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PubMed1989

Conversion of amino acid residues in proteins and amino acid homopolymers to carbonyl derivatives by metal-catalyzed oxidation reactions.

A number of metal-catalyzed oxidation (MCO) systems mediate the oxidative inactivation of enzymes. This oxidation is accompanied by conversion of the side chains of some amino acid residues to carbonyl derivatives (for review, see Stadtman, E. R. (1986) Trends Biochem. Sci. 11, 11-12). To identify the amino acid residues which are sensitive to MCO oxidation, several enzymes/proteins and amino acid homopolymers were exposed to various MCO systems. The carbonyl groups which were formed were converted to their corresponding 3H-labeled hydroxy derivatives. After acid hydrolysis, the labeled free amino acids were separated by ion exchange chromatography. Each protein or polymer gave rise to several different labeled amino acids. The elution profiles of the labeled amino acids obtained from preparations of Escherichia coli glutamine synthetase which had been oxidized by MCO systems comprised of either Fe(II)/O2 or ascorbate/Fe(II)/O2 both in the presence and absence of EDTA were qualitatively the same. From a comparison of the elution profiles of labeled amino acids from various proteins with those obtained from homopolymers, it is evident that the side chains of histidine, arginine, lysine, and proline are particularly sensitive to oxidation by the MCO systems. This conclusion is supported also by direct amino acid analysis of acid hydrolysates which shows that the oxidation of glutamine synthetase, enolase, and phosphoglycerate kinase is associated with the loss of at least 1 histidine residue per subunit. From the results of studies with homopolymers, it is apparent that glutamic semialdehyde is a major product of both proline and arginine residues. In addition, hydroxyproline and unlabeled glutamic acid were identified among the hydrolysis products of oxidized poly-L-proline, and unlabeled aspartic acid was identified as a product of poly-L-histidine oxidation.

Amino Acids↗
PubMed2004

Fibroblast adhesion to micro- and nano-heterogeneous topography using diblock copolymers and homopolymers.

Polymeric substrates of different surface chemistry and length scales were found to have profound influence on cell adhesion. The adhesion of fibroblasts on surfaces of oxidized polystyrene (PS), on surfaces modified with random copolymers of PS and poly(methyl methacrylate) [P(S-r-MMA)] with topographic features, and chemically patterned surfaces that varied in lateral length scales from nanometers to microns were studied. Surfaces with heterogeneous topographies were generated from thin film mixtures of a block copolymer, PS-b-MMA, with homopolymers of PS and PMMA. The two homopolymers macroscopically phase separated and, with the addition of diblock copolymer, the size scales of the phases decreased to nanometer dimensions. Cell spreading area analysis showed that a thin film of oxidized PS surface promoted adhesion whereas a thin film of P(S-r-MMA) surface did not. Fibroblast adhesion was examined on surfaces in which the lateral length scale varied from 60 nm to 6 microm. It was found that, as the lateral length scale between the oxidized PS surfaces decreased, cell spreading area and degree of actin stress fiber formation increased. In addition, scanning electron microscopy was used to evaluate the location of filopodia and lamellipodia. It was found that most of the filopodia and lamellipodia interacted with the oxidized PS surfaces. This can be attributed to both chemical and topographic surface interactions that prevent cells from interacting with the P(S-r-MMA) at the base of the topographic features.

Actins↗
PubMed1999

Modeling homopolymer self-replication: implications for early competition.

We start showing that the rate equation for a homopolymer self-replication may be written as being proportional to mbetapGamma with beta=1 and Gamma=1/2, where m is the monomer concentration and p is the homopolymer total concentration (double helices plus isolated strands). With such values for the exponents beta and Gamma, we examine analytically the asymptotic behavior of our model previously proposed for studying the early polymer evolution. In this model, polymers compete for activated monomers carried into the system under a constant flux. Time changes on their concentrations are determined by the reactions of: spontaneous generation of dimers through non-instructed junction of two monomers; ligation among free monomers and polymers at the end of their chains, so that they can extend their sizes; template-instructed synthesis by which polymers with lengths above a length threshold can catalyse the formation of other polymers; and decomposition of all species. We find out that if the monomer flux intensity is "low" (lesser than the decomposition rate constants), dimer is the dominant species. Under a "high" flux (greater than the template-instructed synthesis rate constant), the longest self-replicating species prevails. For a "middle" flux (between "low" and "high"), the shortest self-replicating polymer is the winner. Whatever the flux intensity, all polymer species ever coexist.

