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PubMed1976

Affinity labeling of Escherichia coli DNA-dependent RNA polymerase with 5-formyl-l-(alpha-D-ribofuranosyl)uracil 5'-triphosphate.

5-Formyl-1-(alpha-D-ribofuranosyl)uracil 5'=triphosphate has been used to affinity label E. coli DNA-dependent RNA polymerase. It is a noncompetitive inhibitor of the enzyme with Ki=0.54 mM. A short preincubation of the enzyme and alpha-fo5UTP is required to achieve maximum inhibition, and the entent of the inhibition is dependent upon the alpha-fo5UTP concentration. When a preincubation mixture of alpha-fo5UTP/enzyme is diluted, the enzyme regains activity with time showing that the inhibition is reversible, presumably occurring by Schiff base formation between an amino group on the enzyme and the formyl group. Upon sodium borohydride reduction of an enzyme/alpha-fo5UTP preincubation mixture the enzyme is irreversibly inhibited. alpha-fo5UTP is more effective in inhibiting the enzyme than alpha-fo5U, and the inhibition is decreased by the presence of ATP, UTP, or GTP in the preincubation mixture, suggesting that inhibition is occurring at a triphosphate binding site. The stoichiometry of binding of alpha-fo5UTP to the enzyme was determined using the gamma-32P-labeled derivative. After a 20-s preincubation of enzyme/alpha-fo5UTP followed by NaBH4 reduction the stoichiometry of binding was 1.1:1 (alpha-fo5UTP bound: inactivated enzyme), and this rose to 2.42:1 after a 10-min preincubation. After a 20-s preincubation the [gamma-32P]-alpha-fo5UTP was shown to be located on the beta subunit of RNA polymerase by cellulose acetate electrophoresis in 6 M urea.

Affinity Labels↗
PubMed1980

Affinity labeling of the digitalis receptor with p-nitrophenyltriazene-ouabain, a highly specific alkylating agent.

Three derivatives of ouabain have been synthesized which alkylate the digitalis receptor. These derivatives were formed through reductive amination of p-nitrophenyltriazene (NPT) ethylenediamine to the periodate-oxidized rhamnose moiety of ouabain. The non-covalent binding of the ouabain derivatives (NPT-ouabain, designated I, II, and III) was followed (i) by their ability to inhibit the activity of sodium- and potassium-activated ATPase ((Na+,K+)-ATPase) purified from the electric organ of Electrophorus electricus, (ii) by the binding of [3H]NPT-ouabain I to the enzyme, and (iii) by the inhibition of [3H]ouabain binding with unlabeled NPT-ouabain I. Covalent modification of the digitalis site of (Na+,K+)-ATPase occurs after long periods of time. At pH 7.5 (25 degrees C) the best alkylating derivative, NPT-ouabain I, gives maximum covalent labeling after 6 h. Only the large polypeptide chain (Mr = 93,000) of the purified enzyme is specifically labeled with [3H]NPT-ouabain I while the glycoprotein chain (Mr = 47,000) is not significantly labeled. Labeling of a microsomal fraction of the electric organ with [3H]NPT-ouabain I gave the same type of gel pattern as that observed with the purified enzyme. [3H]NPT-ouabain I was also used to label the digitalis receptor in highly purified axonal membranes and in cardiac membranes prepared from embryonic chick heart. Although the (Na+,K+)-ATPase in both types of membranes has a low affinity for ouabain, [3H]NPT-ouabain I proved to be a very efficient affinity label for the digitalis receptor. In the complex mixture of polypeptides found in these membrane preparations, only a single polypeptide chain having a Mr = 93,000 is specifically labeled by [3H]NPT-ouabain I.

Affinity Labels↗
PubMed2003

1alpha,25-Dihydroxyvitamin D3-3beta-(2)-bromoacetate, an affinity labeling derivative of 1alpha,25-dihydroxyvitamin D3 displays strong antiproliferative and cytotoxic behavior in prostate cancer cells.

