bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of surfactant type on the synthesis of PMMA using redox initiation and high frequency ultrasound
Authors: Parra Cristina , Albano Carmen , González Gema 
Published: September 2008

AbstractIn the present work, a study of the effect of the surfactant nature on the synthesis of polymethylmethacrylate (PMMA) obtained by high frequency ultrasonic radiation and redox initiation is presented. The surfactants used were an anionic: sodium lauryl sulfate (SLS) and a nonionic: nonylphenol etoxilated. Different morphologies, particle size, and microstructures were obtained depending on the surfactant concentration (0.5, 1.0, 1.5, and 2.0)%. The highest conversion values of PMMA were obtained with SLS, resulting in a highly syndiotactic polymer. High frequency ultrasound is very efficient when ionic surfactants are used. However, for nonionic surfactants ultrasonic irradiation is very inefficient to initiate polymerization, in this case the effect of redox initiation was very marked increasing polymerization conversion. For this, surfactant blends of PMMA/PEO were obtained when redox initiation was used together with high frequency ultrasound. POLYM. ENG. SCI., 2008. © 2008 Society of Plastics Engineers.
Adhesion parameters at the interface in nanoparticulate filled polymer systems
Authors: Kovačević Vera , Vrsaljko Domagoj , Lučić Blagojević Sanja , Leskovac Mirela 
Published: September 2008

AbstractThe interface in particulate filled polymer systems determine to a large extent, the mechanical and morphological properties of composites and polymer blends. The present contribution describes surface free energy measurements and calculations of adhesion parameters at the interface in poly(vinyl acetate) (PVAc) and polyurethane (PU) composites as well as in styrene acrylonitrile/ethylene propylene diene monomer (SAN/EPDM) blends filled with calcium carbonate (CaCO3) nanofillers. The effects that a surface pretreatment of the filler with either silane or stearic acid had on the interface been investigated and related to the resulting properties of the composites and filled polymer blend. The optimal adhesion in the particulate composites and blends was determined by the minimal interfacial energy and optimal coefficient of wetting. The conditions of the optimal adhesion with filler location at the interface, predicting by the thermodynamical models, correlated well with the improvement of the morphological and mechanical properties. POLYM. ENG. SCI., 2008. © 2008 Society of Plastics Engineers.
Synthesis of biodegradable polyhydroxyalcanoate copolymer from a renewable source by alternate feeding
Authors: Pereira Silvia M.F. , Sánchez Rubén J. , Rieumont Jacques , Cabrera Jose G. 
Published: September 2008

AbstractPolyhydroxyalcanoates copolymers with 3‐hydroxybutirate (3HB) and 3‐hydroxyvalerate (3HV) co‐monomers, P3(HB‐co‐x%HV), were produced in fed‐batch culture by Ralstonia eutropha DSM428 using fructose as a single carbon source in the first step and adding propionic acid in the second step by alternating feeding. Polymer yield was 0.18 g/L with a content of 24 mol% of the 3HV fraction determined by 1H NMR. NMR measurements indicated that the polymer obtained is isotactic. The copolymer attained 35% of crystallinity according to X‐ray diffraction measurements, and two (020) planes were observed. Thermal behavior presented melting temperature at 154°C and the crystallization temperature was 65°C. A glass transition temperature was observed at −10°C. Average molecular weight measured by GPC was 4.9 × 105 Dalton. Isothermal radial growth rates of spherulites of P3(HB‐co‐24%HV) were studied. All experimental facts and the analysis of the sequence distribution of diads and triads of 3HB and 3HV units led to the conclusion that it is not a completely statistical random copolymer once it contains different types of segments. POLYM. ENG. SCI., 2008. © 2008 Society of Plastics Engineers.
Photocrosslinkable hyperbranched polyfluorenes containing oxadiazole: synthesis, photophysics and electroluminescence
Authors: Tang Duo‐Feng , Wen Gui‐An , Wei Wei , Huang Wei 
Published: September 2008

