Glycoforms and biological activity: where's the rub?
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Glycoproteins↗
Biomedical subjects
G S Jacob
Publications and source records attributed to G S Jacob.
The isolation by ligand affinity chromatography of a novel form of alpha-L-fucosidase from almond.
An alpha-fucosidase has been extracted from almond meal and purified 163,000-fold to apparent homogeneity using a novel affinity ligand, N-(5-carboxy-1-pentyl)-1,5-dideoxy-1,5-imino-L-fucitol, coupled to Affi-Gel 102. Substrate specificity studies demonstrate that the enzyme hydrolyzes the alpha-fucosidic linkages in Gal(beta 1----3)(Fuc(alpha 1----4]GlcNAc(beta 1----3)Gal(beta 1----4)Glc and Gal(beta 1----4)(Fuc(alpha 1----3]GlcNAc(beta 1----3)Gal(beta 1----4)Glc at similar rates but is unable to hydrolyze Fuc(alpha 1----2)Gal, Fuc(alpha 1----6)GlcNAc, or the synthetic substrate, p-nitrophenyl alpha-L-fucopyranoside. Hence, the enzyme closely resembles an alpha-fucosidase I isolated previously from a commercial preparation of partially purified almond beta-glucosidase (Ogata-Arakawa, M., Muramatsu, T., and Kobata, A. (1977) Arch. Biochem. Biophys. 181, 353-358). However, native and subunit relative molecular masses of 106,000 and 54,000 respectively, different charge and hydrophobicity properties, and the absence of stimulation by NaCl clearly distinguish this enzyme, designated alpha-fucosidase III, from other almond alpha-fucosidases reported previously.
Carbohydrate Conformation↗
Synthesis of the enantiomers of 6-epicastanospermine and 1,6-diepicastanospermine from D- and L-gulonolactone.
The synthesis of the enantiomers of 6-epicastanospermine and of 1,6-diepicastanospermine from the enantiomeric gulonolactones is reported and the structure of the former is established as (1S,6R,7R,8R,8aR)-1,6,7,8-tetrahydroxyoctahydroindolizine. The inhibitory activities of the diastereomers against the amyloglucosidase-catalysed hydrolysis of p-nitrophenyl alpha-D-glucopyranoside were investigated, and the effects of 6-epicastanospermine and of 1,6-diepicastanospermine on 14 human liver glycosidases are reported.
Glycoside Hydrolases↗
Inhibition of alpha-L-fucosidase by derivatives of deoxyfuconojirimycin and deoxymannojirimycin.
Deoxyfuconojirimycin (1,5-dideoxy-1,5-imino-L-fucitol) is a potent, specific and competitive inhibitor (Ki 1 x 10(-8) M) of human liver alpha-L-fucosidase (EC 3.2.1.51). Six structural analogues of this compound were synthesized and tested for their ability to inhibit alpha-L-fucosidase and other human liver glycosidases. It is concluded that the minimum structural requirement for inhibition of alpha-L-fucosidase is the correct configuration of the hydroxy groups at the piperidine ring carbon atoms 2, 3 and 4. Different substituents in either configuration at carbon atom 1 (i.e. 1 alpha- and beta-homofuconojirimycins) and at carbon atom 5 may alter the potency but do not destroy the inhibition of alpha-L-fucosidase. The pH-dependency of the inhibition by these amino sugars suggests very strongly that inhibition results from the formation of an ion-pair between the protonated inhibitor and a carboxylate group in the active site of the enzyme. Deoxymannojirimycin (1,5-dideoxy-1,5-imino-D-mannitol) is also a more potent inhibitor of alpha-L-fucosidase than of alpha-D-mannosidase. This can be explained by viewing deoxymannojirimycin as beta-L-homofuconojirimycin lacking the 5-methyl group. Conversely, beta-L-homo analogues of fuconojirimycin can also be regarded as derivatives of deoxymannojirimycin. This has permitted deductions to be made about the structural requirements of inhibitors of alpha- and beta-D-mannosidases.
