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PubMed1975

Structural determination of the sialic acid polysaccharide antigens of Neisseria meningitidis serogroups B and C with carbon 13 nuclear magnetic resonance.

The application of 13-C nuclear magnetic resonance to the analysis of some sialic acid-containing meningococcal polysaccharide antigens is described. Complete assignments of the spectra of both the native serogroup B and the de-O-acetylated serogroup C polysaccharides have been made. These assignments were based on the corresponding data for some related monomers (sialic acid and its alpha-and beta-methylglycosides) and on supportive chemical evidence. The data indicate that the serogroup B polysaccharide is a 2 yields 8-alpha-linked homopolymer of sialic acid, identical in structure with colominic acid from Escherichia coli, whereas the de-O-acetylated serogroup C polysaccharide is a 2 yield 9-alpha-linked homopolymer. The native serogroup C polysaccharide is O-acetylated (1.16 mol of O-acetyl per sialic acid residue), all the O-acetyl substituents being located only at C-7 and C-8 of the sialic acid residues, and in addition contains unacetylated residues (24%). The polysaccharide contains di-O-acetylated residues (O-acetyl on C-7 and C-8), and at least one of the possible monoacetylated residues at C-7 or C-8.

Antigens, Bacterial↗
PubMed1990

Human immunodeficiency virus reverse transcriptase. Substrate and inhibitor kinetics with thymidine 5'-triphosphate and 3'-azido-3'-deoxythymidine 5'-triphosphate.

3'-Azido-3'-deoxythymidine 5'-triphosphate (AZTTP) was an efficient substrate for the human immunodeficiency virus 1 reverse transcriptase. It was incorporated into both homopolymer and defined sequence DNA-primed RNA templates and DNA-primed DNA templates. The substrate and inhibitor kinetics of both AZTTP and dTTP were dependent on the template-primer and reaction conditions used. dTMP was incorporated into poly(rA).oligo(dT) and into a defined sequence DNA-primed RNA template (when the other three 2'-deoxynucleoside 5'-triphosphates were present) as a conventional substrate, with steady-state Km values of 5-10 microM. The results suggest that the reverse transcriptase was capable of processive DNA polymerization on these DNA-primed RNA templates. In contrast, in the absence of the other three 2'-deoxynucleoside 5'-triphosphates, the time course for incorporation of dTMP into the same defined sequence DNA-primed RNA template was biphasic. A burst of product formation was observed followed by a slow steady-state rate with a Km value of 0.082 microM. AZTMP incorporation into poly(rA).oligo(dT) and into the defined sequence DNA-primed RNA template produced similar biphasic time courses and steady-state Km values. These results were consistent with rate-limiting dissociation of the polymerase.template-primer complex after "forced" termination of polymerization. AZTMP and dTMP were both incorporated into the homopolymer DNA-primed DNA template, poly(dA).oligo(dT), and a defined sequence DNA-primed DNA template as conventional substrates. Their Km values were similar (2-10 microM). The absence of biphasic time courses suggested that dissociation of the DNA-primed DNA templates from the enzyme, after forced termination, was not rate-limiting. This was consistent with a more distributive mode of DNA polymerization. With the defined sequence template-primers and poly(dA).oligo(dT), Ki values for both dTTP and AZTTP were comparable to their Km values. Thus, AZTTP appeared to be a simple competitive substrate-inhibitor with respect to dTTP. AZTTP inhibition of dTMP incorporation into poly(rA).oligo(dT) was linear competitive at low concentrations (0-100 nM) of AZTTP (Ki = 35 nM) but became hyperbolic (decreasing potency) at concentrations of AZTTP above this range. A mechanism for this nonlinear inhibition is discussed.

Antiviral Agents↗
PubMed1991

Enantio- and meso-oligodeoxyribonucleotides.

As sugar-modified oligodeoxyribonucleotides, L-homooligomers (L-dA12 and L-dT12) and a L/D-alternative oligomer ((L-dA-D-dA)6) were synthesized. These oligomers were quite resistant towards phosphodiesterase degradations. L-dA12 formed complexes with poly(dT) and poly(U) at 0 degree C with different stabilities, on the other hand L-dT12 did not show obvious hypochromicities after mixing with complementary natural homopolymers. An alternative sequence, (L-dA-D-dA)6, interacted with both type homopolymers and stabilities of the complexes increased compared to that of L-dA12.

