The fluorinated anesthetic halothane as a potential NMR biologic probe

Fluorinated anesthetics such as halothane preferentially partition into hydrophobic environments such as cell membranes. The ¹⁹F-NMR spectrum of halothane in a rat adenocarcinoma (with known altered lipid metabolism and membrane composition) shows an altered chemical shift pattern compared to the anesthetic in normal tissue. In eight tumor samples examined, the ¹⁹F-NMR spectra exhibit two distinct resonances, compared to a single resonance observed in normal tissues. This is explained by an enhanced or altered hydrophobic component in the tumor tissue giving rise to two discrete halothane environments. Another fluorinated anesthetic, isoflurane, shows similar behavior in distinguishing normal from diseased tissue. Given the large chemical shift range of fluorine and the inherent sensitivity of this nucleus, ¹⁹F-NMR spectra of fluorinated anesthetics can also be used to follow anesthetic degradation by the liver. The ability of fluorinated anesthetics to discriminate tissues and to monitor metabolic processes is potentially useful for in vivo ¹⁹F-NMR surface coil and imaging studies.     

Nucleotide sequence of nuclear 5.7S RNA of mouse cells

Viable tumor cells were examined by ¹⁹F-NMR spectroscopy after treatment with 4-trifluoromethyl 2,6-dinitrophenyl sulphonate (CF₃-DNBS), which is an analog of 2,4,6-trinitrophenyl sulphonate (TNBS). The presence of a strong ¹⁹F-NMR signal from treated cells suggested the binding of the “probe”. Treatment of labelled cells with proteolytic enzymes significantly decreased the signals, suggesting that the label was essentially bound to the cell surface macromolecules. A proportion of the material bound to the cell was removable by dialysis of cell extracts against a structural analog, suggesting that some CF₃-DNBS-cell membrane bonds were not covalent. The existence of such non-covalent bonds has also been confirmed with soluble proteins. By the same approach, it was also found that ¹⁴C-TNBS formed covalent and non-covalent bonds with tumor cells.     

19F-NMR reveals substrate specificity of CYP121A1 in Mycobacterium tuberculosis

Cytochromes P450 are versatile enzymes that function in endobiotic and xenobiotic metabolism and undergo meaningful structural changes that relate to their function. However, the way in which conformational changes inform the specific recognition of the substrate is often unknown. Here, we demonstrate the utility of fluorine (¹⁹F)-NMR spectroscopy to monitor structural changes in CYP121A1, an essential enzyme from Mycobacterium tuberculosis. CYP121A1 forms functional dimers that catalyze the phenol-coupling reaction of the dipeptide dicyclotyrosine. The thiol-reactive compound 3-bromo-1,1,1-trifluoroacetone was used to label an S171C mutation of the enzyme FG loop, which is located adjacent to the homodimer interface. Substrate titrations and inhibitor-bound ¹⁹F-NMR spectra indicate that ligand binding reduces conformational heterogeneity at the FG loop in both the dimer and in an engineered monomer of CYP121A1. However, only the dimer was found to promote a substrate-bound conformation that was preexisting in the substrate-free spectra, thus confirming a role for the dimer interface in dicyclotyrosine recognition. Moreover, ¹⁹F-NMR spectra in the presence of substrate analogs indicate the hydrogen-bonding feature of the dipeptide aromatic side chain as a dicyclotyrosine specificity criterion. This study demonstrates the utility of ¹⁹F-NMR as applied to a multimeric cytochrome P450, while also revealing mechanistic insights for an essential M. tuberculosis enzyme.     

