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PubMed2006

Helical structures from an isotropic homopolymer model.

We present Monte Carlo simulation results for square-well homopolymers at a series of bond lengths. Although the model contains only isotropic pairwise interactions, under appropriate conditions this system shows spontaneous chiral symmetry breaking, where the chain exists in either a left- or a right-handed helical structure. We investigate how this behavior depends upon the ratio between bond length and monomer radius.

Computer Simulation↗
PubMed2003

Stability of a 24-meric homopolymer: comparative studies of assembly-defective mutants of Rhodobacter capsulatus bacterioferritin and the native protein.

The stability of Rhodobacter capsulatus bacterioferritin, a 24-meric homopolymer, toward denaturation on variation in pH and temperature, and increasing concentrations of urea and guanidine.HCl was investigated with native PAGE, and CD and fluorescence spectroscopies. With temperature and urea, the wild-type protein denatured without discernible intermediates in the equilibrium experiments, but with guanidine.HCl (Gnd.HCl) one or more intermediate species were apparent at relatively low Gnd.HCl concentrations. Dissociated subunit monomers, or aggregates smaller than 24-mers containing the high alpha-helical content characteristic of the native protein were not obtained at any pH without a high proportion of the 24-mer being present, and taken together with the other denaturation experiments and the construction of stable subunit dimers by site-directed mutagenesis, this observation indicates that folding of the bacterioferritin monomer could be coupled to its association into a dimer. Glu 128 and Glu 135 were replaced by alanine and arginine in a series of mutants to determine their role in stabilizing the 24-meric oligomer. The Glu128Ala, Glu135Ala and Glu135Arg variants retained a 24-meric structure, but the Glu128Ala/Glu135Ala and Glu128Arg/Glu135Arg variants were stable subunit dimers. CD spectra of the Glu135Arg, Glu128Ala/Glu135Ala, and Glu128Arg/Glu135Arg variants showed that they retained the high alpha-helical content of the wild-type protein. The 24-meric Glu135Arg variant was less stable than the wild-type protein (T(m), [Urea](50%) and [Gnd.HCl](50%) of 59 degrees C, 4.9 M and 3.2 M compared with 73 degrees C, approximately 8 M and 4.3 M, respectively), and the dimeric Glu128Arg/Glu135Arg variant was less stable still (T(m), [Urea](50%) and [Gnd.HCl](50%) of 43 degrees C, approximately 3.2 M and 1.8 M, respectively). The differences in stability are roughly additive, indicating that the salt-bridges formed by Glu 128 and Glu 135 in the native oligomer, with Arg 61 and the amino-terminal amine of neighboring subunits, respectively, contribute equally to the stability of the subunit assembly. The additivity and assembly states of the variant proteins suggest that the interactions involving Glu 128 and Glu 135 contribute significantly to stabilizing the 24-mer relative to the subunit dimer.

Bacterial Proteins↗
PubMed1993

Isolation of rfb gene clusters directing the synthesis of O polysaccharides consisting of mannose homopolymers and serological analysis of lipopolysaccharides.

Four serotypes of two genera, Escherichia coli O8 and O9 and Klebsiella O3 and O5, produce the O polysaccharides consisting of mannose homopolymers. Previously, we reported the isolation and expression of E. coli O9 rfb in E. coli K-12 strains (Kido et al, J. Bacteriol., 171: 3629-3633, 1989). In this study, R' plasmids carrying his-rfb region of the other three strains were isolated and expressed in E. coli K-12 strain. Serological study of lipopolysaccharides (LPS) synthesized in E. coli K-12 strain was carried out. His-linked rfb genes from E. coli O9 and Klebsiella O3 directed the synthesis of O polysaccharides with the same antigenicity as those of the parental strains in E. coli K-12 strain. On the other hand, rfb genes from E. coli O8 and Klebsiella O5 directed the synthesis of O polysaccharides which were antigenically not identical but partially common to those of the parental strains. A rough strain derived from E. coli O8 synthesized LPS which showed the identical antigenicity as the wild strain when the his-rfb region of E. coli O8 was introduced. The results suggest that some genes located distantly from his are additionally required to complete the synthesis of O polysaccharides of E. coli O8 and Klebsiella O5.

Carbohydrate Conformation↗
PubMed1997

Frameshift intermediates in homopolymer runs are removed efficiently by yeast mismatch repair proteins.