AbstractBACKGROUND: Crosslinkable hyperbranched polymers have great potential for use in organic light‐emitting devices and photovoltaics. With this in mind, two crosslinkable hyperbranched polyfluorenes, P5 and P6, containing oxadiazole as the core, and linear polyfluorene P0 were synthesized via palladium‐catalyzed Suzuki coupling. A device was also made.RESULTS: The resulting polymers were characterized using NMR, gel permeation chromatography, differential scanning calorimetry and thermogravimetric analysis. The spectral behavior of the polymers was also investigated. Compared with uncrosslinked P5 and P6, the photoluminescence spectra of crosslinked P5 and P6 were little influenced by the crosslinking. After annealing for 3 h at 200 °C in air, the photoluminescence of P6 (with a greater content of branched units) showed excellent stability compared with that of P5 and P0. The results for the device revealed that photocrosslinking improves the stability of the electroluminescence.CONCLUSION: The crosslinkable polymers obtained can be used in multilayer devices. Copyright © 2008 Society of Chemical Industry
Proteomics integrated with Escherichia coli vector‐based vaccines and antigen microarrays reveals the immunogenicity of a surface sialidase‐like protein of Propionibacterium acnes
Authors: Huang Cheng‐Po , Liu Yu‐Tsueng , Nakatsuji Teruaki , Shi Yang , Gallo Richard R. , Lin Shwu‐Bin , Huang Chun‐Ming 
Published: September 2008

AbstractProteomics is a powerful tool for the identification of proteins, which provides a basis for rational vaccine design. However, it is still a highly technical and time‐consuming task to examine a protein's immunogenicity utilizing traditional approaches. Here, we present a platform for effectively evaluating protein immunogenicity and antibody detection. A tetanus toxin C fragment (Tet‐c) was used as a representative antigen to establish this platform. A cell wall‐anchoring sialidase‐like protein (SLP) of Propionibacterium acnes was utilized to assess the efficacy of this platform. We constructed an Escherichia coli vector‐based vaccine by overexpressing Tet‐c or SLP in E. coli and utilized an intact particle of E. coli itself as a vaccine (E. coli Tet‐c or SLP vector). After ultraviolet (UV) irradiation, the E. coli vector‐based vaccines were administered intranasally into imprinting control region mice without adding exogenous adjuvants. For antibody detection, we fabricated antigen microarrays by printing with purified recombinant proteins including Tet‐c and SLP. Our results demonstrated that detectable antibodies were elicited in mice 6 weeks after intranasal administration of UV‐irradiated E. coli vector‐based vaccines. The antibody production of Tet‐c and SLP was significantly elevated after boosting. Notably, the platform with main benefits of using E. coli itself as a vaccine carrier provides a critical template for applied proteomics aimed at screening novel vaccine targets. In addition, the novel immunogenic SLP potentially serves as an antigen candidate for the development of vaccines targeting P. acnes‐associated diseases.
Therapeutic starvation and autophagy in prostate cancer: A new paradigm for targeting metabolism in cancer therapy
Authors: DiPaola Robert S. , Dvorzhinski Dmitri , Thalasila Anu , Garikapaty Venkata , Doram Donyell , May Michael , Bray K. , Mathew Robin , Beaudoin Brian , Karp C. , Stein Mark , Foran David J. , White Eileen 
Published: September 2008

AbstractBACKGROUNDAutophagy is a starvation induced cellular process of self‐digestion that allows cells to degrade cytoplasmic contents. The understanding of autophagy, as either a mechanism of resistance to therapies that induce metabolic stress, or as a means to cell death, is rapidly expanding and supportive of a new paradigm of therapeutic starvation.METHODSTo determine the effect of therapeutic starvation in prostate cancer, we studied the effect of the prototypical inhibitor of metabolism, 2‐deoxy‐D‐glucose (2DG), in multiple cellular models including a transfected pEGFP‐LC3 autophagy reporter construct in PC‐3 and LNCaP cells.RESULTSWe found that 2DG induced cytotoxicity in PC‐3 and LNCaP cells in a dose dependent fashion. We also found that 2DG modulated checkpoint proteins cdk4, and cdk6. Using the transfected pEGFP‐LC3 autophagy reporter construct, we found that 2DG induced LC3 membrane translocation, characteristic of autophagy. Furthermore, knockdown of beclin1, an essential regulator of autophagy, abrogated 2DG induced autophagy. Using Western analysis for LC3 protein, we also found increased LC3‐II expression in 2DG treated cells, again consistent with autophagy. In an effort to develop markers that may be predictive of autophagy, for assessment in clinical trials, we stained human prostate tumors for Beclin1 by immunohistochemistry (IHC). Additionally, we used a digitized imaging algorithm to quantify Beclin1 staining assessment.CONCLUSIONSThese data demonstrate the induction of autophagy in prostate cancer by therapeutic starvation with 2DG, and support the feasibility of assessment of markers predictive of autophagy such as Beclin1 that can be utilized in clinical trials. Prostate © 2008 Wiley‐Liss, Inc.
Association of HPC2/ELAC2 and RNASEL non‐synonymous variants with prostate cancer risk in African American familial and sporadic cases
Authors: Robbins Christiane M. , Hernandez Wenndy , Ahaghotu Chiledum , Bennett James , Hoke Gerald , Mason Terry , Pettaway Curtis A. , Vijayakumar Srinivasan , Weinrich Sally , Furbert‐Harris Paulette , Dunston Georgia , Powell Isaac J. , Carpten John D. , Kittles Rick A. 
Published: September 2008

