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PubMed2000

Identification of the bile acid-binding site of the ileal lipid-binding protein by photoaffinity labeling, matrix-assisted laser desorption ionization-mass spectrometry, and NMR structure.

The ileal lipid-binding protein (ILBP) is the only physiologically relevant bile acid-binding protein in the cytosol of ileocytes. To identify the bile acid-binding site(s) of ILBP, recombinant rabbit ILBP photolabeled with 3-azi- and 7-azi-derivatives of cholyltaurine was analyzed by a combination of enzymatic fragmentation, gel electrophoresis, and matrix-assisted laser desorption ionization (MALDI)-mass spectrometry. The attachment site of the 3-position of cholyltaurine was localized to the amino acid triplet His(100)-Thr(101)-Ser(102) using the photoreactive 3,3-azo-derivative of cholyltaurine. With the corresponding 7,7-azo-derivative, the attachment point of the 7-position could be localized to the C-terminal part (position 112-128) as well as to the N-terminal part suggesting more than one binding site for bile acids. By chemical modification and NMR structure of ILBP, arginine residue 122 was identified as the probable contact point for the negatively charged side chain of cholyltaurine. Consequently, bile acids bind to ILBP with the steroid nucleus deep inside the protein cavity and the negatively charged side chain near the entry portal. The combination of photoaffinity labeling, enzymatic fragmentation, MALDI-mass spectrometry, and NMR structure was successfully used to determine the topology of bile acid binding to ILBP.

Amino Acid Sequence↗
PubMed1998

Photoaffinity labeling of the human receptor for urokinase-type plasminogen activator using a decapeptide antagonist. Evidence for a composite ligand-binding site and a short interdomain separation.

Binding of urokinase-type plasminogen activator (uPA) to its cellular receptor (uPAR) renders the cell surface a favored site for plasminogen activation. Recently, a 15-mer peptide antagonist of the uPA-uPAR interaction, with an IC50 value of 10 nM, was identified using phage display technology [Goodson, R. J., Doyle, M. V., Kaufman, S. E., and Rosenberg, S. (1994) Proc. Natl. Acad. Sci. 91, 7129-7133]. In the present study, the molecular aspects of the interaction between this peptide and uPAR have been investigated. We have characterized the real-time receptor binding kinetics for the antagonist using surface plasmon resonance and identified critical residues by alanine replacements. The minimal peptide antagonist thus derived (SLNFSQYLWS) was rendered photoactivatable by replacing residues important for uPAR binding with photochemically active derivatives of phenylalanine containing either (trifluoromethyl)diazirine or benzophenone. These peptides incorporated covalently into purified soluble uPAR upon photoactivation, and this was inhibited by preincubation with receptor binding derivatives of uPA. The intact three-domain structure of uPAR was essential for efficient photoaffinity labeling. Proteolytic domain mapping using chymotrypsin revealed a specific labeling of both uPAR domain I and domains II + III dependent on the position of the photoprobe in the antagonist. On the basis of these studies, we propose the existence of a composite ligand binding site in uPAR combined of residues located in distinct structural domains. According to this model, a close spatial proximity between uPAR domain I and either domains II or III in intact uPAR is required for the assembly of this composite binding site. Since the receptor binding properties of the peptide antagonist closely mimic those of uPA itself, these two ligands presumably share coincident binding site in uPAR.

Amino Acid Sequence↗
PubMed1984

Limitations in the use of tritiated methyltrienolone for the photoaffinity labelling of androgen receptor proteins.

In the absence of photoexcitation and under conditions of low ionic strength, the native form of the androgen receptor in rat prostate sediments as a large, 9.2S complex with tritiated androgens, including [3H]methyltrienolone. On photoexcitation, the configuration of labelled receptor complexes changes to a form of lower sedimentation coefficient, 4.2S. Initial experiments indicated that photoaffinity labelling of the androgen receptor protein may be readily achieved and with extensive covalent attachment of [3H]methyltrienolone. However, from ultracentrifugation analyses conducted under denaturing conditions it was established that, at best, only 5-8% of available [3H]methyltrienolone is covalently attached to the receptor protein. The remaining [3H]methyltrienolone is presumably adsorbed or entrapped within the receptor protein and may resist extraction into organic solvents, but it is not authentically bound in an irreversible, covalent manner. Our findings raise doubts concerning the efficiency and usefulness of [3H]methyltrienolone as a photoaffinity reagent for androgen receptor proteins. An additional problem is that photoillumination of [3H]methyltrienolone leads to the attachment of radioactivity to non-receptor proteins present in human plasma.