A change in the number of base pairs within a coding sequence can result in a frameshift mutation, which almost invariably eliminates the function of the encoded protein. A frameshift reversion assay with Saccharomyces cerevisiae that can be used to examine the types of insertions and deletions that are generated during DNA replication, as well as the editing functions that remove such replication errors, has been developed. Reversion spectra have been obtained in a wild-type strain and in strains defective for defined components of the postreplicative mismatch repair system (msh2, msh3, msh6, msh3 msh6, pms1, and mih1 mutants). Comparison of the spectra reveals that yeast mismatch repair proteins preferentially remove frameshift intermediates that arise in homopolymer tracts and indicates that some of the proteins have distinct substrate or context specificities.

Adenosine Triphosphatases↗
PubMed2003

Statistics of copolymer sequences obtained by polymeranalogous reactions of homopolymer globules.

For the first time the macrokinetics of polymeranalogous reaction in a homopolymer globule is considered theoretically. Using mathematical apparatus of the theory of markovian stochastic processes we examined the statistical characteristics of the chemical structure of the emerging copolymers. It is shown that when the reaction is kinetically-controlled the sequence distribution of monomeric units in copolymer chains follows Bernoullian statistics. In the opposite regime, when the reaction is diffusion-controlled it is proved that the resulting primary structure is described by the Levy flight distribution. Such copolymers with nonmarkovian character of the alteration of units in macromolecules can not be synthesized in the bulk or in concentrated solutions by means of standard synthetic polymerization procedures.

Journal Article↗
PubMed2002

Thermophysical properties of fluorinated acrylate homopolymers: mixing and phase separation.

The thermophysical properties of fluorinated acrylate homopolymers are investigated by differential scanning calorimetry (DSC) and optical microscopy and discussed in terms of relative lengths of the fluorinated chain and the hydrocarbon spacer between the acrylate moiety and the fluorinated chain. These compounds exhibit an intrinsic microphase-separation (Isotropic+Isotropic morphology) occurring between the fluorinated chains and the acrylate polymer backbone. It is shown that the enthalpy of mixing is a function of the length of the lateral fluorocarbon chains. The thermophysical behaviour of these materials may be regarded as demixed systems exhibiting an Upper Critical Solution Temperature. The photopolymerization process of one of the monomer is studied by isothermal photocalorimetry. High acrylate double-bond conversion and fast curing rates were obtained thus demonstrating the promising use of these materials for coating and film processing applications using UV-curing techniques.

Journal Article↗
PubMed2004

Plasma protein adsorption to surfaces grafted with dense homopolymer and copolymer brushes containing poly(N-isopropylacrylamide).

Growing polymer chains from surface initiators in principle allows much more dense polymer surface layers to be created than can be produced by grafting of whole (self-excluding) chains. We have utilized aqueous atom transfer radical polymerization to graft a series of cleavable hydrophilic poly(N-isopropylacrylamide) (PNIPAM) homopolymers and block copolymers of substituted acrylamides from polystyrene latex to give brushes of controlled MW and surface density. Average chain separations much less than their free solution radii of gyration have been achieved. Exposure to radiolabeled single proteins or to whole plasma and subsequent analysis by SDS-PAGE shows that PNIPAM brushes decrease protein adsorption relative to the latex surface or other substituted polyacrylamides. The PNIPAM brushes exhibit a second-order phase transition around 30 degrees C as reflected by a decrease in the hydrodynamic thickness of the brush at higher temperatures. Total plasma protein adsorption is increased at 40 degrees C compared to 20 degrees C but there is significant differential adsorption behavior among the proteins detected by gel-electrophoresis analysis.

Acrylic Resins↗
PubMed1999

Evaluation of polyoxyethylene homopolymers for buccal bioadhesive drug delivery device formulations.