Animals↗
PubMed1981

Transformation of E. coli using homopolymer-linked plasmid chimeras.

A number of parameters were explored to increase the transformation efficiency of E. coli with pBR322/eukaryotic DNA chimera, formed via d(A) . d(T) and d(G) . d(C) homopolymer tails. Of the E. coli strains analyzed, E. coli strain RR1 was the most efficient bacterial host. A clear optimum of nucleotide tail length existed for both types of homopolymer. The optimum hybridization temperature for chimera formation was found to be approx. 57 degrees C. In the case of d(A) . d(T)-linked chimeras, 30 min was sufficient for optimum chimera formation. In contrast, d(C) . d(G)-linked chimeras required up to 2 h to give the best yields (as measured by transformation efficiency). Other minor factors affecting the transformation process are also explored and discussed.

Chimera↗
PubMed1995

The inhibition of a leaf proteinase by L-lysine homopolymers.

The role of interlinked positively charged amino acids in the mechanism of inhibition of a monomeric trypsin-like proteinase has been investigated using high molecular mass L-lysine homopolymers ranging from 3.8 to 109 kDa. The data show that the degree of polymerization enhances the inhibitory efficiency which is maximal for homopolymers with more than eighteen interlinked lysine residues. The inhibition is cooperative and, under the maximal inhibition conditions, nine lysine residues of the polymer are involved in the electrostatic binding to the enzyme. A limited conformational change of the protein molecule accompanies the transition from a fully active to a fully inactivated enzyme.

Endopeptidases↗
PubMed1984

Thermodynamical model for insertion and aggregate binding of caffeine to the homopolymer poly(riboadenylate) and model choice by data analysis.

This paper describes the model used to estimate the parameters of caffeine-poly(riboadenylate) (poly(A)) interactions from corresponding 1H-NMR measurements. The model of insertion and aggregate binding describes the non-cooperative insertion of a molecule C into an interspace between two monomers of a homopolymer in competition with aggregate binding. It contains two binding constants, K1 for insertion and K2 for the interaction of monomeric A units of the polymer with C molecules in bound aggregates, and two cooperativity parameters, Kcc for stacking of C molecules within aggregates and tau which is thought to be due to conformational adaptation of the polymer to those bound aggregates which cover more than one A unit. In contrast to other models, the size of a binding site (within the aggregates) is less than one monomeric unit, with n denoting the maximum number of C molecules per A unit in bound aggregates. The model is developed for general n by means of the method of sequence-generating functions. For n = 2 and n = 3, the correctness of the model treatment was checked by the matrix method. The model is applicable to the binding of aggregates to homopolymers, which are flexible enough to fit their structure to the aggregates.

Journal Article↗
PubMed2005

Versatility of the dipolar filter selection: from 1H nuclear spin diffusion experiment to the measurement of nuclear Overhauser effect in homopolymer melts.

Dipolar filters select 1H magnetization according to local dipolar dephasing, which corresponds to site mobility in systems with heterogeneous molecular mobility. Combined with a conventional exchange experiment, it is usually applied to polymeric samples exhibiting structures on the nanometer length scale associated with a strong dynamic contrast. There, the resulting 1H nuclear spin diffusion experiment yields the size of the structure. When the same experiment is applied to homopolymer melts exhibiting a weak dynamic contrast and dynamic heterogeneities on significant shorter length scales, the recorded magnetization decay is in agreement with decays expected from a heterogeneous nanostructure. However, dipolar filters actually can also select mobile parts of the repeat unit, e.g. the end of the alkyl side chains and the subsequent magnetization transfer then can occur via cross relaxation due to non coherent zero-quantum transitions (nuclear Overhauser effect, NOE). The difficulties of distinguishing these two cases are examined and it is demonstrated that NOE experiments exploiting magnetization selection via the dipolar filter allow quantifying the local dynamics of the side chains. This opens new possibilities for measurements of local dynamics in non isotopically labeled homopolymer melts.

Journal Article↗
PubMed1995

Motion of polymer ends in homopolymer and heteropolymer collapse.