1-Deoxynojirimycin↗
Protein dynamics from chemical shift and dipolar rotational spin-echo 15N NMR.
The partial collapse of dipolar and chemical shift tensors for peptide NH and for the amide NH at cross-link sites in cell wall peptidoglycan, of intact lyophilized cells of Aerococcus viridans, indicates NH vector root-mean-square fluctuations of 23 degrees. This result is consistent with the local mobility calculated in typical picosecond regime computer simulations of protein dynamics in the solid state. The experimental root-mean-square angular fluctuations for both types of NH vectors increase to 37 degrees for viable wet cells at 10 degrees C. The similarity in mobilities for both general protein and cell wall peptidoglycan suggests that one additional motion in wet cells involves cooperative fluctuations of segments of cell walls, attached proteins, and associated cytoplasmic proteins.
Bacterial Proteins↗
Aminosugar derivatives as potential anti-human immunodeficiency virus agents.
Recent data suggest that aminosugar derivatives which inhibit glycoprotein processing have potential anti-human immunodeficiency virus (HIV) activity. These inhibitory effects may be due to disruption of cell fusion and subsequent cell-cell transmission of the acquired immunodeficiency syndrome (AIDS) virus. Free virus particles able to bind CD4-positive cells are still produced in the presence of these compounds with only partial reduction of infectivity. We now report a method to score in parallel both the degree of antiviral activity and the effect on cell division of aminosugar derivatives. We find that (i) the compounds 1,4-dideoxy-1,4-imino-L-arabinitol and N-(5-carboxymethyl-1-pentyl)-1,5-imino-L-fucitol partially inhibit the cytopathic effect (giant cell formation, etc.) of HIV and yield of infectious virus; (ii) the compounds N-methyldeoxynojirimycin and N-ethyldeoxynojirimycin reduce the yield of infectious HIV by an order of four and three logarithms, respectively; and (iii) one compound, N-butyldeoxynojirimycin, of the 47 compounds previously screened reduces infectious viral particles by a logarithmic order greater than five at noncytotoxic concentrations. In addition, long-term growth of infected cells in the presence of N-butyldeoxynojirimycin gradually decreases the proportion of infected cells, leading to eventual elimination of HIV from culture. This result suggests that replication is associated with cytolysis. The ability to break the cycle of replication and reinfection has important implications in the chemotherapy of AIDS.
Amino Sugars↗
Metabolism of glyphosate in Pseudomonas sp. strain LBr.
Metabolism of glyphosate (N-phosphonomethylglycine) by Pseudomonas sp. strain LBr, a bacterium isolated from a glyphosate process waste stream, was examined by a combination of solid-state 13C nuclear magnetic resonance experiments and analysis of the phosphonate composition of the growth medium. Pseudomonas sp. strain LBr was capable of eliminating 20 mM glyphosate from the growth medium, an amount approximately 20-fold greater than that reported for any other microorganism to date. The bacterium degraded high levels of glyphosate, primarily by converting it to aminomethylphosphonate, followed by release into the growth medium. Only a small amount of aminomethylphosphonate (about 0.5 to 0.7 mM), which is needed to supply phosphorus for growth, could be metabolized by the microorganism. Solid-state 13C nuclear magnetic resonance analysis of strain LBr grown on 1 mM [2-13C,15N]glyphosate showed that about 5% of the glyphosate was degraded by a separate pathway involving breakdown of glyphosate to glycine, a pathway first observed in Pseudomonas sp. strain PG2982. Thus, Pseudomonas sp. strain LBr appears to possess two distinct routes for glyphosate detoxification.
Biodegradation, Environmental↗
Degradation of glyphosate by Pseudomonas sp. PG2982 via a sarcosine intermediate.