Oligodeoxyribonucleotides↗
PubMed1991

Ubiquitin conjugation by the yeast RAD6 and CDC34 gene products. Comparison to their putative rabbit homologs, E2(20K) AND E2(32K).

The recombinant yeast RAD6 and CDC34 gene products were expressed in Escherichia coli extracts and purified to apparent homogeneity. The physical and catalytic properties of RAD6 and CDC34 were similar but distinct from their putative rabbit reticulocyte homologs, E2(20k) and E2(32k), respectively. Like their reticulocyte counterparts, RAD6 and CDC34 are bifunctional enzymes competent in both ubiquitin:protein ligase (E3)-independent and E3-dependent conjugation reactions. RAD6 and E2(20k) exhibit marked specificity for the conjugation of core histones and catalyze the processive ligation of up to three ubiquitin moieties directly to such model substrates. RAD6 differed from its putative E2(20k) homolog in exhibiting simple saturation behavior in the kinetics of histone conjugation and in being unable to distinguish kinetically between core histones H2A and H2B, yielding identical values of kcat (1.9 min-1) and Km (20 microM). A slow rate of multiubiquitination involving formation of extended ubiquitin homopolymers on the histones was also observed with RAD6 and E2(20k). Comparison of conjugate patterns among native, reductively methylated, and K48R ubiquitin variants demonstrated that the linkage between ubiquitin moieties formed by E2(20k) and RAD6 was not through Lys-48 of ubiquitin, the site previously demonstrated as a strong signal for degradation of the target protein. In contrast, CDC34 differs from its putative homolog, E2(32k), in showing a specificity for conjugation to bovine serum albumin rather than to core histones. Both CDC34 and E2(32k) exhibit a marked kinetic selectivity for processive multiubiquitination via Lys-48 of ubiquitin. Calculations based on a model ubiquitin conjugation reaction indicated that E2(32k) and CDC34 preferentially catalyzed multiubiquitination over ligation of the polypeptide directly to target proteins. Formation of such multiubiquitin homopolymers by E2(32k) and CDC34 suggests these enzymes may commit their respective target proteins to degradation via an E3-independent pathway.

Animals↗
PubMed1977

Artificial hybrid protein containing a toxic protein fragment and a cell membrane receptor-binding moiety in a disulfide conjugate. I. Synthesis of diphtheria toxin fragment A-S-S-human placental lactogen with methyl-5-bromovalerimidate.

In order to study the mechanism of entry of plant seed and bacterial toxins into mammalian cells, methods have been developed to synthesize artificial protein hybrid conjugates containing a moiety which binds to a cell membrane receptor and an active fragment of a toxin protein. Utilizing methyl-5-bromovalerimidate, a disulfide cross-linked conjugate of human placental lactogen (hPL) and diphtheria toxin fragment A (toxin A) was synthesized. The reagent was prepared from 5-bromovaleryl nitrile by Pinner synthesis and then used to amidinate hPL. The bromo group thus introduced was converted to S-sulfonate by nucleophilic displacement with 1 M aqueous sodium thiosulfate at room temperature overnight. The S-sulfonated hPL reacted readily with the-SH gorup of reduced toxin A to form a 1 mol/mol of disulfide conjugate in high yield. Thus when reduced toxin A was incubated with a 4-fold excess of the hPL S-sulfonate at 4 degrees and pH 6.5 for 120 h, a conjugate yield of 50% relative to the toxin A input was obtained. Homopolymer formation was negligible and the product was purified by gel filtration on Sephadex G-150. Purity of the conjugate estimated by quantitative analysis of sodium dodecyl sulfate gels was 90%. The toxin A-hPL conjugate retained the activities of both toxin A and hPL, as reported in the accompanying paper. This method of preparing protein hybrid conjugates appeared to have advantages over previous methods utilizing bifunctional reagents with respect to both yield and freedom from homopolymer formation.

