Protein components of the erythromycin binding site in bacterial ribosomes

Two derivatives of erythromycin have been prepared carrying either an aryl azide or a 4-nitroguaiacol as a photoreactive group. Both derivatives bind to the specific erythromycin ribosomal site as shown by saturation and competition studies. The derivatives were isotopically labeled either with tritium or with 125I, and radioactivity is covalently incorporated to the ribosome upon irradiation at the appropriate wavelength. The ribosomal proteins labeled were identified by either mono- and two-dimensional gel electrophoresis or high performance liquid chromatography. It has been found that protein L22 is the protein mainly, and under some conditions exclusively, labeled by the erythromycin derivatives. These results were confirmed using ribosomes from erythromycin-resistant mutants having a protein L22 with modified electrophoretical mobility. Protein L15 is also labeled in both cases, and the aromatic azide derivative labels to a lesser extent proteins L2 and L4. Competition experiments with erythromycin indicate that labeling in protein L22, and probably in L15, is specific, while the specificity of labeling in proteins L2 and L4 is questionable. These results indicate that the erythromycin derivatives label different ribosomal proteins than the spiramycin type of macrolides (Tejedor, F., and Ballesta, J.P.G. (1985) Biochemistry 24, 467) suggesting that the binding sites of both macrolide types are probably not identical.     

Photoaffinity labeling of procaine-binding sites in normal and sickle cell membranes

A photoaffinity probe, procaine azide, was employed to determine the sites of interaction of procaine in normal and sickle cell erythrocytes. Studies show that the number of binding sites and affinity of procaine to membranes derived from normal and sickled cell erythrocytes were similar, although procaine retards the in vitro formation of irreversibly sickled cells from cells. The results show that procaine azide, a photoaffinity analogue of procaine, is covalently incorporated into both protein (60–70%) and lipid (40–30%) components of the membrane. Sodium dodecyl sulfate-gel electrophoresis of the labeled ghosts show that procaine binds specifically to band 3 and periodic acid-Schiff staining bands in membranes derived from labeled erythrocytes. Binding of procaine or covalent incorporation of procaine azide into membrane proteins does not affect the phosphate transport. Moreover, pre-treatment of intact erythrocytes with 4,4′-diisothiocyano-2,2′-stilbene disulfonate, an anion transport inhibitor, did not affect either the binding or covalent incorporation of procaine azide into erythrocytes. These results indicate that the binding of procaine azide to Band 3 protein occurs at a locus different than that involved in anion translocation process.     

Photoaffinity labeling of a bacterial sialidase with an aryl azide derivative of sialic acid

A photoreactive radioiodinatable derivative of 2-deoxy-2,3-didehydro-5-N-acetylneuraminic acid (NeuAc2en), 5-N-acetyl-9-(4-azidosalicoylamido)-2-deoxy-2,3-didehydroneuram inic acid (ASA-NeuAc2-en) has been synthesized and used to label the active site of Clostridium perfringens sialidase. Like NeuAc2en, its aryl azide derivative is a strong competitive inhibitor of sialidase (Ki approximately 15 microM). The absorbance spectrum of ASA-NeuAc2en shows a characteristic aryl azide peak, which disappears upon photolysis with UV light. When its radioiodinated counterpart 5-N-acetyl-9-(4-iodoazidosalicoylamido)-2-deoxy-2,3-didehydrone uraminic acid ([125I]IASA-NeuAc2en) was photolyzed in the presence of C. perfringens sialidase a 72-kDa protein was labeled. Labeling occurred specifically in the active site since it was inhibited in the presence of NeuAc2en. Chemical cleavage of the photoaffinity-labeled 72-kDa protein demonstrates that specifically labeled peptides involved in the formation of the active site can easily be determined. ASA-NeuAc2en is a valuable new tool for the identification and structural/functional analysis of sialidases and other proteins, recognizing this sialic acid derivative.     

The Synthesis of 5′-O-Triphosphate-4N-(ω-aminoalkyl)deoxycytidine A Useful Precursor to the Generation of Differently Labeled Triphosphates

Abstract

A chemical synthesis is described for 5′-O-triphosphate-4N-[6-(-γ-aminopropylamidosuccinylamido)-hexyl]deoxycytidine (13), the substrate for synthesis of 5′-O-triphosphate deoxycytidine derivatives (17-19) labeled with biotin, fluorescein and photoreactive azide.     