Structural differences between apolipoprotein E3 and E4 as measured by 19F NMR

The apolipoprotein E family contains three major isoforms (ApoE4, E3, and E2) that are directly involved with lipoprotein metabolism and cholesterol transport. ApoE3 and apoE4 differ in only a single amino acid with an arginine in apoE4 changed to a cysteine at position 112 in apoE3. Yet only apoE4 is recognized as a risk factor for Alzheimer''s disease. Here we used ¹⁹F NMR to examine structural differences between apoE4 and apoE3 and the effect of the C-terminal domain on the N-terminal domain. After incorporation of 5-¹⁹F-tryptophan the 1D ¹⁹F NMR spectra were compared for the N-terminal domain and for the full length proteins. The NMR spectra of the N-terminal region (residues 1–191) are reasonably well resolved while those of the full length wild-type proteins are broad and ill-defined suggesting considerable conformational heterogeneity. At least four of the seven tryptophan residues in the wild type protein appear to be solvent exposed. NMR spectra of the wild-type proteins were compared to apoE containing four mutations in the C-terminal region that gives rise to a monomeric form either of apoE3 under native conditions (Zhang et al., Biochemistry 2007; 46: 10722–10732) or apoE4 in the presence of 1 M urea. For either wild-type or mutant proteins the differences in tryptophan resonances in the N-terminal region of the protein suggest structural differences between apoE3 and apoE4. We conclude that these differences occur both as a consequence of the Arg158Cys mutation and as a consequence of the interaction with the C-terminal domain.     

Poliumoside,a caffeic glycoside ester from Teucrium belion

A new caffeic glycoside ester, poliumoside, has been isolated from the aerial parts of Teucrium belion. Its structure, [β-(3′,4′-dihydroxyphenyl)-ethyl]-(3,6-O-α-L-dirhamnopyranosyl)-(4-O-caffeoyl)-β-D-glucopyranoside, was established mainly by high-resolution ¹H NMR and ¹³C NMR spectroscopy.     

Metabolism and biological activity of all-trans 4,4-difluororetinyl acetate

All-trans [11-³H]4,4-difluororetinyl acetate was synthesized by treating methyl all-trans [11-³H]4-oxoretinoate with diethylaminosulfurtrifluoride, followed by reduction and acetylation of the product. After oral administration of the radioactive difluoro analog in oil to rats, difluororetinol, difluororetinyl palmitate and related esters, 4-oxoretinol, 4-oxoretinoic acid and polar conjugated derivatives were identified in the intestine, liver, kidney and / or blood. The major metabolic products were difluororetinyl palmitate and related esters, which were stored in the liver. The presence of the difluoro analog in liver oil from treated rats was confirmed by ¹⁹F-NMR spectroscopy. Neither retinol nor retinyl esters were detected as products of the metabolism of the difluoro analog. Nonetheless, all-trans difluororetinyl acetate showed 26 ± 12% of the biological activity of all-trans retinyl acetate in the rat growth assay. Presumably, the difluoro analog is active per se in growth rather than by conversion to retinol or to one of its known growth-promoting metabolites. In general, however, the difluoro analog was metabolized in a manner very similar to vitamin A. The vitamin A moiety of administered difluororetinyl acetate and retinyl acetate was poorly stored (1.8–3.3%) in the liver of vitamin A-depleted rats, confirming and extending past reports that the liver storage mechanism is severely impaired when initial liver stores are very low.     

Isolation and characterization of Hfr males in Citrobacter freundii

Citrobacter freundii Hfr donor strains were isolated from a C. freundii strain harbouring a temperature-sensitive factor F ts 114 lac ⁺, by selecting for integrative suppression of the ts 114 mutation. Three Hfr strains were characterized, which transfer their chromosomes in a linear and oriented order. The first strain transfers: O-aro ⁺-ilv ⁺-pur ⁺-thr ⁺-leu ⁺-pro ⁺, the second: O-ilv ⁺-pur ⁺-thr ⁺-leu ⁺-pro ⁺ and the third: O-ilv ⁺-aro ⁺-nad ⁺-his ⁺-pro ⁺. The whole chromosome is transferred into the recipient cell within about 145 minutes. From these results we concluded that the linkage map of C. freundii is circular. Mating-pair formation on a membrane filter resulted in more recombinants being formed as compared with mating-pair formation in liquid medium. Furthermore the mating-pairs formed on a membrane were more stable. From one Hfr strain heterogenic F-prime factors could be isolated bearing the F ts 114 lac ⁺ genes from Escherichia coli and the pur ⁺ and/or ilv ⁺ genes from C. freundii. Preliminary mapping by interrupted mating indicated that the linkage map of C. freundii is in general very similar to those of E. coli, Salmonella typhimurium and Klebsiella aerogenes.     