To investigate the polymer coil-to-globule transition we performed simulations for the kinetics of homopolymer and heteropolymer collapse. Our stimulations made use of abstract models of long flexible polymers to obtain extensive statistical sampling. For a variety of these models, the simulations suggest that collapse of long polymers is dominated by diffusion of the polymer ends, which accrete monomers and small aggregates. The growth of the end aggregate was found to be nearly linear in time for homopolymers and largely unaffected by variations in microstructure. In contrast, for heteropolymers the presence of non-aggregating (hydrophilic) monomers dramatically slows and alters the growth of the end mass. In models simulated, the end mass grows roughly as the cube root of time, but still dominates aggregation along the contour. In a model where only pairwise bonding is allowed, the collapse is uniform since more flexible end motion does not result in continued end accretion. The possible significance of our results for biopolymer kinetics is discussed.

Algorithms↗
PubMed2003

Spontaneous formation of nanoparticle vesicles from homopolymer polyelectrolytes.

Nanoparticle vesicles were spontaneously assembled from homopolymer polyamine polyelectrolytes and water-soluble, citrate-stabilized quantum dots. The further addition of silica nanoparticles to a solution of quantum dot vesicles generated stable micrometer-sized hollow spheres whose walls were formed of a thick, inner layer of close-packed quantum dots followed by an outer layer of silica. The method employed here to assemble both the nanoparticle vesicles and the hollow spheres is in direct contrast to previous syntheses that use either tailored block copolymers or oil-in-water emulsion templating. We propose that the formation of charge-stabilized hydrogen bonds between the positively charged amines of the homopolymer polyelectrolytes and the negatively charged citrate molecules stabilizing the quantum dots is responsible for the macroscopic phase separation in this completely aqueous system. The ease and processibility of the present approach gives promise for the production of a diverse array of materials ranging in applications from drug delivery to catalysis to micrometer-scale optical devices.

Journal Article↗
PubMed2005

Preparation of homopolymers and block copolymers in miniemulsion by ATRP using activators generated by electron transfer (AGET).

A new initiating/catalytic system for atom transfer radical polymerization (ATRP) is reported. This system starts with alkyl halides as initiators and transition metal complexes in their oxidatively stable state (e.g., Cu(II)Br2/ligand) as catalysts. The activators are generated by electron transfer (AGET) without involvement of initiating organic radicals. AGET ATRP has a significant advantage over simultaneous reverse and normal initiation (SR&NI) ATRP, because it provides a simple route for synthesizing pure polymers with complex architectures such as star copolymers, block copolymers, etc. Furthermore, AGET ATRP can be also successfully carried out in miniemulsion. Homopolymers and pure block copolymers were successfully synthesized via ATRP in miniemulsion using AGET ATRP. The final products were analyzed via two-dimensional chromatography, which combines high performance liquid chromatography (HPLC) and gel permeation chromatography (GPC). The resulting chromatograms showed that pure linear block copolymers and star block copolymers were prepared without the presence of any homopolymers.

Journal Article↗
PubMed2006

Supramolecular assemblies from amphiphilic homopolymers: Testing the scope.

It has been shown by us in a recent communication that homopolymers, in which each repeat unit contains a hydrophilic and a hydrophobic head group, are capable of forming environment-dependent micellar or inverse micellar assemblies. A systematic structure-property relationship study is carried out here to test the scope of the design. We show here that the molecular design is indeed broadly applicable and that there is a significant gain in the critical aggregation concentrations of these polymers, as compared to the small molecule counterparts. We also show that the design can be tuned to achieve vesicle-type assemblies, which further expands the repertoire of amphiphilic homopolymers in a variety of areas. Characterizations of these assemblies have been carried out using transmission electron microscopy, dynamic light scattering, static light scattering, and dye incorporation experiments.

Hydrophobic and Hydrophilic Interactions↗
PubMed2005

Simulation of interaction forces between nanoparticles in the presence of Lennard-Jones polymers: freely adsorbing homopolymer modifiers.