Animals↗
PubMed1990

The multisubunit structure of synaptophysin. Relationship between disulfide bonding and homo-oligomerization.

Synaptophysin, a major membrane protein of synaptic vesicles, contains four transmembrane regions and two intravesicular loops. Synaptophysin monomers associate into homopolymers that have the potential to form channels in the synaptic vesicle membrane. Here we show that in native synaptophysin, homopolymers are linked by noncovalent forces. The molecule contains unstable intramolecular disulfide bonds that undergo disulfide exchange during solubilization, thereby covalently cross-linking neighboring synaptophysin molecules. The locations of the intramolecular disulfide bonds in synaptophysin were determined, revealing that each of the two intravesicular loops of synaptophysin is circularized by a single disulfide bond. Cross-linking of synaptophysin by disulfide bonds can be triggered in synaptic vesicles and in intact cells by a cycle of reduction and oxidation, suggesting that native synaptophysin is a homomultimer in situ. In addition, chemical cross-linking of native synaptophysin demonstrates that a low molecular weight protein is specifically associated with synaptophysin complexes and is lost upon reduction of the intramolecular disulfide bonds. These data suggest that native synaptophysin forms a noncovalent homomultimeric complex whose structure and interaction with other proteins are dependent on the integrity of its intramolecular disulfide bonds and phospholipid environment.

Adrenal Gland Neoplasms↗
PubMed1990

Kinetics of the binding of mitoxantrone, ametantrone and analogues to DNA: relationship with binding mode and anti-tumour activity.

The kinetics of association and dissociation of DNA complexes of the anti-tumour agents mitoxantrone, ametantrone and related 1,4-bis(alkylamino)anthraquinones have been determined by stopped-flow spectrophotometry, in order to study relationships between structure, kinetic parameters and biological activity. Variations in the structure of the side chains of ametantrone analogues had little effect on the kinetic stability of the complexes, but the mitoxantrone complexes dissociated about an order of magnitude more slowly, suggesting an important role for the two hydroxyl groups on the chromophore of the latter compound. The results are consistent with other n.m.r. and molecular mechanics data, which suggest a binding model where the chromophore intercalates perpendicularly to the DNA base pair axis. Dissociation studies with DNA homopolymers of varying base composition suggest the kinetic mechanism is a mixed parallel/sequential one, with the slowest dissociation processes being from GC-rich sites in both homopolymers and natural DNA. The results suggest guidelines for the design of more tumour-active analogues of the class.

Animals↗
PubMed1975

A DNA polymerase from embryos of Drosophila melanogaster. Purification and properties.

The more than 2,300-fold purification of a DNA polymerase from the embryos of Drosophila melanogaster is described. The enzyme, which forms a single band on gel electrophoresis, has a molecular weight of about 87,000 and a pH optimum of 8.5. A divalent metal is required for activity, Mg2+ being preferred with activated DNA, Mn2+ with homopolymer template-primers. The enzyme is inactivated completely by mercurials; polyamines are also inhibitory with certain templates. The most efficient template-primer is activated DNA, but homopolymers such as poly(dA)-oligo(dT), poly(A)-oligo(dT), and poly(A)-oligo(U) are also utilized with high efficiency. The purified enzyme preparations appear to be devoid of nuclease activity when assayed directly with suitable substrates. In addition, neither primer nor product is degraded after prolonged incubation with the enzyme. In accordance with previous observations on other DNA polymerases, the Drosophila enzyme can replicate single-stranded DNA only under conditions of simultaneous transcription by RNA polymerase.

Ammonium Sulfate↗
PubMed1987

Contribution of the mannan O side-chains to the adjuvant action of lipopolysaccharides.

