bluuebunny/crossref_metadata_2025_split huggingface dataset:
Porphyrin‐based, light‐activated antimicrobial materials
Authors: Bozja Jadranka , Sherrill Jennifer , Michielsen Stephen , Stojiljkovic Igor 
Published: June 2003

AbstractNew light‐activated antimicrobial materials with a potentially wide range of possible uses in civilian settings were synthesized by the grafting of protoporphyrin IX and zinc protoporphyrin IX to nylon fibers. These fibers were shown to be active against Staphylococcus aureus at light exposures of 10,000 lux and greater and against Escherichia coli at 60,000 lux. They were ineffective against both strains in the absence of light. At 40,000 lux, these fibers showed increased antimicrobial activity against S. aureus with increasing exposure time. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2297–2303, 2003
Linear soluble polybenzyls
Authors: Som Abhijit , Ramakrishnan S. 
Published: June 2003

AbstractLinear soluble polybenzyls, although deceptively simple in structure, have been strangely elusive. We report for the first time the synthesis of perfectly linear soluble polybenzyls by the polycondensation of 1,2,4,5‐tetrasubstituted benzenes with formaldehyde using CHCl3/trifluoroacetic acid (TFA) as the medium, wherein TFA served both as an acidic catalyst as well as a cosolvent. The number‐average molecular weights (Mn's) of the polymers, as determined by gel permeation chromatography, varied from about 1000 to 37,000, depending on the nature of the substituent on the benzene ring; Mn was highest when all four substituents were alkoxy groups and was lowest when they were all alkyl groups. This correlated well with susceptibility of the aromatic ring toward electrophilic aromatic substitution, which is the underlying polymerization mechanism. Differential scanning calorimetry of the polymers showed that most of the samples were amorphous with glass‐transition temperatures ranging from about −80° to +80 °C, whereas a few that were either symmetrically substituted or possessed a long alkyl substituent were partially crystalline. Preliminary studies suggested that the methylene unit linking the phenyl rings in these polybenzyls could be readily oxidized to generate conjugated polymers that may be perceived as carbon analogues of polyaniline–poly(arylmethine)s. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2345–2353, 2003
Semicontinuous seeded cationic emulsion polymerization of styrene: The effects of the concentration and type of cationic surfactant
Authors: Ramos Jose , Forcada Jacqueline 
Published: June 2003

AbstractThe objective of this work was to analyze the effects of the concentration and type of cationic surfactant on the kinetic features (instantaneous and overall conversions) and colloidal characteristics [mean particle diameter, particle size distribution (PSD), and surface charge density] in the semicontinuous seeded cationic emulsion polymerization of styrene. 2,2′‐Azobis(N,N′‐dimethyleneisobutyramidine)dihydrochloride was used as an initiator. The surfactants were dodecyltrimethylammonium bromide (DTAB) and hexadecyltrimethylammonium bromide (HDTAB). So that the evolution of some polymeric and colloidal characteristics of the synthesized latices could be followed, the overall and instantaneous conversions were defined and determined gravimetrically. The PSDs and average particle diameters were determined by transmission electron microscopy and photon correlation spectroscopy. The surface charge density was determined by conductimetric titration. The evolution of the instantaneous conversions, the total number of particles, and the PSDs of the different reactions were related to the nucleation, growth, and coagulation processes taking place in the semicontinuous seeded emulsion polymerizations. The PSDs obtained from the reactions carried out with the emulsifier DTAB, at a concentration equal to its critical micelle concentration (cmc) and at a concentration twice its cmc, presented more and smaller particles than those obtained by the addition of HDTAB to the polymerization recipe. At lower emulsifier concentrations equal to half of the cmc, the system had lower colloidal stability with DTAB. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2322–2334, 2003
Photopolymerization of 2‐hydroxyethyl methacrylate: Effect of the medium properties on the polymerization rate
Authors: Valdebenito A. , Encinas M. V. 
Published: June 2003