Our objective was to evaluate the application of polyoxyethylene homopolymers in buccal bioadhesive drug (BBD) delivery device formulations. The bioadhesive strength of four different molecular weight (MW) polyoxyethylene polymers was measured by Instron tensile tester using glass plate and bovine sublingual tissue as substrate surfaces. Several BBD device formulations containing polyoxyethylene polymer (MW 7,000,000) were prepared by direct compression and compression molding processes. The prepared BBD devices were evaluated for their elasticity, in vitro adhesion and drug release characteristics. The in vivo bioadhesion characteristics of a placebo compression molded device were examined in 3 adult healthy male beagle dogs. The bioadhesive strength of polyoxyethylene polymers appeared to be directly related to their molecular weights. When bovine sublingual mucosa or a glass plate was used as model mucosal substrate surface, the rank order of bioadhesive strength of different molecular weight polyoxyethylene polymers was similar. The bioadhesive strength of devices prepared by the compression molding process was greater than those prepared by direct compression, but the kinetics of drug release were independent of the process used for the preparation of the devices. The drug release and the bioadhesive strength of the similarly prepared device formulations appeared to be dependent on the drug:polymer ratios. The elasticity of the BBD devices prepared by compression molding was improved by the inclusion of polyisobutylene polymer in the formulations. When adhered to the oral cavity of the dogs, the compression molded placebo BBD device exhibited adhesion for at least 4 hours and appeared to show no signs of local irritation. In conclusion, BBD devices containing polyoxyethylene polymer (MW 7,000,000) can be prepared by direct compression or compression molding process in order to provide controlled drug release to the oral cavity while maintaining appropriate bioadhesive characteristics.

Administration, Buccal↗
PubMedDate not supplied

[Theoretical model of homopolymer chain adsorption on a homogenous surface].

On the basis of I. M. Lifshitz's theory the adsorption of the homopolymer on the homogenous surface is considered. It is shown that the attraction of monomers to the surface may lead not only to adsorption of the globule or coil but also to the emergence of a new peculiar phase--dislike globule without the fringe, all the monomers of which are stuck to the surface. A two-dimensional phase-diagram is plotted.

Adsorption↗
PubMed2000

Reactivation of acyclovir-resistant thymidine kinase-deficient herpes simplex virus harbouring single base insertion within a 7 Gs homopolymer repeat of the thymidine kinase gene.

HSV infections are treated efficiently and prevented by acyclovir, although resistant strains have been reported. Resistance to acyclovir involves mainly mutations in the viral gene encoding thymidine kinase; mutations may lead to an altered or, more frequently, deficient TK. These acyclovir-resistant TK deficient strains are not able to reactivate from a latent infection in an experimental model, compared to TK positive strains. A case is reported of a bone marrow transplant child who developed HSV infection at 11 days post-transplantation. Acyclovir-resistant HSV 1 was isolated on day 19 post-transplantation. The patient was cured of his infection. A resistant virus was detected 20 months later that harboured the same TK gene mutation as the first resistant virus. This mutation is an insertion of one guanine in a homopolymer repeat of seven guanines located at codon 146 of TK. It has previously been reported and associated with the expression of a deficient TK activity and the ability to reactivate in mice. These results corroborate the clinical relevance of this mutation, which is associated with acyclovir-resistant recurrent infections in humans.

Acyclovir↗
PubMed2001

Complement-dependent platelet degradation and anaphylactoid shock in mice induced by lipopolysaccharide carrying the mannose homopolymer.

Intravenous injection of specified bacterial lipopolysaccharides (LPSs) induced anaphylactoid shock in mice of various strains, including LPS-resistant C3H/HeJ. The reaction was accompanied by occasional mortality of mice within 1 h. Prior to shock, rapid accumulation of blood platelets in the lungs and liver followed by degradation of platelets (or release of their contents) and tissue destruction were observed. In this study, LPS specimens carrying mannose-homopolymer (MHP), which markedly activate the human complement system through the lectin pathway, induced marked platelet degradation and anaphylactoid shock in BALB/c mice. In contrast, in C5-deficient DBA/2 mice, the platelet degradation and anaphylactoid reactions did not occur. Anti-complement agent K-76 COOH (C5 inhibitor) protected BALB/c mice from mortality in the anaphylactoid reaction. K-76 COOH also inhibited platelet degradation, but not accumulation, induced by LPS in mice. Based on these findings, we postulated that strong complement activation by specified LPS preparations induced degradation of platelets that have accumulated in the lungs and liver, resulting in acute inflammation accompanied by severe tissue destruction, especially in the lungs, which in turn leads to anaphylactoid reaction.

Anaphylaxis↗
PubMed2003

Uncommon cytidine-homopolymer dimorphism in 5'-UTR of the human otoferlin gene.

