| 15164054 |
The DNA sequence and comparative analysis of human chromosome 10. |
10.1038/nature02462 |
Nature |
The DNA sequence and comparative analysis of human chromosome 10.
Abstract
- The finished sequence of human chromosome 10 comprises a total of 131,666,441 base pairs. It represents 99.4% of the euchromatic DNA and includes one megabase of heterochromatic sequence within the pericentromeric region of the short and long arm of the chromosome. Sequence annotation revealed 1,357 genes, of which 816 are protein coding, and 430 are pseudogenes. We observed widespread occurrence of overlapping coding genes (either strand) and identified 67 antisense transcripts. Our analysis suggests that both inter- and intrachromosomal segmental duplications have impacted on the gene count on chromosome 10. Multispecies comparative analysis indicated that we can readily annotate the protein-coding genes with current resources. We estimate that over 95% of all coding exons were identified in this study. Assessment of single base changes between the human chromosome 10 and chimpanzee sequence revealed nonsense mutations in only 21 coding genes with respect to the human sequence.
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| 15165149 |
Enniatins of Fusarium sp. strain F31 and their inhibition of Botrytis cinerea spore germination |
10.1021/np0340448. |
J Nat Prod |
Enniatins of Fusarium sp. strain F31 and their inhibition of Botrytis cinerea spore germination
Abstract
- A spectrum of enniatins was isolated from Fusarium sp. strain F31 by bioassay-guided isolation directed against Botrytis cinerea. Two new enniatins, J(2) (7) and J(3) (8), were co-isolated and both contained, in addition to three hydroxyisovaleric acid units, N-methylated l-alanine, l-valine, and l-isoleucine units, differing only in their primary sequence. Two other enniatins, named enniatin J(1) (1) and enniatin K(1) (6), each containing two N-Me-l-Val units and one N-Me-l-Ala or alpha-N-Me-l-butyric acid unit, respectively, were isolated for the first time without directed biosynthesis. The enniatin structures were elucidated by spectroscopic and chemical methods, and the absolute configuration of the amino acids (l) and hydroxyisovaleric acid (d) was consistent with all previously isolated enniatins. The known enniatins B (2), B(1) (4), B(2) (5), and B(4) (3) were also isolated. The minimum inhibitory concentration of pure enniatins against Botrytis cinerea was 75 microg/mL.
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| 15165155 |
Psychrophilin A and cycloaspeptide D, novel cyclic peptides from the psychrotolerant fungus Penicillium ribeum |
10.1021/np0303714. |
J Nat Prod |
Psychrophilin A and cycloaspeptide D, novel cyclic peptides from the psychrotolerant fungus Penicillium ribeum
Abstract
- Two fungal metabolites, psychrophilin A (1) and cycloaspeptide D (2), together with the known cycloaspeptide A (3) were isolated from the psychrotolerant fungus Penicillium ribeum using high-speed countercurrent chromatography (HSCCC) and preparative HPLC. The structures were determined from 1D and 2D NMR techniques, HREIMS, tandem mass spectrometry (ESMS/MS), and X-ray crystallography. The amino acid residues of psychrophilin A (1) and cycloaspeptide D (2) were all found to possess the l configuration by Marfey's method. Psychrophilin A (1) is the first natural cyclic peptide containing a nitro group instead of an amino group.
