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PubMed1995

Affinity labelling of the catalytic and allosteric ATP binding sites on pyruvate kinase type I from Escherichia coli.

The allosterically regulated pyruvate kinase type I (PKI) from E. coli was inactivated by the ATP analog 2',3'-dialdehyde ATP (o-ATP) with a Ki of 3.6 mM. ATP and phosphoenolpyruvate protected the enzyme activity while the allosteric activator fructose 1,6-bisphosphate enhanced the rate of inactivation. Incubation with o-ATP, followed by reduction of the formed Schiff bases with radioactive sodium borohydride, was employed to determine the ATP binding sites of PKI. After tryptic digestion, the purification of the labelled peptides and the sequence analysis allowed to identify four modified lysyl residues, namely Lys173, Lys175, Lys272, and Lys317 of the known DNA-deduced sequence of PKI. The close lysines 173 and 175 reacted with o-ATP in a mutually exclusive way and accounted together for 53% of the recovered radioactivity, the rest being distributed on Lys272 (31%) and Lys317 (16%). When fitted on the available three-dimensional structure of muscle pyruvate kinase, the position of the modified lysines defines both the catalytic and the allosteric ATP binding sites on PKI.

Adenosine Triphosphate↗
PubMed1976

External yeast beta-fructosidase. Affinity labeling of the active site.

Conduritol-B-epoxide, a compound structurally related to the substrates of external yeast beta-fructosidase (beta-D-fructofuranoside fructohydrolase, EC 3.2.1.26), is an active-site directed inhibitor of this enzyme. The inactivation is irreversible and first-order with respect to time and inhibitor concentration. From the kinetic data obtained, it is concluded that one molecule of inhibitor reacts with one molecule of the enzyme causing inactivation. The inactivation is prevented by the presence of substrates. The pH-dependence of inactivation shows two dissociating groups in the enzyme with pKa values 3.05 and 6.8 being involved in the inactivation process. A carboxylate at the active site with pKa 3.05 is suggested to be the reactive group with conduritol-B-epoxide.

Affinity Labels↗
PubMed1989

Affinity labeling of bovine opsin by trans-retinoyl chloromethane.

All-trans-retinoyl chloromethane is a potent irreversible inactivator of bovine opsin in retinal rod outer segments. The inactivation appears to be due to specific modification of the apoprotein at the 11-cis-retinaldehyde binding site. The reaction follows pseudo first order kinetics at 37 degrees C. A moderate dissociation constant for the initial reversible complex of 6.1 mM could be derived with a first order rate constant of 1.8x10(-1) min-1 for the conversion to the irreversible inactivated form. Native rhodopsin or rhodopsin regenerated from opsin by addition of 11-cis-retinaldehyde is completely protected against inactivation by trans-retinoyl chloromethane. All-trans-retinaldehyde does not provide this protection for the irreversible inactivation.

Affinity Labels↗
PubMed1990

N-bromoacetyl-D-leucylglycine. An affinity label for neutral endopeptidase 24.11.

Neutral endopeptidase 24.11 is rapidly inactivated by N-bromoacetyl-D-leucylglycine in a reaction which follows first-order kinetics at pH 8 and 37 degrees C. The concentration dependence of inactivation revealed saturation kinetics with an apparent Ki of 10 mM and kappa inact of 0.4 min-1 at saturating inhibitor concentration. Enzyme can be protected from inactivation by either the substrate Leu5-enkephalin or the competitive inhibitors Phe-Gly or Phe-Ala. Inactivation of enzyme by N-bromo-[14C]acetyl-D-leucylglycine proceeds with the incorporation of a stoichiometric amount of labeled inhibitor. Tryptic digestion of the radioactively labeled enzyme followed by high performance liquid chromatography allowed the isolation of a modified peptide with the sequence T-D-V-H-S-P-G-N-F-R in which histidine (His704) is the modified residue. Site-directed mutagenesis was used to generate a mutant form of the enzyme in which histidine 704 was converted to a glutamine residue. This mutant enzyme retained less than 0.1% of the activity of the native enzyme. These results demonstrate that His704 is at the active site of neutral endopeptidase 24.11 and suggest a catalytic role for this residue.

Affinity Labels↗
PubMed1993

In vivo affinity label of a protein expressed in Escherichia coli. Coenzyme A occupied the AT(D)P binding site of the mutant F1-ATPase beta subunit (Y307C) through a disulfide bond.