AbstractIntroductionThe RNASEL and HPC2/ELAC2 genes have been implicated in hereditary prostate cancer. Further assessment of the role of these genes in sporadic prostate cancer in African American men (AAM) is warranted.MethodsGenotyping of HPC2/ELAC2 variants (S217L, A541T), along with RNASEL variants (R462Q and E541D) was completed in 155 African American sporadic and 88 familial prostate cancer cases, and 296 healthy male controls. Logistic regression analysis was performed and odds ratios (OR) were calculated, while correcting for both age and population stratification using admixture informative markers.ResultsThe HPC2/ELAC2 217L allele was significantly associated with risk of prostate cancer when taking all cases into account (OR = 1.6; 1.0–2.6; P = 0.03). The RNASEL 541D allele was associated with a decrease in risk of prostate cancer in sporadic cases (OR = 0.4; 0.2–0.8; P = 0.01). We did not detect an association between prostate cancer risk and the RNASEL R462Q variant. Results from haplotype analyses of the two RNASEL variants revealed highly significant differences in haplotype allele frequencies between cases and controls suggesting a synergistic effect at the RNASEL locus. One haplotype in particular (462R–541D) is far more frequent in our control population and shows a strong protective effect against prostate cancer (OR = 0.47, P = 8.1 × 10−9).ConclusionsThese results suggest that HPC2/ELAC2 and RNASEL may play a role, however minor, in prostate cancer risk among AAM.
Insights into the DNA cleavage mechanism of human LINE‐1 retrotransposon endonuclease
Authors: Repanas Kostas , Fuentes Gloria , Cohen Serge X. , Bonvin Alexandre M. J. J. , Perrakis Anastassis 
Published: September 2008

AbstractThe human LINE‐1 endonuclease (L1‐EN) contributes in defining the genomic integration sites of the abundant human L1 and Alu retrotransposons. LINEs have been considered as possible vehicles for gene delivery and understanding the mechanism of L1‐EN could help engineering them as genetic tools. We tested the in vitro activity of point mutants in three L1‐EN residues—Asp145, Arg155, Ile204—that are key for DNA cleavage, and determined their crystal structures. The L1‐EN structure remains overall unaffected by the mutations, which change the enzyme activity but leave DNA cleavage sequence specificity mostly unaffected. To better understand the mechanism of L1‐EN, we performed molecular dynamics simulations using as model the structures of wild type EN‐L1, of two βB6‐βB5 loop exchange mutants we have described previously to be important for DNA recognition, of the R155A mutant from this study, and of the homologous TRAS1 endonuclease: all confirm a rigid scaffold. The simulations crucially indicate that the βB6‐βB5 loop shows an anticorrelated motion with the surface loops βA6‐βA5 and βB3‐αB1. The latter loop harbors N118, a residue that alters DNA cleavage specificity in homologous endonucleases, and implies that the plasticity and correlated motion of these loops has a functional importance in DNA recognition and binding. To further explore how these loops are possibly involved in DNA binding, we docked computationally two DNA substrates to our structure, one involving a flipped‐out nucleotide downstream the scissile phosphodiester; and one not. The models for both scenarios are feasible and agree with the hypotheses derived from the dynamic simulations. The reduced cleavage activity we have observed for the I204Y mutant above however, favors the flipped out nucleotide model. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Towards accurate residue–residue hydrophobic contact prediction for α helical proteins via integer linear optimization
Authors: Rajgaria R. , McAllister S. R. , Floudas C. A. 
Published: September 2008

