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PubMed1992

Photoaffinity labeling of the phylloquinone-binding polypeptides by 2-azidoanthraquinone in photosystem I particles.

A photoaffinity label, 2-azido-9,10-anthraquinone, binds at the quinone-binding (Q phi) site with high affinity and can substitute for the secondary acceptor, phylloquinone, in photosystem I reaction center of spinach. Phylloquinone-depleted photosystem I particles reconstituted with azido[3H]anthraquinone were illuminated with UV light and analyzed by sodium dodecylsulfate-polyacrylamide gel electrophoresis. The large core polypeptides (psaA and/or psaB) were selectively labeled. The labeling was competitively inhibited in the presence of anthraquinone. These results indicate that the Q phi site is located on psaA or psaB polypeptides.

Affinity Labels↗
PubMed1992

Highly efficient photoaffinity labeling of the hormone binding domain of atrial natriuretic factor receptor.

A high-efficiency photoaffinity derivative of atrial natriuretic factor (ANF) was developed for studying the peptide binding domain of the receptor protein and for better characterization of this receptor in tissues with a low density of binding sites. The position of the photosensitive residue was chosen on the basis of a molecular conformational model and on structure-activity relationship studies which both indicate that the carboxy-terminal end of the peptide is part of a hydrophobic pole likely to interact deeply within the ANF binding pocket of the receptor. Selection of the photoreactive residue p-benzoylphenylalanine (BPA) as a substitute for arginine in position 125 of the peptide sequence led to a photoaffinity derivative with a high (63%) efficiency of covalent incorporation to the receptor protein. This derivative (BPA-ANF) has a 10-fold lower affinity when compared with ANF, but it is a full agonist in stimulating cGMP production and inhibiting aldosterone secretion in bovine adrenal zona glomerulosa. Photoaffinity labeling with BPA-ANF specifically identifies ANF-R1 and ANF-R2 receptor proteins with a 10-fold higher efficiency than with azido derivatives of ANF or with cross-linking agents. This new ANF derivative therefore appears to be useful for studying ANF receptors in tissues with low levels of expression, for locating receptor following cellular internalization, and for tagging proteolytic fragments of the receptor amenable to amino acid microsequencing.

Affinity Labels↗
PubMed1991

Photoaffinity labelling of the pea chloroplast transcriptional complex by nascent RNA in vitro.

We have used photoaffinity labelling to examine the chloroplast RNA polymerase components which come into contact with nascent transcripts during the in vitro transcription of plastid DNA. The transcripts were synthesized in the presence of a photoactive analogue (4-thio UTP) and alpha-32P-ATP, using enriched pea chloroplast RNA polymerase preparation and a recombinant plasmid containing the plastid 16S rRNA promoter. Brief irradiation of the transcriptional complex crosslinked the photoactive nascent RNA to proximal proteins. Labelling of the transcriptional complex was dependent on 4-thio UTP and template DNA. Two polypeptides of 51 and 54 kDa were consistently crosslinked to the nascent transcripts; about 60% of the total radioactivity of the crosslinked RNA was associated with these polypeptides. In some experiments, two additional polypeptides of 38 and 75 kDa were also found to be associated with about 13% and 17% of the total crosslinked RNA radioactivity, respectively. The UV-crosslinked transcriptional complexes were stable to either DNase or S1 nuclease hydrolysis but partially sensitive to RNase T1. Insensitivity of the complex to hydrolysis with RNase H suggested that the nascent transcripts were not crosslinked to the template. The complexes could also be hydrolysed by proteinase K and thermolysin. No crosslinkage was observed when labelled RNA molecules containing 4-thio UMP residues were added after synthesis to the polymerase preparation. This suggested that the method identified only those polypeptides which came into close contact with the transcript during its synthesis. Antibodies raised against the RNA-protein complex confirmed the presence of the polypeptides in the chloroplast RNA polymerase preparation on Western blots. Preincubation of these antibodies with the chloroplast RNA polymerase inhibited plastid DNA transcription. These data showed that the transcript-binding polypeptides were functional components of the chloroplast transcriptional complex.