When Tyr-307 of the beta subunit of F1-ATPase from a thermophilic Bacillus strain PS3 is replaced by cysteine and expressed in Escherichia coli cells, about a half population of the mutant beta subunit are labeled by Coenzyme A at Cys-307 through a disulfide bond which is cleavable by reducing treatment. The mutant beta subunit can be reconstituted into the alpha 3 beta 3 complex of which ATPase activity is stimulated two-fold by reducing treatment either prior or after reconstitution. Since Tyr-307 has been supposed to be located at one of subdomains which form the ATP binding site of the beta subunit, Coenzyme A binds to the mutant beta subunit as an AT(D)P analogue in E. coli cells and then covalently attaches to Cys-307.

Adenosine Diphosphate↗
PubMed1994

Affinity labeling of Escherichia coli lysyl-tRNA synthetase with pyridoxal mono- and diphosphate.

Pyridoxal 5'-phosphate (PLP) and pyridoxal 5'-diphosphate (PLDP) were used to identify lysyl residues at the phosphate-binding locus in the lysS-encoded and the lysU-encoded lysyl-tRNA synthetases (LysRSs and LysRSu, respectively) from Escherichia coli. Incubation of LysRSs with either reagent, followed by borohydride reduction, resulted in a time-dependent covalent incorporation of the reagent, accompanied with the loss of both tRNA(Lys) aminoacylation and lysine-dependent ATP-PPi exchange activities. By contrast, LysRSu activity was insensitive to prolonged incubation with either reagent, possibly reflecting a difference at the phosphate-binding locus in the two enzyme species. MgATP protected LysRSs against inactivation by PLP or PLDP. Complete inactivation of LysRSs corresponded to the incorporation of 2.6 +/- 0.1 mol of PLP or PLDP per mol of dimeric enzyme. Either reagent was found to label the same set of eight lysyl residues (Lys-25, Lys-82, Lys-114, Lys-132, Lys-156, Lys-185, Lys-364, and Lys-505) as adenosine di- or triphosphopyridoxal (see the preceding paper in this issue). These lysyl residues might represent the subsite for the phosphate moiety of ATP in LysRSs. None of the identified lysyl residues is located within the three sequence motifs considered as characteristic of the class 2 aminoacyl-tRNA synthetases. The present results are discussed on the basis of the crystalline structure of the closely related aspartyl-tRNA synthetase from Saccharomyces cerevisiae.

Affinity Labels↗
PubMed1984

Affinity labelling of 5-aminolevulinic acid dehydratase with 2-bromo-3-(5-imidazolyl)propionic acid.

2-Bromo-3-(5-imidazolyl)propionic acid, a zinc-directed thiol reagent, inactivates the enzyme 5-aminolevulinic acid dehydratase from bovine liver (5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing, EC 4.2.1.24). The substrate, 5-aminolevulinic acid, completely protects against inactivation. The reagent inhibits the zinc-containing enzyme to a greater extent than the zinc-deprived enzyme; and it competes with the zinc chelator 1,10-phenanthroline. The reagent alkylates essential sulfhydryl groups of the enzyme, since the extent of the inactivation depends on the reduction of the enzyme protein by thiol compounds. It is concluded that the zinc site, the substrate site and the essential sulfhydryl groups are in close proximity in the active site.

Affinity Labels↗
PubMed1992

Photolabile derivatives of maltose and maltotriose as ligands for the affinity labelling of the maltodextrin-binding site in porcine pancreatic alpha-amylase.

The 3-azibutyl group was linked through sulfur to the anomeric position of maltose and maltotriose to yield the photolabile thioglycosides 3-azibutyl 1-thio-alpha-maltoside (11) and 3-azibutyl 1-thio-alpha-maltotrioside (12), and to the 4'- and 6'-position of maltose to give the thioethers 4'-S-(3-azibutyl)-4'-thiomaltose (8) and 6'-S-(3-azibutyl)-6'-thiomaltose (15). All four compounds were good competitive inhibitors of the action of porcine pancreatic alpha-amylase. Compound 12 irreversibly deactivated the enzyme to approximately 100% when irradiated together with the protein. The other compounds were much less effective. It is likely that separate areas of the enzyme binding site are chemically modified by the different ligands.

Affinity Labels↗
PubMed1991

Synthesis of histidine-containing dipeptide affinity-labelling agents. Relative inactivation rates of cathepsins B and L.

Peptidyl diazomethyl ketones and fluoromethyl ketones containing histidine in the C-terminal position were synthesized to determine their properties as proteinase inactivators. These were examined chiefly with derivatives of Z-Ala-His. The protection of histidine during conversion of the C-terminal residue to the diazomethyl ketone required unblocking conditions which avoid acid due to the lability of this function. This was achievable with a Cbz-imidazole derivative since aminolysis provided deblocking without disturbance of the diazomethyl ketone function. In the case of the fluoromethyl ketone synthesis using fluoroacetic anhydride (Dakin-West procedure), the desired product could be isolated without ring blocking. The Z-Ala-His products showed enhanced selectivity for inactivation of cathepsin B over L when compared to analogous dipeptide inhibitors.