The bacterium Pseudomonas PG2982 metabolizes glyphosate (N-(phosphonomethyl)glycine) by converting it to glycine, a one-carbon unit, and phosphate. Here we show that this conversion involves the intermediate formation of sarcosine. When cells are incubated with [14C]glyphosate, the 14C can be entrapped in glycine or sarcosine. With added sarcosine, 14C from all three carbons of glyphosate is recovered solely in sarcosine. In experiments with glycine, radioactivity from the carboxymethyl moiety of glyphosate is trapped in glycine as well as serine, whereas radioactivity from the phosphonomethyl carbon is only incorporated into serine. These results are consistent with a pathway involving the conversion of glyphosate to sarcosine by cleavage of its carbon-phosphorus (C-P) bond, followed by the oxidation of sarcosine to glycine and formaldehyde.
Escherichia coli↗
Metabolism of glyphosate in an Arthrobacter sp. GLP-1.
The metabolism of glyphosate [N-(phosphonomethyl)glycine] in a bacterium tentatively identified as an Arthrobacter sp., capable of growth on this herbicide as its sole phosphorus source, has been investigated using solid-state NMR techniques as well as radiotracer analysis. The pathway involves the conversion of glyphosate to glycine, a C1 unit and phosphate. The phosphonomethyl carbon is specifically incorporated into the amino acids serine, cysteine, methionine, and histidine, as well as into purine bases and thymine, indicating the involvement of tetrahydrofolate in single-carbon transfer reactions. Glycine derived from glyphosate is utilized in purine and protein biosynthesis. This pathway for glyphosate degradation in a gram-positive bacterium is similar to that previously reported for Pseudomonas sp. PG2982 [Jacob et al. (1985) J. Biol. Chem. 260, 5899-5905] and is distinct from that reported for soil metabolism of glyphosate where aminomethylphosphonic acid has been shown to be a major metabolite. Preliminary evidence is presented which indicates that the conversion of glyphosate to glycine and the C1 unit involves the intermediate formation of sarcosine. Thus, the primary event in glyphosate degradation by Arthrobacter sp. GLP-1 is the cleavage of its C-P bound. This report constitutes the first demonstration of the metabolism of glyphosate in a gram-positive bacterium.
Arthrobacter↗
Aromatic cross-links in insect cuticle: detection by solid-state 13C and 15N NMR.
Cross-polarization magic-angle-spinning nuclear magnetic resonance spectroscopy has been used to determine insect cuticle composition and cross-link structure during sclerotization or tanning. Unsclerotized cuticle from newly ecdysed pupae of the tobacco hornworm, Manduca sexta L., had a high protein content with lesser amounts of lipid and chitin. Concentrations of chitin, protein, and catechol increased substantially as dehydration and sclerotization progressed. Analysis of intact cuticle specifically labeled with carbon-13 and nitrogen-15 revealed direct covalent linkages between ring nitrogens of protein histidyl residues and ring carbons derived from the catecholamine dopamine. This carbon-nitrogen adduct was present in chitin isolated from cuticle by alkaline extraction and is probably bound covalently to chitin. These data support the hypothesis that the stiffening of insect cuticle during sclerotization results primarily from the deposition of protein and chitin polymers and their crosslinking by quinonoid derivatives of catecholamines.
Animals↗
Solid-state NMR studies of regulation of N-(phosphonomethyl)glycine and glycine metabolism in Pseudomonas sp. strain PG2982.
Lyophilized samples of Pseudomonas sp. PG2982 grown on 13C- and 15N-labeled glyphosate have been analyzed by single and double cross-polarization 13C NMR. Both the carbon and nitrogen metabolism of glyphosate are significantly influenced by the nitrogen source used for the growth of the organism. When ammonium sulfate is the source of nitrogen, the glycyl moiety of glyphosate is utilized intact for the biosynthesis of purines and proteins. But when the organism is grown on glycine as the source of nitrogen, the carbons and nitrogen of glyphosate are scrambled, consistent with incorporation into serine and pyruvate, and hence participation in general metabolism. When both ammonium and glycine are present in the growth medium, regulation of the metabolic fluxes along each of the two major pathways appears to be determined by the intracellular glycine concentration.