Affinity Labels↗
PubMed2002

Photoaffinity labeling of human retinoid X receptor beta (RXRbeta) with 9-cis-retinoic acid: identification of phytanic acid, docosahexaenoic acid, and lithocholic acid as ligands for RXRbeta.

We utilized [20-methyl-(3)H]-9-cis-retinoic acid ([(3)H]9-cis-RA) as a direct photoaffinity probe for the characterization of human recombinant retinoid X receptor beta protein (RXRbeta). The photoaffinity labeling was light- and concentration-dependent, saturable, and protected by unlabeled 9-cis-RA in a concentration-dependent manner, indicating that binding occurred in the RXR retinoid binding site. all-trans-Retinoic acid (atRA) did not affect labeling with the 9-cis derivative, confirming that atRA does not compete for the 9-cis-RA binding site. Several retinoid, fatty acid, and bile acid ligands were evaluated for their ability to recognize the 9-cis-RA binding site. Retinol, atRA glucuronide, 13-cis-RA, dolichol, 5,6-epoxy-RA, and vitamin D(3) did not compete for the 9-cis-RA binding site. However, the saturated diterpenoid phytanic acid (PA) and docosahexaenoic acid, which have been recently shown to activate the nuclear receptor, RXR, competed with 9-cis-RA labeling, showing high affinity for the 9-cis-RA binding site. Oleic acid, arachidonic acid, and butyric acid did not interact. However, the bile acid lithocholic acid competed efficiently with 9-cis-RA for the binding site. These data validated the photoaffinity assay as an excellent system for the identification and evaluation of ligands for RXR.

Alitretinoin↗
PubMed2000

Photoaffinity labeling and site-directed mutagenesis of rat squalene epoxidase.

Squalene epoxidase (SE) (EC 1.14.99.7) is a flavin-requiring, non-cytochrome P-450 oxidase that catalyzes the conversion of squalene to (3S)-2,3-oxidosqualene. Photolabeling and site-directed mutagenesis were performed on recombinant rat SE (rrSE) to elucidate the location and roles of active-site residues important for catalysis. Two new benzophenone-containing analogs of NB-598, a nanomolar inhibitor of vertebrate SE, were synthesized in tritium-labeled form. These photoaffinity analogs (PDA-I and PDA-II) became covalently attached to SE when irradiated at 360 nm. Lys-C digestion and HPLC purification of [3H]PDA-I-labeled rrSE resulted in isolation of a single major peptide. MALDI-TOF mass spectrometry of this peptide indicated a covalent adduct between PDA-I and a tripeptide, Asp-Ile-Lys, beginning at Asp-426 of rat SE. Based on the labeling results, three mutant constructs were made. First, the D426A and K428A constructs showed a 5- to 8-fold reduction in SE activity compared with wild-type enzyme, while little change was observed in the I427A mutant. Second, a set of five mutant constructs was prepared for the conserved region based on the structure of the flavoprotein p-hydroxybenzoate hydroxylase (PHBH). Compared with wild-type, D284A and D407A showed less than 25% SE activity. This reduction also appeared to correlate with reduced affinity of the mutant proteins for FAD. Finally, each of the seven Cys residues of rrSE were individually mutated to Ala. Three Cys substitutions had no effect on SE activity, and substitutions at Cys-500 and Cys-533 showed a 50% lower SE activity. Mutations at Cys-490 and Cys-557 produced proteins with negligible SE activity, implicating these residues as being either structurally or catalytically essential. Chemical modification of wildtype and Cys mutants with a thiol-modifying reagent support the existence of a disulfide bond between Cys-490 and Cys-557.

Affinity Labels↗
PubMed2006

Stereospecific synthesis of a carbene-generating angiotensin II analogue for comparative photoaffinity labeling: improved incorporation and absence of methionine selectivity.

