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PubMed1992

Aphidicolin inhibits DNA polymerizing activity but not nucleolytic activity of Escherichia coli DNA polymerase II.

We have purified the DNA polymerase II of Escherichia coli from the recombinant strain carrying the plasmid which encodes the polB gene. We confirmed that the purified protein, of molecular weight 90,000, possesses a 3'----5' exonuclease activity in addition to DNA polymerizing activity in a single polypeptide. Its DNA polymerizing activity was sensitive to the drug aphidicoline, which is a specific and direct inhibitor of the alpha-like DNA polymerases including eukaryotic replicative DNA polymerases. Aphidicolin had no detectable effect on the 3'----5' exonuclease activity. The inhibition by aphidicolin on the polymerizing activity of polymerase II was competitive with respect to dNTP and uncompetitive with respect to template DNA. This mode of action is the same as that on eukaryotic DNA polymerase alpha. The apparent Ki value calculated from Lineweaver-Burk plots was 55.6 microM.

Aphidicolin↗
PubMed1977

The mechanism of clay catalyzed polymerization of amino acid adenylates.

Amino acid adenylates were adsorbed on montmorillonite when either the interspatial faces or the edges of the latter were blocked. By this method it could be observed that adsorption of the amino acid adenylates takes place mostly on the planes of the clay. However, for polymerization to take place, the edges of the clay have to be free as well and apparently only these molecules polymerize which are attached to the planes of the clay by their amino groups and to the edges of the clay by their phosphate group. Thus all the charges of the molecules which might produce their repulsion from each other would be neutralized. As a consequence of these attachments polymerization on the clay would take place on its planar sites, but only on those neighboring its edges. The question whether neutralization of charges is also the reason why biochemical substrates have to attach themselves by several points to enzymes and thus make biochemistry fit into the framework of general chemistry, is raised.

Adenosine Monophosphate↗
PubMed1975

Interaction of nerve growth factor with tubulin. Studies on binding and induced polymerization.

The interaction of the nerve growth factor with the neurotubule protein has been studied with the aim of elucidating the nature of the large complexes that they form when incubated together and the factors and control this event. The results show that the binding of nerve growth factor to tubulin is followed by the formation of large structures that, in certain experimental conditions, accelerate the rate of tubulin polymerization to form microtubules or catalyze their assembly in conditions where this process does not occur spontaneously. The formation of large nerve growth factor-tubulin complexes starts to occur only at a molar ratio of 1.0-1.5 NaCL or GTP strongly inhibit this proceed without a detectable effect on NGF binding. Two hypotheses are postulated explain these findings. Firstly, that tubulin has two sites with different affinity for nerve growth factor and the polymerization occurs only when the second NGF molecule has interacted with the microtubule protein. Alternatively, free tubulin in solution is the polymerization by hindering site of tubulin-factor complexes present in solution at a 1.1 molar ratio. In both cases, GTP, Na-+ or H-+ will affect the formation of large unsoluble, tubulin-NGF complexes, by changing their conformation or by decreasing electrostatic interactions.

Animals↗
PubMed1988

Thrombin-induced fibrinopeptide B release from normal and variant fibrinogens: influence of inhibitors of fibrin polymerization.

Thrombin preferentially cleaves fibrinopeptides A (FPA) from fibrinogen resulting in the formation of desAA-fibrin from which most of the fibrinopeptides B (FPB) are then released with an enhanced rate. Kinetics of fibrinopeptide release from normal and dysfunctional fibrinogens were investigated in order to further characterize the mechanism of accelerated FPB release during desAA-fibrin polymerization. Dysfunctional fibrinogens London I and Ashford, exhibiting primary polymerization abnormalities (i.e., an abnormality present when all fibrinopeptides have been cleaved), which in the case of fibrinogen London I is believed to be caused by a defect in the D-domain, were shown to exhibit a decreased rate of FPB release compared with normal fibrinogen. While Gly-Pro-Arg-Pro, an inhibitor of fibrin polymerization, was shown to decrease the rate of FPB release from normal fibrinogen by a factor of 5, normal fragment D1, although inhibiting clot formation of normal fibrinogen, did not influence the acceleration of FPB release. On the other hand, the presence of fragment D1 did not enhance FPB release from fibrinogen London I, suggesting that interaction of D-domains in functional isolation with desAA-fibrin E-domains is not sufficient to enhance FPB release. Although clot formation was inhibited by the concentrations of fragment D1 used, the formation of small desAA-fibrin oligomers was hardly affected. Thus, small fibrin polymers, but not desAA-fibrin monomers, act as optimal substrates for the release of FPB by thrombin.