Klebsiella 03 lipopolysaccharide (LPS) and Escherichia coli 09 LPS were previously shown to have potent adjuvant activities in augmenting antibody response and delayed-type hypersensitivity to protein antigens. The R form LPS extracted from the O-specific polysaccharide-less mutants derived from Klebsiella 03 and E. coli 09 strains were characterized by chemical and electrophoretic analyses. The adjuvant activities of the R-LPS in augmenting antibody response and DTH to protein antigens were much weaker than those of the parental LPS. The strength of the adjuvant activities of the R-LPS was similar to that of the activities of Salmonella minnesota LPS and Ra-LPS. By contrast, polyclonal B-cell activation effects of the R-LPS were stronger than those of the parental LPS. The common feature of the parental LPS is that their O-specific polysaccharides are mannose homopolymers (mannans). From these results, it is suggested that mannose homopolymers as the O side-chains of LPS contribute to the action of LPS in enhancing strongly the T-cell dependent immune responses to protein antigens.

Adjuvants, Immunologic↗
PubMed1989

[In vitro anti-HIV activity of phosphorothioate alpha-anomeric oligodeoxynucleotides].

Oligonucleotide analogs consisting exclusively of alpha-anomeric deoxynucleoside units bridged with phosphorothioate linkages have been synthesized and tested in vitro as antiviral agents against human immunodeficiency virus (HIV) in human T cells. Two 28-mers, an homopolymer alpha-S-dC28 and an oligomer alpha-S-anti-rev complementary to the initiation site of the regulatory viral gene rev exhibited antiviral activities comparable to those reported for the corresponding beta-anomeric phosphorothioate analogs. In contrast, a nuclease-resistant homopolymer, alpha-dC28 was inactive. Their preliminary results would indicate that the origin of oligonucleotide phosphorothioate anti-HIV activity is not exclusively correlated with their higher nuclease resistance.

Base Sequence↗
PubMed1989

Mechanism of mRNA binding to bovine mitochondrial ribosomes.

The binding of mRNA to bovine mitochondrial ribosomes was investigated using triplet codons, homopolymers and heteropolymers of various lengths, and human mitochondrial mRNAs. In the absence of initiation factors and initiator tRNA, mitochondrial ribosomes do not bind triplet codons (AUG and UUU) or homopolymers (oligo(U] shorter than about 10 nucleotides. The RNA binding domain on the 28 S mitoribosomal subunit spans approximately 80 nucleotides of the mRNA, judging from the size of the fragments of poly(U,G) and natural mRNAs protected from RNase T1 digestion by this subunit, but the major binding interaction with the ribosome appears to occur over a 30-nucleotide stretch. Human mitochondrial mRNAs coding for subunits II and III of cytochrome c oxidase and subunit 1 of the NADH-ubiquinone oxidoreductase (complex I) were used in studying in detail the binding of mRNA to the small subunit of bovine mitochondrial ribosomes. We have determined that these mRNAs have considerable secondary structure in their 5'-terminal regions and that the initiation codon of each mRNA is sequestered in a stem structure. Little mRNA was bound to ribosomes in a manner conferring protection of the 5' termini from RNase T1 digestion, under standard conditions supporting the binding of artificial templates, but such binding was greatly stimulated by the addition of a mitochondrial extract. Initiation factors and tRNAs from Escherichia coli were unable to stimulate the 5' terminus protected binding of these mRNA molecules, demonstrating a requirement for homologous factors. Our results strongly suggest that mitochondrial initiation factors are required for the proper recognition and melting of the secondary structure in the 5'-terminal region of mitochondrial mRNAs, as a prerequisite for initiation of protein synthesis in mammalian mitochondria.

Animals↗
PubMedDate not supplied

[Molecular weight distribution of polymeric DNA-products, formed upon the action of matrix enzymes].

Models of processive and distributive DNA synthesis and degradation catalysed by matrix enzymes were investigated. Distribution of polymer products dependent on the reaction model chosen, on the type of the matrix and on the enzyme-matrix initial concentration ratio were determined by methods of numerical modeling. Conditions were found where the scattering of the reaction polymer products was minimal. The homopolymer matrix choice of experimental condition may generate a distribution of product that obeys the Poisson distribution. Numerical investigations of polymerization (hydrolysis) processes showed that for a number of heteropolymer matrixes a distribution may exist with scattering much less than that for homopolymer matrixes. Conditions are found when processive and distributive models give different distributions of the reaction product.

Base Sequence↗
PubMedDate not supplied

[Parallel DNA double helices. II. Conformational analysis of regular helices having a second order axis of symmetry].