Affinity Labels↗
PubMed1994

Photoaffinity labeling of the Ah receptor: phylogenetic survey of diverse vertebrate and invertebrate species.

The mammalian aromatic hydrocarbon (Ah) receptor is a soluble protein involved in the regulation of gene expression by halogenated aromatic hydrocarbons such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Little is known, however, about the presence and properties of this receptor in nonmammalian species. In these studies, we sought evidence for an Ah receptor in the liver or liver-equivalent of diverse species of invertebrate and vertebrate animals. Velocity sedimentation analysis of hepatic cytosol labeled with [3H]TCDD gave equivocal results with three species of marine fish. In subsequent studies, photoaffinity labeling with 2-azido-3-[125I]iodo-7,8-dibromodibenzo-p-dioxin was used to identify the Ah receptor. Specific labeling (labeling that could be displaced by an excess of unlabeled ligand) was observed in seven species of teleost and elasmobranch fish, including winter flounder (Pleuronectes americanus), killifish (Fundulus heteroclitus), scup (Stenotomus chrysops), rainbow trout (Oncorhynchus mykiss), brown trout (Salmo trutta), and dogfish (Mustelus canis and Squalus acanthias). Specific labeling was also found in cytosolic fractions prepared from PLHC-1 fish hepatoma cells and livers of a turtle (Chrysemys picta) and a cetacean, the beluga whale Delphinapterus leucas. The fish Ah receptor was sensitive to conditions of tissue preparation; inclusion of proteinase inhibitors in the homogenization buffer stabilized the receptor in some species. There was heterogeneity in the apparent molecular mass of the largest specifically labeled band in each species; these ranged from 105 to 146 kDa, slightly larger on average than mammalian Ah receptors (95-130 kDa). In contrast to the results obtained with teleost and elasmobranch fish, no specifically labeled polypeptides were detectable in cytosol from two agnathan fish species (hagfish Myxine glutinosa and sea lamprey Petromyzon marinus), the tunicate Ciona intestinalis, or any of nine other invertebrate species representing eight classes in four phyla. Overall these results suggest that the Ah receptor evolved at least 450 million years ago, prior to the divergence of bony and cartilaginous fishes. Although the exact relationship between receptor presence and dioxin responsiveness in these species is uncertain, our data predict that the invertebrate species examined in this study, which appear to lack an Ah receptor protein like that seen in mammals and fish, may be less sensitive than vertebrates to the effects of environmental contaminants that act through this transcriptional regulator.

Affinity Labels↗
PubMed1995

Photoaffinity labeling of methyl farnesoate epoxidase in cockroach corpora allata.

The last enzyme in the biosynthetic pathway to juvenile hormone III in the corpora allata of hemimetabolous insects is methyl farnesoate epoxidase, a cytochrome P450 monooxygenase. Assays with intact glands incubated in vitro and with gland homogenates have identified a series of 1,5-disubstituted imidazoles as potent inhibitors of the enzyme. We have designed, synthesized and tested two imidazoles, diazirine-Ice T and benzophenone-Ice T, in which a radiolabeled and photoactivatable diazirine or benzophenone group was introduced to label the hydrophobic substrate binding site of the enzyme. Our results show that these bifunctional compounds inhibit JH III synthesis by intact glands as well as methyl farnesoate epoxidation by gland homogenates. Moreover both compounds selectively label a protein of ca. 55 kDa in corpora allata of the cockroach, Diploptera punctata. These photoaffinity labels, which use an imidazole to coordinate to the heme iron and a photoreactive group to modify the hydrophobic substrate binding pocket, are specific and effective probes for the molecular analysis of methyl farnesoate epoxidase.