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| 15165849 |
Mechanisms of camptothecin resistance by human topoisomerase I mutations |
10.1016/j.jmb.2004.03.077. |
J Mol Biol |
Mechanisms of camptothecin resistance by human topoisomerase I mutations
Abstract
- Human topoisomerase I relaxes superhelical tension associated with DNA replication, transcription and recombination by reversibly nicking one strand of duplex DNA and forming a covalent 3'-phosphotyrosine linkage. This enzyme is the sole target of the camptothecin family of anticancer compounds, which acts by stabilizing the covalent protein-DNA complex and enhancing apoptosis through blocking the advancement of replication forks. Mutations that impart resistance to camptothecin have been identified in several regions of human topoisomerase I. We present the crystal structures of two camptothecin-resistant forms of human topoisomerase I (Phe361Ser at 2.6A resolution and Asn722Ser at 2.3A resolution) in ternary complexes with DNA and topotecan (Hycamtin), a camptothecin analogue currently in widespread clinical use. While the alteration of Asn722 to Ser leads to the elimination of a water-mediated contact between the enzyme and topotecan, we were surprised to find that a well-ordered water molecule replaces the hydrophobic phenylalanine side-chain in the Phe361Ser structure. We further consider camptothecin-resistant mutations at seven additional sites in human topoisomerase I and present structural evidence explaining their possible impact on drug binding. These results advance our understanding of the mechanism of cell poisoning by camptothecin and suggest specific modifications to the drug that may improve efficacy.
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| 15166135 |
Analysis of beta-1,3-glucan assembly in Saccharomyces cerevisiae using a synthetic interaction network and altered sensitivity to caspofungin. |
10.1534/genetics.167.1.35 |
Genetics |
Analysis of beta-1,3-glucan assembly in Saccharomyces cerevisiae using a synthetic interaction network and altered sensitivity to caspofungin.
Abstract
- Large-scale screening of genetic and chemical-genetic interactions was used to examine the assembly and regulation of beta-1,3-glucan in Saccharomyces cerevisiae. Using the set of deletion mutants in approximately 4600 nonessential genes, we scored synthetic interactions with genes encoding subunits of the beta-1,3-glucan synthase (FKS1, FKS2), the glucan synthesis regulator (SMI1/KNR4), and a beta-1,3-glucanosyltransferase (GAS1). In the resulting network, FKS1, FKS2, GAS1, and SMI1 are connected to 135 genes in 195 interactions, with 26 of these genes also interacting with CHS3 encoding chitin synthase III. A network core of 51 genes is multiply connected with 112 interactions. Thirty-two of these core genes are known to be involved in cell wall assembly and polarized growth, and 8 genes of unknown function are candidates for involvement in these processes. In parallel, we screened the yeast deletion mutant collection for altered sensitivity to the glucan synthase inhibitor, caspofungin. Deletions in 52 genes led to caspofungin hypersensitivity and those in 39 genes to resistance. Integration of the glucan interaction network with the caspofungin data indicates an overlapping set of genes involved in FKS2 regulation, compensatory chitin synthesis, protein mannosylation, and the PKC1-dependent cell integrity pathway.
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| 15170751 |
Determining sequences and post-translational modifications of novel conotoxins in Conus victoriae using cDNA sequencing and mass spectrometry |
10.1002/jms.624. |
J Mass Spectrom |
Determining sequences and post-translational modifications of novel conotoxins in Conus victoriae using cDNA sequencing and mass spectrometry
Abstract
- A combination of cDNA cloning and detailed mass spectrometric analyses was employed to identify novel conotoxins from Conus victoriae. Eleven conotoxin sequences were determined using molecular methods: one belonging to the A superfamily (Vc1.1), six belonging to the O superfamily (Vc6.1-Vc6.6) and four members of the T superfamily (Vc5.1-Vc5.4). In order to verify the sequences and identify the post-translational modifications (excluding the disulfide connectivity) of three Conus victoriae conotoxins, vc1a, vc5a and vc6a, deduced from sequences Vc1.1, Vc5.1, and Vc6.1, respectively, liquid chromatography/electrospray ionization ion trap mass spectrometry, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and nanospray ionization ion trap mass spectrometry with collisionally induced dissociation were performed on reduced and alkylated venom fractions. We report that vc1a, the native form of alpha-conotoxin Vc1.1 (an unmodified 16 amino acid residue peptide that has notable pain-relieving capabilities), includes a hydroxyproline and a gamma-carboxyglutamate residue. Conotoxin vc5a is a 10-residue peptide with two disulfide bonds and a hydroxyproline and vc6a is a 25 amino acid peptide with three disulfide bonds.
