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[Affinity labeling of ribosomes from Escherichia coli with 4-(N-2-chloroethyl-N-methylamino) benzyl-5'-phosphamides of oligouridylates of different length].

4-(N-2-chloroethyl-N-methylamino)benzyl-5'-phosphamides of tetra-, penta-, hexauridilates were used for localization of the proteins organizing the mRNA-binding centre of ribosomes from E. coli. These derivatives, alike oligonucleotides, stimulated the binding of phenylalanyl-tRNA to ribosomes. Within the specific ternary complex these derivatives alkylated both 30S and 50S ribosomal subunits with high efficiency. Tetradecauridylic acid protected ribosomal subunits from alkylation. In the 30S ribosomal subunit these derivatives modified 16S RNA and proteins S3, S4, S9, S11, S13, S14, S19. In the 50S subunit these derivatives alkylated 23S RNA and proteins L7/L12, L13, L23, L25, L32. It was found that oligouridylate derivatives of a different length modified different proteins. The data obtained in this paper indicate that the conformation of the ternary complex "70S.CIRCH2NHpU(pU)n-1.tRNAPhe", where tRNAPhe is bound only to P-site of the ribosome differs from the ternary complex where both A- and P-sites of the ribosome are occupied with tRNAPhe.

Affinity Labels↗

Oligodeoxynucleotides containing 4-thiothymidine and 6-thiodeoxyguanosine as affinity labels for the Eco RV restriction endonuclease and modification methylase.

4-Thiothymidine and 6-thiodeoxyguanosine were incorporated into synthetic dodecamers containing the recognition site d(GATATC) of the enzymes Eco RV endonuclease and Eco RV methyltransferase. Upon irradiation with long wavelength UV light (340-360 nm), these oligodeoxynucleotides were photochemically crosslinked to both enzymes. The yields were up to 35% with the methyltransferase, but lower (up to 6%) with the endonuclease. Oligodeoxynucleotides containing 4-thiothymidine generally gave higher yields of crosslinking than those containing 6-thiodeoxyguanosine. Although both specific (i.e. those containing the d(GATATC) sequence) and non-specific (lacking this sequence) photoreactive oligodeoxynucleotides gave rise to crosslinked products, the use of a non-reactive, competitive substrate oligodeoxynucleotide suppressed the crosslinking, indicating that the reaction takes place at the enzymes' active sites. Oligodeoxynucleotides containing 4-thiocyanatothymidine or 6-thiocyanatodeoxyguanosine were also prepared by treatment of the title oligomers with CNBr and KCN. The dodecamers containing 4-thiocyanatothymidine were found to covalently modify both enzymes under study, with levels of crosslinking reaching up to 42% with the endonuclease and up to 12% with the methyltransferase. No crosslinking was observed with oligodeoxynucleotides containing 6-thiocyanatodeoxyguanosine.

Affinity Labels↗

Affinity labeling of cAMP-dependent protein kinase with p-fluorosulfonylbenzoyl adenosine. Covalent modification of lysine 71.

p-Fluorosulfonylbenzoyl 5'-adenosine (FSO2BzAdo) was shown previously to be an irreversible inhibitor of the catalytic subunit of cAMP-dependent protein kinase II from porcine skeletal muscle (Zoller, M. J., and Taylor, S. S. (1979) J. Biol. Chem. 254, 8363-8368). The catalytic subunit of porcine heart cAMP-dependent protein kinase was also inhibited following incubation with FSO2[14C]BzAdo, and inhibition was shown to result from the stoichiometric, covalent modification of a single lysine residue. The amino acid sequence in an extended region around the carboxybenzenesulfonyl lysine (CBS-lysine) was elucidated by characterizing both tryptic and cyanogen bromide peptides containing the 14C-modified residue. The sequence in this region was Leu-Val-Lys-His-Lys-Glu-Thr-Gly-Asn-His-Phe-Ala-Met-Lys(CBS)-Ile-Leu-Asp-Lys-Glu-Lys-Val-Val-Lys-Leu-Lys-Gln-Ile. The covalently modified residue corresponded to lysine 71 in the overall polypeptide chain. Homologies to bovine heart catalytic subunit and to a site modified by FSO2BzAdo in phosphofructokinase are considered.