Human otoferlin, homologous to the Caenorhabditis elegans spermatogenesis factor FER-1 that was shown to be involved in membrane vesicle fusion, belongs to a group of membrane-anchored cytosolic proteins and is found expressed in brain, cochlear inner hair cells and vestibular type I sensory cells. Nonsense and missense mutations of OTOF lead to an autosomal recessive deafness phenotype (DFNB9). We describe here an unusual C-homopolymer dimorphism at position -136 of 5'-UTR of the OTOF short splice form. Although at first identified within a family with a hereditary component of hearing deficiency this C3/C5 dimorphism is found frequently in European populations (0.4 for C3, 0.6 for C5) and does not segregate with the deafness phenotype. The polymorphic site may become useful for studying the origin of different OTOF mutations within various populations, for assessing recombination events within large pedigrees as well as founder effects and for association studies in further deafness phenotypes.

5' Untranslated Regions↗
PubMed1977

Characterization of the nucleoside triphosphate phosphohydrolase (ATPase) activity of RNA synthesis termination factor p. II. Influence of synthetic RNA homopolymers and random copolymers on the reaction.

The ability of various kinds of RNA molecules to activate the ATP hydrolysis reaction catalyzed by the p transcription termination factor from Escherichia coli has been studied. The most active RNA polymers are those containing cytidylate residues and very little ordered structure. Free poly(C) is the most active homopolymer; it is 45 times more active than poly(U), which is the only non-cytidine containing RNA that has detectable activity. Poly(C) has no activity when complexed with poly(I) or when the chain lengths are shorter than 22 nucleotides long. Although cytidylate residues are important they need not be frequent; a random copolymer of uridine and cytidine nucleotides with as few as 1 cytidylate residue out of 20 is as active as poly(C). The extent of activation with poly(C) depends on the ratio of p to poly(C). Poly(C) becomes saturated with p at a ratio of 1.8 ng of p/pmol poly(C), which is equivalent to one p monomer/27 nucleotides. A further increase in this ratio leads to a reduction in p activity. Decreasing the length of the poly(C) does not alter the observed saturation value but does decrease the rate of ATP hydrolysis when the RNA is in excess. The possible relevance of these results to p termination activity is discussed.

Adenosine Triphosphatases↗
PubMedDate not supplied

[The role of topological limitations in the kinetics of homopolymer collapse and self-assembly of biopolymers].

Fast collapse of a linear homopolymer after a spasmodic temperature decrease or deterioration of the solvent quality results in the initiation of folded nonequilibrium globule. The chain line in it is a fractal with the dimension mu less than or equal to 2 at small ranges and 3 at the large ones. This is provided by non-selfintersection of the chain and initiated therefore spatial segregation from each other at all the ranges of the chain regions, globulized each in itself. Further relaxation of the folded globule proceeds very slowly only at the expense of reptation (diffusion crawling) of the chain along itself, and results in the polymer knotting. The model of the folded globule permits explanation from a single viewpoint of a number of globular proteins properties. Predictions are formulated whose checking in a real or computer experiment should reveal the adequacy of our results.

Biopolymers↗
PubMedDate not supplied

[Structure of the B-form of DNA using the homopolymer poly(dA) . poly(dT) as an example. Refinement in accordance with x-ray and energy criteria].

The refinement of the B-form DNA structure was made using homopolymer poly(dA) (dT) as a model system. In the course of refinement 9 conformational and 22 independent experimental parameters (20 intensities of reflections and 2 helical parameters) were used. After the goal-function, including R-factor, helical and conformational parameters, was optimised, the structures with the values of potential energy and R-factor close correspondingly to the optimal values were selected. "The best" conformations obtained according to energy criteria have the value of an axial projection per one nucleotide pair of about 2,9 A that is equal to the corresponding value in the recently discovered relaxed form of DNA in solution. The most probable conformations according to combine energy and structural criteria have better value of the R-factor in comparison with those derived on the basis of X-ray only, although they are slightly less satisfactory according to the energy criteria. The conformation of DNA which have the values of an axial projection per one nucleotide pair--3,29 A; of the angle of rotation of neighboring nucleotide pair relative each other--36 degrees and of the angle of nucleotide pair with an axis of the helix -13,7 degrees seems to be the most accurate description of the doublehelical structure of poly(dA) . poly(dT). The atomic coordinates of the new model may be used in analysis of stereochemistry of the complexes of nucleic acids with polypeptide and proteins, that is in consideration of the problem of protein-nucleic acid recognition.