Blood Coagulation Disorders↗
PubMed1996

Dynamics and morphology of the in vitro polymeric form of elongation factor Tu from Escherichia coli.

Elongation factor Tu from Escherichia coli is known to polymerize at slightly acidic pH and low ionic strength. The structure and dynamics of these aggregates have been examined using imaging and spectroscopic methodologies. Electron microscopy provides evidence for two-dimensional sheets and bundled filaments of EF-Tu, whereas fluorescence microscopy of EF-Tu covalently labeled with tetramethylrhodamine isothiocyanate showed highly branched polymers of EF-Tu several microns in diameter. These polymers were studied using quasi-elastic light scattering to determine the evolution of the translational diffusion coefficient during the polymerization process. The rotational dynamics of the aggregate were investigated using phosphorescence anisotropy of EF-Tu covalently labeled with erythrosin isothiocyanate. A high infinite-time anisotropy was observed, suggesting a lack of motion or entanglement of EF-Tu polymers. A sub-microsecond motion which was slowed in the presence of glycerol may be due to local flexibility of the polymers. The possible relevance of polymeric EF-Tu to its function in vivo is discussed.

Anisotropy↗
PubMed1989

Identifying the site of microtubule polymerization during regrowth of UV-sheared kinetochore fibres using antibodies against acetylated alpha-tubulin.

Areas of reduced birefringence (ARBs) produced on chromosomal fibres of crane-fly spermatocyte spindles by ultraviolet microbeam irradiation move poleward. The ARB is due to the depolymerization of the microtubules in that area, and its poleward motion is due in part to the lengthening of that part of the kinetochore fibre which is left attached to the kinetochore after shearing the microtubules. We tested whether the lengthening of this fibre is due to the polymerization of microtubules at the growing edge of the ARB by staining growing fibres in irradiated spindles with antibodies to tubulin and to acetylated tubulin. We have previously argued that newly-polymerized kinetochore microtubules are not acetylated, whereas older kinetochore microtubules are (Wilson & Forer, 1989). Therefore we expected to see an absence of staining with antibodies to acetylated tubulin at the edge of the ARB if microtubules were polymerizing there. There is no absence of staining, however, which suggests that growth of the sheared microtubules does not occur at the ARB edge. Other possibilities are discussed.

Acetylation↗
PubMed1994

Polymeric 6-aminoquinoline, an activated carbamate reagent for derivatization of amines and amino acids by high-performance liquid chromatography.

A new polymeric reagent containing the 6-aminoquinoline (6-AQ) tag was developed and applied for the off-line derivatization of amines and amino acids in high-performance liquid chromatography (HPLC). The synthesis and characterization of this polymeric reagent are described. An authentic external standard of a typical amine was synthesized and characterized for the determination of the derivatization efficiency. All amines had a derivatization efficiency higher than 50%; the derivatization of amino acids was performed under optimized phase-transfer catalysis reaction conditions. Derivatized amines and amino acids were separated under conventional reversed-phase conditions and determined by UV and FL detectors. To investigate the practical applications, this polymeric reagent was also used to derivatize protein hydrolysates.

Amines↗
PubMed1993

NMR relaxation enhancement in gels polymerized and cross-linked by ionizing radiation: a new approach to 3D dosimetry by MRI.

A new type of tissue-equivalent medium for magnetic resonance imaging of the dose distributions produced by ionizing radiation has been developed. Agarose gel is infused with acrylamide and N,N'-methylene-bis-acrylamide (Bis) comonomers, which are readily polymerized by free radical initiators in de-aerated aqueous solutions. Polymerization and cross-linking induced locally by free radical products of water radiolysis increase the rate of water proton spin relaxation gradually up to doses of about 15 Gy. The slopes of the dose-response curves at 64 MHz are 0.015 and 0.28 s-1 Gy-1 for R1 and R2, respectively. The agarose matrix as well as the high (50% by weight) relative concentration of the cross-linker (Bis) per total comonomer limit the spread of polymerization so that the spatial distribution of the radiation dose is faithfully represented in the resultant spatial distribution of relaxation rates. The gel can be imaged with conventional magnetic resonance imaging devices with high spatial resolution and accuracy. In addition, due to the well established effect of the precipitation of insoluble agglomerates of highly cross-linked acrylamide, the optical turbidity of the gel increases gradually with the absorbed dose. This may provide an additional means of visualizing the dose distribution in three dimensions. The major advantage of the acrylamide-Bis-agarose gels over those that depend on ionic chemical dosimeters, for example, Fricke-infused gels, lies in the lack of diffusion of radiation-induced chemical changes subsequent to or concurrent with irradiation.