Adenosine↗

Affinity labeling of ribonucleotide reductase by the 2',3'-dialdehyde derivatives of ribonucleotides.

Ribonucleotide reductase from Corynebacterium nephridii is rapidly inactivated by the 2',3'-dialdehyde derivatives of CDP (dial-CDP) and ADP (dial-ADP). The analog of CDP causes the progressive inactivation of ribonucleotide reductase activity with Ki of 0.26 mM and a maximum inactivation rate of 0.092 min-1 at saturating concentrations of dial-CDP. The modified enzyme remains inactive even after extensive dialysis. The four common nucleoside diphosphates (ADP, GDP, CDP, and UDP) protect the enzyme against inactivation by dial-CDP. Experiments with [3H]dial-CDP, [14C]dial-ADP, and [32P]dial-ADP demonstrate that the nucleoside moieties of these nucleotide analogs become covalently attached to the enzyme and that inorganic pyrophosphate is eliminated. The stoichiometry of this inactivation, determined with [3H]dial-CDP and [14C]dial-ADP, is 0.6-0.8 site modified per subunit of enzyme. The results suggest that the enzyme catalyzes the elimination of pyrophosphate and that the resulting alpha, beta-unsaturated nucleoside dialdehyde or its corresponding alpha, beta-unsaturated dihydroxymorpholino derivative is attacked by a nucleophilic residue in the active site.

Adenosine Diphosphate↗

Affinity labeling of a cell surface receptor for epidermal growth factor.

The membrane receptor for epidermal growth factor (EGF) on 3T3 cells has been identified and specifically labeled radiochemically using a photoreactive derivative of EGF. Photoreactive EGF, labeled with 125I, was incubated with 3T3 cells and then photolyzed in situ to generate a nitrene capable of reacting with a wide variety of chemical bonds. Analysis of the system by sodium dodecyl sulfate/polyacrylamide gel electrophoresis revealed, besides the band of EGF, only 1 other major radioactive band which migrated at approximately 190,000 daltons. This band was absent when a nonresponsive and nonbinding variant of 3T3 was used. A direct proportionality between binding activity and crosslinked complex formation was demonstrated using a variety of binding conditions. The crosslinked complex in intact cells is accessible to the action of a macromolecule like trypsin at 4 degrees, suggesting a cell surface location for this complex. Upon incubation of cells at 37 degrees, radioactivity from previously formed EGF-receptor crosslinked complex is converted by cellular action to 3 forms of mol wt less than or equal to 58,000 daltons. These are not accessible to trypsin action upon intact cells.

Affinity Labels↗

Molecular properties of the apamin-binding component of the Ca2+-dependent K+ channel. Radiation-inactivation, affinity labelling and solubilization.

Radiation-inactivation was used to assess the functional size of the apamin-binding component of the Ca2+-dependent K+ channel. The amount of specific binding of 125I-apamin to receptors in synaptic membranes of rat cortex decayed exponentially with increasing doses of ionizing radiation and target size analysis was consistent with a relative molecular mass of 250 000 +/- 20 000 for the 125I-apamin receptor. Analysis on sodium dodecyl sulfate gels following covalent cross-linking of 125I-apamin to its receptor in a synaptosomal membrane preparation from rat cortex revealed a single labelled polypeptide chain of Mr = 33 000 +/- 2000 in the presence of protease inhibitors. Our results suggest that the Ca2+-dependent K+ channel from rat cortex is an oligomeric structure of Mr = 250 000 +/- 20 000 containing an apamin-binding subunit of Mr = 33 000 +/- 2000. The apamin-binding component of the Ca2+-dependent K+ channel from rat synaptosomes was solubilized using detergents such as sodium cholate or 3-[(3-cholamidopropyl)dimethylammonio]-1-propane sulfonate. Phospholipids did not increase the stability of the apamin-binding component during the solubilization. Binding of apamin to its solubilized receptor is reversible and saturable. The dissociation constant of the apamin-receptor complex is 40-150 pM, the rates constants of association and dissociation being 3.2 X 10(6) M-1s-1 and 1.4 X 10(-4)s-1 respectively. These binding characteristics are similar to those found for the membrane-bound apamin receptor.

Affinity Labels↗

Periodate-oxidized AMP as a substrate, an inhibitor and an affinity label of human placental alkaline phosphatase.