AbstractA new optimization‐based method is presented to predict the hydrophobic residue contacts in α‐helical proteins. The proposed approach uses a high resolution distance dependent force field to calculate the interaction energy between different residues of a protein. The formulation predicts the hydrophobic contacts by minimizing the sum of these contact energies. These residue contacts are highly useful in narrowing down the conformational space searched by protein structure prediction algorithms. The proposed algorithm also offers the algorithmic advantage of producing a rank ordered list of the best contact sets. This model was tested on four independent α‐helical protein test sets and was found to perform very well. The average accuracy of the predictions (separated by at least six residues) obtained using the presented method was ∼66% for single domain proteins. The average true positive and false positive distances were also calculated for each protein test set and they are 8.87 and 14.67 Å, respectively. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Molecular dynamics of amicyanin reveals a conserved dynamical core for blue copper proteins
Authors: Rizzuti Bruno , Sportelli Luigi , Guzzi Rita 
Published: September 2008

AbstractMolecular dynamics simulation has been carried out for the blue copper protein amicyanin from two different sources, Paracoccus denitrificans and Paraccocus versutus, to investigate the structural and dynamical properties common to the two molecules and to identify prominent features shared with proteins of the same family, the monomeric cupredoxins. The two amicyanins have almost identical secondary and tertiary structure. In the simulation, they differ for the number of hydrogen bonds in the main chain and the conformation of some β‐strands. However, they strictly maintain the arrangement of the portions of the β‐barrel that are conserved in the folding architecture of the blue copper proteins. Paracoccus versutus amicyanin equilibrates more rapidly, shows lower atomic deviation values, and is less rigid with respect to Paracoccus denitrificans amicyanin. Principal component analysis reveals that the conformational subspaces corresponding to eigenvectors with the same index for each of the two molecules are not necessarily equivalent. Nevertheless, a core scaffold with constrained dynamics exist for both amicyanins. In addition, two fairly flexible regions that are located on the opposite side with respect to the interaction sites with the partner molecules in the redox process have been evidenced in the protein structure. This description of amicyanin, with a few mobile regions remote from the active site and a rigid scaffold including most of the protein β‐barrel, has a close similarity with that of azurin and plastocyanin, two other cupredoxins previously investigated in simulation. Furthermore, similarities in the distribution of the atomic fluctuations indicate that amicyanin, azurin, and plastocyanin possess common dynamical features, in spite of differences in their structure. On the basis of these findings, we suggest that topological constraints imposed by the folding in correspondence of protein regions that are the most conserved determine the protein dynamics of the cupredoxin family. The dynamical properties of the cupredoxins might be controlled for functional advantages that include the binding mechanism with the biological partners and the collective inner motions of the protein matrix required for the electron transfer, whereas long‐range conformational changes in the redox reaction should be excluded. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Substrate directs enzyme dynamics by bridging distal sites: UDP‐galactopyranose mutase
Authors: Yao Xiaohui , Bleile Dustin W. , Yuan Yue , Chao Jay , Sarathy Karunan P. , Sanders David A. R. , Pinto B. Mario , O'Neill Melanie A. 
Published: September 2008

AbstractUDP‐Galactopyranose mutase (UGM) is a flavoenzyme that catalyzes interconversion of UDP‐galactopyranose (UDP‐Galp) and UDP‐galactofuranose (UDP‐Galf); its activity depends on FAD redox state. The enzyme is vital to many pathogens, not native to mammals, and is an important drug target. We have probed binding of substrate, UDP‐Galp, and UDP to wild type and W160A UGM from K. pneumoniae, and propose that substrate directs recognition loop dynamics by bridging distal FAD and W160 sites; W160 interacts with uracil of the substrate and is functionally essential. Enhanced Trp fluorescence upon substrate binding to UGM indicates conformational changes remote from the binding site because the fluorescence is unchanged upon binding to W70F/W290F UGM where W160 is the sole Trp. MD simulations map these changes to recognition loop closure to coordinate substrate. This requires galactose‐FAD interactions as Trp fluorescence is unchanged upon substrate binding to oxidized UGM, or binding of UDP to either form of the enzyme, and MD show heightened recognition loop mobility in complexes with UDP. Consistent with substrate‐directed loop closure, UDP binds 10‐fold more tightly to oxidized UGM, yet substrate binds tighter to reduced UGM. This requires the W160‐U interaction because redox‐switched binding affinity of substrate reverses in the W160A mutant where it only binds when oxidized. Without the anchoring W160‐U interaction, an alternative binding mode for UDP is detected, and STD‐NMR experiments show simultaneous binding of UDP‐Galp and UDP to different subsites in oxidized W160A UGM: Substrate no longer directs recognition loop dynamics to coordinate tight binding to the reduced enzyme. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Fuzzy domains: New way of describing flexibility and interdependence of the protein domains
Authors: Yesylevskyy Semen O. , Kharkyanen Valery N. 
Published: September 2008

