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Affinity Labels (1):
Recent article
Affinity Labels
Gastroenterology (139)5 2010
Abstract
We aim to select and validate an affinity peptide that binds to esophageal dysplasia for future clinical studies.
Peptide selection was performed using phage display by removing nonspecific binders using Q-hTERT (intestinal metaplasia) cells and achieving specific binding against OE33 (esophageal ad...
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PMID: 20637198
PDF is available here.
PDF is available here.
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Food Microbiology (27)4 2010
Abstract
We obtained a dynamic range of greater than 3 logs for differentiating viable vs. dead cells. The viability and morphological characteristics of the stressed cells after one-week incubation at 25 degrees C, in air, and under nutrient-poor conditions were investigated. Our results indicated that, ove...
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PMID: 20417391
PDF is available here.
PDF is available here.
Molecular Pharmacology (75)1 2009
Abstract
P-glycoprotein (P-gp), an ATP-dependent drug efflux pump, has been implicated in multidrug resistance of several cancers due to its over-expression. Here rationally designed second-generation P-gp inhibitors are disclosed, based on dimerized versions of the substrates quinine and quinidine. These dim...
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PMID: 18945821
PDF is available here.
PDF is available here.
Abstract
We will discuss affinity-based methods and their applications, focusing on their unique advantages. In addition, we will describe emerging methods with potential value to proteomics, as well as the challenges that remain for proteomic studies....
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PMID: 19811078
PDF is available here.
PDF is available here.
Abstract
We prepared an affinity probe displaying picomolar potency toward several MMPs, and a related photoaffinity probe incorporating a photoactivatable azido group exhibiting subnanomolar affinity toward these targets. By a combination of silver-staining detection and MALDI peptide mass fingerprints, a s...
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PMID: 19271733
PDF is available here.
PDF is available here.
EMBO Journal (28)8 2009
Abstract
We have earlier shown that microglia, the immune cells of the CNS, release microparticles from cell plasma membrane after ATP stimulation. These vesicles contain and release IL-1beta, a crucial cytokine in CNS inflammatory events. In this study, we show that microparticles are also released by astro...
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PMID: 19300439
PDF is available here.
PDF is available here.
Abstract
Defining protein complexes is a vital aspect of cell biology because cellular processes are often carried out by stable protein complexes and their characterization often provides insights into their function. Accurate identification of the interacting proteins in macromolecular complexes is easiest...
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PMID: 19521826
PDF is available here.
PDF is available here.
ChemBioChem (10)4 2009
Abstract
Photogenerated quinine methides (QMs) can act as highly specific light-controllable protein affinity labeling reagents, broadening their applications to the study of protein-ligand and protein-protein interactions. The reactions between QMs and nucleophiles are less heterogeneous than those of other...
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PMID: 19197921
PDF is available here.
PDF is available here.
Electrophoresis (30)3 2009
Abstract
We describe three kinds of 2-DE using phosphate-affinity PAGE for the analysis of phosphoprotein isotypes. The first dimension is a urea-PAGE, IEF/NEPHGE, or SDS-PAGE, which are widely used. The second dimension is a phosphate-affinity SDS-PAGE using a phosphate-binding tag molecule, Phos-tag (Mn(2+...
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PMID: 19156764
PDF is available here.
PDF is available here.
Abstract
We address these limitations by a novel integrated method, which we applied and benchmarked for the human protein phosphatase 2A system. We identified a total of 197 protein interactions with high reproducibility, showing the coexistence of distinct classes of phosphatase complexes that are linked t...
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PMID: 19156129
PDF is available here.
PDF is available here.
Abstract
The effectiveness of an affinity column cleanup procedure followed by LC with fluorescence detection was established for the determination of aflatoxins and ochratoxin A in high-sugar-content traditional Turkish foods. Traditional foods, such as baklava (finely layered pastry filled with nuts and st...
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PMID: 19714981
PDF is available here.
PDF is available here.
Abstract
We describe a comprehensive methodology that uses our recently developed dual-tag affinity purification system for the enrichment and identification of mammalian protein complexes. The protocol covers a series of separate but sequentially related techniques focused on the facile monitoring and purif...