AbstractThe effect of solvent properties on the polymerization rate of 2‐hydroxyethyl methacrylate (HEMA) was examined with the photoreaction of 4,4′‐azobis(2‐amidinopropane) and photoinduced electron transfer of a thioxanthone derivative and triethanolamine as the radical source. The polymerization rate of HEMA was markedly affected by pH and the medium polarity. The rate increased over a pH range of 6–8. The dependence of the polymerization rate on the amine concentration photoinitiated by the bimolecular system was different in water and acetonitrile as solvents. In aqueous medium, pH 9.5, the rate increased with the amine concentration reaching a constant value at 0.025 M amine; further amine addition inhibited the polymerization. In organic media the inhibition effect was not observed. Triethanolamine addition did not change the polymerization rate photoinitiated by the azo compound. Photochemical studies of the thioxanthone were carried out under the polymerization conditions. These studies allowed us to simulate the dependence of the polymerization rate on the amine concentration. The results are explained in terms of the interaction of the ketone excited states with the amine in the different media. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2368–2373, 2003
Thermal properties and fracture toughness of epoxy resins cured by phosphonium and pyrazinium salts as latent cationic initiators
Authors: Park Soo‐Jin , Heo Gun‐Young , Suh Dong‐Hack 
Published: June 2003

AbstractIn this work, the latent thermal cationic initiators triphenyl benzyl phosphonium hexafluoroantimonate (TBPH) and benzyl‐2‐methylpyrazinium hexafluoroantimonate (BMPH) were newly synthesized and characterized with IR, 1H NMR, and P NMR spectroscopy. The thermal and mechanical properties of difunctional epoxy [diglycidyl ether of bisphenol A (DGEBA)] resins cured by 1 phr of either TBPH or BMPH were investigated. The DGEBA/TBPH system showed a higher curing temperature and a higher critical stress intensity factor than the epoxy/BMPH system. This could be interpreted in terms of the slow thermal diffusion rate and bulk structure of the four phenyl groups in TBPH. However, the decomposition activation energy derived from the Coats–Redfern method was lower for epoxy/TBPH. This result was probably due to the fact that a broken short‐chain structure was developed by the steric hindrance of TBPH in the difunctional epoxy resin. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2393–2403, 2003
Preparation, thermal properties, and flame retardance of epoxy–silica hybrid resins
Authors: Liu Ying‐Ling , Wu Chuan‐Shao , Chiu Yie‐Shun , Ho Wen‐Hsuan 
Published: June 2003

AbstractA novel epoxy system was developed through the in situ curing of bisphenol A type epoxy and 4,4′‐diaminodiphenylmethane with the sol–gel reaction of a phosphorus‐containing trimethoxysilane (DOPO–GPTMS), which was prepared from the reaction of 9,10‐dihydro‐9‐oxa‐10‐phosphaphenanthrene‐10‐oxide (DOPO) with 3‐glycidoxypropyltrimethoxysilane (GPTMS). The preparation of DOPO–GPTMS was confirmed with Fourier transform infrared, 1H and 31P NMR, and elemental analysis. The resulting organic–inorganic hybrid epoxy resins exhibited a high glass‐transition temperature (167 °C), good thermal stability over 320 °C, and a high limited oxygen index of 28.5. The synergism of phosphorus and silicon on flame retardance was observed. Moreover, the kinetics of the thermal oxidative degradation of the hybrid epoxy resins were studied. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2354–2367, 2003
Fibrillar structure of resorbable microblock copolymers based on 1,5‐dioxepan‐2‐one and ε‐caprolactone
Authors: Andronova Natalia , Finne Anna , Albertsson Ann‐Christine 
Published: June 2003

