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PubMed2000

Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.

The synergism between apolar and polar interactions in the carbohydrate recognition by human lysozyme (HL) was probed by site-directed mutagenesis and affinity labeling. The three-dimensional structures of the Tyr63-->Leu mutant HL labeled with 2',3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose (L63-HL/NAG-NAG-EPO complex) and the Asp102-->Glu mutant HL labeled with the 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine were revealed by X-ray diffraction at 2.23 and 1.96 A resolution, respectively. Compared to the wild-type HL labeled with the 2', 3'-epoxypropyl beta-glycoside of N,N'-diacetylchitobiose, the N-acetylglucosamine residue at subsite B of the L63-HL/NAG-NAG-EPO complex markedly moved away from the 63rd residue, with substantial loss of hydrogen-bonding interactions. Evidently, the stacking interaction with the aromatic side chain of Tyr63 is essential in positioning the N-acetylglucosamine residue in the productive binding mode. On the other hand, the position of the galactose residue in subsite B of HL is almost unchanged by the mutation of Asp102 to Glu. Most hydrogen bonds, including the one between the carboxylate group of Glu102 and the axial 4-OH group of the galactose residue, were maintained by local movement of the backbone from residues 102-104. In both structures, the conformation of the disaccharide was conserved, reflecting an intrinsic conformational rigidity of the disaccharides. The structural analysis suggested that CH-pi interactions played an important role in the recognition of the carbohydrate residue at subsite B of HL.

Affinity Labels↗
PubMed1987

Reaction of (bromoacetamido)nucleoside affinity labels with ribonuclease A: evidence for steric control of reaction specificity and alkylation rate.

Four new bromoacetamido pyrimidine nucleosides have been synthesized and are affinity labels for the active site of bovine pancreatic ribonuclease A (RNase A). All bind reversibly to the enzyme and react covalently with it, resulting in inactivation. The binding constants Kb and the first-order decomposition rate constants k3 have been determined for each derivative. They are the following: 3'-(bromoacetamido)-3'-deoxyuridine, Kb = 0.062 M, k3 = 3.3 X 10(-4) s-1; 2'-(bromoacetamido)-2'-deoxyxylofuranosyluracil, Kb = 0.18 M, k3 = 1700 X 10(-4) s-1; 3'-(bromoacetamido)-3'-deoxyarabinofuranosyluracil, Kb = 0.038 M, k3 = 6.6 X 10(-4) s-1; and 3'-(bromoacetamido)-3'-deoxythymidine, Kb = 0.094 M, k3 = 2.7 X 10(-4) s-1. 3'-(Bromoacetamido)-3'-deoxyuridine reacts exclusively with the histidine-119 residue, giving 70% of a monoalkylated product substituted at N-1, 14% of a monoalkylated derivative substituted at N-3, and 16% of a dialkylated species substituted at both N-1 and N-3. Both 2'-(bromoacetamido)-2'-deoxyxylofuranosyluracil and 3'-(bromoacetamido)-3'-deoxyarabinofuranosyluracil react with absolute specificity at N-3 of the histidine-12 residue. 3'-(Bromoacetamido)-3'-deoxythymidine alkylates histidines-12 and -119. The major product formed in 57% yield is substituted at N-3 of histidine-12. A monoalkylated derivative, 8% yield, is substituted at N-1 of histidine-119. A disubstituted species is formed in 14% yield and is alkylated at both N-3 of histidine-12 and N-1 of histidine-119. A specific interaction of the "down" 2'-OH group, unique to 3'-(bromoacetamido)-3'-deoxyuridine, serves to orient the 3'-bromoacetamido residue close to the imidazole ring of histidine-119. The 2'-OH group of 3',5'-dinucleoside phosphate substrates may serve a similar role in the catalytic mechanism, allowing histidine-119 to protonate the leaving group in the transphosphorylation step. (Bromoacetamido)nucleosides are bound in the active site of RNase A in a variety of distinct conformations which are responsible for the different specificities and alkylation rates.

Acetamides↗
PubMed1982

Affinity labeling of purified ornithine decarboxylase by alpha-difluoromethylornithine.