Conformational analysis of double helices of DNA with parallel arranged sugar-phosphate chains connected by twofold symmetry has been performed. Homopolymers poly(dA).poly(dA), poly(dC).poly(dC), poly(dG).poly(dG) and poly(dT).poly(dT) were studied. For each of the homopolymers all variants of H-bond pairing were checked. The maps of closing of sugar-phosphate backbone were previously computed. By the optimization of potential energy the dihedral angles and helix parameters of relatively stable conformations of parallel stranded polynucleotides were calculated. The dependence of conformational energy on the nucleic base character and the base pair type were studied. Two main conformational regions for favourable "parallel" helix of polynucleotides were found. The former of these two regions coincide with the region of typical conformational parameters of B-DNA. On an average the conformational energy of "parallel" DNA is close to the energy of canonic "antiparallel" B-DNA.

DNA↗
PubMed1989

Recognition of (dG)n.(dC)n sequences by endonuclease G. Characterization of the calf thymus nuclease.

We report the purification of endonuclease G (Ruiz-Carrillo, A., and Renaud, J. (1987) EMBO J. 6, 401-407) from calf thymus nuclei and whole tissue. The enzyme has been enriched 29,000-fold, and the activity was unambiguously identified with a 26-kDa protein after renaturation following sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The native nuclease behaves as a 50-kDa species by gel filtration, suggesting that it is composed of two subunits, presumably identical. In terms of absolute amounts, endonuclease G (endo G) is a nuclear enzyme although it was also detected in purified mitochondria. Endo G is highly specific for (dG)n.(dC)n tracts in DNA, nicking either strand of relaxed substrates with similar kinetics. The sensitivity of the homopolymer tracts is proportional to their length (from n = 8 to 29), insofar as the flanking sequences are constant. However, the overall rate of cleavage is influenced by the composition of the flanking DNA. Minor cleavage sites contain shorter (dG)n.(dC)n clusters (n = 3-7). Endo G efficiently cleaves (dC)n but not (dG)n runs in single-stranded DNA, suggesting that it may recognize an asymmetric strand conformation of the homopolymer tracts. Endo G does not recognize other homo(co)-polymer sequences or cruciform structures in DNA.

Animals↗
PubMed1988

Murine immune response to the Neisseria meningitidis group C capsular polysaccharide. II. Specificity.

As a means of further understanding the regulation of diversity and the development of protective immunity to the Neisseria meningitidis group C capsular polysaccharide (MCPS), we have generated and characterized, in detail, a panel of mAb against MCPS, a homopolymer of alpha(2----9)-sialic acid. Whereas the serum response to MCPS is restricted to the IgM and IgG3 isotypes, the panel of mAb includes, in addition, both IgG1 and IgG2b. Among 15 mAb of four isotypes, seven different specificities were observed based on direct binding in a fluorescence ELISA and precipitation in gel. Although all the mAb were derived from mice immunized with bacteria encapsulated with the native MCPS (strain C11), only 7 of 15 reacted with MCPS alone. Seven of 15 reacted with a natural O-acetyl-negative variant (OAc-, strain MC19) polysaccharide as well as with MCPS. Five of these reacted as much as 3 logs better with OAc- than MCPS and the other two reacted better with MCPS than OAc-. One mAb appeared to be alpha(2----9)-linkage specific as it reacted not only with MCPS and OAc-, but also with the capsular polysaccharide of Escherichia coli K92, a polymer of sialic acid linked alternately alpha(2----8) and alpha(2----9). None of the mAb reacted with the capsular polysaccharide of E. coli K1, a homopolymer of alpha(2----8)-sialic acid. In general, there was a good correlation between the ability to precipitate Ag in gel and to agglutinate bacteria; however, 3 of 15 mAb, all IgG3, did not conform to this rule in that they precipitated Ag but did not agglutinate bacteria of the relevant capsular specificity. Antibodies of both IgM and IgG isotypes and of both major specificities, MCPS-specific and those binding MCPS and OAc-, were bactericidal for strain C11, whereas only those reactive with OAc- were able to kill strain MC19.