Acrylamide↗
PubMedDate not supplied

Recent studies of the interaction of rabbit dimeric IgA with its polymeric immunoglobulin receptor.

Rabbit secretory components (SC) constitute a highly heterogeneous population of glycoprotein molecules that are present in secretions as free or bound forms to polymeric immunoglobulins (Ig). Two SC families are known, one of high molecular weight (approximately equal to 80 Kd) composed of five (perhaps six) domains related to Ig variable domains, and one of low molecular weight (approximately equal to 55 Kd). An account of our most recent experimental data is reviewed in this article. We have shown: 1) that both the high and low Mr SC families possess the same relative avidity for binding to dimeric IgA of the g-subclass; 2) that the first NH2-terminal domain of SC derived from the high and low Mr polypeptides is necessary and sufficient for efficient non-covalent binding to dimeric IgA of the g-subclass; 3) that the low Mr SC polypeptide derives from the high Mr SC by the internal deletion of the entire second and third domains, suggesting that these domains are not involved in the binding reaction with polymeric Ig; 4) that the heterogeneity of rabbit secretory components is, in large part, due to the expression of several polymorphic forms (allotypes) susceptible to be recognized by specific alloantisera; the biochemical characterization of the three known SC allotypes (t61, t62 and t63) reveals that t62 and t63 are structurally very similar to each other and markedly divergent from the t61 homologue; 5) that by using non-cross-reactive alloantisera, the major immunodominant allotopes are confined within the COOH-terminal domains 3, 4 and 5 of SC; 6) that the location of the residues involved in the attachment of the carbohydrate unit within domain 1 varies according to the allotype: t61 is N-linked glycosylated at position 70, whereas about 75% of t62 molecules are devoid of sugars; the remaining 25% of t62 molecules are glycosylated at residue position 90; these oligosaccharide chain units are linked to asparagine residues in the acceptor site consensus sequence, Asn-X-Thr/Ser; 7) that the presence of the carbohydrate unit in domain 1 is not required for efficient binding of this domain to polymeric Ig: indeed, after enzymatic deglycosylation, domain 1 exhibits a relative binding avidity which is indistinguishable from that of the native glycosylated domain 1.

Amino Acid Sequence↗
PubMed1988

Polymerization of turtle alpha-macroglobulin through newly exposed sulfhydryls reveals the location of ex-thiolester bonds.

Green turtle alpha-macroglobulin, which has previously been shown to contain thiolester bonds, formed linear polymers after being treated with proteinases. Biochemical analyses showed that the polymerization proceeded through disulfide-bond formation between monomers. The only sulfhydryl groups available for such polymerization after proteinase treatment were those created as the product of thiolester hydrolysis. Electron micrographs of polymers revealed H-shaped monomeric units aligned lengthwise in linear polymers. The average length per monomeric unit in the polymer estimated from the discrete distribution of polymer lengths was approximately 80% of the average length of free monomers, indicating that monomers overlapped each other within a region of about 4 nm. From such observations we concluded that the newly produced sulfhydryl groups were located on the four arms of the H-shaped molecule. The location of sulfhydryls can be taken as the site of the exposure of thiolesters which were originally sequestered in the hydrophobic interior of the molecule. Since the structure of turtle alpha-macroglobulin is very similar to that of human serum alpha 2-macroglobulin the results predict a similar location of sulfhydryls in human alpha 2-macroglobulin after proteinase treatment. The observed polymerization property is unique to sea turtle alpha-macroglobulin and has not been observed with human alpha 2-macroglobulin or other homologous proteins.

Animals↗
PubMedDate not supplied

Polymerizing properties of pepstatin A.