Ornithine decarboxylase (L-ornithine carboxy-lyase, EC 4.1.1.17) purified from rat liver was affinity-labeled by alpha-[5-14C]difluoromethylornithine. On analysis by SDS-polyacrylamide gel electrophoresis, the radioactivity migrated as a single major peak that coincided with a single protein band of Mr 50,000. Calculation from bound radioactivity indicated that ornithine decarboxylase has two active sites, one for each subunit, and that pure enzyme should have a specific activity of about 1.4 x 10(6) nmol CO2/h per mg protein.

Affinity Labels↗
PubMed1988

Affinity labeling at the A-site of Escherichia coli ribosomes by a non-hydrolyzable gamma-amide analog of GTP.

gamma-Amides of GTP and affinity and photoaffinity derivatives of gamma-amides of GTP: gamma-anilide of GTP, gamma-(4-azido)anilide of GTP, gamma-[N-(4-azidobenzyl)-N-methyl]amide of GTP, gamma[4-N-(2-chloroethyl)-N-methylaminobenzyl]amide of GTP and gamma-[4-N-(2-oxoethyl)-N-methylaminobenzyl]amide of GTP substituted efficiently for GTP in the EF-Tu-dependent transfer of aminoacyl-tRNA to the ribosome but, in contrast to GTP, they were not hydrolyzed in this process. They represent a new class of non-hydrolyzable GTP analogs with preserved gamma-phosphodiester bond. The radioactive analog of GTP: gamma-[4-N-(2-chloroethyl)-N-methylamino[14C]benzyl]amide of GTP was used as an affinity labeling probe for the identification of components of the GTPase center formed in the EF-Tu-dependent transfer reaction of aminoacyl-tRNA to the ribosomal A-site. Within a six-component complex of poly(U)-programmed E. coli ribosomes with elongation factor Tu, Phe-tRNA(Phe) (at the A-site), tRNA(Phe) (at the P-site) and the [14C]GTP analog, mainly the ribosomal 23S RNA and to a lesser extent the ribosomal proteins L17, L21, S16, S21 and the ribosomal 16S RNA were labeled by the reagent. No significant modification of EF-Tu was detected.

Affinity Labels↗
PubMed1981

Potential thyroliberin affinity labels. 1. Chloroacetyl-substituted phenylalanylpyrrolidines.

Six analogues of thyroliberin (TRH) that have a chloroacetyl substituent at the amino terminus have been prepared as potential affinity labels for the TRH receptor. These compounds are N-(chloroacetyl)-L-alanyl-L-phenylalanylpyrrolidine (ClAc-Ala-Phe-Pyrr; 14), N-[m-(chloroacetyl)benzoyl]-L-phenylalanylpyrrolidine (m-ClAcBz-Phe-Pyrr; 11a), N-[m-(chloroacetyl)benzoyl]-L-alanyl-L-phenylalanylpyrrolidine (m-ClAcBz-Ala-Phe-Pyrr; 15a), N-[p-(chloroacetyl)benzoyl]-L-phenylalanylpyrrolidine (p-ClAcBz-Phe-Pyrr; 11b), and N-[p-(chloroacetyl)benzoyl]-L-alanyl-L-phenylalanylpyrrolidine (p-ClAcBz-Ala-Phe-Pyrr; 15b). Pyroglutamyl-L-phenylalanylpyrrolidine was also synthesized as a model agonist. Weak agonist activity was observed for 11a, 11b, and 15b. These three analogues do not contain the amide group of the pyroglutamyl moiety that was previously thought to be essential for intrinsic activity. No significant antagonist activity was observed for these compounds at the doses tested.

Affinity Labels↗
PubMed1986

Characterization of benzodiazepine binding sites after short-wave photo-affinity labeling with flunitrazepam.