Affinity Labels↗
PubMed1980

[Affinity labeling of inorganic pyrophosphatase from yeast by methylphosphate].

Yeast inorganic pyrophosphatase is specifically and irreversibly inactivated by methylphosphate. The high rate of inhibition, the protective effect of the substrate, the strict correlation between the degree of inhibition and the amount of the protein-bound reagent and the effect of saturation of the enzyme with methylphosphate provide evidence in favour of the reaction in the active center. Modification of two chemically identical enzyme subunits proceeds at different rates and results in a formation of phosphorylated subunits with different stability of the phosphate bond, which is indicative of the mutual effects of the pyrophosphatase subunits. The reaction between the modified enzyme and hydroxylamine suggests that the interaction between pyrophosphatase and methylphosphate entails modification of the carboxylic groups of two active centers, resulting in a formation of the acylphosphate bonds.

Affinity Labels↗
PubMed1984

Affinity labeling of spinach ferredoxin-NADP+ oxidoreductase with periodate-oxidized NADP+.

Periodate-oxidized NADP+ (dialdehyde-NADP+) inactivated soluble ferredoxin-NADP+ oxidoreductase and combined covalently to the enzyme. This inactivation was first order with respect to dialdehyde-NADP+ and followed saturation kinetics, indicating that the enzyme initially forms a reversible complex with the inactivator. NADP+ afforded complete protection against inactivation, while spinach ferredoxin was uneffective. In the presence of exogenous ferredoxin and illuminated thylakoids, the nucleotide analog functioned as a coenzyme for the reductase, although with rather lower efficiency than NADP+. It also acted as a competitive inhibitor with respect to NADPH in diaphorase activity. Incorporation of radioactivity from periodate-oxidized [3H]NADP+ gave a stoichiometry of 0.85 mol of reagent/mol of reductase, indicating that the modification of a single residue in the flavoprotein is responsible for the loss of enzymatic activity.

Affinity Labels↗
PubMed1990

ATP binding site of mitochondrial creatine kinase. Affinity labelling of Asp-335 with C1RATP.

The ATP binding site of mitochondrial creatine kinase from chicken heart has been studied by modifying the purified enzyme with a 14C-labelled ATP analogue, C1RATP, in which the reactive label was covalently bound to the gamma-phosphate group of ATP. The modified enzyme was digested by pepsin, and a single radioactive nonapeptide was isolated by HPLC. Amino acid analysis and direct sequence determination revealed that the isolated peptide corresponds to amino acids 335-343 within the C-terminal region of Mi-CK, this peptide being highly preserved throughout evolution. Asp-335 is very likely the site of modification by C1RATP. The specificity of the ATP analogue for the active site of creatine kinase was demonstrated by the inhibition of the enzymatic activity of Mi-CK by C1RATP and by the prevention of this inhibition bij ADP.

Adenosine Triphosphate↗
PubMed1983

Affinity labeling and partial purification of nerve growth factor receptors from rat pheochromocytoma and human melanoma cells.

A cell surface glycoprotein receptor for nerve growth factor (NGF) has been identified by covalent crosslinking to 125I-labeled NGF (125I-NGF). Either ethyldimethylisopropyl-aminocarbodiimide or hydroxysuccinimidyl-p-azidobenzoate causes highly specific crosslinking of 125I-NGF to a similar receptor species on rat pheochromocytoma PC12 cells and on human melanoma A875 cells. The NGF-receptor complex migrates as a broad band in NaDodSO4/polyacrylamide gel electrophoresis with an apparent Mr of approximately equal to 100,000. Because the NaDodSO4-denatured complex apparently contains a single Mr 13,000 NGF chain, the apparent molecular weight of the receptor itself is 87,000. Inhibition of protein glycosylation by tunicamycin generates smaller 125I-NGF-receptor complexes. The mobility of the smallest of these in NaDodSO4 gel electrophoresis corresponds to a Mr of 90,000 for the complex and, hence, 77,000 for the carbohydrate-deficient receptor. A second NGF-receptor complex with a Mr of 225,000 also is obtained from A875 cells but only occasionally from PC12 cells. Tunicamycin treatment decreases the molecular weight of these species by 10,000-15,000. Substantial purification of the Mr 100,000 NGF-receptor complex was achieved by lectin affinity chromatography on columns of wheat germ agglutinin linked to Affi-Gel 15. The specific absorption of NGF-receptor complexes to these columns indicates that the receptor is a glycoprotein that contains N-acetyl-D-glucosamine.

Adrenal Gland Neoplasms↗
PubMed1990

Anionic subsites of the acetylcholinesterase from Torpedo californica: affinity labelling with the cationic reagent N,N-dimethyl-2-phenyl-aziridinium.