Ammonia↗
Solid-state NMR studies of Klebsiella pneumoniae grown under nitrogen-fixing conditions.
The carbon and nitrogen metabolism of Klebsiella pneumoniae M5a1 has been characterized using 13C and 15N labeling with detection by cross-polarization magic-angle spinning solid-state NMR. Cells grown on ammonium typically require some 20 h to derepress fully for nitrogenase when transferred to medium devoid of any source of fixed nitrogen. We have established that during this period some cellular proteins are catabolized with the liberated nitrogen being used for the synthesis of purines needed for formation of ribosomal RNA. The 20-h derepression period can be shortened to 6 h by the introduction of fixed nitrogen in certain specific forms. Serine is the most successful agent we have examined for shortening the derepression period and glycine among the least successful. We attribute this difference to the advantage of serine over glycine in providing both specific and nonspecific carbon and nitrogen sources for complete purine synthesis. These determinations were made by tracing the metabolism of 13C- and 15N-labeled chemical bonds from the 2 amino acids during derepression.
Bacterial Proteins↗
Direct measurement of poly(beta-hydroxybutyrate) in a pseudomonad by solid-state 13C NMR.
Four narrow lines are observed in the high-resolution cross-polarization magic-angle spinning 13C NMR spectra of intact, lyophilized samples of Pseudomonas sp. LBr, in addition to the broader lines normally associated with bacterial cellular material. These narrow lines arise from poly(beta-hydroxybutyrate). The cellular carbon contained in this storage material can be measured quantitatively and nondestructively from the solid-state NMR spectra. We find that cells starved for phosphorus store up to 50% of their total carbon as poly(beta-hydroxybutyrate). When such cells are used to inoculate medium containing a source of phosphorus, all of the poly(beta-hydroxybutyrate) is metabolized by the time the culture has reached midlogarithmic growth phase.
Carbon Isotopes↗
Analysis of chitin structure by nuclear magnetic resonance spectroscopy and chitinolytic enzyme digestion.
Solid-state 13C-NMR analysis of chitin prepared from cuticle of the tobacco hornworm, Manduca sexta (L.), and of crab yielded spectra that demonstrate a high degree of chemical homogeneity (greater than 95%) for the preparations. The chemical shifts of the well-resolved carbon signals from both samples matched closely those of the monomeric unit 2-acetamido-2-deoxy-D-glucopyranoside (GlcNAc). Chromatographic analysis of products from the digestion of chitin by the binary chitinase system (endo splitting chitinase and exo splitting beta-N-acetylglucosaminidase) isolated from M. sexta molting fluid showed that the major product from both chitin preparations is GlcNAc. Also detected was a minor product (product U) that had a chromatographic retention time on the carbohydrate analysis column intermediate between those of chitin penta- and hexasaccharides. Gel filtration chromatography of U indicated that U had an apparent molecular weight intermediate between that of GlcNAc and of N,N'-diacetylchitobiose. Cation-exchange chromatography of U after acid hydrolysis revealed the presence of glucosamine only. Derivatization with trinitrobenzenesulfonate showed the presence of a free amino group in U. Solution proton and carbon NMR spectroscopy were used to identify U as a N-monoacetylchitobiose [O-beta-D-2-amino-2-deoxyglucopyranosyl- (1----4)-2-acetamido-2-deoxy-beta-D-glucopyranose] with the residue at the nonreducing end deacetylated. These studies showed that chitin prepared from alkali- and heat-treated insect or crab cuticle contains trace levels of deacetylated residues that are released as a dead-end product, N-monoacetylchitobiose, after digestion by the binary enzyme system.
Acetylglucosamine↗
Characterization of peptidoglycan stem lengths by solid-state 13C and 15N NMR.
