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Photo-sensitive peptidyl-tRNA's were used to scan the environment of the peptidyl-transferase center of the ribosome. The specificity of the previously described labeling in the 18-S fragment of 23-S rRNA by Boc-Phe(N3)-Phe-tRNA (4-azido-N-t-butoxycarbonyl-phenylalanyl-phenylalanyl-tRNA) was demonstrated by the ability of the covalently anchored molecule to serve as donor substrate in peptide bond formation. Labeling patterns were also obtained with Boc-Phe(N3)-Phe-Phe-tRNA bound at the acceptor site and with Boc-Phe(N3)-(Gly)n-Phe-tRNA (n = 2,4). The results indicate that subsequences within the 18-S fragment of 23-S rRNA are located close to the acceptor site as well as along the path where the peptide moiety adheres to the ribosome. Identification of the labeled sequences is expected to shed light on the spatial arrangement as well as functional role of rRNA in the peptidyl transferase center.
In this study we report on the synthesis, kinetic characterization and application of a novel biotinylated and active-site-directed inactivator of cathepsin B. Thus the peptidyldiazomethane biotinyl-Phe-Ala-diazomethane has been synthesized by a combination of solid-phase and solution methodologies and has been shown to be a very efficient inactivator of bovine and human cathepsin B. The respective apparent second-order rate constants (k0bs./[I]) for the inactivation of the human and bovine enzymes by this reagent, namely approximately 5.4 x 10(4) M-1.min-1 and approximately 7.8 x 10(4) M-1.min-1, compare very favourably with those values determined for the urethane-protected analogue benzyloxycarbonyl-Phe-Ala-chloromethane first described by Green & Shaw [(1981) J. Biol. Chem. 256, 1923-1928], thus demonstrating that the presence of the biotin moiety at the P3 position is compatible with inhibitor effectiveness. The utilization of this reagent for the detection of cathepsin B in electrophoretic gels, using Western blotting and in combination with a streptavidin/alkaline phosphatase detection system, is also demonstrated. Given that the peptidyldiazomethanes exhibit a pronounced reactivity towards cysteine proteinases, we feel that the present label may well constitute the archetypal example of a wide range of reagents for the selective labelling of this class of proteinase, even in a complex biological milieu containing additional classes of proteinases.
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The bifunctional reagent 4,4'-diisothiocyanostilbene-2,2'-disulfonate (DIDS) reacts with hemoglobin to give various products whose properties are dependent on the ligation state of the protein during the reaction. A major product obtained after reaction of (carbonmonoxy)hemoglobin with DIDS was a high oxygen affinity derivative [P50 = 1.4 mmHg, control P50 = 6 mmHg; 50 mM [bis(2-hydroxyethyl)-amino]tris(hydroxymethyl)methane (Bis-Tris), pH 7.4, 0.1 M Cl-, 25 degrees C] which contained two molecules of DIDS per tetramer resulting from adduct formation at each beta-chain amino terminus. In contrast, a major product of the reaction of deoxyhemoglobin with DIDS consisted of hemoglobin which had incorporated one molecule of DIDS per tetramer and was cross-linked between the beta-chain amino termini. This cross-linked hemoglobin was found to have a greatly decreased O2 affinity (P50 = 28 mmHg). Inhibition of the T to R transition due to the structural constraint produced by cross-linking the beta amino termini is likely to be a major factor in the decreased O2 affinity of this product. The structural and functional properties of this molecule make it a potential candidate for a cell-free blood substitute.
[3H]-14 beta-(Bromoacetamido)-7,8-dihydromorphine ([3H]H2BAM) was synthesized and tested for its ability to selectively label mu opioid receptors in bovine striatal membranes. Incubating membranes with N-tosyl-L-phenylalanine chloromethyl ketone and dithiothreitol before the addition of [3H]H2BAM reduced nonspecific [3H]H2BAM binding so that [3H]H2BAM binding to opioid receptors was up to 70% of the total [3H]H2BAM binding and was dependent on [3H]H2BAM concentration, incubation time, and pH of the reaction. At pH 7.5, [3H]H2BAM bound selectively to the mu opioid receptor, but mainly noncovalently. After the initial binding of [3H]H2BAM to the receptor, membranes were washed and then incubated at 37 degrees C in 50 mM Tris-HCl, pH 8.5, for 3 h, a time that resulted in greater than 80% of the [3H]H2BAM associated with the receptor becoming covalently bound to the opioid receptor. The mu-selective peptide [D-Ala2,(Me)Phe4,Gly(ol)5]enkephalin inhibited [3H]H2BAM labeling of membranes, while delta- or kappa-selective compounds were ineffective. Both NaCl and the nonhydrolyzable guanine nucleotide analog guanylyl 5'-imidodiphosphate reduced the incorporation of [3H]H2BAM into membranes. When [3H]H2BAM-labeled striatal membranes were separated under reducing conditions on a sodium dodecyl sulfate-polyacrylamide gel, two proteins with molecular weights of 54,000 and 44,000 were specifically labeled. The 54-kDa protein was present in a greater amount than the 44-kDa protein. Both proteins bound to wheat germ agglutinin-Sepharose and concanavalin A-Sepharose, suggesting that both proteins contain multiple carbohydrate moieties. Despite the inclusion of protease inhibitors, the 44-kDa protein may be a proteolytic fragment of the 54-kDa protein.(ABSTRACT TRUNCATED AT 250 WORDS)
Methylenetetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclohydrolase are inactivated in parallel by carbodiimide-activated folic acid in an NADP-dependent reaction. Modification with tritium-labelled reagent resulted in the incorporation of 1 mole 3H-folate per mole polypeptide, which demonstrates that these activities share a single folate binding site.
