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Pcp oligomers

D Rivas, A Ginebreda, A Elosegi, J Pozo, S Pérez, C Quero, D Barceló
Characterization of river ecosystems must take into consideration both structural and functional aspects. For the latter, a convenient and simple approach for routine monitoring is based on the decomposition of organic matter measured in terms of breakdown of natural organic substrates like leaf litter, wood sticks. Here we extended the method to a synthetic organic material using polymer probes characterized by MALDI-TOF/MS. We first characterized several commercial available polymers, and finally selected polycaprolactonediol 1250 (PCP 1250), a polyester oligomer, as the most convenient for further studies...
December 15, 2016: Science of the Total Environment
Sergei Kalynych, Maia Cherney, Mihnea Bostina, Isabelle Rouiller, Miroslaw Cygler
Bacteria have evolved cellular control mechanisms to ensure proper length specification for surface-bound polysaccharides. Members of the Polysaccharide Copolymerase (PCP) family are central to this process. PCP-1 family members are anchored to the inner membrane through two transmembrane helices and contain a large periplasm-exposed domain. PCPs are known to form homooligomers but their exact stoichiometry is controversial in view of conflicting structural and biochemical data. Several prior investigations addressing this question indicated a nonameric, hexameric, or tetrameric organization of several PCP-1 family members...
January 2015: Protein Science: a Publication of the Protein Society
Hanwei Liu, Tao Zou, Jin-Ming Gao, Liwei Gu
Procyanidin dimers, trimers, and tetramers are absorbable, whereas larger oligomers are not. Procyanidins in cranberries are bioactive components that help prevent chronic diseases; however, 85% of cranberry procyanidins are large oligomers or polymers with a degree of polymerization above four. The objective of this study was to depolymerize cranberry procyanidins, particularly the polymers, into absorbable oligomers. Partially purified cranberry procyanidins (PCP) were obtained using chromatographic methods...
November 1, 2013: Food Chemistry
Nobuhiro Yanai, Takashi Uemura, Wataru Kosaka, Ryotaro Matsuda, Tetsuhiro Kodani, Meiten Koh, Takashi Kanemura, Susumu Kitagawa
The dynamics of oligo(vinylidene fluoride) (OVDF) confined in regular nanochannels of a porous coordination polymer (PCP) was studied by means of dielectric spectroscopy. The OVDF chains in the PCP nanopores showed two Arrhenius-type relaxation processes at lower temperatures than the relaxation temperature observed for the neat OVDF, showing the enhanced mobility of the confined OVDF.
April 14, 2012: Dalton Transactions: An International Journal of Inorganic Chemistry
Jeramie J Adams, Navamoney Arulsamy, Dean M Roddick
The syntheses of Ir(I) and Ir(III) complexes incorporating the electron-withdrawing pincer ligand (1,3-C(6)H(4)(CH(2)P(CF(3))(2))(2)) ((CF(3))PCPH) with (PPh(3))(3)Ir(CO)H and subsequent chemistry are reported. Under ambient conditions, reaction of 1 equiv. (CF(3))PCPH with (PPh(3))(3)Ir(CO)H gave the mono-bridged complex [Ir(CO)(PPh(3))(2)(H)](2)(μ-(CF(3))PCPH) (1). Reaction of (PPh(3))(3)Ir(CO)H with excess (CF(3))PCPH and MeI gave the doubly-bridged complex [Ir(CO)(PPh(3))(H)](2)(μ-(CF(3))PCPH)(2) (2), whereas the tetrameric oligomer [Ir(CO)(PPh(3))(H)](4)(μ-(CF(3))PCPH)(4) (2-sq) was obtained from a 1:1 ligand:metal mixture in benzene in the presence of excess MeI...
October 21, 2011: Dalton Transactions: An International Journal of Inorganic Chemistry
Kane Larue, Robert C Ford, Lisa M Willis, Chris Whitfield
Neisseria meningitidis serogroup B and Escherichia coli K1 bacteria produce a capsular polysaccharide (CPS) that is composed of α2,8-linked polysialic acid (PSA). Biosynthesis of PSA in these bacteria occurs via an ABC (ATP-binding cassette) transporter-dependent pathway. In N. meningitidis, export of PSA to the surface of the bacterium requires two proteins that form an ABC transporter (CtrC and CtrD) and two additional proteins, CtrA and CtrB, that are proposed to form a cell envelope-spanning export complex...
May 13, 2011: Journal of Biological Chemistry
Magdalene Papadopoulos, Renato Morona
In Shigella flexneri, the polysaccharide copolymerase (PCP) protein Wzz(SF) confers a modal length of 10 to 17 repeat units (RUs) to the O-antigen (Oag) component of lipopolysaccharide (LPS). PCPs form oligomeric structures believed to be related to their function. To identify functionally important regions within Wzz(SF), random in-frame linker mutagenesis was used to create mutants with 5-amino-acid insertions (termed Wzz(i) proteins), and DNA sequencing was used to locate the insertions. Analysis of the resulting LPS conferred by Wzz(i) proteins identified five mutant classes...