DNA↗
PubMed1981

Quantitative isolation of oligo- and polyadenosine-diphosphoribosylated proteins by affinity chromatography from livers of normal and dimethylnitrosamine-treated Syrian hamsters. In vivo and in vitro metabolism of the homopolymer.

Polyadenosine- and adenosine-diphosphoribosylated proteins of hamster liver were quantitatively isolated with the aid of m-aminophenyl boronic acid glutaryl hydrazide polyacrylamide affinity resin by selective adsorption at pH 8.2 and elution at pH 4.0. Polymer-free proteins, DNA, and RNA are readily separated from adenosine-diphosphoribosylated proteins. The total quantity of proteins that is covalently modified by the homopolymer is 14.3 micrograms/mg of DNA or 37.4 micrograms/g of liver in controls and 38.7 micrograms/mg of DNA or 116 micrograms/g of liver in dimethylnitrosamine-treated hamsters. Polymer content increases from 9 to 15 nmol/mg of DNA to 42 to 118 nmol/mg of DNA following treatment with dimethylnitrosamine. Pulse labeling with [14C]ribose results in a parallel doubling in dimethylnitrosamine-treated animals of the specific activities of adenosine- diphosphoribose and NAD+ and of the [14C]ribose content of polyadenosine-diphosphoribose of chain length between 20 and 40, indicating chain elongation of pre-existing larger polymers. Two groups of proteins that are isolated as polyadenosine-diphosphoribose adducts are increased significantly after treatment with dimethylnitrosamine, one minor component of a mass between 100-112 X 10(3) daltons, and a major group exhibiting a mass of 158-162 X 10(3) daltons. Polyadenosine-diphosphoribose synthetase activity of isolated hepatic nuclei is increased by 32-37% after dimethylnitrosamine treatment, and since the change in glycohydrolase activity is negligible relative to the increase in synthetase, the augmentation of polyadenosine-diphosphoribosylated proteins can be explained by the increased synthetase of nuclei. The molecular size distribution of DNA in liver nuclei of control and dimethylnitrosamine-treated hamsters is indistinguishable.

Adenosine Diphosphate Ribose↗
PubMed1995

Use of vaccinia virus poly(A) polymerase for RNA 3'-end labeling with a chain-terminating nucleotide or a short 3' homopolymer tract.

Conditions are described for the 3'-end labeling of RNA with 32P 3'-dATP (3'-deoxyadenosine-5'-triphosphate), a chain-terminating nucleotide, using the poly(A) polymerase (PAP) encoded by vaccinia virus. Reaction time, divalent cation species and concentration, and the requirement for both subunits of the PAP were investigated. In the presence of Mn2+, vaccinia PAP is able to tail RNA primers with tracts of 3'-oligo(U), oligo(C) and oligo(G). Conditions for the addition of labeled 3'-homopolymer tracts were characterized. The use of low nucleotide concentrations in this study revealed an apparently fixed divalent cation concentration optimum of 0.1 mM, distinct from the previously noted requirement for a 1:1 divalent cation:NTP complex. This indicates a possible requirement for multiple divalent cations in nucleotidyl transfer by vaccinia PAP.

Cations, Divalent↗
PubMed1994

The FAR domain defines a new Xenopus laevis zinc finger protein subfamily with specific RNA homopolymer binding activity.

The zinc finger motif defines a large superfamily of nucleic acid binding proteins. Conserved amino acid sequence elements associated with structurally variant zinc finger clusters define subfamilies of zinc finger proteins (ZFPs). The FAR domain (Finger Associated Repeats) is a novel type of repeat element found at the amino-terminus in a subfamily of Xenopus laevis ZFPs. Northern blot analyses of three different members of the FAR subfamily (XFO 6, XFO 9-3 and XFG 68) revealed that each of these genes is transcribed during oogenesis, embryogenesis and in all investigated tissues of adult animals thereby indicating a ubiquitous distribution of transcripts. All FAR-ZFPs tested so far have specific RNA homopolymer binding activity; they associate preferentially with poly(U). The FAR repeats possess limited primary sequence homology with a sequence in the nucleolar shuttling protein NO38, within a region that contains a casein kinase II phosphorylation site.

Amino Acid Sequence↗