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PMID: 19488716
PDF is available here.
PDF is available here.
Abstract
We also focus on the MRI contrast properties of the labeled cells, as well as on the feasibility of in vivo detection of immunizing circulating cells by MRI, with direct implications in cell-based anticancer therapy using lymphocytes....
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PMID: 19347287
PDF is available here.
PDF is available here.
Abstract
In recognition of the fact that a relatively small percentage of 'named' genes in databases have any experimental proof for their annotation, attention is shifting towards the more accurate assignment of functions to individual genes in a genome. The central objective will be to reduce our reliance...
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PMID: 19347659
PDF is available here.
PDF is available here.
Molecular Pharmacology (75)1 2009
Abstract
We have synthesized a series of stereoisomers of fenoterol and its derivatives and characterized their receptor binding and pharmacological properties. We tested the hypothesis that the stereochemistry of an agonist determines selectivity of receptor coupling to different G protein(s). We found that...
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PMID: 18838481
PDF is available here.
PDF is available here.
Abstract
Biochemistry (Washington) (47)39 2008
Abstract
We have thus designed and synthesized several perfluorophenyl azido (pfpa) CQ analogues for PfCRT photolabeling studies. One particularly useful probe (AzBCQ) places the pfpa group at the terminal aliphatic N of CQ via a flexible four-carbon ester linker and includes a convenient biotin tag. This pr...
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PMID: 18767816
PDF is available here.
PDF is available here.
Acta Crystallographica Section D (64)Pt 9 2008
Abstract
The putative outer membrane c-type cytochrome OmcF from Geobacter sulfurreducens contains a single haem group and shows homology to soluble cytochromes c(6), a class of electron-transfer proteins that are typically found in cyanobacterial photosynthetic electron-transfer chains. OmcF was overexpress...
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PMID: 18703839
PDF is available here.
PDF is available here.
Abstract
The specific recognition and binding of biological molecules by antibodies is fundamentally important. Natural antibodies are multivalent, having at least two identical ligand-binding sites; this permits them to bind tightly at cell surfaces, which present multiple copies of their target ligands. An...
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PMID: 18538444
PDF is available here.
PDF is available here.
Bioconjugate Chemistry (19)8 2008
Abstract
Cholesteryl ester transfer protein (CETP) transfers neutral lipids between different types of plasma lipoprotein. Inhibitors of CETP elevate the fraction of plasma cholesterol associated with high-density lipoproteins and are being developed as new agents for the prevention and treatment of cardiova...
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PMID: 18646836
PDF is available here.
PDF is available here.
Abstract
We synthesized labeling reagents that contain: 1) a benzenesulfonamide ligand that directs specifically to bovine carbonic anhydrase II (bCA), 2) an electrophilic epoxide group for protein labeling, 3) an exchangeable hydrazone bond linking the ligand and the epoxide group, and 4) an iodophenyl or a...
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PMID: 18494012
PDF is available here.
PDF is available here.
Clinical Chemistry (54)7 2008
Abstract
The PLA may offer significant advantages over conventional methods for screening the interactions of ligands with their receptors. The assay may prove useful for parallel analyses of large numbers of samples in the screening of inhibitor libraries for promising agents. The technique provides dose-re...
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PMID: 18499900
PDF is available here.
PDF is available here.
Abstract
Ethanol and zolpidem share similar discriminative stimulus effects most likely through GABA(A) receptors that contain alpha(1) subunits, however, antagonism by Ro15-4513 of zolpidem generalization from the lower training dose of ethanol (1.0 g/kg) may involve additional zolpidem-sensitive GABA(A) re...
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PMID: 18482161
PDF is available here.
PDF is available here.
Chemical Society Reviews (37)7 2008
Identification of the cellular targets of bioactive small organic molecules using affinity reagents.
Abstract
The elucidation of molecular targets of bioactive small organic molecules remains a significant challenge in modern biomedical research and drug discovery. This tutorial review summarizes strategies for the derivatization of bioactive small molecules and their use as affinity probes to identify cell...
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PMID: 18568161
PDF is available here.
PDF is available here.