In this report we describe that 1,25(OH)(2)D(3)-3-BE, a VDR-affinity labeling analog of 1,25(OH)(2)D(3), showed strong and dose-dependent growth-inhibitory effect in several epithelial cells, i.e., keratinocytes (primary cells), MCF-7 breast cancer, PC-3, and LNCaP prostate cancer and PZ-HPV-7 immortalized normal prostate cell-lines. Furthermore, 10(-6) M of 1,25(OH)(2)D(3)-3-BE induced apoptosis specifically in LNCaP and PC-3 cells; and the effect was much less pronounced at lower doses. We also showed that the effect (of 1,25(OH)(2)D(3)-3-BE) was not due to probable degradation (hydrolysis) of 1,25(OH)(2)D(3)-3-BE or random interaction of this molecule with cellular proteins. Tissue- or cell-specific action of 1,25(OH)(2)D(3) and its mimics is not common due to the ubiquitous nature of VDR. Furthermore, variable effects of 1,25(OH)(2)D(3) and its analogs in various cell-lines potentially limits their application as anticancer agents. We showed that 1,25(OH)(2)D(3)-3-BE displayed similar growth-inhibitory and cytotoxic activities towards androgen sensitive LNCaP and androgen-independent PC-3 cell-lines. Therefore, these results raise the possibility that 1,25(OH)(2)D(3)-3-BE or similar VDR-cross linking analogs of 1,25(OH)(2)D(3) might be considered for further development as potential candidates for prostate cancer.

Affinity Labels↗
PubMed2003

Dermorphin-based potential affinity labels for mu-opioid receptors.

Dermorphin and [Lys7]dermorphin, selective micro -opioid receptor ligands originating from amphibian skin, have been modified with various electrophiles in either the 'message' or 'address' sequences as potential peptide-based affinity labels for micro -receptors. Introduction of the electrophilic isothiocyanate and bromoacetamide groups on the para position of Phe3 and Phe5 was accomplished by incorporating Fmoc-Phe(p-NHAlloc) into the peptide followed by selective deprotection and modification. The corresponding amine-containing peptides were also prepared. The pure peptides were evaluated in radioligand binding experiments using Chinese hamster ovary (CHO) cells expressing micro - and delta-opioid receptors. In dermorphin, introduction of the electrophilic groups in the 'message' domain lowered the binding affinity by > 1000-fold; only [Phe(p-NH2)3]dermorphin retained nanomolar affinity for micro -receptors. Modifications in the 'address' region of both dermorphin and [Lys7]dermorphin were relatively well tolerated. In particular, [Phe(p-NH2)5,Lys7]dermorphin showed similar affinity to dermorphin, with almost 2-fold higher selectivity for micro -receptors. [Phe(p-NHCOCH2Br)5]- and [Phe(p-NHCOCH2Br)5,Lys7]dermorphin exhibited relatively high affinity (IC50 = 27.7 and 15.1 nm, respectively) for micro -receptors. However, neither of these peptides inhibited [3H]DAMGO binding in a wash-resistant manner.

Affinity Labels↗
PubMed1983

Human placental estradiol 17 beta-dehydrogenase. Identification of a single histidine residue affinity-labeled by both 3-bromoacetoxyestrone and 12 beta-bromoacetoxy-4-estrene-3,17-dione.

Human placental estradiol 17 beta-dehydrogenase (EC 1.1.1.62) was affinity-labeled at pH 6.3 by 3-bromo[2'-14C]acetoxyestrone and 12 beta-bromo-[2'-14C] acetoxy-4-estrene-3,17-dione (both are substrates) in separate incubations. The affinity-alkylated enzyme samples were then treated separately as described below. Amino acid compositions of both samples revealed radioactive 3-carboxymethylhistidine. Tryptic digests of each sample were prepared, applied to Sephadex G-50, and 3-carboxymethylhistidine-bearing fractions identified. These peptides were further purified by cation exchange chromatography, gel filtration, and paper electrophoresis. The purified, 3-carboxymethylhistidine-bearing peptides labeled by the two steroids had identical electrophoretic mobilities at pH 6.5, 3.5, and 1.9. The amino acid sequence of the radioactive peptide alkylated by 3-bromo[2'-14C]acetoxyesterone was determined as: Leu-Ala-3-[14C]CmHis-Ser-Lys. The smaller quantity of peptide obtained from the inactivation with 12 beta-bromo[2'-14C]acetoxy-4-estrene-3,17-dione precluded the determination of its complete sequence. However, the first 3 residues were found to be Leu-Ala-3-[14C]CmHis and the amino acid composition showed that serine and lysine were also present. It is concluded that the steroid-binding site of human placental estradiol 17 beta-dehydrogenase contains a histidine residue which proximates the upper A-ring region of the steroid as it undergoes the reversible binding step.