A stereospecific convergent synthesis of N-[(9-fluorenyl)methoxycarbonyl]-p-[3-(trifluoromethyl)-3H-diazirin-3-yl]-l-phenylalanine (Fmoc-12, Fmoc-Tdf) and its incorporation into the C-terminal position of the angiotensin II (AngII) peptide to form (125)I[Sar(1),Tdf(8)]AngII ((125)I-13) is presented. This amino acid photoprobe is a highly reactive carbene-generating diazirine phenylalanine derivative that can be used for photoaffinity labeling. Using model receptors, we compared the reactivity and the Met selectivity of 12 to that of the widely used and reputedly Met-selective p-benzoyl-l-phenylalanine (Bpa) photoprobe. Wild-type and mutant AngII type 2 receptors, a G protein-coupled receptors, were photolabeled with (125)I-13 as well as with (125)I[Sar(1),Bpa(8)]AngII ((125)I-14), and the respective incorporation yields were assessed. The carbene-generating 12 was more reactive toward inert residues and was not Met-selective compared to the biradical ketone-generating Bpa, allowing for more precise determination of ligand contact points in peptidergic receptors.

Angiotensin II↗
PubMed1990

Biologically active aromatic retinoids bearing azido photoaffinity-labeling groups and their binding to cellular retinoic acid-binding protein.

Retinoids bearing azido photoaffinity-labeling groups (azidoretinoids) have potential as probes for investigating the molecular mechanisms of action of all-trans-retinoic acid (RA) as mediated by its cellular retinoic acid-binding protein (CRABP) and nuclear receptor proteins. Two new azidoretinoids, 3-azido-4-[2-(5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-naphthalenyl)-1E- propen-1-yl]-benzonic acid and 4-(4-azido-5,6,7,8-tetrahydro-5,5,8,8-tetramethyl-2-anthracenyl)be nzoic acid were synthesized, and evaluated for their in vitro biological potency, and binding affinity for CRABP. Like RA, these aromatic azides had significant activity in modulating cell differentiation in retinoid-deficient hamster tracheal organ culture (ED500.02 nM and 0.03 nM, respectively) and in the inhibition of the induction of ornithine decarboxylase in mouse epidermis (ED50 7.0 nmol and 0.5 nmol, respectively). They also possessed high binding affinity for CRABP (ID50 0.9 microM and 0.85 microM, respectively). The tritiated aromatic azides were further evaluated for their ability to bind covalently to CRABP after photolysis. On photolysis at -78 degrees C, the two radiolabeled azidoretinoids formed stable adducts with CRABP. Treatment of the adducts with either RA or p-chloromercuriphenylsulfonic acid (CMPS) and subsequent dialysis did not cause any dissociation, indicating the formation of a covalent bond. In contrast, treatment of the unirradiated complexes with RA or CMPS led to dissociation of the complex. Synthesis of affinity labels and characterization of CRABP-retinoid complexes should provide useful information on the ligand-binding regions and insights into the mechanism of action of RA.

Affinity Labels↗
PubMed1986

A stopped-flow apparatus for photoaffinity labeling studies in the milliseconds time range. Application in investigations of the nicotinic acetylcholine receptor.

A photoaffinity labeling method is described to label a protein covalently in various transient covalent states. The method uses a combination of an especially adapted stopped-flow apparatus with a Q-switched Nd: YAG DCR-2A laser (wavelength 266 nm, i.e. four-fold the primary frequency, pulse duration 4 ns, pulse energy 15 mJ). The construction of the mixing cell, the triggering device and the set-up for determining the dead time of the stopped-flow apparatus is described. The dead time is 2.4 ms. In combination with a specific photolabel the method has been used for labeling functional states (resting, activated, desensitized, antagonist-blocked) of the nicotinic acetylcholine receptor from Torpedo marmorata electric tissue.

Affinity Labels↗
PubMed1985

Photoaffinity labelling of a nuclear matrix nucleoside triphosphatase and its modulation in the acute-phase response.