Brain Research (1215) 2008
Abstract
We compare cellular labeling methods of rat marrow stromal cells that were labeled with 5-bromo-2-deoxyuridine (BrdU), 1,1'-dioctadecyl-3,3,3',3'-tetramethylindocarbocyanine perchlorate (DiI) and fluorescence in situ hybridization (FISH). Our data show that (i) BrdU uniformly labeled the nuclei, (ii...
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PMID: 18468584
PDF is available here.
PDF is available here.
Abstract
A bidirectional affinity system was used to screen for marine natural products that bound to Escherichia coli proteins. A system was developed and applied to isolate the natural product sceptrin from an Agelas conifera extract and its affinity partner MreB from E. coli lysate. The use of a dual immu...
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PMID: 18479102
PDF is available here.
PDF is available here.
Abstract
We reported that chimeric hexitol (HNA) and altritol (ANA) nucleotide monomers with an anhydrohexitol sugar moiety are easily available and proved their chemistry to be compatible with DNA and RNA synthesis. In this communication we describe a novel analytical platform based on HNA and ANA units to...
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PMID: 18378134
PDF is available here.
PDF is available here.
Abstract
We illustrate the use of SPR-MS to solve proteomics-based research questions, describing applications that use very different types of immobilized components: such as small (drug or messenger) molecules, peptides, DNA and proteins. We evaluate the current possibilities and limitations and discuss th...
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PMID: 18532910
PDF is available here.
PDF is available here.
Abstract
A nanoscale sensor employing fluorescent resonance energy transfer interactions between fluorescent quantum dots (QDs) and organic quencher molecules can be used for the multiplexed detection of biological antigens in solution. Detection occurs when the antigens to be detected displa...
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PMID: 18500912
PDF is available here.
PDF is available here.
Abstract
We isolated EBNA5 containing protein complexes using a modified tandem affinity purification (TAP) method and identified the protein components by LC-MS/MS analysis of tryptic digests on a LTQ-FT-ICR mass spectrometer. The modified TAP tag contained a Protein A domain and a StrepTagII sequence separ...
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PMID: 18457437
PDF is available here.
PDF is available here.
Bioorganic Chemistry (36)3 2008
Abstract
We have now synthesized a nonhydrolyzable reactive cGMP analog, Rp-guanosine-3',5'-cyclic-S-(4-bromo-2, 3-dioxobutyl)monophosphorothioate (Rp-cGMPS-BDB). Rp-cGMPS-BDB irreversibly inactivates PDE3A (K(I)=43.4+/-7.2muM and k(cart)=0.007+/-0.0006 min(-1)). The effectiveness of protectants in decreasin...
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PMID: 18394675
PDF is available here.
PDF is available here.
Abstract
We demonstrated the noninvasive imaging of glycans in live developing zebrafish, using a chemical reporter strategy. Zebrafish embryos were treated with an unnatural sugar to metabolically label their cell-surface glycans with azides. Subsequently, the embryos were reacted with fluorophore conjugate...
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PMID: 18451302
PDF is available here.
PDF is available here.
Bioconjugate Chemistry (19)5 2008
Abstract
During recent years, quantitative proteome profiling has taken advantage of incorporating the traditional stable isotope dilution analysis into global scale or discovery-based proteomic experiments that use mass spectrometers as detectors to allow the pairwise study of differently expressed proteins...
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PMID: 18407682
PDF is available here.
PDF is available here.
Abstract
To prepare thiol-reactive ifenprodil derivatives designed as potential probes for cysteine-substituted NR2B containing NMDA receptors, electrophilic centers were introduced in different areas of the ifenprodil structure. Intermediates and final compounds were evaluated by binding studies and by elec...
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PMID: 18434149
PDF is available here.
PDF is available here.
Abstract
We present a method for the fluorescent profiling of PKS, NRPS, and FAS multidomain modular synthases in their whole proteomes using complementary metabolic and activity based probes. After first examining the reactivity of these activity based probes with a variety of purified recombinant PKS, NRPS...
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PMID: 18376827
PDF is available here.
PDF is available here.