17-Hydroxysteroid Dehydrogenases↗
PubMed2004

13-Demethyl-13-substituted-13,14-dihydroretinols as potential affinity labels of retinol-binding proteins: syntheses and stability studies.

13-Demethyl-13-substituted-13,14-dihydroretinols were synthesized and their stability under various conditions was measured in order to evaluate whether they would be useful as affinity labels of retinol binding proteins and retinol metabolizing enzymes. The 13-chloro analog could not be isolated because it eliminated HCl under the Wittig reaction conditions of its preparation. The trans- and cis-13,14-epoxy analogs are stable in non-protic organic solvents, but undergo an elimination reaction under various chromatographic conditions and in mixtures of organic solvents with water or alcohol. The 13-hydroxy and 13-methoxy analogs are stable in aqueous solutions and are therefore suitable for biological studies.

Affinity Labels↗
PubMed1984

Affinity-labeled somatomedin-C receptors and binding proteins from the human fetus.

We investigated the ontogeny of the human placental membrane somatomedin-C (Sm-C)/insulin-like growth factor I (IGF-I) receptor by affinity labeling with the cross-linking agent disuccinimidyl suberate (DSS). Specific Sm-C receptors, identified from as early as 6 weeks gestation, demonstrated no apparent structural changes through the course of gestation. Second trimester human fetal brain membranes cross-linked to [125I]Sm-C exhibited an identical pattern of receptor binding. These findings in both placenta and fetal brain membrane are consistent with the proposed heterotetrameric structure of the Sm-C/IGF-I receptor. Using a similar DSS cross-linking technique, we identified Sm-C-binding proteins in second trimester amniotic fluid [apparent molecular mass (Mr), 38,000 and 35,000] and term cord plasma (Mr, 41,000, 38,000, and 35,000). Identically sized binding components (Mr, 35,000-45,000) were also found in membrane preparations of preterm placenta and brain after cross-linking. Evidence that these binding species represent contamination of preterm membrane preparations with soluble amniotic fluid and/or fetal plasma Sm-C-binding proteins and that they are not derived from membrane receptors is as follows: (1) these binding species, like amniotic fluid and cord plasma binding proteins, were insensitive to competition with insulin (in concentrations as high as 0.6 mg/ml), a characteristic not shared with membrane receptor binding components; (2) these binding species were largely removed from placental membranes by extensive washing and appeared in the supernate when membrane preparations were incubated at 4 C for 18 h, indicating that they were soluble and not an integral part of the particulate membrane; (3) limited proteolysis of placental membrane preparations did not result in the appearance of similar binding species; and (4) preparation of preterm placental membranes in the presence of protease inhibitors did not eliminate these binding species. Use of traditional methodology to study binding of somatomedin to receptors in membranes prepared from preterm human tissues may be misleading because of contamination by amniotic fluid and/or plasma-derived binding proteins.

Affinity Labels↗
PubMed1988

Identification of amino acid residues involved in substrate recognition by the catalytic subunit of bovine cyclic AMP dependent protein kinase: peptide-based affinity labels.

Two peptide-based affinity inactivators Ac-Leu-(BrAc)Orn-Arg-Ala-Ser-Leu-Gly (4) and Ac-Leu-Arg-(BrAc)Orn-Ala-Ser-Leu-Gly (5) were prepared as probes for the study of the nature of the active-site residues in the catalytic subunit of cyclic AMP dependent protein kinase. Under conditions of inhibitor in excess, both peptides inactivated the catalytic subunit by an apparent biphasic process. A fast phase, which inactivated the protein by approximately 40%, was followed by a slow phase that accounted for the loss of the remaining enzyme activity. Protection experiments with the kinase substrates showed that the slow phase of inactivation was active site directed, while the fast phase was not. Studies with radioactively labeled peptides 4 and 5 indicated incorporation of two peptide residues per molecule of the catalytic subunit upon complete inactivation. This observation is consistent with the occurrence of one alkylation event in each phase of the inactivation. The protein was proteolyzed subsequent to its modification with radioactive peptides. High-performance liquid chromatography afforded two radioactive peptide fragments in each case, which were sequenced by Edman degradation. Peptide 4 alkylated Thr-197 and Glu-346, while peptide 5 modified Cys-199 and also Glu-346. Data are presented to support the conclusion that Thr-197 and Cys-199 are located at or near the active site.