Pepstatin A, a pentapeptide aspartyl protease inhibitor, can spontaneously polymerize into filaments having a helical substructure and, after negative staining, characteristic diameters ranging from 6 to 12 nm. Optical diffraction analysis demonstrated that these filaments consist of a 6-nm-wide strand helically wound with a periodic pitch of 25 nm. Selected images suggest that these filaments may actually be composed of two, intertwined 6-nm-wide strands, an hypothesis not at variance with the diffraction data. These filaments may extend over several micrometers. At low ionic strength and neutral pH, the critical concentration for pepstatin A filament assembly is 0.1 mM. At higher pepstatin A concentrations or in physiological salt solutions, a variety of higher order structures were observed, including ribbons, sheets, and cylinders with both regular and twisted or irregular geometries. Pepstatin A polymerized into these higher order structures loses its ability to inhibit the aspartyl protease of the human immunodeficiency virus type 1. These results have implications not only for model studies on the polymerization of small peptides into higher order structures, but also for the practical development of soluble protease inhibitors.

Microscopy, Electron↗
PubMed2004

Pyrophosphorolysis by Type II DNA polymerases: implications for pyrophosphorolysis-activated polymerization.

We find that Type II DNA polymerases can catalyze pyrophosphorolysis, the reverse reaction of DNA polymerization. This property is applied utilizing pyrophosphorolysis-activated polymerization (PAP), a method of nucleic acid amplification using serial coupling of pyrophosphorolysis and polymerization. PAP can be used for ultrarare allele detection (detection of minimal residual disease and cancer risk assessment through measurement of mutation load) and for microarray-based scanning for unknown mutations. Herein, we show that Type II DNA polymerases efficiently catalyze template-dependent pyrophosphorolysis to activate oligonucleotides blocked at their 3' termini with acyclonucleotides in which a 2-hydroxyethoxymethyl group substitutes for the 2'-deoxyribofuranosyl sugar. Type II archeon DNA polymerases Vent (exo-) and Pfu (exo-) can be utilized for PAP or a bidirectional form of PAP with acyclonucleotide-blocked oligonucleotides, but not with dideoxynucleotide-blocked oligonucleotides. In contrast, a Type I DNA polymerase, TaqFS, can utilize either acyclonucleotide-blocked or dideoxynucleotide-blocked oligonucleotides. These findings expand the potential of nascent PAP technology.

Alleles↗
PubMed2005

Turbidity as a probe of tubulin polymerization kinetics: a theoretical and experimental re-examination.

We report here an examination of the validity of the experimental practice of using solution turbidity to study the polymerization kinetics of microtubule formation. The investigative approach proceeds via numerical solution of model rate equations to yield the time dependence of each microtubule species, followed by the calculation of the time- and wavelength-dependent turbidity generated by the calculated distribution of rod lengths. The wavelength dependence of the turbidity along the time course is analyzed to search for generalized kinetic regimes that satisfy a constant proportionality relationship between the observed turbidity and the weight concentration of polymerized tubulin. An empirical analysis, which permits valid interpretation of turbidity data for distributions of microtubules that are not long relative to the wavelength of incident light, is proposed. The basic correctness of the simulation work is shown by the analysis of the experimental time dependence of the turbidity wavelength exponent for microtubule formation in taxol-supplemented 0.1 M Pipes buffer (1 mM GTP, 1 mM EGTA, 1 mM MgSO4, pH 6.4). We believe that the general findings and principles outlined here are applicable to studies of other fibril-forming systems that use turbidity as a marker of polymerization progress.

Animals↗
PubMed2006

Current status of polymeric gene delivery systems.

Gene therapy provides great opportunities for treating diseases from genetic disorders, infections and cancer. To achieve successful gene therapy, development of proper gene delivery systems could be one of the most important factors. Several non-viral gene transfer methods have been developed to overcome the safety problems of their viral counterpart. Polymer-based non-viral gene carriers have been used due to their merits in safety including the avoidance of potential immunogenecity and toxicity, the possibility of repeated administration, and the ease of the establishment of good manufacturing practice (GMP). A wide range of polymeric vectors have been utilized to deliver therapeutic genes in vivo. The modification of polymeric vectors has also shown successful improvements in achieving target-specific delivery and in promoting intracellular gene transfer efficiency. Various systemic and cellular barriers, including serum proteins in blood stream, cell membrane, endosomal compartment and nuclear membrane, were successfully circumvented by designing polymer carriers having a smart molecular structure. This review explores the recent development of polymeric gene carriers and presents the future directions for the application of the polymer-based gene delivery systems in gene therapy.