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| 15176835 |
On-resin native chemical ligation for cyclic peptide synthesis |
10.1021/jo049839d. |
J Org Chem |
On-resin native chemical ligation for cyclic peptide synthesis
Abstract
- A novel cysteine derivative, N(alpha)-trityl-S-(9H-xanthen-9-yl)-l-cysteine [Trt-Cys(Xan)-OH] has been introduced for peptide synthesis, specifically for application to a new strategy for the preparation of cyclic peptides. The following steps were carried out to synthesize the cyclic model peptide cyclo(Cys-Thr-Abu-Gly-Gly-Ala-Arg-Pro-Asp-Phe): (i). side-chain anchoring of Fmoc-Asp-OAl via its free beta-carboxyl as a p-alkoxybenzyl ester to a solid support; (ii). stepwise chain elongation of the peptide by standard Fmoc/tBu solid-phase chemistry; (iii). removal of the N-terminal Fmoc group; (iv). coupling of Trt-Cys(Xan)-OH; (v). selective Pd(0)-promoted cleavage of the C-terminal allyl ester; (vi). coupling of the C-terminal residue, i.e., H-Phe-SBzl, preactivated as a thioester; (vii). selective removal of the N(alpha)-Trt and S-Xan protecting groups under very mild acid conditions; (viii). on-resin cyclization by native chemical ligation in an aqueous milieu; and (ix). final acidolytic cleavage of the cyclic peptide from the resin. The strategy was evaluated for three supports: poly[N,N-dimethacrylamide-co-poly(ethylene glycol)] (PEGA), cross-linked ethoxylate acrylate resin (CLEAR), and poly(ethylene glycol)-polystyrene (PEG-PS) graft resin supports. For PEGA and CLEAR, the desired cyclic product was obtained in 76-86% overall yield with initial purities of approximately 70%, whereas for PEG-PS (which does not swell nearly as well in water), results were inferior. Solid-phase native chemical ligation/cyclization methodology appears to have advantages of convenience and specificity, which make it promising for further generalization.
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| 15178353 |
Differential agonistic and antagonistic effects of the urotensin-II ligand SB-710411 at rodent and primate UT receptors |
10.1016/j.ejphar.2004.03.059. |
Eur J Pharmacol |
Differential agonistic and antagonistic effects of the urotensin-II ligand SB-710411 at rodent and primate UT receptors
Abstract
- SB-710411 (Cpa-c[d-Cys-Pal-d-Trp-Lys-Val-Cys]-Cpa-amide) inhibited [(125)I]urotensin-II rat and monkey UT receptor binding (pK(i)s 7.50+/-0.07 and 6.82+/-0.06). However, whereas SB-710411 antagonized urotensin-II-induced inositol phosphate formation at the rat UT receptor (pK(b) 6.54+/-0.05), this ligand functioned as an agonist at the monkey UT receptor (pEC(50) 6.56+/-0.35, E(max) 5.27+/-0.65-fold over basal). Indeed, in contrast to the rat UT receptor (and rat isolated arteries), SB-710411 exhibited intrinsic activity in monkey arteries acting as an efficacious vasoconstrictor (pEC(50)s 5.03+/-0.18 to 5.71+/-0.21, E(max)s 101+/-4 to 218+/-58% KCl). These data demonstrate that caution must be taken when extrapolating the pharmacology of a specific ligand(s) between the rodent and primate UT receptors.
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| 15199155 |
SENP1 enhances androgen receptor-dependent transcription through desumoylation of histone deacetylase 1 |
10.1128/MCB.24.13.6021-6028.2004. |
Mol Cell Biol |
SENP1 enhances androgen receptor-dependent transcription through desumoylation of histone deacetylase 1
Abstract
- SUMO (also called Sentrin) is a ubiquitin-like protein that plays an important role in regulating protein function and localization. It is known that several nuclear receptors are modified by SUMO; however, the effect of desumoylation in regulating nuclear receptor function has not been elucidated. Here we show that androgen receptor (AR)-mediated transcription is markedly enhanced by SENP1, a member of SUMO-specific protease family. SENP1's ability to enhance AR-dependent transcription is not mediated through desumoylation of AR, but rather through its ability to deconjugate histone deacetylase 1 (HDAC1), thereby reducing its deacetylase activity. HDAC1's repressive effect on AR-dependent transcription could be reversed by SENP1 and by deletion of its sumoylation sites. RNA interference depletion of endogenous HDAC1 also reduced SENP1's effect. Thus, SENP1 could regulate AR-dependent transcription through desumoylation of HDAC1. These studies provide insights on the potential role of desumoylation in the regulation of nuclear receptor activity.