Affinity Labels↗
PubMed1993

Structural arrangement of the codon-anticodon interaction area in human placenta ribosomes. Affinity labelling of the 40S subunits by derivatives of oligoribonucleotides containing the AUG codon.

Using the derivatives of the oligoribonucleotides pAUGUn and AUGUnC (n = 0; 3) bearing an alkylating group at either the 5' or 3' end, respectively (mRNA analogues), the affinity labelling of the human placenta 40S ribosomal subunits has been investigated in model initiation complexes obtained in the presence of the ternary complex eIF-2.GTP.Met-tRNA(fMet). The regions of 18S rRNA and ribosomal proteins labelled with these mRNA analogues were identified. The sites of covalent attachment of the pAUGUn derivatives with a reactive group at the 5' end were located between 18S rRNA positions 976 and 1164. The derivative of AUGU3C with an alkylating group at the 3' end modified 18S rRNA mainly at the 593-673 region. The main targets of the 3' end derivative of AUGC were located between positions 1610 and 1869. The proteins S3/S3a, S6, S7 and S14/S15 were modified by both types of the oligoribonucleotide derivatives regardless of the point of the reactive group attachment to the oligonucleotide moiety. The proteins S2 and S4 were modified by both the 3' end derivative of AUGC and 5' end derivative of pAUGU3; and the protein S8 was modified by the 3' end derivative of AUGC. The proteins S5 and S9 were labelled by the 5' end derivative of pAUGU3, and the protein S17 was modified by the 5' end derivative of pAUG.

Affinity Labels↗
PubMed1985

Cellular receptors for type beta transforming growth factor. Ligand binding and affinity labeling in human and rodent cell lines.

Type beta transforming growth factor (beta TGF) purified from human platelets to homogeneity as judged by NH2-terminal amino acid sequence analysis has been labeled with 125I to characterize its interaction with cellular receptors. Binding of 125I-beta TGF to target cells is temperature- and time-dependent, specific, saturable, and reversible. About 1.6-1.9 X 10(4) binding sites/cell with high affinity for beta TGF (Kd = 5.6-7.8 X 10(-11) M and 9.1-14 X 10(-11) M, respectively) are found in NRK-49F and BALB/c 3T3 cells. beta TGF receptors do not appear to undergo acute down-regulation by the ligand. Specific binding of 125I-beta TGF has been observed in several human, rat, and mouse fibroblast lines and in some, but not all, tumor-derived cell lines examined. 125I-beta TGF has been cross-linked to intact cells and isolated membrane preparations using disuccinimidyl suberate. Cells and isolated membranes from human, rat, and mouse origin affinity labeled with 125I-beta TGF exhibit a major labeled species of approximately 280 kilodaltons that has the properties of high affinity and specificity expected from a physiologically relevant beta TGF receptor. Minor labeled species of 70-90 kilodaltons are also labeled by 125I-beta TGF, but they correspond to molecular species with low apparent affinity (Kd approximately 10(-8) M) for 125I-beta TGF.

Affinity Labels↗
PubMed1993

Affinity labelling of sorbitol dehydrogenase from sheep liver with alpha-bromo-beta-(5-imidazolyl)propionic acid.