Photoaffinity labelling has been used to identify the major nuclear matrix nucleoside triphosphatase (NTPase) as a 46 kD polypeptide, which appears to represent the same polypeptide photolabelled in nuclear envelope. Nuclear matrix NTPase and its photolabelling were selectively decreased in the acute phase response of rat liver, which also encompasses decreases (30%) in RNA transport in vitro and nuclear envelope NTPase. These results, and quantitative considerations suggest that the NTPase correlatively linked to RNA transport is not solubilized by detergents; it appears to represent a nuclear matrix component.

Affinity Labels↗
PubMedDate not supplied

Synthesis and binding of new polyfluorinated aryl azides to alpha-chymotrypsin. New reagents for photoaffinity labeling.

The preparation of several new, water-soluble, polyfluorinated aryl azide reagents for use in photoaffinity labeling studies is described. The ability of some of these reagents and their nonfluorinated controls to noncovalently bind to alpha-chrymotrypsin is reported. It is found that polyfluorination does not interfere with ligand binding.

Affinity Labels↗
PubMed1986

Reconstitution of Escherichia coli ribosomes containing puromycin-modified S14: functional effects of the photoaffinity labeling of a protein essential for tRNA binding.

In previous work we have shown that puromycin photoaffinity labels two proteins, L23 and S14, from separate sites of high affinity on Escherichia coli ribosomes [Jaynes, E. N., Jr., Grant, P. G., Giangrande, G., Wieder, R., & Cooperman, B. S. (1978) Biochemistry 17, 561-569; Weitzmann, C. J., & Cooperman, B. S. (1985) Biochemistry 24, 2268-2274], that puromycin-modified S14 is separable from native S14 by reverse-phase high-performance liquid chromatography (RP-HPLC), and that ribosomal proteins prepared by RP-HPLC can be reconstituted into active 30S subunits [Kerlavage, A. R., Weitzmann, C. J., & Cooperman, B. S. (1984) J. Chromatogr. 317, 201-212]. In this work we definitively identify puromycin-modified S14 by tryptic fingerprinting, an analysis that also provides evidence that the single tryptophan-containing peptide in S14 is the site of puromycin photoincorporation. We show that reconstituted 30S subunits, in which all of the S14 present is stoichiometrically modified with puromycin and all other ribosomal components are present in unmodified form, lack Phe-tRNAPhe binding activity and further that 70S ribosomes containing such reconstituted 30S subunits have substantially diminished binding activity to both the A and P sites, as differentiated through use of tetracycline. Suitable control experiments strongly indicate that this loss of activity is a direct consequence of puromycin photoincorporation.

Affinity Labels↗
PubMed1993

Molecular structures, conformational analysis, and preferential modes of binding of 3-aroyl-2-arylbenzo[b]thiophene estrogen receptor ligands: LY117018 and aryl azide photoaffinity labeling analogs.

Structural and computational modeling studies were performed on the antiestrogen LY117018 (3) and two photoaffinity labeling analogs, in which an azide replaces the basic ether side chain (methyl ether tetrafluoro azide 7 and its protio analog 8). These studies were undertaken in order to determine the conformational preferences of these compounds and to propose favorable orientational modes for their binding to the estrogen receptor. In the crystallographic studies, we found that, unlike tetrafluoro azide 7, which adopts a face-to-face stacking of the p-hydroxyphenyl and benzoyl groups in the solid state, the pendant rings in the corresponding protio analog 8 are found in a predominantly offset pi-stacked array. In LY117018, which has an ether on the benzoyl ring, stacking of the pendant rings does not occur in the crystal structure; it assumes a T-shape, with the benzoyl group oriented perpendicular to the benzo[b]thiophene nucleus. In modeling studies, analogs of LY117018, 7, and 8 were subjected to a conformational grid search by molecular mechanics, and for each compound, three low-energy conformers (and their atropisomers) were obtained. These conformers were further geometry optimized by semiempirical molecular orbital calculations. For each compound, one of the three minimum-energy conformers is quite similar to the solid-state geometry. The computational structure of the tetrafluoro azide showed the greatest stacking between the benzoyl group and the p-methoxyphenyl ring, but less stacking than was observed in the crystallographic structure. The orientational preferences of these benzo[b]thiophene ligands with the estrogen receptor were analyzed with the receptor volume mapping technique, a method based on the correspondence of the hydroxyl groups and the volume that the benzo[b]thiophene compound shares with a composite molecular volume of high-affinity estradiol-type ligands (the receptor excluded volume, RExV). If the benzo[b]thiophene nucleus is overlapped with the steroid AB rings, the best overlap with the RExV is achieved, but there is poor correspondence of the hydroxyl groups. An orientation and conformation in which the benzoyl group of the 3-benzoyl-2-aryl-benzo[b]thiophenes occupies a 7 alpha-like position relative to the steroid produces both ample volume overlap with the RExV and close approximation of the hydroxyl groups and is presented as the putative bioactive conformation.