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| 15199170 |
Thiostrepton-resistant mutants of Thermus thermophilus |
10.1093/nar/gkh644. |
Nucleic Acids Res |
Thiostrepton-resistant mutants of Thermus thermophilus
Abstract
- Ribosomal protein L11 and its associated binding site on 23S rRNA together comprise one of the principle components that mediate interactions of translation factors with the ribosome. This site is also the target of the antibiotic thiostrepton, which has been proposed to act by preventing important structural transitions that occur in this region of the ribosome during protein synthesis. Here, we describe the isolation and characterization of spontaneous thiostrepton-resistant mutants of the extreme thermophile, Thermus thermophilus. All mutations were found at conserved positions in the flexible N-terminal domain of L11 or at conserved positions in the L11-binding site of 23S rRNA. A number of the mutant ribosomes were affected in in vitro EF-G-dependent GTP hydrolysis but all showed resistance to thiostrepton at levels ranging from high to moderate. Structure probing revealed that some of the mutations in L11 result in enhanced reactivity of adjacent rRNA bases to chemical probes, suggesting a more open conformation of this region. These data suggest that increased flexibility of the factor binding site results in resistance to thiostrepton by counteracting the conformation-stabilizing effect of the antibiotic.
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| 15202729 |
ISAtx-247 (Isotechnika/Roche) |
None |
Curr Opin Investig Drugs |
ISAtx-247 (Isotechnika/Roche)
Abstract
- ISAtx-247 is a ciclosporin A analog under development by Isotechnika and Roche as an immunosuppressant for the potential prevention of organ rejection after transplantation, and for the potential treatment of autoimmune diseases such as rheumatoid arthritis, psoriasis and type 1 diabetes. A phase II renal transplantation study had been completed by June 2003.
|
| 15205345 |
Inhibition of breast cancer metastasis by selective synthetic polypeptide against CXCR4 |
10.1158/0008-5472.CAN-03-3958. |
Cancer Res |
Inhibition of breast cancer metastasis by selective synthetic polypeptide against CXCR4
Abstract
- Metastasis shares many similarities with leukocyte trafficking. Among those chemokine receptors thought to be involved in hemopoietic cell homing, stromal cell-derived factor-1 and its receptor CXC chemokine receptor-4 (CXCR4) have received considerable attention. Like hemopoietic cell homing, levels of stromal cell-derived factor-1 are high at sites of breast cancer metastasis including lymph node, lung, liver, and the marrow. Moreover, CXCR4 expression is low in normal breast tissues and high in malignant tumors, suggesting that a blockade of CXCR4 might limit tumor metastasis. We therefore investigated the role of a synthetic antagonist 14-mer peptide (TN14003) in inhibiting metastasis in an animal model. Not only was TN14003 effective in limiting metastasis of breast cancer by inhibiting migration, but it may also prove useful as a diagnostic tool to identify CXCR4 receptor-positive tumor cells in culture and tumors in paraffin-embedded clinical samples.
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| 15208328 |
Mutational analysis of ionizable residues proximal to the cytoplasmic interface of membrane spanning domain 3 of the multidrug resistance protein, MRP1 (ABCC1): glutamate 1204 is important for both the expression and catalytic activity of the transporter. |
10.1074/jbc.m403832200 |
J. Biol. Chem. |
Mutational analysis of ionizable residues proximal to the cytoplasmic interface of membrane spanning domain 3 of the multidrug resistance protein, MRP1 (ABCC1): glutamate 1204 is important for both the expression and catalytic activity of the transporter.