Uptake of bicarbonate ion in darkness by isolated chloroplast envelope membranes and intact chloroplasts of spinach

Bicarbonate uptake by isolated chloroplast envelope membranes and intact chloroplasts of spinach (Spinacia oleracea L. var. Viroflay) in darkness exhibited a similar dependency upon temperature, pH, time, and concentrations of isolated or attached envelope membranes. This similarity in uptake properties demonstrates the usefulness of the envelope membranes for the study of chloroplast permeability. Maximal rates for dark HCO₃^- uptake by isolated envelope membranes and intact chloroplasts were more than sufficient to account for the maximal rates of photosynthetic CO₂ fixation observed with intact chloroplasts. The active species involved in the uptake process was found to be HCO₃^- and not CO₂. The significance of HCO₃^- uptake and its relationship to carbonic anhydrase and ribulose diphosphate carboxylase is discussed. Conditions for maximal HCO₃^- uptake in darkness by intact chloroplasts were found to be similar to those required for maximal photosynthetic CO₂ fixation, suggesting that HCO₃^- uptake by the envelope membrane may regulate photosynthetic CO₂ fixation.     

Canna indica flower: New source of anthocyanins

In this study the red flowers of Canna indica (Cannaceae) were extracted by using sonicator and isolation of anthocyanins have been carried out. Four anthocyanin pigments have been isolated apart from quercetin and lycopene. They are Cyanidin-3-O-(6′′-O-α-rhamnopyranosyl)-β-glucopyranoside (1), Cyanidin-3-O-(6′′-O-α-rhamnopyranosyl)-β-galactopyranoside (2), Cyanidin-3-O-β-glucopyranoside (3) and Cyanidin-O-β-galactopyranoside (4). These compounds were isolated by using HPLC and their structures were subsequently determined on the basis of spectroscopic analyses, i.e., ¹H NMR, ¹³C NMR, HMQC, HMBC, ESI-MS, FTIR, UV–Visible etc. The isolated compounds showed good antioxidant activity thus makes it suitable for use in food coloration and as a nutraceutical. Thus it is a promising pigment source for food applications.     

Thinking outside the crystal: Complementary approaches for examining transporter mechanism

As the number of high-resolution structures of membrane proteins continues to rise, so has the necessity for techniques to link this structural information to protein function. In the case of transporters, function is achieved via coupling of conformational changes to substrate binding and release. Static structural data alone cannot convey information on these protein movements, but it can provide a high-resolution foundation on which to interpret lower resolution data obtained by complementary approaches. Here, we review selected biochemical and spectroscopic methods for assessing transporter conformational change. In addition to more traditional techniques, we present ¹⁹F-NMR as an attractive method for characterizing conformational change in transporters of known structure. Using biosynthetic labeling, multiple, non-perturbing fluorine-labeled amino acids can be incorporated throughout a protein to serve as reporters of conformational change. Such flexibility in labeling allows characterization of movement in protein regions that may not be accessible via other methods.     

The protein patterns of intracytoplasmic membranes and reaction center particles isolated fromRhodopseudomonas capsulata

Intracytoplasmic membranes of wild type strain 37 b 4 and mutant strains A1a car^-bchl^-, A1a car^-bchl⁺ ofRhodopseudomonas capsulata were isolated. The membrane proteins were solubilized and separated by polyacrylamide gel electrophoresis (methods of Takayamaet al., 1964; Weber and Osborn, 1969). The band patterns were compared with each other. From the strain A1a car^-bchl⁺ reaction center particles were isolated by treatment of membrane with Triton X-100 followed by sucrose density gradient centrifugation. The reaction center particles were found to be enriched in reaction center bacteriochlorophyll. This pigment shows a reversible bleaching at 855 nm and a blue shift at 798 nm. The light harvesting bacteriochlorophyll portion of this fraction was 14–22% of the total bacteriochlorophyll content. The three main proteins of the reaction center particles amount to about 80% of the total protein of the particles. The molecular weights of the main proteins were estimated to be 32000, 27500 and 22500 daltons.     