Affinity Labels↗
PubMed1979

5-Fluoro-2'deoxyuridine 5'-(p-azidophenyl phosphate), a potential photoaffinity label of thymidylate synthetase.

5-Fluoro-2'-deoxyuridine 5'-(p-azidophenyl phosphate) (1), a potential photoaffinity labeling reagent for thymidylate synthetase from a methotrexate-resistant strain of Lactobacillus casei, has been synthesized and characterized. UV254 irradiation of mixtures of thymidylate synthetase with 1, containing 14C-labeled phenyl and 3H-labeled pyrimidine rings, in the presence of excess 5,10-methylenetetrahydrofolate, the cofactor for the reaction, produced two complexes, separable from the native enzyme by polyacrylamide gel electrophoresis, in which only the 3H-containing moiety was bound to the protein. When mixtures of enzyme and 1 were irradiated in the absence of cofactor, complexes separable from the native enzyme were not observed. However, the 14C-containing component of 1 was now bound to the protein in the absence of the 3H-containing portion. The results are discussed in terms of the topography of the enzyme active site.

Affinity Labels↗
PubMed1978

8-Azido-adenosine 5'-triphosphate as a photoaffinity label for bacterial F1 ATPase.

1. 8-Azido-adenosine 5'-triphosphate (n83ATP) is a suitable photoaffinity label for F1 ATPase from Micrococcus luteus. The nucleotide is a substrate in the presence of bivalent cations and inhibits the enzyme irreversibly upon irradiation with ultraviolet light above 300 nm. 2. More than 80% of the label is covalently bound to the beta subunits in the presence of bivalent cations. Labeling and inactivation is decreased by protection with ADP, ATP or adenyl-5'-yl imidodiphosphate. To a much smaller degree the alpha subunits also become labeled. 3. n83AMP does not specifically bind to the beta subunits upon irradiation. Like n83ATP and n83ADP, it also labels the alpha subunits to a small extent. 4. The F1 ATPase is inactivated after a single beta subunit per F1 complex has become labeled. A cooperativity of the beta subunits carrying nucleotide binding sites is suggested.

Adenine Nucleotides↗
PubMed1997

Differentiation of substrate-binding sites in pyruvate kinase by selective photoaffinity labeling.

The four substrate-binding sites in porcine liver pyruvate kinase have been labeled with the photoaffinity reagent 8-azido-2'-O-dansyl-[alpha-32P]ATP (AD-ATP) under different experimental conditions. In the dark, the native pyruvate kinase was reversibly and competitively inhibited by AD-ATP, with KI = 2.8 microM and KADP = 0.18 mM. Under UV-irradiation, the enzyme was covalently labeled in the presence of Mg2+ by AD-ATP and inactivated irreversibly. Measurement of this photoinactivation process in the presence of various concentrations of ADP gave KI = 4.0 microM and KADP = 0.2 mM. A linear plot of the relative specific activity of the partially photolabeled enzyme after gel-filtration vs. the number of label per pyruvate kinase molecule introduced in the presence of Mg2+ shows that each covalent label completely inactivates a tetrameric pyruvate kinase molecule. In the strict absence of Mg2+, up to three substrate-binding sites in each pyruvate kinase molecule can be labeled by AD-ATP without decreasing enzyme activity. Subsequent addition of Mg2+ enables AD-ATP to label the remaining site and inactivate the enzyme. These observations show that there are one catalytic and three non-catalytic substrate-binding sites in each pyruvate kinase molecule. A probable structural reason for possible functional differentiation of intrinsically identical substrate-binding sites in all tetrameric enzymes is suggested.

