver tissue was digested with three proteases, that is, trypsin, pepsin and thermolysin, with different specificities, separately. Use of trypsin alone resulted in identification of 622 N-glycosites, while using pepsin and thermolysin resulted in identification of 317 additional N-glycosites. Among the 317 additional N-glycosites, 98 (30.9%) could not be identified by trypsin in theory because the corresponding in silico tryptic peptides are either too small or too big to detect in mass spectrometer. This study clearly demonstrated that the coverage of N-glycosites could be significantly increased due to the adoption of multiple enzyme digestion. A total number of 939 N-glycosites were identified confidently, covering 523 noredundant glycoproteins from human liver tissue, which leads to the establishment of the largest data set of glycoproteome from human liver up to now.
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| 19165845 |
(1)H and (13)C NMR assignments of eight nitrogen containing compounds from Nocardia alba sp.nov (YIM 30243(T)) |
10.1002/mrc.2393. |
Magn Reson Chem |
(1)H and (13)C NMR assignments of eight nitrogen containing compounds from Nocardia alba sp.nov (YIM 30243(T))
Abstract
- An unprecedented new natural product named nocarsin A (1), 5H-4a,6,7a-triazacyclopenta[cd]indene-5,7(6H)-dione (1), together with seven known compounds lumichrome (2), cyclo (L-Leu-L-Tyr) (3), cyclo (L-Ala-L-Ile) (4), cyclo (L-Ala-L-Leu) (5), cyclo (L-Val-L-Ala) (6), 5-methyluracil (7) and uracil (8), was isolated from Nocardia alba sp.nov (YIM 30243(T)), which was isolated from a soil sample collected from Yunnan Province, P. R. China. NMR techniques including COSY, HSQC, ROESY, and HMBC were used to elucidate the structures of these compounds. We report the unambiguous assignments of the (1)H and (13)C NMR spectra of the new compound nocarsin A (1).
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| 19168442 |
Cdc2-like kinases and DNA topoisomerase I regulate alternative splicing of tissue factor in human endothelial cells. |
10.1161/circresaha.108.183905 |
Circ. Res. |
Cdc2-like kinases and DNA topoisomerase I regulate alternative splicing of tissue factor in human endothelial cells.
Abstract
- Tumor necrosis factor (TNF)-alpha-stimulated human umbilical vein endothelial cells express 2 naturally occurring forms of tissue factor (TF), the primary initiator of blood coagulation: the soluble alternatively spliced isoform and the full-length TF isoform. The regulatory pathways enabling this phenomenon are completely unknown. Cdc2-like kinases and DNA topoisomerase I regulate alternative splicing via phosphorylation of serine/arginine-rich proteins. In this study, we examined effects of serine/arginine-rich protein kinases on TF splicing following stimulation with TNF-alpha. Human endothelial cells were pretreated with specific inhibitors or small interfering RNAs against Cdc2-like kinases and DNA topoisomerase I before stimulation with TNF-alpha. TF levels were determined by semiquantitative RT-PCR, real-time PCR, and Western blotting. Cellular procoagulant activity was analyzed in a chromogenic TF activity assay. All 4 known Cdc2-like kinases forms were expressed in human endothelial cells. Selective inhibition of Cdc2-like kinases and DNA topoisomerase I elicited distinct changes in TF biosynthesis in TNF-alpha-stimulated endothelial cells, which impacted endothelial procoagulant activity. This study is the first to demonstrate that serine/arginine-rich protein kinases modulate splicing of TF pre-mRNA in human endothelial cells and, consequently, endothelial procoagulant activity under inflammatory conditions.
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| 19172738 |
Phosphorylation-dependent binding of 14-3-3 terminates signalling by the Gab2 docking protein |
10.1038/emboj.2008.159. |
EMBO J |
Phosphorylation-dependent binding of 14-3-3 terminates signalling by the Gab2 docking protein
Abstract
- Grb2-associated binder (Gab)2 functions downstream of a variety of receptor and cytoplasmic tyrosine kinases as a docking platform for specific signal transducers and performs important functions in both normal physiology and oncogenesis. Gab2 signalling is promoted by its association with specific receptors through the adaptor Grb2. However, the molecular mechanisms that attenuate Gab2 signals have remained unclear. We now demonstrate that growth factor-induced phosphorylation of Gab2 on two residues, S210 and T391, leads to recruitment of 14-3-3 proteins. Together, these events mediate negative-feedback regulation, as Gab2(S210A/T391A) exhibits sustained receptor association and signalling and promotes cell proliferation and transformation. Importantly, introduction of constitutive 14-3-3-binding sites into Gab2 renders it refractory to receptor activation, demonstrating that site-selective binding of 14-3-3 proteins is sufficient to terminate Gab2 signalling. Furthermore, this is associated with reduced binding of Grb2. This leads to a model where signal attenuation occurs because 14-3-3 promotes dissociation of Gab2 from Grb2, and thereby uncouples Gab2 from the receptor complex. This represents a novel regulatory mechanism with implications for diverse tyrosine kinase signalling systems.