Several peptides of acetylcholinesterase of Torpedo californica labelled with the alkylating reagent [3H]N,N-dimethyl-2-phenyl-aziridinium (DPA) were localized within the primary structure. One peptide had the sequence KPQELIDVE (positions 270-278); the incorporation of DPA into this peptide could be specifically suppressed by propidium, which suggests that it is part of the peripheral anionic site. The incorporation of DPA into two other peptides was insensitive to propidium but could be prevented by edrophonium; the sequence of one of the peptides assumed to be part of the anionic site in the catalytic centre was found to be DLFR (positions 217-220). Decamethonium efficiently blocked alkylation by DPA in all three investigated peptides.

Acetylcholinesterase↗
PubMed1988

Iodination of peptidyl chloromethyl ketones for protease affinity labels.

The specificity of peptidyl chloromethyl ketones has been used to label proteases in complex biological systems by incorporating tyrosine into the structure for eventual radioiodination. Contrary to results with iodination of proteins, a mild reagent, that is, one which iodinates at neutrality, was unsuitable, giving complex mixtures with poor reproducibility, apparently because of side reactions at the chloromethyl ketone group. On the other hand, iodine monochloride in acetic acid provided clean products. In the cases examined where a tyrosine residue was not appropriate for the specificity of the target protease, this residue was located well displaced from the primary specificity site. The resultant diiodotyrosine-containing derivatives were generally highly active as protease inhibitors. The p-aminobenzoyl group was used as an alternative to tyrosine as an iodinatable component.

Affinity Labels↗
PubMed1978

Identification of cysteine-10 of protein S18 as part of the mRNA-binding site of Escherichia coli ribosomes by affinity-labeling studies with a chemically reactive A-U-G analog.

The reaction of a bromoacetamidophenyl derivative of the initiation codon A-U-G (A-U-G) with tight couples of Escherichia coli ribosomes leads to an exclusive crosslinking of label to protein S18. This crosslinking inhibits A-U-G-directed fMet-tRNAfMet binding into the puromycin-sensitive site of ribosomes and stimulates elongation-factor-dependent binding of Met-tRNAmMet. It is, therefore, concluded that protein S18 is located at or near the aminoacyl-tRNA binding site of E. coli ribosomes. Peptide as well as amino acid analysis shows that the reaction between A-U-G and ribosomes took place at cysteine-10 of protein S18. A-U-G could not be crosslinked to ribosomal proteins of the temperature-sensitive E. coli strain 258ts, where arginine-11 of protein S18 is replaced by a cysteine residue.

Affinity Labels↗
PubMed1979

Analysis of the allosteric properties of rabbit muscle phosphofructokinase by means of affinity labeling with a reactive ATP analog.

A reactive ATP analog, N6-(6-bromoacetamidohexyl)-AMP-PCP, reacted specifically with the ATP inhibitory site of rabbit skeletal muscle phosphofructokinase without affecting the active site. Modification resulted in the incorporation of 1.01 mol of the reagent per mol of enzyme subunit. The modified enzyme was insensitive to allosteric inhibition by ATP and to activation by AMP at pH 7.2, where the native enzyme exhibits allosteric kinetic behavior. These observations demonstrate that we had succeeded in obtaining PFK fixed in the T state. Using the kinetic parameters of this modified enzyme, the kinetic properties of native enzyme can be quantitatively accounted for by the allosteric model of Monod-Wyman-Changeux. Further, the reagent was shown to have reacted with a specific cysteine residue near or at the ATP inhibitory site, and the sequence around the cysteine was determined as Cys-Lys-Asp-Phe-Arg.

Adenosine Triphosphate↗
PubMed1976

Affinity labelling of tRNA nucleotidyltransferase from baker's yeast with tRNAPhe modified on the 3'-terminus.

2'-Deoxy-2'-amino-cytidylic acid can be incorporated into position 75 of tRNAPhe from yeast by tRNA nucleotidyltransferase yielding tRNAPhe-C-C(2'NH2). tRNAPhe-C-C(2'NH2) can be reacted with the N-hydroxysuccinimide esters of bromoacetic acid of mercuriacetic acid to yield the derivatives tRNAPhe-C-C(2'NHCOCH2Br) and tRNAPhe-C-C(2'NHCOCH2Hg+OH-). Each of these reactive tRNAs inactivates tRNA nucleotidyltransferase from yeast with similar kinetics. The enzyme can be protected against inhibition by its substrates tRNAPhe-C and tRNAPhe-C-C as well as ATP and CTP. A covalent, isolatable 1:1 complex between tRNAPhe-C-C(2'NHCOCH2Br) and the enzyme was formed, but could not be found when the enzyme had previously been inactivated with p-hydroxymercuribenzoate.

Affinity Labels↗