Human placental alkaline phosphatase (EC 3.1.3.1) was inactivated by periodate-oxidized AMP. The inactivation showed saturation kinetics and could be partially prevented by the substrate AMP or the product inhibitor inorganic phosphate. Oxidized AMP was itself a substrate for this enzyme, with an apparent Km of 0.67 mM. The hydrolytic products of oxidized AMP were identified as oxidized adenosine hemiacetals. Oxidized AMP was also found to be a non-competitive inhibitor with respect to p-nitrophenyl phosphate, with identical Kis and Kii values of 0.15 mM. Our results indicate that oxidized AMP could combine with the enzyme to form a binary complex, followed by reaction with the proximal lysyl amino group to yield a Schiff base. The latter was reduced with NaBH4 and identified by t.l.c. The incorporation of only 1.5 molecules of oxidized [14C]AMP per enzyme subunit resulted in a complete inactivation of the enzyme. The modified enzyme showed higher apparent Km for the substrates and higher Ki for inorganic phosphate, but lower [32P]phosphate incorporation, than the native enzyme. These results support the conclusion that a lysine residue is involved in the phosphate-binding site of human placental alkaline phosphatase.

Adenosine Monophosphate↗

Identification of an electron transfer locus in plastocyanin by chromium(II) affinity labeling.

Cu(II)--plastocyanin from French beans (Phaseolus vulgaris) is reduced quantitatively by Cr(II)aq ions to give a substitution-inert Cr(III) adduct of Cu(I)--plastocyanin. Enzymatic proteolysis of this derivative by thermolysin led to the identification of the Cr(III) binding peptide. This contains four potential ligands for the metal ion: aspartate-42 and -44 and glutamate-43 and -45. In the three-dimensional fold of plastocyanin, this stretch is very close to tyrosine-83. The emission intensity and its pH dependence observed for the tyrosines in this tryptophan-devoid protein differ markedly in the Cr(III) adduct. That difference is interpreted as reflecting proximity and interaction between the latter metal ion and tyrosine-83. The distance between the copper center and the suggested Cr(III) binding site is approximately 12 A. The intervening region contains an array of highly invariant aromatic residues. These are proposed to be involved in the electron transfer process. A mechanism for that process is presented that involves interaction between the d electrons of the metal ions with d pi-pi* delocalization through a weakly coupled pi* system. The rationale of this electron transfer pathway for the reactivity of plastocyanin with inorganic redox agents is discussed.

Affinity Labels↗

Monobromobimane as an affinity label of the xenobiotic binding site of rat glutathione S-transferase 3-3.

Monobromobimane (mBBr), besides being a substrate in the presence of glutathione, inactivates rat liver glutathione S-transferase 3-3 at pH 7.5 and 25 degrees C as assayed using 1-chloro-2,4-dinitrobenzene (CDNB). The rate of inactivation is enhanced about 5-fold by S-methylglutathione. Substrate analogs bromosulfophthalein and 2,4-dinitrophenol decrease the rate of inactivation at least 20-fold. Upon incubation for 60 min with 0.25 mM mBBr and S-methylglutathione, the enzyme loses 91% of its activity toward CDNB and incorporates 2.14 mol of reagent/mol of subunit, whereas incubation under the same conditions but with added protectant 2,4-dinitrophenol yields an enzyme that is catalytically active and contains only 0.89 mol of reagent/mol of subunit. mBBR-modified enzyme is fluorescent, and fluorescence energy transfer occurs between intrinsic tryptophan and covalently bound bimane in modified enzyme. Both Tyr115 and Cys114 are modified, but Tyr115 is the initial reaction target and its modification correlates with loss of activity toward CDNB. The fact that the activity toward mBBr is retained by the enzyme after modification suggests that rat isozyme 3-3 has two binding sites for mBBr.

Affinity Labels↗

Affinity labeling of phosphoglycerate kinase by 5'-[p-(fluorosulfonyl)benzoyl]-1,N6-ethenoadenosine.