Affinity Labels↗
PubMed1995

Photoaffinity labeling of lysosomal membrane proteins with [125I]diiodotyrosine, a system h ligand.

Percoll-purified rat thyroid FRTL-5 cell lysosomes were photoaffinity-labeled with [125I]diiodotyrosine to identify proteins which bind diiodotyrosine, a ligand for lysosomal transport system h. SDS-PAGE and autoradiography of these membranes showed specific labeling of a 70-kDa protein and weak labeling of three smaller proteins. [125I]Diiodotyrosine photolabeling of the 70-kDa protein was specifically competed against by ligands of lysosomal transport system h ligands. The 70-kDa protein was photolabeled more strongly in lysosomal membranes isolated from thyrotropin-stimulated cells when compared with those grown in the absence of thyrotropin, consistent with previous demonstrations that thyrotropin stimulates system h transport. The 70-kDa protein may represent some portion of the system h carrier protein.

Affinity Labels↗
PubMed1990

Guanosine 3',5'-cyclic nucleotide binding proteins of bovine retina identified by photoaffinity labeling.

Cyclic GMP-binding proteins present in membrane fractions of bovine retina and, in particular, rod outer segments (ROS) were identified by photoaffinity labeling with 8-azido-[32P]cGMP. Two soluble proteins and two membrane-associated proteins were specifically labeled. The soluble proteins, 93 and 72 kDa, corresponded respectively to the alpha subunit of ROS cGMP phosphodiesterase and cGMP-dependent protein kinase. One of the two membrane-associated proteins, 53 kDa, was present in all particulate retinal fractions. Its function is unknown. It is distinct from cAMP-dependent protein kinase or the 63-kDa cGMP-activated channel from ROS. The second membrane-associated protein, 37 kDa, was present only in fractions that did not contain ROS. The molecular mass of this protein was similar to that of a cGMP-binding protein previously attributed to rod cells.

Affinity Labels↗
PubMed1992

Photoaffinity labeling of the primary fibrin polymerization site: isolation and characterization of a labeled cyanogen bromide fragment corresponding to gamma-chain residues 337-379.

Human fibrinogen and the plasmin-generated fibrinogen fragment D were photoaffinity labeled specifically with the peptide [14C]Gly-Pro-Arg-N(4-azido-2-nitrophenyl)Lys amide. In the case of fibrinogen, greater than 85% of the incorporated radioactivity was found in the gamma chain. Similarly, when fragment D (Mr, 90,000) was labeled with the same derivatized peptide, virtually all the radioactivity was found in the gamma-chain portion. The labeled fragment D was treated with CNBr and an initial purification was achieved by two gel-filtration steps. The labeled material was purified further by HPLC and was also compared with CNBr digests of unlabeled material. Amino acid analysis and gas-phase sequencing showed the labeled fragment to be gamma-chain residues 337-379.

Amino Acid Sequence↗
PubMed1982

Photoaffinity labeling of chromatin. Synthesis and properties of arylazido derivatives of 9-aminoacridine: potential photolabels for chromatin studies.

The syntheses and properties of potential photoaffinity labels for the proteins in chromatin studies are described. One compound, N,N'-bis-(9-acridinyl)-4-aza-4-(4-azidobenzoyl)-1,7-diaminoheptane dihydrochloride, has been studied more closely. This photolabel shows high affinity towards DNA (Ka approximately 3 x 10(5) M-1) and photoreacts with histones at wavelengths in the range 260-450 nm. The photoreaction was monitored fluorimetrically, and labeling of histones H1, H2A/H2B and H3 was observed. When chromatin was photolabeled, labeling of H1 was exclusively quenched by NaCl at concentrations which are known to cause dissociation of this histone from the DNA. It is inferred that only DNA-associated proteins are photolabeled by the reagent.

Affinity Labels↗
PubMed1983

Photoaffinity labeling of brain adenylate cyclase preparations with azido[125 I]iodocalmodulin.