Fluorescent photochemical surface labeling of intact human erythrocytes.

A photolabile nitrene precursor, 3-azido-(2,7)-naphthalene disulfonate (ANDS), has been synthesized and used as a membrane-impermeable probe. The aryl azide was nonfluorescent. When activated by light, a highly reactive nitrene was generated which was capable of nonspecific covalent modifications of hydrophilic regions of cell surfaces. The products of the photolysis were highly fluorescent and modified proteins could be identified by their characteristic fluorescence after electrophoresis on sodium dodecyl sulfate polyacrylamide gels. When intact human erythrocytes were labeled with ANDS, Protein 3, the major membrane protein, and the sialoglycoproteins were modified. No proteins of apparent molecular weight greater than Protein 3 were labeled by ANDS, suggesting that none of these membrane components was exposed to the hydrophilic external surface of the red blood cell. When open erythrocyte stroma were labeled with ANDS, virtually all protein bands detectable by Coomassie blue staining could be shown to contain some fluorescence label. The significance of these findings are discussed with relation to the use of various aryl azides as surface labels of membranes.     

3,4-Dihydroxyphenylacetic acid is a potential aldehyde dehydrogenase inducer in murine hepatoma Hepa1c1c7 cells

3,4-Dihydroxyphenylacetic acid (DOPAC) is one of the major colonic microflora-produced catabolites of quercetin glycosides, such as quercetin 4′-glucoside derived from onion. Here, we investigated whether DOPAC modulates the aldehyde dehydrogenase (ALDH) activity and protects the cells from the acetaldehyde-induced cytotoxicity in vitro. DOPAC was shown to enhance not only the total ALDH activity, but also the gene expression of ALDH1A1, ALDH2 and ALDH3A1 in a concentration-dependent manner. DOPAC simultaneously stimulated the nuclear translocation of NFE2-related factor 2 and aryl hydrocarbon receptor. The pretreatment of DOPAC completely protected the cells from the acetaldehyde-induced cytotoxicity. The present study suggested that DOPAC acts as a potential ALDH inducer to prevent the alcohol-induced abnormal reaction.     

Efficient and selective photoaffinity labeling of the estrogen receptor using two nonsteroidal ligands that embody aryl azide or tetrafluoroaryl azide photoreactive functions

3-(4-Azido-2,3,5,6-tetrafluorobenzoyl)-6-hydroxy-2-(4- hydroxyphenyl)benzo[b]thiophene 1 (tetrafluoroaryl azide, TFAA) and its protio analogue 3-(4-azidobenzoyl)-6- hydroxy-2-(4-hydroxyphenyl)benzo[b]thiophene 2 (protioaryl azide, PAA), photoaffinity labeling (PAL) reagents for the estrogen receptor (ER), have been prepared in high specific activity tritium-labeled form (19 Ci/mmol) and shown to undergo selective and efficient photocovalent attachment to ER from rat uterus. Both azides 1 and 2 demonstrate high binding affinity for ER as determined by both a competitive binding assay (relative binding affinities: estradiol = 100; TFAA = 9.3; PAA = 66) and a direct binding assay (Kd: estradiol = 0.24 nM; TFAA = 2.64 nM; PAA = 0.37 nM). When unlabeled TFAA and PAA are irradiated at greater than 315 nm, they demonstrate site-specific photoinactivation of ER that reaches 43% and 55%, respectively, by 30 min. Specific photocovalent attachment to ER can be effected by irradiation of the tritium-labeled azides; the covalent attachment efficiency is good (1 = 20-30%, 2 = ca. 25%) and the selectivity of ER labeling is high. Characterization of the photolabeled proteins by SDS-polyacrylamide gel electrophoresis shows specific labeling of a major component at Mr 60,000 and a minor species at Mr 46,000, the same two species that are labeled by [3H]tamoxifen aziridine, a well-characterized affinity label for ER. The ER-specific antibodies H222Sp gamma and D547Sp gamma show a clean precipitation of only these two species. In the MCF-7 human breast cancer cell line, PAA is a full estrogen agonist in terms of stimulation of cell proliferation and induction of progesterone receptor. These two azides provide the first system in which the photocovalent attachment efficiency of an aryl azide can be compared to its tetrafluorosubstituted aryl azide analogue in a complex biological receptor system. Azides 1 and 2 are the most efficient and selective PAL reagents prepared to date for ER, and they should be useful in further studies of the hormone-binding domain of this protein.     