AbstractThe copolymerization of 1,5‐dioxepan‐2‐one (DXO) and ε‐caprolactone, initiated by a five‐membered cyclic tin alkoxide initiator, was performed in chloroform at 60 °C. Copolymers with different molar ratios of DXO (25, 40, and 60%) were synthesized and characterized. 13C NMR spectroscopy of the carbonyl region revealed the formation of copolymers with a blocklike structure. Differential scanning calorimetry measurements showed that all the copolymers had a single glass transition between −57 and −49 °C and a melting temperature in the range of 30.1–47.7 °C, both of which were correlated with the amount of DXO. An increase in the amount of DXO led to an increase in the glass‐transition temperature and to a decrease in the melting temperature. Dynamic mechanical thermal analysis measurements confirmed the results of the calorimetric analysis, showing a single sharp drop in the storage modulus in the temperature region corresponding to the glass transition. Tensile testing demonstrated good mechanical properties with a tensile strength of 27–39 MPa and an elongation at break of up to 1400%. The morphology of the copolymers was examined with polarized optical microscopy and atomic force microscopy; the films that crystallized from the melt showed a short fibrillar structure (with a length of 0.05–0.4 μm) in contrast to the untreated solution‐cast films. © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2412–2423, 2003
Amino‐functionalized latex particles obtained by a multistep method: Development of a new immunoreagent
Authors: Ramos Jose , Martín‐Molina Alberto , Sanz‐Izquierdo M. Pilar , Rus Antonio , Borque Luis , Hidalgo‐Álvarez Roque , Galisteo‐González Francisco , Forcada Jacqueline 
Published: June 2003

AbstractCationic latex particles with surface amino groups were prepared by a multistep batch emulsion polymerization. In the first one, two or three steps, monodisperse cationic latex particles to be used as the seed were synthesized. In the third and fourth steps, the amino‐functionalized monomer aminoethylmethacrylate hydrochloride was used to synthesize the final functionalized latex particles. Three different azo initiators 2,2′‐azobisisobutyramidine dihydrochloride, 2,2′‐azobisdimethylenisobutyramidine dihydrochloride, and 2,2′‐azobisisobutyronitrile were used as initiators. Hexadecyltrimethylammonium bromide was the emulsifier. To characterize the final latices, conversions were obtained gravimetrically, and particle size distributions and average particle diameters were determined by transmission electron microscopy and photon correlation spectroscopy. The amount of amino groups was determined by conductimetric titrations. Colloidal aspects were ascertained by measuring the electrophoretic mobilities. Activation of these particles with glutaraldehyde produced an efficient reagent for latex‐enhanced immunoassay. The covalent coupling efficiency (protein covalently bound with respect to the total amount of protein adsorbed) was compressed between 50 and 80%. The developed immunoreagent was applied to the measurement of serum ferritin concentration in a new turbidimetric procedure that was compared with a commercial nephelometric method; the results obtained with both methods demonstrated that the two procedures correlated well (r = 0.992). © 2003 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 2404–2411, 2003
Reaction mechanism of caspases: Insights from QM/MM Car–Parrinello simulations
Authors: Sulpizi M. , Laio A. , VandeVondele J. , Cattaneo A. , Rothlisberger U. , Carloni P. 
Published: June 2003

AbstractCaspases are fundamental targets for pharmaceutical interventions in a variety of diseases involving disregulated apoptosis. Here, we present a quantum mechanics/molecular mechanics Car–Parrinello study of key steps of the enzymatic reaction for a representative member of this family, caspase‐3. The hydrolysis of the acyl–enzyme complex is described at the density functional (BLYP) level of theory while the protein frame and solvent are treated using the GROMOS96 force field. These calculations show that the attack of the hydrolytic water molecule implies an activation free energy of ca. ΔFA ≈ 19 ± 4 kcal/mol in good agreement with experimental data and leads to a previously unrecognized gem‐diol intermediate that can readily (ΔFA ≈ 5 ± 3 kcal/mol) evolve to the enzyme products. Our findings assist in elucidating the striking difference in catalytic activity between caspases and other structurally well‐characterized cysteine proteases (papains and cathepsins) and may help design novel transition‐state analog inhibitors. Proteins 2003;52:212–224. © 2003 Wiley‐Liss, Inc.
Free energy calculations for the relative binding affinity between DNA and λ‐repressor
Authors: Saito Minoru , Sarai Akinori 
Published: June 2003