A partially purified calmodulin-sensitive adenylate cyclase from bovine cerebral cortex was photoaffinity labeled with azido[125 I]iodocalmodulin. Sodium dodecyl sulfate gel electrophoresis followed by autoradiography revealed several cross-linked polypeptides ranging in molecular weight from 37000 to 200000. The calmodulin-sensitive enzyme was submitted to a number of purification steps to determine if any of the calmodulin binding polypeptides copurified with adenylate cyclase activity. Fractionation procedures used included Bio-Gel A5M and Ultragel AcA 34 gel chromatography, isoelectric focusing, and native gradient gel electrophoresis. One cross-linked peptide having a molecular weight of 170000 correlated with adenylate cyclase activity through all purification steps. Native gradient gel electrophoresis in the presence of 0.03% deoxycholate gave one peak of adenylate cyclase activity with a Stokes radius of 40 A, consistent with a molecular weight of 140000-150000. It is proposed that the molecular weight of the adenylate cyclase catalytic subunit is 150,000 and that each catalytic subunit interacts with one calmodulin.

Adenylyl Cyclases↗
PubMed1986

Photoaffinity labelling of carnitine acetyltransferase with S-(p-azidophenacyl)thiocarnitine.

A photolabile reagent, p-azidophenacyl-DL-thiocarnitine, was synthesized and tested as a photoaffinity label for carnitine acetyltransferase (EC 2.3.1.7) from pigeon breast. p-Azidophenacyl-DL-thiocarnitine is an active-site-directed reagent for this acetyltransferase, since it is a competitive inhibitor (Ki 10 microM) versus carnitine. U.v. irradiation of a mixture of p-azidophenacyl-DL-thiocarnitine and enzyme produces irreversible inhibition. Acetyl-DL-carnitine protects the enzyme from inhibition by photoactivated p-azidophenacyl-DL-thiocarnitine. In the presence of 30 mM-2-mercaptoethanol as a scavenger, the relationship between loss of activity and photoincorporation of reagent suggests that one molecule of reagent is incorporated per molecule of inhibited enzyme. However, peptide maps of enzyme labelled with p-azidophenacyl[14C]thiocarnitine indicate that several (about six) tryptic peptides (of a possible 60-65) are modified. The presence of 5 mM-acetyl-DL-carnitine significantly decreases the incorporation of reagent in each labelled tryptic peptide.

Acetyltransferases↗
PubMed1993

Synthesis and characterization of a new photocrosslinking CTP analog and its use in photoaffinity labeling E. coli and T7 RNA polymerases.

A new photocrosslinking CTP analog that functioned as a substrate during transcription was synthesized and used to photoaffinity label E. coli and bacteriophage T7 RNA polymerases. This analog, 5-((4-azidophenacyl)thio) cytidine-5'-triphosphate (5-APAS-CTP) contains an aryl azide group approximately 10 A from the nucleotide base and specifically replaced CTP during synthesis of RNA by both polymerases. Analog was placed at the 3' end or internally within RNA. Both polymerases inefficiently incorporated two 5-APAS-CMP molecules sequentially, as was found for the related 5-APAS-UMP. Analog was placed at the 3' end of RNA in transcription complexes paused at the site of Q-modification of E. coli RNA polymerase, downstream of the lambda PR' promoter (+16), a pause that requires specific DNA sequences but no apparent RNA hairpin. Crosslinking was examined in the presence and absence of the NusA protein, which enhances the transcriptional pause at this site and is required for Q modification of the polymerase. Crosslinking of the 3' end of the RNA to NusA was not observed, consistent with our earlier results involving a NusA-enhanced pause site downstream from an RNA hairpin.

Affinity Labels↗
PubMed1990

Progesterone photoaffinity labels P-glycoprotein in multidrug-resistant human leukemic lymphoblasts.