双向凝胶电泳中三种蛋白质检测方法的比较

高通量双向电泳是蛋白质组学的核心 ,双向电泳凝胶上蛋白质点的检测方法应具有灵敏度高、线性范围宽和兼容质谱鉴定等优点 .采用差异凝胶电泳 (differencegelelectrophoresis ,DIGE)技术以Cy3(1 (5 carboxypentyl) 1′ propylindocarbocyaninehalideN hydroxysuccinimidylester)和Cy5 (1 (5 carboxypentyl) 1′ methylindodicarbocyaninehalideN hydroxysuccinimidylester)荧光分别标记正常和TNF α处理细胞的蛋白质 ,用Cy2 (3 (4 carboxymethyl)phenylmethyl) 3′ ethyloxacarbocyaninehalideN hydroxysuccinimidylester)荧光标记正常和TNF α处理细胞蛋白质的等量混合样品作为内标 ,混合 3种荧光标记的蛋白质后 ,在同一等电聚焦胶条进行聚焦 ,然后在聚丙烯酰胺凝胶上进行第二向电泳 ,用 3种波长的激光激发扫描得到凝胶图象 ,DIGE中多个样品在同一条件下电泳 ,因而匹配率高 ,且引入内标使蛋白质点的检测与定量更为准确 .DIGE技术与质谱相结合 ,实现了高通量和相对准确定量 .与硝酸银和考马斯亮蓝染色结果相比较 ,DIGE技术具有灵敏度高、线性范围宽和不影响后续质谱鉴定等优点     

Reaction of Azide Ion with 1-(2,3-Anhydrolyxofuranosyl)Uracil. Isolation of 1-(2-Amino-2-deoxy-β-D-Xylo-Furanosyl)uracil and 1-(3-Amino-3-deoxy-β-D-arabinofuranosyl)uracil

Abstract

The reaction of the 2′,3′-lyxoepoxide (1) with ammonium azide gives two products; namely, the 3′-arabino azide (2a) and in low yield 2′-xylo azide (3a). After debenzoylation and reduction the resulting mixture of amines was resolved by chromatography on a weak cation exchanger, Amberlite IRC-50, and afforded crystalline 1-(3-amino-3-deoxy-β-D-arabinofuranosyl)uracil (2c) and 1-(2-amino-2-deoxy-β-D-xylofuranosyl)uracil (3c) in the ratio of 4:1.     

Internal and external membrane proteins of the cyanobacterium, Synechococcus cedrorum

The protein composition and architecture of the photosynthetic membranes from the cyanobacterium, Synechococcus cedrorum, were analyzed with the aid of site-specific labels. Using membranes labeled with ³⁵S, about 50 membrane proteins can be detected by sodium dodecyl sulfate acrylamide gel electrophoresis. Approximately half of the proteins are accessible to modification by the impermeant probe, lactoperoxidase, indicating that they have surface-exposed domains. At least six of these external proteins can be removed by EDTA washing; the correspondence in molecular weights between five of these EDTA-extractable proteins and those of typical chloroplast coupling factor preparations may indicate that they are subunits of a membrane-bound ATPase. The photoactive, lipophilic compound, [¹²⁵I]iodonaphthyl azide, was used to label protein domains in contact with the lipid bilayer. Iodonaphthyl azide modification led to a labeling pattern significantly different from that seen with lactoperoxidase. In particular, proteins in the 13 000–20 000 dalton range that were labeled poorly or not at all by lactoperoxidase were heavily modified by iodonaphthyl azide.Photosystem I and II particles, extracted from the membrane by digitonin treatment, were iodinated by lactoperoxidase after isolation. The PS I particles acted as a relatively tight complex, with most of the proteins remaining inaccessible to surface modification. The PS II particles, on the other hand, responded as a more open structure, with most of the subunits yielding to lactoperoxidase iodination. Similar studies on a highly fluorescent, temperature-sensitive mutant of S. cedrorum revealed a different organization of the PS II complex. This mutant, when grown at 40°C, inserts a 51 kdalton polypeptide in place of a 53 kdalton protein. This protein also replaces the 53 kdalton species in the PS II complex of the mutant after 40°C growth. The structure of this complex is altered in that more sites become accessible to lactoperoxidase. This is particularly true of the 51 kdalton protein, which is barely labeled in wild-type PS II complexes.     