The metal-directed alkylating agent DL-alpha-bromo-beta-(5- imidazolyl)propionic acid (BrImPpOH) is shown to be an affinity-labelling reagent for sheep liver sorbitol dehydrogenase (SDH). As previously found for horse liver alcohol dehydrogenase (ADH), it modifies a cysteine ligand to the active-site zinc. In this case it is selectively incorporated (over 90%) at Cys43 in each of the four polypeptide chains/protomers of sheep liver SDH. Incorporated reagent and residual activity correlated. The first order inactivation constant, K2, and KEI, the dissociation constant for SDH and BrImPpOH, have been determined at different pH. The reactivity of BrImPpOH for SDH is higher than that for horse liver and yeast ADH. The protection of SDH against BrImPpOH inactivation by buffers and other molecules shows some similarities to that with horse liver ADH. However, sheep liver SDH bound BrImPpOH, imidazole and phosphate ions much weaker than liver ADH. The pKa values from the plot of log (k2/KEI) against pH are approximately 7.0 and 8.8-8.9. The former pKa value probably represents ionization of an imidazole group and the latter the zinc/water ionization in SDH. These pKa values are similar to those found for horse liver ADH. They are apparently not noticeably influenced by a second cysteine ligand in liver ADH being replaced by a proposed glutamic acid residue as a ligand to the catalytic zinc in SDH. The plot of logk2 against pH shows pKa values around 7.0 and 9.2 for the SDH-BrImPpOH-complex. The pKa of 7.0 is the same as for log(k2/KEI), and indicates no significant perturbation due to the binding of BrImPpOH to SDH. The pKa around 9.2 indicates perturbation of the zinc/water ionization or the ionization of Cys43.

Affinity Labels↗
PubMed1978

High yield photoreagents for protein crosslinking and affinity labeling.

4-Nitrophenyl ethers are proposed as new high-yield photoreagents for protein crosslinking and affinity labeling. These are totally unreactive in the dark under biological conditions, but react quantitatively with amines at pH 8 upon irradiation with 366-nm light. The reaction of monoalkoxy-p-nitrobenzenes with an amine yields the corresponding free alcohol and substituted nitrophenylamine. In essence, the nitrophenyl group is transferred from the alcohol to the amine. Bifunctional affinity reagents of this type could be especially useful for placing the p-nitrophenyl chromophore adjacent to a binding site without blocking it. The corresponding 2-methoxy-4-nitrophenyl ethers react with amines by displacement of the methoxyl group. Thus, bifunctional reagents of this class could be photocrosslinkers. A maleimide-containing 2-methoxy-4-nitrophenyl ether was attached to human fetal hemoglobin at gamma-cysteine F9 stoichiometrically. Subsequent ultraviolet irradiation yielded a gamma-gamma crosslinked hemoglobin in 80% yield. The oxygenation properties of the derivative indicate that it is locked in a high affinity conformation and that all cooperativity is lost.

Journal Article↗
PubMed1981

Affinity labeling of multiplication stimulating activity receptors in membranes from rat and human tissues.

Plasma membranes from rat adipocytes and liver and from human placenta have been labeled by covalent cross-linking to membrane-bound 125I-labeled multiplication stimulating activity (125I-MSA) with three different bishydroxysuccinimide esters: disuccinimidyl suberate, disuccinimidyl succinate, and ethyleneglycolyl bis(succinimidyl succinate). Dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiographic analysis of the 125I-MSA-labeled material in the presence of dithiothreitol reveals one single-labeled protein migrating with an apparent Mr = 255,000 regardless of the kind and concentration of cross-linker used. Electrophoresis in the absence of reductant indicates that the affinity-labeled species is not disulfide-linked to any other protein in the native plasma membrane, but contains internal disulfide bonds that compact its structure. The labeling of the Mr = 255,000 species increases with increasing concentrations of 125I-MSA between 0.3 and 3 nM. Labeling is abolished in a competitive manner by nonradioactive MSA but not by similar concentrations of insulin, proinsulin, or epidermal growth factor in all three tissues examined. The unique labeling of this Mr = 225,000 membrane component and its selective inhibition by MSA suggest that this protein is a plasma membrane receptor for MSA.

Adipose Tissue↗
PubMed2002

Solid phase synthesis and evaluation of Tyr-Tic-Phe-Phe(p-NHCOCH(2)Br) ([Phe(p-bromoacetamide)(4)]TIPP), a potent affinity label for delta opioid receptors.

Derivatives of the delta opioid receptor selective peptide Tyr-Tic-Phe-Phe-OH (TIPP) containing a p-bromoacetamide moiety on the phenyl ring of Phe(3) or Phe(4) were prepared by solid phase synthesis. [Phe(p-NHCOCH(2)Br)(4)]TIPP exhibited high affinity for cloned delta receptors (IC(50) = 5.4 nM), and incubation with only 2.5 nM resulted in 85% wash resistant inhibition of radioligand binding to delta receptors. Therefore, this peptide is a potent affinity label for further study of delta opioid receptors.