We show for the first time that [3H]progesterone ([3H]PRG) can directly photoaffinity label membrane proteins prepared from a multidrug-resistant human leukemic lymphoblastic cell line CEM/VLB5K. A 170-kDa protein in CEM/VLB5K cell membranes was specifically labeled by [3H]PRG, which we identified as P-glycoprotein (Pgp) by immunoprecipitation with monoclonal antibody C219. The anticancer drug vinblastine and multidrug resistance reversing agent verapamil as well as several steroidal hormones were examined for their ability to interfere with [3H]PRG binding to Pgp. We found that 200-fold molar excess of vinblastine strongly inhibited (93%) the binding of [3H]PRG to Pgp compared with verapamil (80%), progesterone (78%), testosterone (46%), dexamethasone (25%), and aldosterone (56%). The results of this study provide direct evidence that progesterone can bind to Pgp and support the hypothesis that under physiological conditions Pgp may play a role in the excretion of progesterone from certain cells. Importantly, our results show that under our conditions vinblastine and verapamil are better able to compete with [3H]PRG for binding to Pgp than are other steroids, including testosterone, corticosteroids, and mineralocorticoids.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed1987

Photoaffinity labeling of rat liver carbamoyl phosphate synthetase I by 8-azido-ATP.

8-Azido-ATP has been found to serve as a photoaffinity label for two distinct ATP sites on rat liver carbamoyl phosphate synthetase I and to allow preliminary localization of these sites. In the dark, 8-azido-ATP acted as a competitive inhibitor with respect to ATP. Ultraviolet irradiation of carbamoyl phosphate synthetase I in the presence of 8-azido-ATP led to an irreversible loss of activity. ATP specifically protected against this inactivation. The incorporation of 2 mol of 8-azido-ATP per mol of enzyme was required for complete inactivation. To localize the 8-azido-ATP-binding sites to discrete regions of carbamoyl phosphate synthetase I which appear to be structural domains, the enzyme was photolabeled with [gamma-32P]8-azido-ATP and subjected to limited proteolytic digestion. The resulting model for the functional roles of the domains is that there is one ATP site on each of the two large internal structural domains of the enzyme. Each of these domains was found to contain the consensus sequences A and B common to many other nucleotide-binding proteins (Walker, J.E., Saraste, M., Runswick, M. J., and Gay, N. J. (1982) EMBO J. 1, 945-951). In addition, there is extensive structural and possibly functional interaction of the smaller N-terminal domain with one of the internal ATP-binding domains, analogous to a subunit interaction observed with the evolutionarily related Escherichia coli carbamoyl phosphate synthetase.

Adenosine Triphosphate↗
PubMed1989

Human liver thermostable phenol sulfotransferase: photoaffinity labeling with 2-iodo-4-azidophenol.

Phenol sulfotransferase (PST) catalyzes the sulfate conjugation of phenolic drugs, neurotransmitters, and xenobiotic compounds. Human tissues contain at least two forms of PST, which differ in their substrate specificities, inhibitor sensitivities, physical properties, and regulation. One form of the enzyme is thermostable (TS) and catalyzes the sulfate conjugation of micromolar concentrations of "simple" phenols. The other form of PST is thermolabile and catalyzes the sulfate conjugation of micromolar concentrations of dopamine and other phenolic monoamines. Quantitative structure-activity relationship (QSAR) analyses of substrate kinetic data obtained with purified human liver TS PST made it possible to design a photoreactive substrate for this form of the enzyme. Because of the very high affinity of TS PST for 2-halogenated phenols, 2-iodo-4-azidophenol (IAP) was synthesized and tested for this purpose. The Km predicted for IAP on the basis of QSAR analysis was 95 nM. The apparent Km determined experimentally was 52 nM. UV irradiation of partially purified human liver TS PST in the presence of [125 I]IAP and 3'-phosphoadenosine-5'-phosphosulfate, the sulfate donor for the reaction, resulted in the radioactive labeling of two proteins, with molecular weights of 32,000 and 34,000, by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Inhibitors of the reaction catalyzed by TS PST, including 2,6-dichloro-4-nitrophenol-3'-phosphoadenosine- 5'-phosphate and NaCl, as well as 2-iodophenol, a competing substrate, inhibited the photolabeling of both of these proteins by [125I]IAP in a concentration-dependent fashion. Partially purified TS PST was then radioactively labeled with [125]IAP and was subjected to gel filtration high performance liquid chromatography to verify that the photo-affinity-labeled proteins detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis coeluted with TS PST enzyme activity. Photoaffinity labeling of TS PST will be useful in studies of the molecular characteristics of the protein and its active site, as well as in the purification of this important drug-metabolizing enzyme.