Preparation and characterization of a biologically active spin-labeled sea anemone toxin

A derivative of the polypeptide cardiostimulant anthopleurin-B(AP-B) labeled with the spin label 1-oxyl 2,2,6,6-tetramethyl-4-piperidinyloxycarbonyl azide has been prepared and characterized. The product was found by mass spectrometry to be labeled at a single site, which amino acid sequencing showed to be the N-terminus. It also retained positive inotropic activity when assayed on isolated guinea pig atria. The spin-labeled (SL) product was found to exist in two distinct conformations by reversed-phase HPLC and in at least two conformations by electron spin resonance spectroscopy (ESR) over thepH range 2–9. The ESR data also show evidence for multimetric states of SL-AP-B over thepH range 2–9, with maximum aggregation at pH 4.5–5, and a slow disaggregation when thepH is adjusted to 8–9. The presence of multiple conformers of SL-AP-B and its tendency to aggregate render it unsuitable for high-resolution NMR structural studies of the isolated ligand, but the retention of activity may make it useful for studies of the sodium-channel-bound form of the molecule.Abbreviations AP-A anthopleurin-A - AP-B anthopleurin-B - ATX Ia toxin Ia fromAnemonia sulcata - Sh I neurotoxin I fromStichodactyla helianthus - TFA trifluoroacetic acid - SL-AP-B AP-B labeled at the N-terminus with the spin label 1-oxyl 2,2,6,6-tetramethyl-4-piperidinyloxycarbonyl azide     

Gas chromatographic/mass spectrometric methodology for simultaneous assay of salsolinol, dopamine, norepinephrine, dihydroxyphenylacetic acid and dihydroxyphenylethanol

Synthesis of deuterated (2H4)salsolinol from (2H4)dopamine via a Pictet-Spengler condensation is described. This (2H4)salsolinol is an ideal internal standard to determine picomole (ng) amounts of salsolinol (SAL) in a variety of sample types including urine, plasma, beverages and fruits. The deuterated standard is completely free of contamination by the non-deuterated species. The extraction procedure described is fast, highly efficient and does not lead to artifactual salsolinol formation even in the face of high dopamine concentrations. As well as SAL the method described allows simultaneous determination of norepinephrine (NE), dopamine (DA) and its two metabolites dihydroxyphenylacetic acid (DOPAC) and dihydroxyphenylethanol (DOPET). Each of the analytes is measured as its trifluoroacetyl derivative. Using trifluoroacetic anhydride in conjunction with trifluoroethanol allows simultaneous one-step derivatization of the acid function of DOPAC. All compounds were measured in the single ion monitoring (SIM) mode and quantified using appropriate deuterated internal standards. SAL, DA, DOPET, DOPAC and NE have been quantified in a variety of food and beverage sources. Soy sauce and dried banana have been identified as rich dietary sources of SAL. These data suggest diet should be considered a potentially important source of 'mammalian alkaloids' such as SAL, and the presence of SAL in mammalian systems is not necessarily evidence for an in vivo Pictet-Spengler condensation.     

Synthesis and Biological Activity of the Mono- and Diamino Analogues of 2′-Deoxyadenosine,Cordycepin, 9-(3-Deoxy-α-D-Threo-Pentofuranosyl)-Adenine (A Structural Component of Agrocin 84) and 9-(2-Deoxy-α-D-Threo-Pentofuranosyl)Adenine