The dNTP binding pocket of human immunodeficiency virus type 1 reverse transcriptase (RT) and DNA polymerase beta (beta-pol) were labeled using a photoreactive analog of dCTP, exo-N-[beta-(p-azidotetrafluorobenzamido)-ethyl]-deoxycytidine-5'- triphosphate (FABdCTP). Two approaches of photolabeling were utilized. In one approach, photoreactive FABdCTP and radiolabeled primer-template were UV-irradiated in the presence of each enzyme and resulted in polymerase radiolabeling. In an alternate approach, FABdCTP was first UV-cross-linked to enzyme; subsequently, radiolabeled primer-template was added, and the enzyme-linked dCTP analog was incorporated onto the 3'-end of the radiolabeled primer. The results showed strong labeling of the p66 subunit of RT, with only minor labeling of p51. No difference in the intensity of cross-linking was observed with either approach. FABdCTP cross-linking was increased in the presence of a dideoxyterminated primer-template with RT, but not with beta-pol, suggesting a significant influence of prior primer-template binding on dNTP binding for RT. Mutagenesis of beta-pol residues observed to interact with the incoming dNTP in the crystal structure of the ternary complex resulted in labeling consistent with kinetic characterization of these mutants and indicated specific labeling of the dNTP binding pocket.
Transport of pyridoxal 5-phosphate (PLP) into erythrocytes was inhibited by inhibitors of anion transport including stilbene disulfonate compounds, indicating that it is mediated by Band 3 protein. When erythrocytes were treated with PLP and large amounts of free lysine and NaBH4, two membrane-spanning fragments of Band 3 (Mr = 17,000 and 35,000) were specifically labeled. When the cells were pretreated with 4,4'-dinitrostilbene 2,2'-disulfonate, the labeling in the 35,000-dalton fragment was inhibited. Erythrocytes labeled by PLP in both the 17,000- and 35,000-dalton fragments transported PLP at a decreased rate, whereas the cells labeled in only the 17,000-dalton fragment had essentially the same transport activity as the control when 4,4'-dinitrostilbene 2,2'-disulfonate was removed. The extent of inhibition of transport of inorganic phosphate in the labeled cells was similar to that of PLP. The results indicate that the 35,000-dalton fragment participates in the anion transport of the cell membrane.
A new photocross-linking 5-C-base-substituted UTP analogs, carrying 4-azidoperfluorobenzoyl and 4-azidoaniline residues were synthesized. Two flavivirus proteins NS5 and NS3 are shown to be labelled after RNA synthesis in the presence of the analogs, irradiation (lambda > 300 nm) and subsequent [alpha-32P]NTP incorporation.
Dihydrofolate reductases from different species contain several highly conserved arginines, some of which have been shown by x-ray crystallography to have their guanido groups near the p-aminobenzoyl glutamate moiety of enzyme-bound methotrexate. The orientation of one of these (Arg-52) appears to be completely reversed in comparing the crystal structures of Escherichia coli with Lactobacillus casei enzyme (Bolin, J. T., Filman, D. J., Matthews, D. A., Hamlin, R. C., and Kraut, J. (1982). J. Biol. Chem. 257, 13650-13662). We synthesized a novel antifolate containing a glyoxal group designed to react specifically with active-site guanido groups which are able to approach the p-aminobenzoyl carbonyl of methotrexate. The binding of this compound to the enzyme was competitive with dihydrofolate (DHF) in ordinary buffers. In borate buffer at pH 8.0 it inactivated dihydrofolate reductases from both E. coli and L. casei at similar maximum rates, while the chicken liver enzyme was more slowly inactivated. The inactivation was stoichiometric, paralleled the loss of the glyoxal chromophore, and showed saturation kinetics. Inhibitor binding and thus inactivation was enhanced by NADPH, while DHF protected the enzyme. This allowed calculation of the Kd for DHF which was found to be identical with its Km. The stoichiometrically inactivated enzyme displayed the 340-nm chromophore characteristic of 4-aminopteridines bound to dihydrofolate reductase confirming active-site labeling with normal orientation of the ligand. The ligand remained covalently bound to inactivated enzyme upon denaturation at low pH but dissociated at neutral pH. Computer graphic modeling of the crystal structures predicted reaction of Arg-31 but not Arg-52 in L. casei dihydrofolate reductase and of only Arg-52 in the E. coli enzyme. Purification of the CNBr fragments from the inactivated enzymes gave a single labeled peptide for each species. The particular peptide tagged in each case was unaffected by the presence of NADPH and was in excellent agreement with the crystallographic predictions.