Yeast phosphoglycerate kinase is irreversibly inactivated upon incubation with 5'-[p-(fluorosulfonyl)-benzoyl]-1-N6-ethenoadenosine (5'-FSB epsilon A), an analogue to the nucleotide substrate. Marked protection against inactivation occurs with MgATP, ATP, MgADP, ADP, and 3-phosphoglycerate, suggesting that a part of the catalytic center is modified. The time dependence of the inactivation is characterized by a nonlinear kinetic profile. Curve fitting of various models for ligand binding to the enzyme suggested a two-site model. Modification of one of the sites appears to protect the catalytically essential site from modification. Stoichiometric studies show that the relationship between moles of 5'-FSB epsilon A incorporated per mole of enzyme and the residual enzymatic activity also shows nonlinear behavior. An extrapolated value of 1.5 mol of bound label/mol of enzyme corresponds to complete inactivation. The apparent overall pseudo first-order rate constant for the reaction between phosphoglycerate kinase and 5'-FSB epsilon A, as well as the separate rate constants for the modification, exhibit saturation behavior with respect to the concentration of 5'-FSB epsilon A, indicative of a rapid reversible binding of the reagent to the enzyme prior to modification.

Adenosine↗

C-terminal incorporation of fluorogenic and affinity labels using wild-type and mutagenized carboxypeptidase Y.

The ability to carry out specific C-terminal modification or labeling of peptides and proteins has a broad range of applications. It is well established that this may be achieved by protease-catalyzed transacylation reactions and that carboxypeptidase Y (CPD-Y) is suitable for this due to its broad specificity and stability in the presence of denaturants. Furthermore, CPD-Y is characterized by a S'1 binding site that is open to solvent and, thus, capable of catalyzing a transpeptidation reaction with nucleophiles that extend beyond the perimeter of the active site. However, one major drawback with CPD-Y is that the yield of the reaction is highly dependent on the nature of the leaving group; e.g., with large apolar leaving groups the yield of the reaction does not exceed 15%. In the present publication it is demonstrated that mutants of CPD-Y, designed for low leaving group dependence, efficiently incorporate biocytin amide as well as a new fluorescent nucleophile, N'-Abz-Lysine amide (ablysin amide), into peptides and proteins.

Affinity Labels↗

A transition-state analysis of the enzyme catalysis in the affinity labelling of horse-liver alcohol dehydrogenase by bromoacids.

The effect of temperature on the inactivation of liver alcohol dehydrogenase and on the alkylation of a model thiol free in solution by bromoacetate, 2-bromopropionate, 3-bromopropionate and 2-bromo-3-(5-imidazolyl)-propionate has been studied and the thermodynamic activation parameters calculated. All the bromoacids had a favourable entrôpy of activation in reaction with the enzyme compared to the model reaction with the thiolate anion of cysteine. This results from the formation of a reversible bromoacid-enzyme complex prior to the irreversible inactivation. The enthalpy of activation is however unfavourable, due to the lower intrinsic reactivity of the metal-thiol in the enzyme, compared to the thiolate anion of cysteine. The difference in free energy of activation between the enzyme reaction and the model reaction was used to measure catalysis. The efficiency of the enzyme catalysis of alkylation increased in the order: bromoacetate less than 2-bromopropionate less than 3-bromopropionate less than 2-bromo-3-(5-imidazolyl)propionate. Promotion by imidazole of enzyme inactivation by bromoacetate is a pure enthalpy effect. This is due to imidazole when bound to the active-site metal improving the intrinsic reactivity of the metal-thiol of Cys-46.

Acetates↗

Identification by affinity labeling of potential sites in 23-S rRNA interacting with the 3' end of tRNA.

A derivative of tRNAPhe carrying at its 3' end a photolyzable group was chemically synthesized by coupling p-azidobenzoylglycylhydrazide to periodate-oxidized tRNA. The reaction converts the 3'-terminal ribofuranoside residue into a six-membered ring. The binding of p-azidobenzoylglycylhydrazide-tRNA to 70-S ribosomes resembles the binding of Phe-tRNA in its requirement for poly(U) and Mg2+ dependence. Irradiation at wavelengths greater than 300 nm of complexes of p-azidobenzoylglycylhydrazide-tRNA and 70-S ribosomes results in the covalent binding of approximately 20% of the reversibly bound tRNA to the ribosomes. The labeling occurs predominantly at a single site in 23-S rRNA within the sequence included in the 18-S fragment. To identify the modified sequence, an RNase A digest of 23-S rRNA was fractionated on a hydrophobic matrix (Porapak Q) and adsorbed and non-adsorbed fractions were compared by fingerprint analysis. A relatively intense spot was observed in the expected region in the fingerprint of the adsorbed fraction. The presence of an unusual nucleotide in the sequence of this oligonucleotide was demonstrated by a mobility-shift analysis of a partial nuclease P1 digest. The sequence derived is G*-A-A-G-C (the asterisk denoting the site of modification). Sequences at six positions in the 23-S rRNA are compatible with the sequence of the oligonucleotide determined. Of the six positions five are located within nucleotides 1467-1887. This region of approximately 400 nucleotides is likely to include the sequence interacting with the 3' end of tRNA and possibly forming part of the peptidyl-transferase center.