色氨酸类似物标记法研究DsbA蛋白的结构环境

用生物标记的方法将色氨酸类似物标记在DsbA蛋白中的色氨酸位置,分析标记蛋白质的谱学性质、色氨酸结构环境和潜在应用前景.5-OH-Trp标记的DsbA蛋白具有315 nm激发的荧光发射光谱;¹⁹F-NMR 能分辨5-F-Trp标记的DsbA蛋白的两个F-Trp残基(Trp76和Trp126),Trp76化学位移变化反映二硫键交换引起的结构转化.进一步将利用标记蛋白的独特荧光和¹⁹F-NMR性质,研究DsbA蛋白的氧化还原及与底物蛋白的结合作用.     

Halo lipids. V. Synthesis,nuclear magnetic resonance spectra and cytostatic properties of halo analogues of alkyllysophospholipids

A series of fluorine- and chlorine-containing analogues of alkyllysophospholipids has been synthesised as potential antimetabolites of phospholipids. These compounds include various structural isomers of racemic long-chain alkyldeoxyhaloglycerophosphocholines and N,N-dimethylethanolamines, alkyldeoxyhaloglycerophosphoric acids, and alkyl esters. ¹H- and ¹⁹F-NMR spectroscopic data are presented and analysed. Alkyldeoxyhaloglycerophosphocholines were found to exhibit a strong inhibitory effect on the proliferation of Ehrlich ascites carcinoma cells in vitro.     

Oritavancin Binds to Isolated Protoplast Membranes but not Intact Protoplasts of Staphylococcus aureus

Solid-state NMR has been used to examine the binding of N′-4-[(4-fluorophenyl)benzyl)]chloroeremomycin, a fluorinated analogue of oritavancin, to isolated protoplast membranes and whole-cell sucrose-stabilized protoplasts of Staphylococcus aureus, grown in media containing [1-¹³C]glycine and l-[?-¹⁵N]lysine. Rotational-echo double-resonance NMR was used to characterize the binding by estimating internuclear distances from ¹⁹F of oritavancin to ¹³C and ¹⁵N labels of the membrane-associated peptidoglycan and to the ³¹P of the phospholipid bilayer of the membrane. In isolated protoplast membranes, both with and without 1 M sucrose added to the buffer, the nascent peptidoglycan was extended away from the membrane surface and the oritavancin hydrophobic side chain was buried deep in the exposed lipid bilayer. However, there was no N′-4-[(4-fluorophenyl)benzyl)]chloroeremomycin binding to intact sucrose-stabilized protoplasts, even though the drug bound normally to the cell walls of whole cells of S. aureus in the presence of 1 M sucrose. As shown by the proximity of peptidoglycan-bridge ¹³C labels to phosphate ³¹P, the nascent peptidoglycan of the intact protoplasts was confined to the membrane surface.     

Agglutination factor in the cell body of Chlamydomonas eugametos

Chlamydomonas eugametos gametes agglutinate via the surfaces of their flagella. The mating-type minus (mt ^-) agglutination factor is a high-molecular-weight glycoprotein called PAS-1.2, present on the exterior surface of the flagellar membrane. During flagellar regeneration, mt ^- gametes were able to agglutinate as soon as the flagella protruded as short stumps. This was also observed when protein synthesis was blocked, indicating that gametes possess a pool of PAS-1.2. When the exterior surface of flagella-less gametes was extracted and the proteins were subjected to gel electrophoresis, large quantities of PAS-1.2 were detected. Using anti-PAS-1.2 serum, the presence of PAS-1.2-like material was visualized on the plasma membrane of mt ^- gamete cell bodies. By assaying the biological activity of extracts of the cell bodies and of isolated flagella, it was calculated that the plasma membrane of the cell bodies contains 25 times the activity present in the flagella and could, therefore, represent a large pool of mt ^- agglutination factor.     