Membranes prepared from rat cerebral cortex were irradiated with short-wave UV light in the presence of flunitrazepam (FZ). This photo-affinity labeling (PAL) drastically reduces the potency of FZ binding to these membranes, but the binding of 3H-beta-carboline-3-carboxylate ethyl ester (3H-BCCE) was found to be essentially unchanged. 3H-BCCE binding was therefore determined in the presence of an antagonist (BCCE itself), an agonist (FZ) and a compound reported to discriminate between multiple benzodiazepine sites (CL 218,872). The results with BCCE are consistent with a single population of sites, but FZ binds to some of the sites with a reduced affinity (KI = 30 nM) and to the remaining sites with a very low affinity (KI approximately equal to 1 microM). CL 218,872 shows a reduced affinity but appears to interact with all of the sites. Taken together, these results indicate that the binding domains for BCCE and FZ are not identical, and that CL 218,872 interacts more strongly with the antagonist domain.

Affinity Labels↗
PubMed1976

Cobalt(III) affinity-labeled aspartokinase. Formation of substrate and inhibitor adducts.

The kinase active site of the aspartokinase-homoserine dehydrogenase enzyme complex of Excherichia coli has been affinity labeled both with substrates aspartate and adenosine triphosphate and feedback inhibitor threonine. Co(III) exchange-inert adducts of aspartokinase and inhibitor or substrates were produced in situ by oxidation of Co(II) with H2O2. Emzyme-Co(III)-adenosine 5'-triphosphate (ATP), enzyme-Co(III)-aspartate, and enzyme-Co(III)-threonine ternary adducts were produced in this manner. The formation of the enzyme-Co(III)-threonine adduct leads us to conclude that threonine inhibits the kinase activity of this enzyme complex by binding in the first coordination sphere of the catalytic metal ion cofactor, a conclusion which is consistent with evidence derived from previous nuclear magnetic resonance data obtained in this laboratory. The quaternary adducts formed by H2O2 oxidation in the presence of aspartokinase, Co(II), ATP, aspartate, and threonine comprised a mixture of both ezyme-Co(III)-ATP-aspartate and enzyme-Co(III)-ATP-threonine adducts. The formation of the quaternary aspartate-containing adduct was unexpected, since the presence of threonine was expected to prevent access of the aspartate to the active site; most significantly however, the the sum of the numbers of aspartate plus threonine molecules incorporated per active site is one. We believe that this shows direct steric overlap between the metal-adjacent binding sites for aspartate and threonine. Aspartate or threonine can not occupy the kinase active site simultaneously; this conclusion is consistent with the direct competitive inhibition of aspartate by threonine observed in steady-state kinetic studies.

Adenosine Triphosphate↗
PubMed1980

Photo-induced affinity labeling of Escherichia coli ribosomes by chloramphenicol.

In order to obtain more information about the binding site for chloramphenicol (D-threo diastereoisomer) on the bacterial ribosome, photo-affinity labeling experiments of this receptor have been performed with [3H]chloramphenicol itself. Control experiments show that this drug can be split photochemically by ultraviolet irradiation, whereas the ribosome is not modified structurally or functionally by such a treatment. When photolysis of a mixture of chloramphenicol and ribosomes is performed under critical conditions, some proteins like L1, L11, S3 and S4 are radiolabeled. L11, S3 and S4 are radiolabeled specifically as demonstrated by photo-incorporation experiments with isotopically diluted [3H]chloramphenicol or by comparison of the results obtained here with reversible experiments performed by the isotopic dilution method. When the D-erythro diastereoisomer of chloramphenicol is photo-incorporated into the bacterial ribosome, proteins are radiolabeled only in a non-specific way. These results show that this material could be used as an efficient scavenger. When finally D-threo [3H]chloramphenicol is photo-incorporated in the presence of a large amount of the D-erythro diastereoisomer, the radiolabeling pattern obtained for the proteins is quite different from that expected: while L11 is still labeled fairly extensively, L27 is the most radiolabeled protein found.

Affinity Labels↗
PubMed1992

Human immunodeficiency virus type 1 reverse transcriptase. Affinity labeling of the primer binding site.