Lyophilized whole cells of Aerococcus viridans (Gaffkya homari) grown on a synthetic medium containing D-[2-13C, 15N]Ala, or containing both L-[1-13C]Lys and D-[15N]Ala, have been examined by double cross-polarization magic-angle spinning 13C and 15N nuclear magnetic resonance. Results from the double-labeled alanine experiment confirm the absence of metabolic scrambling of alanine by A. viridans. Results from the combined single-label experiment can be used to count directly the number of adjacent L-Lys and D-Ala units in peptide chains of cell-wall peptidoglycan. This count leads to the conclusion that there are no terminal D-Ala or D-Ala-D-Ala units in uncross-linked chains of the peptidoglycan of A. viridans.
Alanine↗
The role of gastrointestinal endoscopy in a developing country.
Eight-thousand-six-hundred-and-eighty patients were examined endoscopically over a period of six years. Significant pathological lesions were detected in 79.6% of the cases. While duodenal ulcers were seen at the same frequency as in the West, the number of gastric ulcers were considerably fewer, the ratio of gastric to duodenal ulcer being 1:8.4. Gastric cancer was also observed less commonly than in the West, but gastric lymphoma constituted 21% of all gastric malignancies. By endoscoping all bleeders within 24 hours we were able to identify the source of bleeding in 90.9% of the cases, and a lesion was detected in 96.8%. Direct visualisation of the duodenal and jejunal mucosa supported by histological examination was of paramount importance in the early detection of Immunoproliferative Small Intestinal Disease (IPSID) and its differentiation from other diseases such as tuberculosis, bilharzial jejunitis and Crohn's disease which are seen in our population.
Adolescent↗
Solid-state NMR determination of glyphosate metabolism in a Pseudomonas sp.
The metabolism of the broad-spectrum herbicide, glyphosate (N-phosphonomethylglycine) in a soil Pseudomonas sp. PG2982 has been determined by cross-polarization magic-angle spinning 15N and 13C NMR of intact lyophilized cells. Using samples grown on 13C- and 15N-labeled glyphosate, we find that PG2982 does not metabolize glyphosate to aminomethylphosphonate as has been reported for mixed cultures of soil microbes. Rather, the phosphonomethyl carbon-nitrogen bond in glyphosate is cleaved, releasing glycine. Solid-state NMR analysis reveals that 20% of this glycine is used in the synthesis of purines, 35% is incorporated into protein as glycyl residues, with an additional 35% incorporated as seryl residues. The phosphonomethyl carbon of glyphosate is ultimately incorporated into a number of sites, including the C-2 and C-8 positions of the purine rings of nucleic acids, methyl groups of methionine and thymidine, and the methylene group of serine. The pattern of phosphonomethyl carbon incorporation indicates the involvement of tetrahydrofolate, a coenzyme which facilitates single-carbon transfers. This is the first complete determination of the metabolism of glyphosate in a pure culture, and the first bacterial metabolic study using both single and double cross-polarization solid-state NMR.
Biodegradation, Environmental↗
Solid-state 13C and 15N nuclear magnetic resonance studies of alanine metabolism in Aerococcus viridans (Gaffkya homari).
Transport and metabolism of D- and L-alanine by Aerococcus viridans (Gaffkya homari) have been studied using cross-polarization magic-angle spinning 13C and 15N NMR spectroscopy of lyophilized whole cells, isolated cell walls, and crude extracts. For equimolar concentrations in the growth medium, about 10 times more D-alanine than L-alanine is transported into the cells. Examination of cells labeled with D-[13C]alanine and L-[epsilon-15N]lysine by double cross-polarization magic-angle spinning 15N NMR indicates that only about 20% of the D-alanine present in cell-wall peptidoglycan comes directly from the growth medium. The rest is produced by de novo synthesis. Most of the labeled D-alanine is found within peptidoglycan precursors or inverted to L-alanyl residues of soluble proteins.
Alanine↗