The distribution of phosphatidylinositol in microsomal membranes from rat liver after biosynthesis de novo. Evidence for the existence of different pools of microsomal phosphatidylinositol by the use of phosphatidylinositol-exchange protein

1. The phosphatidylinositol-exchange protein from bovine brain was used to determine to what extent phosphatidylinositol in rat liver microsomal membranes is available for transfer. 2. The microsomal membranes used in the transfer reaction contained either phosphatidyl[2-³H]inositol or ³²P-labelled phospholipid. The ³²P-labelled microsomal membranes were isolated from rat liver after an intraperitoneal injection of [³²P]P_i. The ³H-labelled microsomal membranes and rough- and smooth-endoplasmic-reticulum membranes were prepared in vitro by the incorporation of myo-[2-³H]inositol into phosphatidylinositol by either exchange in the presence of Mn²⁺ or biosynthesis de novo in the presence of CTP and Mg²⁺. 3. Tryptic or chymotryptic treatment of the microsomes impaired the biosynthesis de novo of phosphatidylinositol. It was therefore concluded that the biosynthesis of phosphatidylinositol and/or its immediate precursor CDP-diacylglycerol takes place on the cytoplasmic surface of the microsomal membrane. 4. Under the conditions of incubation 42% of the microsomal phosphatidyl[2-³H]inositol was transferred with an estimated half-life of 5min; 38% was transferred with an estimated half-life of about 1h; the remaining 20% was not transferable. Identical results were obtained irrespective of the method of myo-[2-³H]inositol incorporation. 5. Both measurement of phosphatidylinositol phosphorus in the microsomes after transfer and the transfer of microsomal [³²P]phosphatidylinositol indicate that phosphatidyl[2-³H]-inositol formed by exchange or biosynthesis de novo was homogeneously distributed throughout the microsomal phosphatidylinositol. 6. We present evidence that the slowly transferable pool of phosphatidylinositol does not represent the luminal side of the microsomal membrane; hence we suggest that this phosphatidylinositol is bound to membrane proteins.     

Spliceosome Sm proteins D1, D3, and B/B' are asymmetrically dimethylated at arginine residues in the nucleus

We report a novel modification of spliceosome proteins Sm D1, Sm D3, and Sm B/B′. L292 mouse fibroblasts were labeled in vivo with [³H]methionine. Sm D1, Sm D3, and Sm B/B′ were purified from either nuclear extracts, cytosolic extracts or a cytosolic 6S complex by immunoprecipitation of the Sm protein-containing complexes and then separation by electrophoresis on a polyacrylamide gel containing urea. The isolated Sm D1, Sm D3 or Sm B/B′ proteins were hydrolyzed to amino acids and the products were analyzed by high-resolution cation exchange chromatography. Sm D1, Sm D3, and Sm B/B′ isolated from nuclear fractions were all found to contain ω-N^G-monomethylarginine and symmetric ω-N^G,N^G′-dimethylarginine, modifications that have been previously described. In addition, Sm D1, Sm D3, and Sm B/B′ were also found to contain asymmetric ω-N^G,N^G-dimethylarginine in these nuclear fractions. Analysis of Sm B/B′ from cytosolic fractions and Sm B/B′ and Sm D1 from cytosolic 6S complexes showed only the presence of ω-N^G-monomethylarginine and symmetric ω-N^G,N^G′-dimethylarginine. These results indicate that Sm D1, Sm D3, and Sm B/B′ are asymmetrically dimethylated and that these modified proteins are located in the nucleus. In reactions in which Sm D1 or Sm D3 was methylated in vitro with a hemagglutinin-tagged PRMT5 purified from HeLa cells, we detected both symmetric ω-N^G,N^G′-dimethylarginine and asymmetric ω-N^G,N^G-dimethylarginine when reactions were done in a Tris/HCl buffer, but only detected symmetric ω-N^G,N^G′-dimethylarginine when a sodium phosphate buffer was used. These results suggest that the activity responsible for the formation of asymmetric dimethylated arginine residues in Sm proteins is either PRMT5 or a protein associated with it in the immunoprecipitated complex.     