Affinity Labels↗

Design of opioid peptides for a potential delta-receptor affinity label function: comparison with the mu-specific Tyr-D-Ala-Gly-(Me)Phe-chloromethyl ketone.

To find a delta-opioid receptor preferring peptide structure containing an Asp residue in a potentially interacting position, Tyr-Pro-Phe-Asp, Tyr-D-Ala-Phe-Asp, Tyr-D-Ala-Gly-Phe-Asp, Tyr-D-Ala-Gly-Phe-Asp alpha- and beta-methyl ester and Tyr-Gly-Gly-Phe-Asp peptides were synthesized and their biological activities were analyzed in vitro in mouse vas deferens and longitudinal muscle strip of guinea pig ileum. Changing the beta-methyl ester for an alkylating chloromethyl ketone moiety in the delta-receptor-selective agonist Tyr-D-Ala-Gly-Phe-Asp-beta-methyl ester enhanced further the delta-receptor preference. The delta-receptor selective chloromethyl ketone but not the beta-methyl ester gave a very slow washout after prolonged incubation in the mouse vas deferens bioassay; however, it was still readily displaceable by naloxone. The washout pattern of mu-specific Tyr-D-Ala-Gly-(Me)Phe chloromethyl ketone did not differ in the bioassays from that of the corresponding Gly5-ol derivative. Both chloromethyl ketones gave irreversible characteristics in the receptor binding assay.

Affinity Labels↗

Affinity labeling of 3 alpha, 20 beta-hydroxysteroid dehydrogenase with a nucleoside analog.

Incubation of 3 alpha, 20 beta-hydroxysteroid dehydrogenase (3 alpha, 20 beta-HSD; E.C.1.1.1.53) with the nucleoside 5'-p-fluorosulfonylbenzoyladenosine (FSA) caused a time-dependent and irreversible loss in enzyme activity. Both 3 alpha- and 20 beta-hydroxysteroid oxidoreductase activities decreased at equal rates by a first order kinetic process (in 0.05M phosphate buffer at pH 6.0 and 25 degrees C, t1/2 = 170 min). Incubation of 3 alpha, 20 beta-HSD was quenched by addition of 2-mercaptoethanol which instantaneously reacts with the fluorosulfonyl group of FSA. The cofactor NADH protected 3 alpha, 20 beta-HSD against inactivation by FSA, in a concentration-dependent manner. However, progesterone did not protect 3 alpha, 20 beta-HSD against inactivation by FSA. Evidently, FSA causes inactivation of the enzyme by irreversibly binding to the NADH-binding region at the active site of 3 alpha, 20 beta-HSD. Both 3 alpha- and 20 beta-hydroxysteroid oxidoreductase activities disappeared at equal rates under a variety of enzyme-inactivating conditions. These results suggest that both 3 alpha- and 20 beta-activities occur at the same active site of 3 alpha, 20 beta-HSD.

20-Hydroxysteroid Dehydrogenases↗

Catechol O-methyltransferase. 7. Affinity labeling with the oxidation products of 6-aminodopamine.