Abstract

The mono- and diamino analogues of 9-(2-deoxy-α-D-erythro-pen-tofuranosyl)adenine la, 9-(2-deoxy-α-D-threo-pentofuranosyl)adenine 4a, 9-(3-deoxy-α-D-erythro-pentofuranosyl)adenine 2a and 9-(3-deoxy-α-D-threo-pentofuranosyl)adenine 3a were synthesized by triphenylphosphine reduction of the corresponding azido compounds. The azido group was introduced by a substitution reaction with lithium azide on mesylates or, more directly, by reaction with lithium azide, triphenylphosphine and carbon tetrabromide. Of the newly synthesized compounds, only 3′-amino-2′,3′-dideoxyadenosine proved, albeit slightly, inhibitory to murine leukemia L1210 and mammary carcinoma FM3A, and human B-lymphoblast Raji, T-lymphoblast Molt/4F and T-lymphocyte MT-4 cell proliferation in vitro (50 % inhibitory dose : 43.1-323 μM). None of the compounds inhibited human immunodeficiency virus-induced cytopathogenicity in MT-4 cells.     

Measurement of 3,4-dihydroxyphenylacetic acid and 3-methoxytyramine specific activity rat striatum.

A method is described for the simultaneous determination in rat striatum of the specific activities of tyrosine, dopamine, 3,4-dihydroxyphenylacetic acid (DOPAC), and 3-methoxytyramine (3-MT) after administration of [³H]tyrosine. [³H]Tyrosine was given intraventricularly to nonanesthetized rats, and the animals were killed by exposure to microwave radiations. Combined chromatographic elutions on Dowex 50W-X4 columns and alumina or solvent extractions were devised to separate the compounds. Fluorimetric, mass-fragmentographic, and radiometric techniques were used for their detection. Recovery was 94% for tyrosine, 72% for dopamine, 63% for DOPAC, and 50% for 3-MT. Concentrations of the labeled compounds in rat striatum 15 min after the [³H]tyrosine injection were at least five to eight times higher than background. Identity of the final fractions containing 3-MT and DOPAC tissue extracts was verified by thin-layer chromatography. α-Methyltyrosine pretreatment of rats markedly reduced the formation of labeled dopamine. DOPAC, and 3-MT from [³H]tyrosine.     

Site-specific, covalent attachment of proteins to a solid surface

Immobilized and site-specifically labeled proteins are becoming invaluable tools in proteomics. Here, we describe a strategy to attach a desired protein to a solid surface in a covalent, site-specific manner. This approach employs an enzymatic posttranslational modification method to site-specifically label a target protein with an azide; an alternative substrate for protein farnesyl transferase containing an azide group was developed for this purpose. A bio-orthogonal Cu(I)-catalyzed cycloaddition reaction is then used to covalently attach the protein to agarose beads bearing an alkyne functional group. We demonstrate that both the azide incorporation and the capture steps can be performed on either a purified protein target or on a protein present within a complex mixture. This approach involves the use of a four-residue tag which is significantly smaller than most other tags reported to date and results in covalent immobilization of the target protein. Hence it should have significant applicability in protein science.     

Fluorescent labeling of Taqman oligonucleotide probes via Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) click chemistry

We describe an approach to the synthesis of TaqMan oligonucleotide probes that is based on Cu(I)-catalyzed alkyne-azide cycloaddition (CuAAC) click chemistry when oligonucleotides containing an internal alkynyl group at the pyrimidine position are labeled post-synthetically with a f luorescent azide. TaqMan probes were constructed with f luorescein in different internal positions and a BHQ1 quencher on the 3′-end. Our previously designed alkynylated deoxyuridine or deoxycytidine phosphoramidites have been employed for the synthesis of alkynyl oligonucleotides. It was demonstrated that the synthesized TaqMan probes can detect accumulation of PCR product in real-time. The closer to the label the 3′-terminal quencher, the higher the quenching efficiency, but the efficiency of probe hybridization to DNA template is reduced in this case.     

Photoaffinity labeling of the erythropoietin receptor and its identification in a ligand-free form.