Affinity Labels↗
PubMed1997

Identification of the nonsubstrate steroid binding site of rat liver glutathione S-transferase, isozyme 1-1, by the steroid affinity label, 3beta-(iodoacetoxy)dehydroisoandrosterone.

3beta-(Iodoacetoxy)dehydroisoandrosterone (3beta-IDA), an analogue of the electrophilic substrate, Delta5-androstene-3,17-dione, as well as an analogue of several other steroid inhibitors of glutathione S-transferase, was tested as an affinity label of rat liver glutathione S-transferase, isozyme 1-1. A time-dependent loss of enzyme activity is observed upon incubation of 3beta-IDA with the enzyme. The rate of enzyme inactivation exhibits a nonlinear dependence on 3beta-IDA concentration, yielding an apparent Ki of 21 microM. Upon complete inactivation of the enzyme, a reagent incorporation of approximately 1 mol/mol of enzyme subunit or 2 mol/mol of enzyme dimer is observed. Protection against inactivation and incorporation is afforded by alkyl glutathione derivatives and nonsubstrate steroid ligands such as 17beta-estradiol-3,17-disulfate but, surprisingly, not by Delta5-androstene-3,17-dione or any other electrophilic substrate analogues tested. These results suggest that the site of reaction is within the nonsubstrate steroid binding site of the enzyme, which is distinguishable from the electrophilic substrate binding site, near the active site of the enzyme. Two cysteine residues, Cys17 and Cys111, are modified in nearly equal amounts, despite an average reagent incorporation of 1 mol/mol enzyme subunit. Isolation of enzyme subunits indicates the presence of unmodified, singly labeled, and doubly labeled subunits, consistent with mutually exclusive modification of cysteine residues across enzyme subunits; i.e., modification of Cys111 on subunit A prevents modification of Cys111 on subunit B and similarly for Cys17. Molecular modeling analysis suggests that Cys17 and Cys111 are located in the nonsubstrate steroid binding site, within the cleft between the subunits of the dimeric enzyme.

Affinity Labels↗
PubMedDate not supplied

X-ray structural analysis of the ligand-recognition mechanism in the dual-affinity labeling of c-type lysozyme with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine.

In spite of the belonging to the same c-type lysozyme family, hen egg-white lysozyme (HEWL) was much less susceptible to the dual-affinity labeling with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine (Galbeta1,4GlcNAc-Epo) than human lysozyme (HL). The three-dimensional structures of the HEWL labeled with single Galbeta1,4GlcNAc-Epo and the Glu102-mutant HL labeled with double Galbeta1,4GlcNAc-Epo were determined by X-ray crystallography at resolutions of 1.85 and 2.0 A, respectively. The overall conformation and the interaction mode of the carbohydrate ligand part in the singly labeled HEWL and the doubly labeled Glu102-mutant HL were basically identical to those of the correspondingly labeled wild-type HL with minor alterations in some stereochemical parameters. A detailed comparison of the structures revealed the key protein-carbohydrate and carbohydrate-carbohydrate interactions essential for the dual labeling. It was suggested that the difference in the efficiency of the dual labeling was caused by the structural difference between Gln104 in HL and Asn103 in HEWL. The relevance to our previous study and the carbohydrate-carbohydrate interaction on cell-surface membranes were discussed.

Affinity Labels↗
PubMed1977

Fluorescence energy transfer between heterologous active sites of affinity-labeled aspartokinase of Escherichia coli.

The distance between aspartokinase and homoserine dehydrogenase active sites was determined using fluorescence energy transfer between modified substrates. The fluorescent 1,N(6)-ethenoadenosine 5'-triphosphate was bound at the kinase active site by Co(III) affinity labeling. Reduced thionicotinamide adenine dinucleotide phosphate quenched the fluorescence of bound nucleotide. Fluorescence depolarization measurements led to a delimitation of the value of the dipolar orientation factor to the range 0.3 to 2.8. The distance between the fluorescent probe and the quencher was 29 +/- 4 A. In the presence of threonine, this distance increased to 36 +/- 5 A. Threonine binding either increased the intersite distance by ca. 7 A or caused a reorientation of the probe at the dehydrogenase site.

Affinity Labels↗