The force between two nanoscale colloidal particles dispersed in a solution of freely adsorbing Lennard-Jones homopolymer modifiers is calculated using the expanded grand canonical Monte Carlo simulation method. We investigate the effect of polymer chain length (N), nanoparticle diameter (sigma(c)), and colloid-polymer interaction energy (epsilon(cp)) on polymer adsorption (Gamma) and polymer-induced forces (F(P)(r)) between nanoparticles in the full thermodynamic equilibrium condition. There is a strong correlation between polymer adsorption and the polymer-mediated nanoparticle forces. When the polymer adsorption is weak, as in the case of smaller diameters and short polymer chain lengths (sigma(c) = 5, N = 10), the polymers do not have any significant effect on the bare nanoparticle interactions. The adsorbed amount increases with increasing particle diameter, polymer chain length, and colloid-polymer interaction energy. In general, for strong polymer-particle adsorption the polymer-governed force profiles between nanoparticles show short-range repulsion and long-ranged attraction, suggesting that homopolymers would not be ideal for achieving stabilization in nanoparticle dispersions. The attraction is likely due to bridging, as well as polymer segment-segment interactions. The location and magnitude of attractive minimum in the force profile can be controlled by varying N and epsilon(cp). The results show partial agreement and some marked differences with previous theoretical and experimental studies of forces in the limit of flat walls in an adsorbing polymer solution. The difference could be attributed to incorporation of long-ranged colloid-polymer potential in our simulations and the influence of the curvature of the nanoparticles.

Journal Article↗
PubMed2004

Dewetting behavior of a block copolymer/homopolymer thin film on an immiscible homopolymer substrate.

Numerous previous studies have established that the addition of a microphase-ordered AB diblock copolymer to a thin homopolymer A (hA) film can slow, if not altogether prevent, film rupture and subsequent film dewetting on a hard substrate such as silica. However, only a few reports have examined comparable phenomena when the hA/AB blend resides on a soft B-selective surface, such as homopolymer B (hB). In this work, the dewetting kinetics of thin films composed of polystyrene (PS) and a symmetric poly(styrene-b-methyl methacrylate) (SM) diblock copolymer on a poly(methyl methacrylate) substrate is investigated by hot-stage light microscopy. Without the SM copolymer, the dewetting rate of the PS layer is constant under isothermal conditions and exhibits Arrhenius behavior with an apparent activation energy of approximately 180 kJ/mol. Addition of the copolymer promotes a crossover from early- to late-stage dewetting kinetics, as evidenced by measurably different dewetting rates. Transmission electron microscopy reveals the morphological characteristics of dewetted PS/SM films as functions of film thickness and SM concentration.

Journal Article↗
PubMed2006

Diblock copolymer surfactant transport across the interface between two homopolymers.

Dynamics of adsorption and desorption of a diblock copolymer to an interface between two homopolymers was measured using dynamic secondary-ion mass spectrometry (SIMS). Thin films were constructed consisting of a layer of saturated polybutadiene with 90% 1,2-addition (sPB90), followed by a layer of saturated polybutadiene with 63% 1,2-addition (sPB63), and finally by another layer of the sPB90 homopolymer. A sPB90-sPB63 diblock copolymer was initially included only in the top sPB90 layer of the film at a volume fraction of 0.05. The thin films were annealed at ambient temperature for times ranging between 0.2 and 108 h, and the concentration profiles of the diblock copolymer through the films were measured using SIMS. The dynamics of adsorption and desorption of the diblock copolymer at the two sPB90-sPB63 interfaces was gauged by comparing the different transient concentration profiles. The sorption process was modeled as diffusion in an external field, generated from self-consistent field theory (SCFT). All parameters for the model were determined independently. Although the model neglects the dynamics of conformational change, experimental results matched theory very well.

Polymers↗
PubMed2000

Polyarginine enters cells more efficiently than other polycationic homopolymers.

Homopolymers or peptides containing a high percentage of cationic amino acids have been shown to have a unique ability to cross the plasma membrane of cells, and consequently have been used to facilitate the uptake of a variety of biopolymers and small molecules. To investigate whether the polycationic character of these molecules, or some other structural feature, was the molecular basis for the effect, the ability of a variety of homopolymers to enter cells was assayed by confocal microscopy and flow cytometry. Polymers of L- or D-arginine containing six or more amino acids entered cells far more effectively than polymers of equal length composed of lysine, ornithine and histidine. Peptides of fewer than six amino acids were ineffective. The length of the arginine side-chain could be varied without significant loss of activity. These data combined with the inability of polymers of citrulline to enter cells demonstrated that the guanidine headgroup of arginine was the critical structural component responsible for the biological activity. Cellular uptake could be inhibited by preincubation of the cells with sodium azide, but not by low temperature (3 degrees C), indicating that the process was energy dependent, but did not involve endocytosis.

Biological Transport↗
PubMed2004

Ordered microstructures by assembly of ABC 3-miktoarm star terpolymers and linear homopolymers.