Preparation,characterization, biological activity and metabolism of all-trans retinoyl fluoride

All-trans retinoyl fluoride was prepared by treating all-trans retinoic acid with diethylaminosulfurtrifluoride. The crystalline product, which was characterized by melting point, infrared, ¹H-NMR, ¹⁹F-NMR and elementary analysis, showed λ_max at 382 nm in hexane (ε = 4.98·10⁴ M^?1·cm^?1) and at 392 nm in methanol (ε = 4.60·10⁴ M^?1·cm^?1). Its biological activity in the rat growth assay, relative to all-trans retinyl acetate, was 22% ± 10%. Upon oral administration for 5 days to vitamin A-depleted rats, retinoyl fluoride (1020 μg) was rapidly metabolized to a polar metabolite fraction and, in the intestine, to an unstable retinol-like metabolite, purpotedly 15-fluororetinol. Upon administering intraperitoneally smaller doses (47–94 μg) of [11-³H]retinoyl fluoride, which was synthesized from [11-³H] retinoic acid, radioactive retinoic acid was noted in the liver and plasma but not in the intestine. As expected, a radioactive polar fraction appeared in the intestine and liver, but radioactive retinol, retinyl ester and some common oxidation products were not detected. Of the administered radioactivity, 72% was excreted in the urine, and only 4% was found in the feces over a 7-day period. Hydrolysis of the urine gave a radioactive fraction with a polarity similar to that of retinoic acid. Retinoyl fluoride also reacts readily with glycine to yield N-retinoyl glycine. Thus, the biological activity of retinoyl fluoride can be attributed to the formation of retinoic acid, probably by way of N-retinoyl derivatives. A possible pathway for its metabolism is presented.     

Action of the multifunctional peptide BP100 on native biomembranes examined by solid-state NMR

Membrane composition is a key factor that regulates the destructive activity of antimicrobial peptides and the non-leaky permeation of cell penetrating peptides in vivo. Hence, the choice of model membrane is a crucial aspect in NMR studies and should reflect the biological situation as closely as possible. Here, we explore the structure and dynamics of the short multifunctional peptide BP100 using a multinuclear solid-state NMR approach. The membrane alignment and mobility of this 11 amino acid peptide was studied in various synthetic lipid bilayers with different net charge, fluidity, and thickness, as well as in native biomembranes harvested from prokaryotic and eukaryotic cells. ¹⁹F-NMR provided the high sensitivity and lack of natural abundance background that are necessary to observe a labelled peptide even in protoplast membranes from Micrococcus luteus and in erythrocyte ghosts. Six selectively ¹⁹F-labeled BP100 analogues gave remarkably similar spectra in all of the macroscopically oriented membrane systems, which were studied under quasi-native conditions of ambient temperature and full hydration. This similarity suggests that BP100 has the same surface-bound helical structure and high mobility in the different biomembranes and model membranes alike, independent of charge, thickness or cholesterol content of the system. ³¹P-NMR spectra of the phospholipid components did not indicate any bilayer perturbation, so the formation of toroidal wormholes or micellarization can be excluded as a mechanism of its antimicrobial or cell penetrating action. However, ²H-NMR analysis of the acyl chain order parameter profiles showed that BP100 leads to considerable membrane thinning and thereby local destabilization.     

Rapid Synthesis of 2′ and 3′ Fluorinated Nucleotides and Their Use in 19F-NMR-Spectroscopy of Nucleotide-Binding Enzymes

Abstract

Improved methods have been developed for the syntheses of nucleoside analogs with fluorine atoms in the furanose moiety. 5′-O-mono and triphosphates of these analogs were used in stuctural studies on adenylate kinase using ¹⁹F-NMR.