|
| 19179285 |
Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite |
10.1073/pnas.0812623106. |
Proc Natl Acad Sci U S A |
Mammalian metallopeptidase inhibition at the defense barrier of Ascaris parasite
Abstract
- Roundworms of the genus Ascaris are common parasites of the human gastrointestinal tract. A battery of selective inhibitors protects them from host enzymes and the immune system. Here, a metallocarboxypeptidase (MCP) inhibitor, ACI, was identified in protein extracts from Ascaris by intensity-fading MALDI-TOF mass spectrometry. The 67-residue amino acid sequence of ACI showed no significant homology with any known protein. Heterologous overexpression and purification of ACI rendered a functional molecule with nanomolar equilibrium dissociation constants against MCPs, which denoted a preference for digestive and mast cell A/B-type MCPs. Western blotting and immunohistochemistry located ACI in the body wall, intestine, female reproductive tract, and fertilized eggs of Ascaris, in accordance with its target specificity. The crystal structure of the complex of ACI with human carboxypeptidase A1, one of its potential targets in vivo, revealed a protein with a fold consisting of two tandem homologous domains, each containing a beta-ribbon and two disulfide bonds. These domains are connected by an alpha-helical segment and a fifth disulfide bond. Binding and inhibition are exerted by the C-terminal tail, which enters the funnel-like active-site cavity of the enzyme and approaches the catalytic zinc ion. The findings reported provide a basis for the biological function of ACI, which may be essential for parasitic survival during infection.
|
| 19182791 |
Chfr is linked to tumour metastasis through the downregulation of HDAC1 |
10.1038/ncb1837. |
Nat Cell Biol |
Chfr is linked to tumour metastasis through the downregulation of HDAC1
Abstract
- Chfr is a ubiquitin ligase that functions in the mitotic checkpoint by delaying entry into metaphase in response to mitotic stress. It has been suggested that Chfr is a tumour suppressor as Chfr is frequently silenced in human cancers. To better understand how Chfr activity relates to cell-cycle progression and tumorigenesis, we sought to identify Chfr-interacting proteins using affinity purification combined with mass spectrometry. Histone deacetylase 1 (HDAC1), which represses transcription by deacetylating histones, was newly isolated as a Chfr-interacting protein. Chfr binds and downregulates HDAC1 by inducing its polyubiquitylation, both in vitro and in vivo. Ectopic expression of Chfr in cancer cells that normally do not express it results in downregulation of HDAC1, leading to upregulation of the Cdk inhibitor p21(CIP1/WAF1) and the metastasis suppressors KAI1 and E-cadherin. Coincident with these changes, cells arrest in the G1 phase of the cell cycle and become less invasive. Collectively, our data suggest that Chfr functions as a tumour suppressor by regulating HDAC1.
|
| 19211551 |
Combined X-ray and NMR analysis of the stability of the cyclotide cystine knot fold that underpins its insecticidal activity and potential use as a drug scaffold |
10.1074/jbc.M900021200. |
J Biol Chem |
Combined X-ray and NMR analysis of the stability of the cyclotide cystine knot fold that underpins its insecticidal activity and potential use as a drug scaffold
Abstract
- Cyclotides are a family of plant defense proteins that are highly resistant to adverse chemical, thermal, and enzymatic treatment. Here, we present the first crystal structure of a cyclotide, varv F, from the European field pansy, Viola arvensis, determined at a resolution of 1.8 A. The solution state NMR structure was also determined and, combined with measurements of biophysical parameters for several cyclotides, provided an insight into the structural features that account for the remarkable stability of the cyclotide family. The x-ray data confirm the cystine knot topology and the circular backbone, and delineate a conserved network of hydrogen bonds that contribute to the stability of the cyclotide fold. The structural role of a highly conserved Glu residue that has been shown to regulate cyclotide function was also determined, verifying its involvement in a stabilizing hydrogen bond network. We also demonstrate that varv F binds to dodecylphosphocholine micelles, defining the binding orientation and showing that its structure remains unchanged upon binding, further demonstrating that the cyclotide fold is rigid. This study provides a biological insight into the mechanism by which cyclotides maintain their native activity in the unfavorable environment of predator insect guts. It also provides a structural basis for explaining how a cluster of residues important for bioactivity may be involved in self-association interactions in membranes. As well as being important for their bioactivity, the structural rigidity of cyclotides makes them very suitable as a stable template for peptide-based drug design.