Abstract
We describe a method for bestowing light sensitivity onto endogenous ion channels that does not rely on exogenous gene expression. The method uses a synthetic photoisomerizable small molecule, or photoswitchable affinity label (PAL), that specifically targets K+ channels. PALs contain a reactive ele...
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PMID: 18311146
PDF is available here.
PDF is available here.
Abstract
The yeast two-hybrid system has evolved from a method mainly used in basic research to a collection of versatile screening systems with the potential to affect many different aspects of drug discovery today....
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PMID: 18348685
PDF is available here.
PDF is available here.
Molecular Pharmacology (73)4 2008
Abstract
These results establish that Lys411 participates in substrate binding via an ionic association with the substrate gamma-carboxylate; however, this is not essential for transport. An unmodified alpha-carboxylate is required for high-affinity substrate binding to RFC, whereas the gamma-carboxyl is not...
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PMID: 18182479
PDF is available here.
PDF is available here.
European Journal of Pharmacology (582)1-3 2008
Abstract
Our results indicate that meperidine, remifentanil and tramadol interact with alpha(2)-adrenoceptors in mouse brain showing different affinity for alpha(2A)-, alpha(2B)- and alpha(2C)-adrenoceptors. In contrast, the micro-agonist sufentanil did not show any alpha(2)-adrenoceptor interaction. These e...
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PMID: 18234187
PDF is available here.
PDF is available here.
Bioconjugate Chemistry (19)3 2008
Abstract
Optical imaging of bacterial infection in living animals is usually conducted with genetic reporters such as light-emitting enzymes or fluorescent proteins. However, there are many circumstances where genetic reporters are not applicable, and there is a need for exogenous synthetic probes that can s...
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PMID: 18260609
PDF is available here.
PDF is available here.
Abstract
We describe methods for each of these assays, identify recent improvements in these assays and outline the strengths and limitations of each approach....
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PMID: 18314058
PDF is available here.
PDF is available here.
Abstract
We report a novel and versatile synthesis protocol to access a variety of functionalised p-nitrophenyl phosphonate (PNPP) inhibitors from a common azide functionalised precursor using click chemistry. The obtained PNPPs were successfully used to covalently label serine hydrolases in their active sit...
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PMID: 18219423
PDF is available here.
PDF is available here.
Proteomics (8)4 2008
Abstract
MALDI-MS is an extremely flexible technique and can be synergistically used in conjunction with established bioanalytical methods such as PAGE or SPR. To that end, slight modifications on the sample target plate may be necessary. Those can involve the use of hydrophobic coatings for improved sample...
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PMID: 18210370
PDF is available here.
PDF is available here.
ChemBioChem (9)2 2008
Abstract
Clinical laboratory (54)11-12 2008
Abstract
This article has been designed to give a brief overview of antigen-antibody reactions, especially in the form used in immunoassays. The different types of label and assay design have been described briefly. The report has not been designed as a brief text book, so that diagrams referring to assay pr...
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PMID: 19216249
PDF is available here.
PDF is available here.
AADE editors' journal (110) 2008
Abstract
The use of mass spectrometry in protein identification has revolutionized the field of proteomics. Coupled to various affinity purification techniques, mass spectrometry is used to identify protein-protein interactions. This chapter looks at the use of these affinity purification techniques in the i...
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PMID: 18227982
PDF is available here.
PDF is available here.
Abstract
We cloned twelve additional subfamily Ialpha enzymes from an evolutionarily divergent set of organisms. Nine were purified to homogeneity after heterologous expression in Escherichia coli in native, intein-tagged or His(6)-tagged forms. The two Saccharomyces cerevisiae isoforms were recombinantly pr...
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PMID: 17964807
PDF is available here.
PDF is available here.
Abstract
Many elegant methodologies have been devised to explore RNA-protein as well as RNA-RNA interactions. Although the characterization of messages targeted by a specific RNA-binding protein (RBP) has been accelerated by the application of microarray technologies, reliable methods to describe the endogen...
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PMID: 18369976
PDF is available here.
PDF is available here.
Bioconjugate Chemistry (19)1 2008
Abstract
We have used the site-directed incorporation of cysteine nucleophiles at the periphery of an antibody's binding site, paired with the chemical design of weakly electrophilic ligands, to produce receptor-ligand pairs that conjugate specifically and permanently (Corneillie et al. (2004) Bioconjugate C...