Affinity modification of the primer site of HIV1-RT was performed with an oligonucleotide derivative containing a photoreactive azido group at the 5' end of d(pT)10. The affinity of HIV1-RT for d(pT)10 and for its derivative was first estimated by measuring the Michaelis constants of these two oligonucleotides acting as primers in the retrotranscription of poly(rA). The enzyme was then inactivated under UV-irradiation at 303-365 nm in the presence of ArN3-d(U*T9); the dependence of the rate of inactivation on primer concentration was found to be consistent with the Km value. Last, selectivity of affinity modification was demonstrated through elongation of the covalently bound primer and selective protection of inactivation by d(pT)10 or tRNA(Lys).

Affinity Labels↗
PubMedDate not supplied

A comparison of 11 beta-chloromethylestradiol and tamoxifen aziridine as affinity labeling reagents for estrogen receptors.

The tritium-labeled from of 11 beta-chloromethylestradiol was prepared by metal hydride reduction of the 17-keto derivative. Affinity labeling experiments were carried out using [3H] 11 beta-chloromethylestradiol and [3H]tamoxifen aziridine with estrogen receptor from crude, calf uterine cytosol and partially purified (heparin-sepharose chromatography) preparations. Both compounds formed highly stable receptor complexes. Estrogen specific, covalent binding, however, was indicated only for [3H]tamoxifen aziridine. An equilibrium dissociation constant of 2.8 x 10(-10) M was determined for the receptor-[3H] 11 beta-chloromethylestradiol interaction. Measurement of hormone dissociation kinetics at 30 degrees C revealed a slow, single phase dissociation of 11 beta-chloromethylestradiol from the receptor (dissociation rate constant, 1.3 x 10(-3) min-1). This contrasted with the normal biphasic dissociation pattern of estradiol in which the dissociation rate constant for the slower component was 16.7 x 10(-3) min-1. The results indicate that 11 beta-chloromethylestradiol readily converts the estrogen receptor to a high affinity binding form and suggest that the radiolabeled hormone may prove useful for studies of estrogen action.

Affinity Labels↗
PubMed1987

Ketononestrol aziridine, an agonistic estrogen receptor affinity label: study of its bioactivity and estrogen receptor covalent labeling.

Ketononestrol aziridine [(6R,TS)1-(N-aziridinyl)6,7-bis-(4-hydroxyphenyl)5-nonamone (KNA)], an aziridine derivative of hexestrol, is an estrogenic affinity label for the estrogen receptor (ER). It has an apparent relative binding affinity 8% that of estradiol and shows time-dependent irreversible binding to the ER in uterine cytosol preparations and intact human breast cancer cells (MCF-7). The agonistic activity of KNA is evident in MCF-7 cells in culture, where it increases the cell growth rate and elevates the level of progesterone receptor. KNA was prepared in high specific activity tritium-labeled form by iodination of a methanesulfonate precursor, followed by catalytic tritium-iodine exchange and aziridinylation; the material prepared has high radiochemical purity and a specific activity of 67 Ci/mmol. The covalent attachment of [3H]KNA to the ER can be followed directly by a solvent precipitation assay. In cytosol preparations of uterine ER, labeling with [3H]KNA proceeds in a time-, concentration-, and temperature-dependent manner; labeling is efficient and selective and, by competition studies, was shown to be estrogen specific. ER in intact MCF-7 cells can also be covalently labeled by treatment with [3H]KNA. Receptor covalently labeled with [3H]KNA sediments as a 4S species on high salt sucrose gradients, and its sedimentation position is shifted by treatment with monoclonal antireceptor antibodies. On sodium dodecyl sulfate-polyacrylamide gels, the principal labeled species migrates with a mol wt of 66,000. KNA should prove to be a useful probe for studies on receptor structure, function, and chromatin interactions, particularly when the behavior of a receptor-agonist complex is being investigated.

Affinity Labels↗
PubMed1992

Identification of amino acids modified by the bifunctional affinity label 5'-(p-(fluorosulfonyl)benzoyl)-8-azidoadenosine in the reduced coenzyme regulatory site of bovine liver glutamate dehydrogenase.