Adenosine Triphosphate↗
PubMed1998

Molecular constituents of the replication apparatus in the plasmodium of Physarum polycephalum: identification by photoaffinity labelling.

The plasmodium of Physarum polycephalum has long been considered a model system for syncytically growing cells, but important details of the DNA replication apparatus, such as the DNA polymerase epsilon and other replication factors, have not been detected. In this study, a new variation of photoaffinity labelling and immunoblotting was used to detect DNA polymerases and other factors in nuclear extracts of P. polycaphalum. Proteins were specifically cross-linked with photoreactive arylazido-dCMP residues incorporated during extension of template-primer DNA. The DNA synthesized in situ was 32P-labelled. After nucleolytic removal of protruding DNA, the proteins were separated by SDS-gel electrophoresis, electroblotted on membranes and subjected to autoradiography. The alpha, delta, epsilon and beta-like DNA polymerases were labelled, as were histones and replication-factor-like proteins. Cytoplasmic extracts were devoid of these species. Abundant proliferating-cell nuclear antigen and replication protein A large subunit were labelled and found to be of unusual mass. A number of subunits of purified DNA polymerase holoenzymes were labelled. In contrast, only the DNA-polymerizing subunits could be labelled in nuclear extracts. Higher-order complexes in the nuclear extract may make subunits inaccessible to photo-cross-linking. Complex formation is promoted by beta-poly(L-malate), a plasmodium-specific putative storage and carrier molecule that supports DNA replication in the synchronized nuclei. Percoll, a polyvinylpyrrolidone-coated colloidal silica, partially disrupted these complexes. A 200 kDa fragment of DNA polymerase epsilon and a 135 kDa beta-like DNA polymerase did not participate in the complexes, suggesting functions unlike those of the other polymerases. DNA polymerase molecules were intact during proliferation of plasmodia, but were nicked before their clearance from the nuclei at growth arrest.

Animals↗
PubMed2004

Photoaffinity labeling of the anionic sites in Caco-2 cells mediating saturable transport of hydrophilic cations ranitidine and famotidine.

The H(2) antagonists, ranitidine and famotidine, exhibit saturable absorptive transport across Caco-2 cell monolayers and human intestine via a yet unidentified mechanism. A photoreactive derivative of famotidine has been synthesized and evaluated as a photoaffinity probe for the putative transporter protein(s). The probe irreversibly inhibited ranitidine transport across Caco-2 cell monolayers and irreversibly increased the transepithelial electrical resistance (TEER) after UV activation. Photoaffinity labeling was protected by a molar excess of famotidine.

Biological Transport↗
PubMed1989

Photoaffinity labeling of the purified skeletal muscle calcium antagonist receptor by a novel benzothiazepine, [3H]azidobutyryl diltiazem.

Previous photoaffinity-labeling studies with [3H]azidopine, (+) [3H]PN200-110, and [3H]LU 49888 have demonstrated that 1,4-dihydropyridines (nifedipine-like drugs) and phenylalkylamines (verapamil-like drugs) bind exclusively to the 165-kDa alpha 1 subunit of skeletal muscle calcium channels. However, it has not been conclusively determined whether benzothiazepines (diltiazem-like drugs), which represent the third group of calcium antagonists, also bind to the alpha 1 subunit. Here we report data obtained with a newly developed benzothiazepine photoaffinity probe, [3H]azidobutyryl diltiazem. This drug competes with diltiazem for the benzothiazepine-binding site and, in purified calcium channel preparations, specifically labels the 165-kDa polypeptide which does not change its electrophoretic mobility upon disulfide reduction. These data show that benzothiazepines, just like 1,4-dihydropyridines and phenylalkylamines, bind to the alpha 1 subunit of the skeletal muscle calcium channels.

Affinity Labels↗