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PMID: 18062660
PDF is available here.
PDF is available here.
Abstract
Biospecific interactions are used in many capturing and bioseparation steps. A typical situation is the coupling of a biospecific ligand to a chromatographic stationary phase for affinity chromatography. This approach has two possible drawbacks. The first is that a chromatographic column may be awkw...
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PMID: 18287648
PDF is available here.
PDF is available here.
Abstract
The analysis of peptide mixtures from urine and plasma samples using bare (uncapped) SiO2 nanoparticles (NPs) with atmospheric-pressure matrix-assisted laser desorption/ionization mass spectrometry (AP-MALDI-MS) has been reported. The method was based on the adsorption of positively charged peptides...
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PMID: 18186457
PDF is available here.
PDF is available here.
Protein Science (2)10 2008
Abstract
Abstract
We describe the synthesis and characterisation of dye oligomers containing dansyl-, 7-nitro-2,1,3-benzoxadiazol-4-yl- (NBD), coumarin-343, 5(6)-carboxyfluorescein and sulforhodamine B2 moieties based on polyamidoamine (PAMAM) dendrimers. The PAMAM dendrimers were synthesised by an improved protocol...
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PMID: 18752247
PDF is available here.
PDF is available here.
MR and iron magnetic nanoparticles. Imaging opportunities in preclinical and translational research.
Abstract
We demonstrated that magnetic resonance imaging at 1.5 T allows the detection of ultrasmall superparamagnetic iron oxide nanoparticle conjugated antibody specifically bound to human tumor cells in vitro and in vivo, and that the magnetic resonance signal intensity correlates with the concentration o...
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PMID: 18564611
PDF is available here.
PDF is available here.
Laryngoscope (118)1 2008
Abstract
This initial study using new high-resolution MALDI-TOF mass spectrometry coupled with bead fractionation is suitable for automated protein profiling and has the capability to simultaneously identify potential biomarker proteins for HNSCC. In addition, we were able to show improvement with the MALDI-...
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PMID: 18043497
PDF is available here.
PDF is available here.
Abstract
Affinity hydrogels based on poly(ethylene glycol) diacrylate and a metal-ion-chelating ligand, glycidyl methacrylate-iminodiacetic acid, have been developed to systematically decrease protein release rates from hydrophilic tissue engineering scaffolds formed in situ. In the current w...
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PMID: 17580324
PDF is available here.
PDF is available here.
Genes & Development (21)23 2007
Abstract
We exploited an RNA-based affinity purification method to isolate ribonucleoproteins (RNPs) assembled on individual human Y RNAs. Silver staining and mass spectrometry revealed that the Ro and La proteins assemble with all Y RNAs, while additional proteins associate with specific Y RNAs. Unexpectedl...
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PMID: 18056422
PDF is available here.
PDF is available here.
Abstract
A bifunctional high molecular weight (Mr, 64,500 Da) beta-1-3, 1-4 glucan 4-glucanohydrolase was purified to homogeneity from Thermomonospora sp., exhibiting activity towards lichenan and xylan. A kinetic method was used to analyze the active site that hydrolyzes lichenan and xylan. The experimental...
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PMID: 17689169
PDF is available here.
PDF is available here.
Neuropharmacology (53)7 2007
Abstract
We have used a newly available GABA-A/benzodiazepine receptor inverse agonist that is selective for the alpha5 subtype (a5IA) to evaluate the role of this subtype in mediating these effects of alcohol on the brain. After pre-treatment with a5IA, we found almost complete blockade of the marked impair...
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PMID: 17888460
PDF is available here.
PDF is available here.
Biochemistry (Washington) (46)45 2007
Abstract
We characterize its ATPase activity and demonstrate that it has biochemical features reminiscent of those of other ATP-binding cassette multidrug transporters: a relatively high Km for ATP (1.9 mM), inhibition by orthovanadate, and the ability to specifically bind an azidoATP analogue at the nucleot...
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PMID: 17956128
PDF is available here.
PDF is available here.