Bovine liver glutamate dehydrogenase reacts with the bifunctional affinity label 5'-(p-(fluorosulfonyl)benzoyl)-8-azidoadenosine (5'-FSBAzA) in a two-step process: a dark reaction yielding about 0.5 mol of -SBAzA/mol of subunit by reaction through the fluorosulfonyl moiety, followed by photoactivation of the azido group whereby covalently bound -SBAzA becomes cross-linked to the enzyme [Dombrowski, K. E., & Colman, R. F. (1989) Arch. Biochem. Biophys. 275, 302-308]. We now report that the rate constant for the dark reaction is not reduced by ADP or GTP, but it is decreased 7-fold by 2 mM NADH and 40-fold by 2 mM NADH + 0.2 mM GTP, suggesting that 5'-FSBAzA reacts at the GTP-dependent NADH inhibitory site. The amino acid residues modified in each phase of the reaction have been identified. Modified enzyme was isolated after each reaction phase, carboxymethylated, and digested with trypsin, chymotrypsin, or thermolysin. The digests were fractionated by chromatography on a phenylboronate agarose column followed by HPLC. Gas-phase sequencing of the labeled peptides identified Tyr190 as the major amino acid which reacts with the fluorosulfonyl group; Lys143 was also modified but to a lesser extent. The predominant cross-link formed during photolysis is between modified Tyr190 and the peptide Leu475-Asp476-Leu477-Arg478, which is located near the C-terminus of the enzyme. Thus, 5'-FSBAzA is effective in identifying critical residues distant in the linear sequence, but close within the regulatory nucleotide site of glutamate dehydrogenase.

Adenosine↗
PubMed1982

Potential affinity labels for the opiate receptor based on fentanyl and related compounds.

Derivatives of fentanyl, 3-methylfentanyl, sufentanil, and lofentanil, possessing chemo- or photoaffinity functionalities, were synthesized as potential affinity reagents for the opiate receptor. Opiate receptor binding constants (IC50) were determined in competition experiments with [3H]naloxone and [3H]naltrexone. Affinity-labeling experiments were generally unsuccessful, although some irreversible attachment was achieved with alpha-diazoamide 17 and aryl azide 23.

Affinity Labels↗
PubMed1983

Evaluation of N-bromoacetyl-L-thyroxine as an affinity label for the thyroxine (T4)-binding site in human T4-binding globulin.

The T4 analog N-bromoacetyl-L-T4 (BrAcT4) has been investigated as a possible affinity labeling reagent for identification of amino acids located within the T4-binding site in T4-binding globulin (TBG). As shown by fluorescence measurements involving displacement of 8-anilino-1-naphthalene-sulfonic acid from TBG, BrAcT4 is an effective competitor for the T4-binding site in TBG, with an association constant one seventh that of T4. Covalent modification of TBG by BrAcT4 was a slow process; after 48 h at a 10:1 molar ratio of [14C] BrAcT4 to TBG, incorporation of the 14C label reached 0.58 mol/mol protein or 77% of the theoretical value, correcting for 0.25 mol residually bound T4 in the original TBG sample. When [14C] BrAcT4 was reacted with TBG in the presence of T4, a partial inhibition of 25% in the degree of modification was obtained. The low inhibition of incorporation of label in the presence of T4 may be attributed to displacement of T4 from the binding site by BrAcT4 during the 20-h reaction time. To determine the effect of modification of the protein on binding activity, TBG was reacted with [14C]BrAcT4, and the binding capacity of modified TBG was determined by equilibrium dialysis. Three different TBG and three different [14C]BrAcT4 preparations were used. In two experiments, there was no reduction in binding capacity of modified TBG compared to that of control, although 0.6 and 0.48 mol label were incorporated per mol protein. In the third experiment, the decrease in binding capacity of modified TBG was 45% of the expected value. The lack of correspondence between the reduction in binding capacity and the degree of modification indicates that instead of reacting with amino acids within the T4-binding site, BrAcT4 derivatizes amino acids that are near but not actually part of the site. Covalent attachment of BrAcT4 to amino acids outside the T4-binding site places this compound in the category of an exoaffinity labeling reagent with regard to TBG and limits its usefulness for unequivocal identification of amino acids in the protein that participate directly in binding T4.