6-Aminodopamine (6-NH2DA) and various analogs of 6-NH2DA have been evaluated for their ability to inactivate purified catechol O-methyltransferase (COMT) in vitro. The inactivation of COMT by these agents could be prevented by including an antioxidant in the preincubation mixture or by excluding oxygen; however, catalase did not protect the enzyme from inactivation. Substrate protection studies and kinetic studies suggested that the loss of enzyme activity resulted from the alkylation of an amino acid residue at the active site of COMT by the quinoid types products which were generated upon air oxidation of 6-NH2DA. In addition, we have explored in more detail the reactivity toward COMT of specific intermediates in the oxidation pathways of 6-NH2DA by using various 6-NH2DA analogs. From the above studies we have concluded that 6-aminodopamine-p-quinone (6-NH2DAQ) is perhaps the most toxic species toward COMT. However, the aminochromes which are formed from 6-NH2DAQ are also effective in inactivating COMT. The results of these studies have provided a useful model system for observing the interaction of 6-NH2DA and its oxidation products with proteins; in addition, it has provided additional insight into the topography of the active site of COMT.

Aerobiosis↗

Catechol O-methyltransferase. 12. Affinity labeling the active site with the oxidation products of 5,6-dihydroxyindole.

5,6-Dihydroxyindole (5,6-DHI) and a series of 4- and/or 7-methylated analogues of 5,6-DHI have been synthesized and evaluated for their ability to inactivate purified rat liver catechol O-methyltransferase (COMT). The inactivation of COMT by these agents could be prevented by excluding oxygen from the incubation of mixtures, indicating the necessity for their oxidation to the corresponding aminochromes. Substrate protection studies and kinetic studies suggested that the loss of enzyme activity resulted from the modification of a crucial amino acid residue at the active site of COMT through reaction with the quinoid oxidation products. The COMT inhibitory activity of the 4- and/or 7-methylated analogues of 5,6-DHI argue against a mechanism involving a 1,4 Michael addition reaction at positions 4 or 7 on the aminochrome. Considering the number of potential electrophilic centers on the basic aminochrome structure, the site of the reaction might change depending on the aromatic substitution pattern. The preferred pathway of reaction may be determined in part by the juxtaposition of the protein nucleophile to the possible sites of attack on the electrophilic ligand but also in part on the reactivity of the electrophilic site which might change with substitution on the aromatic ring.

Aerobiosis↗

New reactive coenzyme analogues for affinity labeling of NAD+ and NADP+ dependent dehydrogenases.

Reactive coenzyme analogues omega-(3-diazoniumpyridinium)alkyl adenosine diphosphate were prepared by reaction of omega-(3-aminopyridinium)alkyl adenosine diphosphate with nitrous acid. In these compounds the nicotinamide ribose is substituted by hydrocarbon chains of varied lengths (n-ethyl to n-pentyl). The diazonium compounds are very unstable and decompose rapidly at room temperature. They show a better stability to 0 degree C. Lactate and alcohol dehydrogenase do not react with any of the analogues. Glyceraldehyde-3-phosphate dehydrogenase reacts rapidly with the diazoniumpentyl compound. Decreasing the length of the alkyl chain significantly decreases the inactivation velocity. 3 alpha, 20 beta-Hydroxysteroid dehydrogenase reacts at 0 degree C with the ethyl homologue and slowly with the propyl compound. The butyl- and pentyl analogues do not inactivate at 0 degree C. Tests with 14C-labeled 2-(3-diazoniumpyridinium)ethyl adenosine diphosphate show that complete loss of enzyme activity results after incorporation of 2 moles of inactivator into 1 mole of tetrameric enzyme. 4-(3-Acetylpyridinium)butyl 2'-phospho-adenosine diphosphate, a structural analogue of NADP+, was prepared by condensation of adenosine-2,3-cyclophospho-5'-phosphomorpholidate with (3-acetylpyridinium)butyl phosphate, followed by hydrolysis of the cyclic phosphoric acid with 2':3'-cyclonucleotide-3'-phosphodiesterase. Because of the redox potential (-315 mV) and the distance between the pyridinium and phosphate groups, this analogue is a hydrogen acceptor and its reduced form a hydrogen donor in tests with alcohol dehydrogenase from Thermoanaerobium brockii. The reduced form of the coenzyme analogue also is a hydrogen donor with glutathione reductase. With other NADP+-dependent dehydrogenases the compound has been shown to be a competitive inhibitor against the natural coenzyme. The acetyl group reacts with bromine to form the bromoacetyl group. This reactive bromoacetyl analogue is a specific active-site directed irreversible inhibitor of isocitrate dehydrogenase.

Affinity Labels↗