|
| 19214948 |
Largamides A-C, tiglic acid-containing cyclodepsipeptides with elastase-inhibitory activity from the marine cyanobacterium Lyngbya confervoides |
10.1055/s-0029-1185332. |
Planta Med |
Largamides A-C, tiglic acid-containing cyclodepsipeptides with elastase-inhibitory activity from the marine cyanobacterium Lyngbya confervoides
Abstract
- Three unusual tiglic acid-containing cyclodepsipeptides, possessing the revised regioisomeric structures for largamides A-C (1-3), have been isolated from the marine cyanobacterium Lyngbya confervoides collected from southeastern Florida. The two-dimensional structures were determined by NMR spectroscopy and the absolute configurations by chiral HPLC analysis of degradation products. Compounds 1-3 are moderate inhibitors of mammalian elastase activity in vitro with IC(50) values ranging from 0.53 to 1.41 microM.
|
| 19224155 |
Safety, pharmacokinetic and pharmacodynamic studies of batifiban injection following single- and multiple-dose administration to healthy Chinese subjects |
10.1007/s11596-009-0103-7. |
J Huazhong Univ Sci Technolog Med Sci |
Safety, pharmacokinetic and pharmacodynamic studies of batifiban injection following single- and multiple-dose administration to healthy Chinese subjects
Abstract
- Batifiban, a synthetic cyclic peptide, is a potent platelet glycoprotein GPIIb/IIIa antagonist which may be useful in the treatment and prevention of acute coronary syndromes. The pharmacokinetics and pharmacodymanic (inhibition of platelet aggregation) effects, and tolerability of batifiban were investigated in healthy subjects following single bolus injection with doses of 55, 110, or 220 microg/kg, or multiple doses of an bolus followed intravenous infusion for 24 h (180 microg/kg plus 2.0 microg/min.kg, and 220 microg/kg plus 2.5 microg/min.kg) in this phase I clinical trial. Plasma levels of batifiban and areas under the curve were found to be proportional to doses. Batifiban was rapidly eliminated with a half-life of approximately 2.5 h. Significant differences were noted for plasma levels of batifiban and areas under the curve between males and females. No significant differences in the terminal half-life were found between males and females. Batifiban reversibly inhibited ex vivo platelet aggregation in a dose- and concentration-dependent manner, consistent with its mechanism as a GPIIb/IIIa antagonist. Single and multiple intravenous doses of batifiban were found to be safe and well tolerated in healthy subjects. These results support a bolus injection plus intravenous infusion regimen of batifiban for the treatment and prevention of acute coronary syndromes.
|
| 19245260 |
Cottoquinazoline A and cotteslosins A and B, metabolites from an Australian marine-derived strain of Aspergillus versicolor |
10.1021/np800777f. |
J Nat Prod |
Cottoquinazoline A and cotteslosins A and B, metabolites from an Australian marine-derived strain of Aspergillus versicolor
Abstract
- An Australian marine-derived isolate of Aspergillus versicolor (MST-MF495) yielded the known fungal metabolites sterigmatocystin, violaceol I, violaceol II, diorcinol, (-)-cyclopenol, and viridicatol, along with a new alkaloid, cottoquinazoline A (1), and two new cyclopentapeptides, cotteslosins A (2) and B (3). Structures for 1-3 and the known compounds were determined by spectroscopic analysis. The absolute configurations of 1-3 were addressed by chemical degradation and application of the C(3) Marfey's method. The use of "cellophane raft" high-nutrient media as a device for up-regulating secondary metabolite diversity in marine-derived fungi is discussed. The antibacterial properties displayed by A. versicolor (MST-MF495) were attributed to the phenols violaceol I, violaceol II, and diorcinol, while cotteslosins 2 and 3 were identified as weak cytotoxic agents.
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