Affinity Labels↗
PubMed1991

Self-catalysed affinity labeling of Q beta replicase.

The spatial neighbourhood of the active center of Q beta replicase can be selectively modified by the method of self-catalysed affinity labeling. In the template-directed, mainly intramolecular enzymatic catalysis, the product [32P]GpG becomes specifically attached to the beta subunit. Using limited digestion of the radioactively labeled polypeptide by cyanogen bromide or N-chlorosuccinimide, we have mapped the attachment site to the region of subunit beta between Trp93 and Met130. Under our reaction conditions, Lys95 is the amino acid most likely to be modified, suggesting that Lys95 lies near the nucleotide binding site in the active center.

Affinity Labels↗
PubMed1980

Altered physical states of the membrane-bound acetylcholine receptor after affinity labelling.

The study of the interacstion of the bifunctional cholinergic ligand alpha-bromoacetylcholine with the membrane-bound acetylcholine receptor has allowed the identification of physically altered states of the receptor following affinity labelling. Depending on the integrity of a disulphide bond in the receptor, the ligand can either trigger the normal conversion of affinity states in unmodified membranes (apparent Kd's of approximately 0.5-1 microM and 5-10 nM in the low and high affinity states, respectively) or reversibly lock the reduced receptor in an agonist-insensitive state. Antagonists like d-tubocurarine release the receptor from this state, in accordance with in vivo observations. The integrity of a disulphide bond available for affinity acylation after reduction of the receptor appears to be essential for correct ligand discrimination and for the occurrence of ligand-induced state transitions of the membrane-bound receptor in vitro.

Acetylcholine↗
PubMed1983

Steroid derivatives for electrophilic affinity labelling of glucocorticoid binding sites: interaction with the glucocorticoid receptor and biological activity.

To investigate the possible use of electrophilic affinity labelling for the characterization of glucocorticoid receptors, different chemically reactive derivatives of deoxycorticosterone (deoxycorticosterone 21-mesylate and deoxycorticosterone 21-(1-imidazole) carboxylate), dexamethasone (dexamethasone 21-mesylate, dexamethasone 21-iodoacetate and dexamethasone 21-bromoacetate) and progesterone (21-chloro progesterone) were tested for their ability to bind irreversibly to the glucocorticoid receptor from goat lactating mammary gland. Using partially purified receptor, only one of the steroids tested, dexamethasone 21-mesylate (DXM-M) was found more effective than dexamethasone (DXM) in preventing exchange of radioactive dexamethasone in the receptor binding site. The affinity of DXM-M for the glucocorticoid receptor, measured by competitive binding assay, was 1/15 that of DXM. Polyacrylamide gel electrophoresis in sodium dodecyl sulphate of the [3H]-DXM-M labeled glucocorticoid receptor revealed a specific covalently radiolabeled fraction corresponding to an apparent molecular weight of 75,000 to 80,000. The biological activity of DXM-M was studied in RPMI 3460-clone 6 Syrian hamster melanoma cells, a cell line which is sensitive to growth inhibition by glucocorticoids. Like DXM, DXM-M inhibits the growth of RPMI 3460-clone 6 cells and it acts as a slowly reversible glucocorticoid agonist at concentrations which correlate with the affinity of DXM-M for the glucocorticoid receptor in vitro.

Affinity Labels↗
PubMed1975

Affinity labeling of the ribonucleic acid component adjacent to the peptidyl recognition center of peptidyl transferase in Escherichia coli ribosomes.

N-Iodacetylphenylalanyl-tRNA was used as an affinity label for localizing the RNA components intimately related to the peptidyl transferase activity of Escherichia coli ribosomesmthis analogue could specifically alkylate a unique nucleotide chain of 23-S RNA. The alkylation was strongly enhanced by poly(U), and was dependent on the presence of both 50- and 30-S subunits; Chloramphenicol inhibited the reaction, wheras blasticidin S stimulated it. The alkylated RNA base was found to be adenine. The nucleotide chain attacked by N-iodoacetylphenylalanyl-tRNA seemed to be localized at or near to the peptidyl recognition center of peptidyl transferase.

Acyltransferases↗