July 2010: Journal of Bacteriology
Vladimir N Malashkevich, Natalya G Dulyaninova, Udupi A Ramagopal, Melissa A Liriano, Kristen M Varney, David Knight, Michael Brenowitz, David J Weber, Steven C Almo, Anne R Bresnick
S100A4, a member of the S100 family of Ca(2+)-binding proteins, regulates carcinoma cell motility via interactions with myosin-IIA. Numerous studies indicate that S100A4 is not simply a marker for metastatic disease, but rather has a direct role in metastatic progression. These observations suggest that S100A4 is an excellent target for therapeutic intervention. Using a unique biosensor-based assay, trifluoperazine (TFP) was identified as an inhibitor that disrupts the S100A4/myosin-IIA interaction. To examine the interaction of S100A4 with TFP, we determined the 2...
May 11, 2010: Proceedings of the National Academy of Sciences of the United States of America
Benjamin M Hogan, Heather Verkade, Graham J Lieschke, Joan K Heath
The rapid embryonic development and high fecundity of zebrafish contribute to the great advantages of this model for the study of developmental genetics. Transient disruption of the normal function of a gene during development can be achieved by microinjecting mRNA, DNA or short chemically stabilized anti-sense oligomers, called morpholinos (MOs), into early zebrafish embryos. The ensuing develop ment of the microinjected embryos is observed over the following hours and days to analyze the impact of the microinjected products on embryogenesis...
2008: Methods in Molecular Biology
Ante Tocilj, Christine Munger, Ariane Proteau, Renato Morona, Leanne Purins, Eunice Ajamian, John Wagner, Magdalene Papadopoulos, Luisa Van Den Bosch, John L Rubinstein, James Féthière, Allan Matte, Miroslaw Cygler
The chain length distribution of complex polysaccharides present on the bacterial surface is determined by polysaccharide co-polymerases (PCPs) anchored in the inner membrane. We report crystal structures of the periplasmic domains of three PCPs that impart substantially different chain length distributions to surface polysaccharides. Despite very low sequence similarities, they have a common protomer structure with a long central alpha-helix extending 100 A into the periplasm. The protomers self-assemble into bell-shaped oligomers of variable sizes, with a large internal cavity...
February 2008: Nature Structural & Molecular Biology
Guiling Zhang, Jing Ma, Jin Wen
The packing structures and packing effects on excitation energies of oligomers of polyfuran (PFu), polypyrrole (PPy), polycyclopentidene (PCp), polythiophene (PTh), polyphosphole (PPh), and polysilole (PSi) are comparatively studied by employing molecular dynamics (MD) simulations and time-dependent density functional theory (TDDFT) calculations. The dependence of packing structures on the main group of heteroatoms in the five-membered heterocyclic oligomers is exhibited from MD simulations. The planarity of backbones and the population of pi-stacked structures increase with the heteroatoms going from group 14 to group 16; i...
October 11, 2007: Journal of Physical Chemistry. B
Dieter Leupold, Klaus Teuchner, Jürgen Ehlert, Klaus-Dieter Irrgang, Gernot Renger, Heiko Lokstein
Stepwise two-photon excited fluorescence (TPEF) spectra of the photosynthetic antenna complexes PCP, CP47, CP29, and light-harvesting complex II (LHC II) were measured. TPEF emitted from higher excited states of chlorophyll (Chl) a and b was elicited via consecutive absorption of two photons in the Chl a/b Qy range induced by tunable 100-fs laser pulses. Global analyses of the TPEF line shapes with a model function for monomeric Chl a in a proteinaceous environment allow distinction between contributions from monomeric Chls a and b, strongly excitonically coupled Chls a, and Chl a/b heterodimers/-oligomers...
September 1, 2006: Journal of Biological Chemistry
Nathan J Hillson, Christopher T Walsh
Nonribosomal peptide synthetases (NRPS), fatty acid synthases (FAS), and polyketide sythases (PKS) are multimodular enzymatic assembly lines utilized in natural product biosynthesis. Previous data on FAS and PKS subunits have indicated that they are homodimers and that some of their catalytic functions can work in trans. When NRPS assembly lines have been probed for comparable formation of stable oligomers, no evidence had been forthcoming that species other than monomer forms were active. In this work we focus on the six-domain (Cy1-Cy2-A-C1-PCP-C2) enzyme VibF from the vibriobactin synthetase assembly line, which contains three other proteins, VibB, VibE, and VibH, that--when purified and mixed with VibF and the substrates ATP, threonine, 2,3-dihydroxybenzoate (DHB), and norspermidine--produce the iron chelator vibriobactin...