AbstractWe proposed the innovative method of domain identification based on the concept of the fuzzy domains. In this method each residue of the protein can belong to several domains simultaneously with certain weights, which reflect to what extent this residue shares the motion pattern of the given domain. Our method allows describing the fuzzy boundaries between the domains and the gradual changes of the motion pattern from one domain to the other. It provides the reasonable compromise between the continuous change of the protein dynamics from one residue to the other and the discrete description of the structure in terms of small number of domains. We suggested quantitative criterion, which shows the overall degree of domain flexibility in the protein. The concept of the fuzzy domains provides an innovative way of visualization of domain flexibility, which makes the gradual transitions between the domains clearly visible and comparable to available experimental and structural data. In the future, the concept of the fuzzy domains can be used in the coarse‐grained simulations of the domain dynamics in order to account for internal protein flexibility. Proteins 2009. © 2008 Wiley‐Liss, Inc.
The selenoproteome of Clostridium sp. OhILAs: Characterization of anaerobic bacterial selenoprotein methionine sulfoxide reductase A
Authors: Kim Hwa‐Young , Zhang Yan , Lee Byung Cheon , Kim Jae‐Ryong , Gladyshev Vadim N. 
Published: September 2008

AbstractSelenocysteine (Sec) is incorporated into proteins in response to UGA codons. This residue is frequently found at the catalytic sites of oxidoreductases. In this study, we characterized the selenoproteome of an anaerobic bacterium, Clostridium sp. (also known as Alkaliphilus oremlandii) OhILA, and identified 13 selenoprotein genes, five of which have not been previously described. One of the detected selenoproteins was methionine sulfoxide reductase A (MsrA), an antioxidant enzyme that repairs oxidatively damaged methionines in a stereospecific manner. To date, little is known about MsrA from anaerobes. We characterized this selenoprotein MsrA which had a single Sec residue at the catalytic site but no cysteine (Cys) residues in the protein sequence. Its SECIS (Sec insertion sequence) element did not resemble those in Escherichia coli. Although with low translational efficiency, the expression of the Clostridium selenoprotein msrA gene in E. coli could be demonstrated by 75Se metabolic labeling, immunoblot analyses, and enzyme assays, indicating that its SECIS element was recognized by the E. coli Sec insertion machinery. We found that the Sec‐containing MsrA exhibited at least a 20‐fold higher activity than its Cys mutant form, indicating a critical role of Sec in the catalytic activity of the enzyme. Furthermore, our data revealed that the Clostridium MsrA was inefficiently reducible by thioredoxin, which is a typical reducing agent for MsrA, suggesting the use of alternative electron donors in this anaerobic bacterium that directly act on the selenenic acid intermediate and do not require resolving Cys residues. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Crystal structure of the hexamer of human heat shock factor binding protein 1
Authors: Liu Xueqi , Xu Lingfeng , Liu Yiwei , Tong Xiaohang , Zhu Guangyu , Zhang Xuejun C. , Li Xuemei , Rao Zihe 
Published: September 2008

AbstractHeat shock response (HSR) is a ubiquitous cellular mechanism that copes with a variety of stresses. This response is mediated by a family of transcriptional activators, heat shock factors (HSFs), which are under tight regulation. HSF binding protein 1 (HSBP1) is a negative regulator of HSR and is reported to bind specifically with the active trimeric form of HSF1, thus inhibiting its activity. HSBP1 contains heptad‐repeats in the primary sequence and was believed to stay in a trimer form in solution. We report the crystal structure of the trimerization domain of the M30I/L55P mutant of human HSBP1 at 1.8 Å resolution. In this crystal form, the HSBP1 fragment of residues 6–53 forms a continuous, 11‐turn long helix. The helix self‐associates to form a parallel, symmetrical, triple coiled‐coil helix bundle, which further assembles into a dimer of trimers in a head‐to‐head fashion. Solution study confirmed that the wild‐type HSBP1 shares similar biophysical properties with the crystallized variant. Furthermore, we identified Ser31, which buried its polar side chain in the hydrophobic interior of the helix bundle, as a stability weak‐spot. Substitution of this residue with Ile increases the melting temperature by 24°C, implicating that this conserved serine residue is maintained at position 31 for functional purposes. Proteins 2009. © 2008 Wiley‐Liss, Inc.