Agglutination Tests↗
PubMed1988

Mechanism of ferritin iron uptake: activity of the H-chain and deletion mapping of the ferro-oxidase site. A study of iron uptake and ferro-oxidase activity of human liver, recombinant H-chain ferritins, and of two H-chain deletion mutants.

To study the functional differences between human ferritin H- and L-chains and the role of the protein shell in the formation and growth of the ferritin iron core, we have compared the kinetics of iron oxidation and uptake of ferritin purified from human liver (90% L) and of the H-chain homopolymer overproduced in Escherichia coli (100% H). As a control for iron autocatalytic activity, we analyzed the effect of Fe(III) on the iron uptake reaction. The results show that the H-chain homopolymer has faster rates of iron uptake and iron oxidation than liver ferritin in all the conditions analyzed and that the difference is reduced in the conditions in which iron autocatalysis in high: i.e. at pH 7 and in presence of iron core. We have also analyzed the properties of two engineered H-chains, one lacking the last 22 amino acids at the carboxyl terminus and the other missing the first 13 residues at the amino terminus. These mutant proteins assemble in ferritin-like proteins and maintain the ability to catalyze iron oxidation. The deletion at the carboxyl terminus, however, prevents the formation of a stable iron core. It is concluded that the ferritin H-chain has an iron oxidation site which is separated from the sites of iron transfer and hydrolysis and that either the integrity of the molecule or the presence of the amino acid sequences forming the hydrophobic channel is necessary for iron core formation.

Chromosome Deletion↗
PubMed1986

Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides.

The enzyme exonuclease I from Escherichia coli hydrolyzes successive nucleotides from the 3'-termini of single-stranded deoxyribonucleotide homopolymers. When the reaction is stopped after partial hydrolysis, only intact starting material and small oligomers can be isolated. The distribution of oligomeric products varies with the base composition of the polymer but the largest oligomer that can be isolated from the reaction of exonuclease I with homopolymers of deoxyadenylate, deoxythymidylate, or deoxycytidylate is a decamer. These results suggest a model in which exonuclease I possesses at least two nucleotide binding sites. When both sites are filled, with 11-mers and longer polymers, the enzyme does not dissociate from the polymer during hydrolysis. When, with smaller oligomers, only a single site is filled, the reaction partitions at each oligomer between hydrolysis and dissociation. The kinetics of the reactions of exonuclease I with purified polydeoxyriboadenylates of defined size distributions have been investigated. The maximum rates of hydrolysis are nearly independent of polymer size while the apparent Michaelis constants are inversely proportional to the polymer size. A simple steady state model yields a kinetic equation that is consistent with our results. Competition experiments indicate that the rate at which exonuclease I associates with the 3'-terminus of a polydeoxyribonucleotide is independent of the polymer's chain length.

Binding Sites↗
PubMed1982

Chemically related antigens compete for presentation by accessory cells to T cells.

Immune responsiveness of guinea pigs to dinitrophenyl-poly-L-lysine (DNP-PLL) and to the lysine-rich random copolymer of L-glutamic acid and L-lysine (GL) are both controlled by the "poly-L-lysine gene." We demonstrate that accessory cells of responder strains can be made incapable of presenting DNP-PLL to response T cells in assays for proliferation by in vitro exposure of the cells to GL before and during their exposure to DNP-PLL. The inhibition was not rapidly reversible, because GL preexposed accessory cells that were cultured for 2 hr in GL-free medium were still refractory to pulsing with DNP-PLL. In contrast, DNP-PLL had only a moderate inhibitory effect on accessory cell presentation of GL. Unconjugated poly- and oligo-lysines also inhibited the ability of accessory cells to present DNP-PLL, but inhibitory activity was displayed only by homopolymers containing eight to 12 or more residues in the chain. The homopolymers of D-lysine, L-arginine, and L-glutamic acid, and lysine-free glutamic acid-rich copolymers had little or no inhibitory effect. The results are interpreted to mean that antigens to which responsiveness is regulated by the same Ir gene compete for presentation by accessory cells. This may reflect a competition for the Ir gene product of the antigen-presenting cell.

Animals↗