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4-(N-2-chloroethyl-N-methyl)aminobenzyl-5'-phosphoamide of the heptauridylic acid was used to localize the structures organizing mRNA-binding site of ribosomes from E. coli. Both rRNA and proteins undergo modification in the ribosome 10-18 and 82-90% of the total ribosomal subunit modification, respectively. Using the method of two-dimensional electrophoresis in the acrylamide gel the proteins S5, S11, S13 and L2, L7/L12, L31 which are labelled by the analog of mRNA were identified. We assume these proteins to be located in the vicinity of mRNA-binding centre of ribosomes.
Cyclic GMP-stimulated cyclic nucleotide phosphodiesterase (PDE2) is the second most abundant of this class of enzymes in platelets. PDE2 probably plays an important role in the regulation of elevated intracellular concentrations of cAMP and cGMP in platelets inhibited by prostacyclin and/or nitric oxide. The cAMP and cGMP PDEs have catalytic domains with 28-40% identity, but vary in their substrate specificity and affinity. As a first step toward the goal of identifying important amino acids in the substrate binding site pocket, we have employed the affinity analog 8-[(4-bromo-2, 3-dioxobutyl)thio]adenosine-3'5' cyclic monophosphate (8-BDB-TcAMP) to inactivate PDE2 and observe the pattern of protection by substrates and their products. Incubation of purified platelet PDE2 with 8-BDB-TcAMP (2-10 mM) resulted in a time-dependent, irreversible inactivation of the enzyme with a second-order rate constant of 0.013 min(-1) mM(-1). Both substrates, cAMP and cGMP, as well as the products of hydrolysis by PDE2, AMP and GMP, exhibited concentration-dependent protection against inhibition by 8-BDB-TcAMP, but no protection was noted with ADP or ATP, which are not hydrolyzed by the enzyme. This compound, 8-BDB-TcAMP, and similar affinity reagents should prove useful in delineating amino acids in the active site of PDE2.
An N-hydroxysuccinimide ester of [3H]methotrexate has been employed to covalently label a specific binding protein that resides in the plasma membrane of L1210 cells. Incorporation of radioactivity into this protein accounted for 55% of total cellular labeling, was half-maximal at a reagent concentration of 27 nM, and was blocked either by prior exposure to unlabeled reagent or by the addition of excess methotrexate. A role for this protein in methotrexate transport was supported by the observations that: (a) similar concentrations of reagent were required for both labeling of the binding protein and irreversible inhibition of transport; (b) the amount of labeled binding protein was comparable to observed levels of transport protein; (c) protection against labeling was afforded by thiamin pyrophosphate, a potent competitive inhibitor of methotrexate transport; and (d) labeling of the binding protein was not observed in a subline of L1210 cells that has a defect in the ability to transport methotrexate. The binding protein could be solubilized from the membrane by various ionic and non-ionic detergents and the covalent bond between the incorporated [3H]methotrexate and the protein was stable to a variety of conditions, including high concentrations of mercaptoethanol and hydroxylamine and extremes of pH. The labeled protein fractionated as a nearly symmetrical peak on Sephacryl S-300 and it appeared as a single band (Mr = 36,000) after electrophoresis in polyacrylamide gel containing sodium dodecyl sulfate.
A number of retinoid derivatives have been synthesized for use as labels for cellular retinol-binding protein. Introduction of substituents abolished the binding of the derivatives to the protein, except in the case of the photo-reactive derivative, 4-azidoretinol. This compound was found to compete successfully with all-trans-retinol for binding to cellular retinol-binding protein, with a high relative binding affinity. Irradiation of a complex of 4-azidoretinol and a semi-purified preparation of cellular retinol-binding protein from liver resulted in a firm attachment stable to SDS-gel electrophoresis. It is therefore suggested that the irradiated product is held together covalently. A method for the synthesis of 4-azidoretinol is described.
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Effects of temperature and d-cis-diltiazem (DTZ) on [3H]nitrendipine (NTD) and [3H]nimodipine (NIM) binding to skeletal muscle t-tubular membranes were studied. A decrease in temperature from 37 degrees C to 10 degrees C decreased KD and increased Bmax slightly. DTZ increased binding by increasing Bmax under all conditions and also decreased KD for NTD at 37 degrees C. The binding protein labeled with [3H]isothiocyanate dihydropyridine revealed a molecular weight of 36,000. The binding site for NTD was solubilized by deoxycholate and dihydropyridine binding was still stimulated by DTZ in the solubilized form.