Pure human recombinant erythropoietin (EP) was acylated through a primary amino residue with a cross-linking reagent, N-[[3-[[4-[(p-azido-m-[125I]iodophenyl)azo]benzoyl]amino] propanoyl]oxy]-succinimide (Denny-Jaffe reagent), which is photoreactive and cleavable at the azo residue. The resulting conjugated hormone (DJ-EP) was purified from unmodified EP by reverse-phase high-pressure liquid chromatography and maintained its capacity to bind to receptors for EP on erythroid progenitor cells. The receptor for EP was previously identified as two related proteins of 100 and 85 kDa molecular mass by chemical cross-linking to 125I-EP. Recently, D'Andrea and co-workers [(1989) Cell 57, 277-285] cloned a cDNA that codes for a protein of 55-66 kDa, which is thought to be the EP receptor. In this report, cross-linking to the receptor through the monofunctional DJ-EP labeled the same 140- and 125-kDa molecular mass bands (100- and 85-kDa proteins) cross-linked with 125I-EP and disuccinimidyl suberate. Furthermore, cleavage of the azo bond of the DJ-EP receptor complex by sodium dithionite (80 degrees C, 5 min) demonstrated that proteins of 105 and 90 kDa were labeled in ligand-free form by DJ-EP. This result demonstrates that artifactual cross-linking of multiple proteins or other artifacts of cross-linking do not explain the difference in molecular mass of the EP receptor identified by cross-linking and the receptor identified by expression cloning.     

Axonal transport of actin in rabbit retinal ganglion cells

We labeled proteins in the cell bodies of rabbit retinal ganglion cells with [35S]methionine and subsequently observed the appearance of radioactive actin in tissues containing the axons and synaptic terminals of these neurons, i.e., the optic nerve (ON), optic tract (OT), lateral geniculate nucleus (LGN) and the superior colliculus (SC). The temporal sequence of appearance of labeled actin (which was identified by its specific binding to DNase I, its electrophoretic mobility, and its peptide map) in these tissues indicated that actin is an axonally transported protein with a maximum transport velocity of 3.4--4.3 mm/d. The kinetics of labeling actin were similar to the kinetics of labeling two proteins (M1 and M2) which resemble myosin; these myosin-like proteins were previously found to be included in the groups of proteins (groups III and IV) transported with the third and fourth most rapid maximum velocities. The similarity in transport between actin and myosin-like proteins supports the idea that a number of proteins in the third and fourth transport groups may be functionally related by virtue of their involvement in a force-generating mechanism and suggests the possibility that these proteins may be axonally transported as a preformed force-generating unit.     

Accumulation of Golgi-processed secretory proteins in an organelle of high density upon reduction of ATP concentration in rat hepatocytes.

We have previously shown that when rat hepatocytes are incubated with 4 mM azide, which reduces the intracellular ATP concentration to about 30% of its normal level, secretory proteins are reversibly arrested within the cell. Analysis of haptoglobin after 150 min of azide incubation shows that its carbohydrates have been processed by Golgi enzymes (Persson, R., Ahlstr?m, E., and Fries, E. (1988) J. Cell Biol. 107, 2503-2510). Here, we have further characterized the site of arrest. Subcellular fractionation by density gradient centrifugation showed that albumin and haptoglobin fractionated like a marker for the endoplasmic reticulum. Localization of albumin by immunoelectron microscopy showed, however, that it occurred in flattened cisternae and that the endoplasmic reticulum was devoid of the protein. A possible explanation for these results is that the azide treatment blocks transport through the Golgi complex, leading to an accumulation of secretory proteins in a pre- or early Golgi compartment of high density. This compartment could contain sufficient amounts of Golgi enzymes to carry out the observed carbohydrate processing upon prolonged incubation or possibly acquire them as an effect of the azide treatment.     

Redirecting lipoic acid ligase for cell surface protein labeling with small-molecule probes

Live cell imaging is a powerful method to study protein dynamics at the cell surface, but conventional imaging probes are bulky, or interfere with protein function, or dissociate from proteins after internalization. Here, we report technology for covalent, specific tagging of cellular proteins with chemical probes. Through rational design, we redirected a microbial lipoic acid ligase (LplA) to specifically attach an alkyl azide onto an engineered LplA acceptor peptide (LAP). The alkyl azide was then selectively derivatized with cyclo-octyne conjugates to various probes. We labeled LAP fusion proteins expressed in living mammalian cells with Cy3, Alexa Fluor 568 and biotin. We also combined LplA labeling with our previous biotin ligase labeling, to simultaneously image the dynamics of two different receptors, coexpressed in the same cell. Our methodology should provide general access to biochemical and imaging studies of cell surface proteins, using small fluorophores introduced via a short peptide tag.