Ordered microstructures assembled from the mixture of the ABC 3-miktoarm star terpolymers and the linear homopolymers have been investigated by using dynamic density functional theory. The simulations reveal that completely different ordered microphase pattern is found with addition of a few percent homopolymers that is identical in component to one of the arms on the ABC 3-miktoarm star terpolymer. For example, the original density pattern of ABC 3-miktoarm star terpolymers with parameters of N(A)=N(B)=N(C)=10 and chi(AB)=0.90, chi(BC)=chi(CA)=0.45 is in a perfectly ordered knitting feature. However, with gradual addition of the linear polymer same as block C on ABC 3-miktoarm star terpolymer into the system, the density patterns evolve with the volume fraction of the linear polymer from the ordered knitting patterns into the hexagonal patterns. Furthermore, with addition of linear polymers same as block A, lamellar microstructure has finally resulted. The simulation points out a way for designing and manufacturing nanomaterials with totally different microstructures.

Journal Article↗
PubMed1986

OH-induced free radicals in purine nucleosides and their homopolymers: e.s.r. and spin-trapping with 2-methyl-2-nitrosopropane.

Free radicals produced by X-irradiation of N2O-saturated aqueous solutions of purine nucleosides (2'-deoxyadenosine, adenosine, 2'-deoxyguanosine, 3'-deoxyadenosine, guanosine and inosine) and the corresponding homopolymers (poly A and poly I) have been investigated by the technique of spin-trapping and e.s.r. spectroscopy. 2-Methyl-2-nitrosopropane was used as a spin-trap. For 2'-deoxyadenosine and 2'-deoxyguanosine, the resulting spin-adducts were separated by Bio-Gel P-2 column chromatography and analysed by e.s.r. spectroscopy. For homopolymers, e.s.r. spectra were recorded at 50 degrees C after enzymatic digestion to obtain signals with narrower line width. The e.s.r. signal consisting of only a primary triplet without further splittings, which is consistent with assignment to the trapping of an H-abstraction radical at the C4' position of the sugar moiety, was observed in all cases. For 2'-deoxyguanosine an e.s.r. signal consisting of a secondary triplet was observed. Examinations using other spin-trapping reagents such as PBN, 4-PyOBN and DMPO provided no positive evidence supporting the proposal that this was due to an alpha-nitrogen. The e.s.r. signal consisting of a secondary doublet which further splits into a doublet was observed for 2'-deoxyadenosine, adenosine, 3'-deoxyguanosine, 2'-deoxyguanosine, and inosine, and tentatively associated with a radical centered in the sugar moiety.

Adenosine↗
PubMed1998

A comparison of guanosine-quartet inhibitory effects versus cytidine homopolymer inhibitory effects on rat neointimal formation.

Phosphorothioate oligodeoxynucleotides (PS oligos) manifest antisense and G-quartet aptameric inhibitory effects on vascular smooth muscle cell (SMC) proliferation. PS oligo cytidine homopolymers also have nonsequence-specific, non-G-quartet inhibitory effects on in vitro and in vivo SMC proliferation. In this study, we compared the effects of S-dC18 and S-dC28, 18-mer and 28-mer cytidine homopolymers, respectively, which lack guanosines, with those of ZK10, a G-tetrad forming compound, on in vitro SMC proliferation and in vivo neointimal formation. ZK10 significantly inhibited in vitro human aortic SMC proliferation. At the same molar concentration, ZK10 had significantly greater inhibitory potency on SMC proliferation than either S-dC18, S-dC28, or 7DG-ZK10, which is a modified ZK10 with ten 7-deaza guanosine substitutions. ZK10 was significantly more potent than S-dC18 and S-dC28 in inhibiting PDGF-induced in vitro SMC migration. S-dC18, S-dC28, and ZK10 treatment significantly reduced the intima/media area ratio after rat carotid artery balloon injury compared with the values of the control groups. ZK10 was a more potent inhibitor of neointimal formation than the same chain length S-dC18. ZK10 formed higher-order structures, as shown on gel electrophoresis, in contrast to S-dC28 and 7DG-ZK10. Therefore, the 18-mer ZK10 has comparable in vivo SMC inhibitory effects to the 28-mer S-dC28, a fact that may have ramifications for the development of optimal PS oligos to inhibit angioplasty restenosis.

Angioplasty, Balloon↗