Affinity Labels↗
PubMed1977

Poly(4-thiouridylic acid) as messenger RNA and its application for photoaffinity labelling of the ribosomal mRNA binding site.

Poly(4-thiouridylic acid) [poly(s4U)] synthesized by polymerization of 4-thiouridine 5'-diphosphate with Escherichia coli polynucleotide phosphorylase (EC 2.7.7.8) acts as messenger RNA in vitro in a protein-synthesizing system from E. coli. It stimulates binding of Phe-tRNA to ribosomes both in the presence of EF-Tu-Ts at 5 mM Mg2+ concentration and nonenzymatically at 20 mM Mg2+ concentration. It codes for the synthesis of polyphenylalanine. Poly(s4U) competes with poly(U) for binding to E. coli ribosomes. Light of 330 nm photoactivates poly(s4U) thus making it a useful photoaffinity label for the ribosomal mRNA binding site. Upon irradiation of 70-S ribosomal complexes, photoreaction occurs with ribosomal proteins as well as 16-S RNA. Ribosomes pre-incubated with R17 RNA are protected against the photoaffinity reaction. The labelling of 16-S RNA can be reduced by treatment of ribosomes with colicin E3.

Affinity Labels↗
PubMed1994

The melanocortin (MC3) receptor from rat hypothalamus: photoaffinity labelling and binding of alanine-substituted alpha-MSH analogues.

Membrane preparations of cells expressing the cloned rat hypothalamus melanocortin receptor, MC3, have been photoaffinity labelled using a radiolabelled photoreactive analogue of alpha-MSH, [125I-Tyr2,Nle4,D-Phe7,ATB-Lys11]alpha-MSH. SDS-PAGE followed by autoradiography showed a single band at 53-56 kDa for the native receptor or 35 kDa after deglycosylated with PNGase F, consistent with the predicted cDNA sequence. Receptor binding studies with alpha-MSH, gamma-MSH and [Nle4,D-Phe7]alpha-MSH established that alpha-MSH and gamma-MSH had similar affinities while [Nle4,D-Phe7]alpha-MSH bound 100 times more strongly. These results suggest that the receptor recognises the conserved 'core sequence' (-Met-Glu/Gly-His-Phe-Arg-Trp-) of MSH/ACTH peptides. The binding affinities of alanine-substituted analogues of alpha-MSH were determined to investigate the role of individual residues in ligand-receptor interactions. While in the terminal regions only the replacement of Tyr2 reduced the affinity of the peptide, replacement of Met4, Phe7, Arg8 and Trp9 within the peptide core led to a significant loss of affinity. Glu5 appeared unimportant for receptor recognition.

Affinity Labels↗
PubMed1991

Direct photoaffinity labeling of gizzard myosin with vanadate-trapped adenosine diphosphate.

The active-site topology of smooth muscle myosin has been investigated by direct photoaffinity-labeling studies with [3H]ADP. Addition of vanadate (Vi) and Co2+ enabled [3H]ADP to be stably trapped at the active site (t1/2 greater than 5 days at 0 degrees C). The extraordinary stability of the myosin.Co2+.[3H]ADP.Vi complex allowed it to be purified free of excess [3H]ADP before irradiation began and ensured that only active-site residues became labeled. Following UV irradiation, approximately 10% of the trapped [3H]ADP became covalently attached at the active site. All of the [3H]ADP incorporated into the 200-kDa heavy chain, confirming earlier results using untrapped [alpha-32P]ATP [Maruta, H., & Korn, E. (1981) J. Biol. Chem. 256, 499-502]. After extensive trypsin digestion of labeled subfragment 1, HPLC separation methods combined with alkaline phosphatase treatment allowed two labeled peptides to be isolated. Sequence analysis of both labeled peptides indicated that Glu-185 was the labeled residue. Since Glu-185 has been previously identified as a residue at the active site of smooth myosin using [3H]UDP as a photolabel [Garabedian, T. E., & Yount, R. G. (1990) J. Biol. Chem. 265, 22547-22553], these results provide further evidence that Glu-185, located immediately adjacent to the glycine-rich loop, is located in the purine binding pocket of the active site of smooth muscle myosin.

Adenosine Diphosphate↗