Animals↗
PubMed2005

Mechanism of horseradish peroxidase-catalyzed heme oxidation and polymerization (beta-hematin formation).

Horseradish peroxidase (HRP) catalyzes the polymerization of free heme (beta-hematin formation) through its oxidation. Heme when added to HRP compound II (FeIV=O) causes spectral shift from 417 nm (Compound II) to 402 nm (native, FeIII) indicating that heme may be oxidized via one-electron transfer. Direct evidence for one-electron oxidation of heme by HRP intermediates is provided by the appearance of an E.s.r signal of a 5,5-dimethyl-1-pyrroline N-oxide (spin trap)-heme radical adduct (a1H=14.75 G, a2H=4.0 G) in E.s.r studies. Heme-polymerization by HRP is inhibited by spin trap indicating that one-electron oxidation product of heme ultimately leads to the formation of heme-polymer. HRP, when incubated with diethyl pyrocarbonate (DEPC), a histidine specific reagent, shows concentration dependent loss of heme-polymerization indicating the role of histidine residues in the process. We suggest that HRP catalyzes the formation of heme-polymer through one-electron oxidation of free heme.

Catalysis↗
PubMed2004

Lipoxygenase-catalyzed polymerization of phenolic lipids suggests a new mechanism for allergic contact dermatitis induced by urushiol and its analogs.

Lipoxygenase was found to catalyze the oxidative polymerization of phenolic lipids containing a (Z,Z)-pentadiene in the side chain, the model compounds of urushiol and its analog, yielding methanol-soluble and insoluble polymers. The structural analysis of the resulted polymers suggested that the polymerization occurred at both the phenol and the unsaturated side chain. The key step of the polymerization was the generation of the hydroperoxide at the unsaturated side chain by lipoxygenase. The decomposition of hydroperoxide and concomitant dehydrogenation of phenol ring catalyzed by lipoxygenase might produce radicals that could be coupled to form cross-linked polymers. This lipoxygenase-mediated reaction implies a new mechanism for contact allergy of urushiol and its analogs.

Catalysis↗
PubMed2006

8-Chloro-adenosine inhibits growth at least partly by interfering with actin polymerization in cultured human lung cancer cells.

A key feature of actin is its ability to bind and hydrolyze ATP. 8-Chloro-adenosine (8-Cl-Ado), which can be phosphorylated to the moiety of 8-Cl-ATP in living cells, inhibits tumor cell proliferation. Therefore we tested the hypothesis that 8-Cl-Ado can interfere with the dynamic state of actin polymerization. We found that 8-Cl-Ado inhibited the growth of human lung cancer cell line A549 and H1299 in culture, and arrested the target cells in G2/M phase evidenced by fluorescence-activated cell sorting (FACS). Immunocytochemistry showed that the normal organization of microfilaments was disrupted in 8-Cl-Ado-exposed cells, which is accompanied by the decrease of cell size and the alteration of cell shape, and by aberrant mitosis and apoptosis in targeted cells. Furthermore, in vitro light scattering assays revealed that 8-Cl-ATP could directly inhibit the transition of G-actin to F-actin. DNase I inhibition assays showed that the G/F-actin ratio, a surrogate marker of actin polymerization status in living cells, was significantly increased in 8-Cl-Ado-exposed A549 and H1299 cells, compared to the G/F-actin ratio in unexposed cells. Taken together, these results indicate that 8-Cl-Ado exposure can alter the dynamic properties of actin polymerization, disrupt the dynamic instability or the rearrangement ability of actin filaments. Therefore, our data suggest that 8-Cl-Ado may exert its cytotoxicity at least partly by interfering with the dynamic instability of microfilaments, which may correlate with its inhibitory effects on cell proliferation and cell death.

2-Chloroadenosine↗
PubMed2004

Ring opening polymerization of L-lactide initiated by creatinine.

L-lactide was first successfully ring-opening polymerized in bulk using creatinine initiator. Poly(L-lactide)(PLLA) synthesized possesses a moderate molecular weight (MW) (Mn = 1.56 x 10(4)) and pretty narrow MW distribution (PDI = 1.28). Influence of temperature, time and creatinine dosage on the polymerization and formed PLLA's properties were examined. The polymerization mechanism is postulated according to (1)HNMR characterization of the propagation species and the synthesized PLLA product.

Biocompatible Materials↗