Abstract
- The multidrug resistance protein MRP1 is an ATP-dependent transporter of organic anions and chemotherapeutic agents. A significant number of ionizable amino acids are found in or proximal to the 17 transmembrane (TM) helices of MRP1, and we have investigated 6 of these at the cytoplasmic interface of TM13-17 for their role in MRP1 expression and transport activity. Opposite charge substitutions of TM13 Arg(1046) and TM15 Arg(1131) did not alter MRP1 expression nor did they substantially affect activity. In contrast, opposite charge substitutions of TM16 Arg(1202) and Glu(1204) reduced protein expression by >80%; however, MRP1 expression was not affected when Arg(1202) and Glu(1204) were replaced with neutral or same-charge residues. In addition, organic anion transport levels of the R1202L, R1202G, and R1202K mutants were comparable with wild-type MRP1. In contrast, organic anion transport by E1204L was substantially reduced, whereas transport by E1204D was comparable with wild-type MRP1, with the notable exception of GSH. Opposite charge substitutions of TM16 Arg(1197) and TM17 Arg(1249) did not affect MRP1 expression but substantially reduced transport. Mutants containing like-charge substitutions of Arg(1197) or Arg(1249) were also transport-inactive and no longer bound leukotriene C(4). In contrast, substrate binding by the transport-compromised E1204L mutant remained intact. Furthermore, vanadate-induced trapping of azido-ADP by E1204L was dramatically increased, indicating that this mutation may cause a partial uncoupling of the catalytic and transport activities of MRP1. Thus, Glu(1204) serves a dual role in membrane expression of MRP1 and a step in its catalytic cycle subsequent to initial substrate binding.
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| 15217277 |
Three cyclooctapeptides and one glycoside from Microtoena prainiana |
10.1021/np040021x. |
J Nat Prod |
Three cyclooctapeptides and one glycoside from Microtoena prainiana
Abstract
- Three new cyclic octapeptides, microtoenins A-C (1-3), and a new glycoside, 3'''-O-methylcrenatoside (4), along with several known compounds, were isolated from the ethanolic extract of the stems of Microtoena prainiana. Their structures were determined by spectral and chemical evidence. At a concentration of 0.01 mg/mL, 3'''-O-methylcrenatoside (4), crenatoside (5), and isocrenatoside (6) inhibited angiotensin converting enzyme (ACE) activity by more than 30%.
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| 15231824 |
Agonist-dependent dissociation of human somatostatin receptor 2 dimers: a role in receptor trafficking. |
10.1074/jbc.m407310200 |
J. Biol. Chem. |
Agonist-dependent dissociation of human somatostatin receptor 2 dimers: a role in receptor trafficking.
Abstract
- G-protein-coupled receptors (GPCRs) represent the largest and most diverse family of cell surface receptors. Several GPCRs have been documented to dimerize with resulting changes in pharmacology and signaling. We have previously reported, by means of photobleaching fluorescence resonance energy transfer (pbFRET) microscopy and fluorescence correlation spectroscopic analysis in live cells, that human somatostatin receptor (hSSTR) 5 could both homodimerize and heterodimerize with hSSTR1 in the presence of the agonist SST-14. By contrast, hSSTR1 remained monomeric when expressed alone regardless of agonist exposure in live cells. However, the effect of the agonist on other hSSTR members remains unknown. Using pbFRET microscopy and Western blot, we provide evidence for agonist-dependent dissociation of self-associated hSSTR2 stably expressed in CHO-K1 and HEK-293 cells. Furthermore, the dissociation of the hSSTR2 dimer occurred in a concentration-dependent manner. Moreover, blocking receptor dissociation using a cross-linker agent perturbed receptor trafficking. Taking these data together, we suggest that the process of GPCR dimerization may operate differently, even among members of the same family, and that receptor dissociation as well as dimerization may be important steps for receptor dynamics.
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