January 28, 2003: Biochemistry
I Francesconi, W D Wilson, F A Tanious, J E Hall, B C Bender, R R Tidwell, D McCurdy, D W Boykin
Dicationic 2,4-bis(4-amidinophenyl)furans 5-10 and 2, 4-bis(4-amidinophenyl)-3,5-dimethylfurans 14 and 15 have been synthesized. Thermal melting studies revealed high binding affinity of the compounds to poly(dA-dT) and to the duplex oligomer d(CGCGAATTCGCG)2. All of the new compounds were effective against Pneumocystis carinii pneumonia in the immunosuppressed rat model with up to 200-fold increase in activity compared to the control compound pentamidine. No toxicity was noted for 5, 7-10 at the dose of 10 micromol/kg/d; however, the isopropyl analogue 7 showed toxicity comparable to pentamidine at the dosage of 20 micromol/kg/d...
June 17, 1999: Journal of Medicinal Chemistry
D W Boykin, A Kumar, G Xiao, W D Wilson, B C Bender, D R McCurdy, J E Hall, R R Tidwell
The syntheses of 12 new 2,5-bis[4-(N-alkylamidino)phenyl]furans are reported. The interaction of these dicationic furans with poly(dA-dT) and with the duplex oligomer d(CGCGAATTCGCG)2 was determined by Tm measurements, and the effectiveness of these compounds against the immunosuppressed rat model of Pneumocystis carinii was evaluated. At the screening dose of 10 mumol/kg, 9 of the 14 N-alkylamidino furans described here are more active than the parent compound 1. Substitution of an alkyl group of the amidino nitrogen, except for in 9, 13, and 15, resulted in higher affinity for DNA than the parent compound as judged by the larger delta Tm values and suggests enhanced van der Waals interactions in the bis-amidine-DNA complex...
January 1, 1998: Journal of Medicinal Chemistry
M M Hingorani, S S Patel
The equilibrium nucleotide binding and oligomerization of bacteriophage T7 gene 4 helicases have been investigated using thymidine 5'-triphosphate (dTTP), deoxythymidine 5'-(beta, gamma-methylenetriphosphate)(dTMP-PCP), thymidine 5'-diphosphate (dTDP), adenosine 5'-triphosphate (ATP), and adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S). In the presence of nucleotide ligands, T7 helicases self-assemble into hexamers with six potential nucleotide binding sites that are nonequivalent both in the absence and in the presence of single-stranded DNA...
February 20, 1996: Biochemistry
M M Hingorani, S S Patel
Protein-DNA interactions of bacteriophage T7 DNA primase/helicase protein 4A' with small synthetic oligodeoxynucleotides were investigated using a 20-base-paired hairpin duplex, and 10-, 30-, and 60-base-long single-stranded DNA. The effect of nucleotide cofactors on DNA binding was examined using membrane binding assays which showed that 4A' binds DNA optimally only in the presence of MgdTMP-PCP, the nonhydrolyzable analog of dTTP. About 20% of single-stranded DNA binding was observed in the presence of MgdTDP, but none was detectable in the absence of nucleotides...
November 23, 1993: Biochemistry
H C Schröder, M Kelve, H Schäcke, W Pfleiderer, R Charubala, R J Suhadolnik, W E Müller
2',5'-Oligoadenylates (2-5As) inhibit the type I DNA topoisomerase activity both in uninfected and HIV-1-infected human T cell line H9 as well as the purified enzyme (calf thymus). Topoisomerase I activity was determined by measuring the relaxation of negatively supercoiled pBR322 DNA. Inhibition of topoisomerase I by 2-5A depends on the chain length of the oligomer and the presence of 5'-phosphate. The 5'-triphosphate of the 2-5A hexamer was most active (almost total inhibition of DNA relaxation at 10 microM concentration); the 2-5A core trimer (at 100 microM) displayed no significant effect...
February 1994: Chemico-biological Interactions
E Romaniuk, L W McLaughlin, T Neilson, P J Romaniuk
In order to make efficient use of T4 RNA ligase in a program involving chemical-enzymatic oligoribonucleotide synthesis, the sequence effects of the acceptor oligomer have been refined. The reaction of the donor molecules pCp and pUpUpUpCp with a series of trinucleoside diphosphates ApApN, CpNpA and NpCpA (where N = U, C, A or G) was examined. High-performance liquid chromatography was used for simultaneous analysis of all substrates, intermediates and products. For all trinucleoside bisphosphates tested a substantial amount of the intermediate A(5')pp(5')Cp or A(5')pp(5')UpUpUpCp was observed...
July 1982: European Journal of Biochemistry
J Imai, P F Torrence
The oligonucleotides A5'pp5'A2'p5'A2'p5'A and A5'ppp5'A2'p5'A2'p5'A were prepared by reaction of AMP or ADP, respectively, with the 5'-(phosphoimidazolidate) of A2'p5'A2'p5'A. A5'pppp5'A2'(p5'A)n (n = 1-3) were synthesized by reaction of p5'A2'(p5'A)n (n = 1-3) with adenosine 5'-trimetaphosphate. All structures were confirmed by enzyme digestion and 1H and 31P nuclear magnetic resonance (NMR). The products A5'pppp5'A2'p5'A and A5'pppp5'A2'p5'A2'p5'A were found to be identical with two of the products of the 2-5A synthetase catalyzed reaction of Ap4A with ATP, thus confirming the structural assignments made by earlier investigators...
February 14, 1984: Biochemistry
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