AbstractThe change in the binding free energy between DNA and λ‐repressor resulting from a base substitution, thymine (T)→deoxyuracil (abbreviated as U), was evaluated by the free energy perturbation method on the basis of molecular dynamics simulations for the DNA–λ‐repressor complex in water with all degrees of freedom and including long‐range Coulomb interactions. The binding free energy change that we calculated (1.47 ± 0.40 kcal/mol) was in good agreement with an experimental value (1.8 kcal/mol). We clarified why the small difference between T and U (CH3 in T is replaced with H in U) caused such a significant change in the binding free energy: The substitution of CH3 in T with H in U lowered the dissociated‐state free energy level due to the gain of the hydration free energy. Furthermore, the T→U substitution raised the free energy level in the associated state due to the loss of the favored van der Waals (vdW) interactions with the λ‐repressor amino acid residues. In other words, the amino acid residues of λ‐repressor can recognize the CH3 in T through the vdW interactions with the CH3. This recognition is enhanced in a water environment, because the hydrophobic CH3 prefers the amino acid residues of λ‐repressor to water molecules. Proteins 2003;52:129–136. © 2003 Wiley‐Liss, Inc.
A new bioinformatic approach to detect common 3D sites in protein structures
Authors: Jambon Martin , Imberty Anne , Deléage Gilbert , Geourjon Christophe 
Published: June 2003

AbstractAn innovative bioinformatic method has been designed and implemented to detect similar three‐dimensional (3D) sites in proteins. This approach allows the comparison of protein structures or substructures and detects local spatial similarities: this method is completely independent from the amino acid sequence and from the backbone structure. In contrast to already existing tools, the basis for this method is a representation of the protein structure by a set of stereochemical groups that are defined independently from the notion of amino acid. An efficient heuristic for finding similarities that uses graphs of triangles of chemical groups to represent the protein structures has been developed. The implementation of this heuristic constitutes a software named SuMo (Surfing the Molecules), which allows the dynamic definition of chemical groups, the selection of sites in the proteins, and the management and screening of databases. To show the relevance of this approach, we focused on two extreme examples illustrating convergent and divergent evolution. In two unrelated serine proteases, SuMo detects one common site, which corresponds to the catalytic triad. In the legume lectins family composed of >100 structures that share similar sequences and folds but may have lost their ability to bind a carbohydrate molecule, SuMo discriminates between functional and non‐functional lectins with a selectivity of 96%. The time needed for searching a given site in a protein structure is typically 0.1 s on a PIII 800MHz/Linux computer; thus, in further studies, SuMo will be used to screen the PDB. Proteins 2003;52:137–145. © 2003 Wiley‐Liss, Inc.
Interaction of agitoxin2, charybdotoxin, and iberiotoxin with potassium channels: Selectivity between voltage‐gated and Maxi‐K channels
Authors: Gao Ying‐Duo , Garcia Maria L. 
Published: June 2003

AbstractTo gain insight into the molecular determinants that define the specificity of interaction of pore‐blocking peptides, such as agitoxin 2 (AgTX2), charybdotoxin (ChTX), and iberiotoxin (IbTX) with the Shaker‐type voltage‐gated potassium channel Kv1.3, or the large‐conductance Ca2+‐activated K+ (Maxi‐K) channel, homology models of these channels were generated based on the crystal structure of the bacterial, KcsA, potassium channel. Peptide–channel complexes were analyzed to evaluate the predicted interaction interfaces between the peptides and the channels' outer vestibules. The docking model, for either AgTX2 or ChTX with the Kv1.3 channel, predicts a novel hydrogen bonding interaction between the Asn30 side‐chain of the peptide and the Asp381 side‐chain of the channel. This interaction is consistent with the >500‐fold decreased potency of both AgTX2 and ChTX mutants at position 30 for the Shaker channel [(Ranganathan et al., Neuron 1996;16:131–139); (Goldstein et al., Neuron 1994;12:1377–1388)]. This hydrogen bonding interaction also suggests that Gly30 in IbTX may be the critical determinant for its lack of activity against Shaker Kv channels. The model of the Maxi‐K channel reveals a narrower and more structurally restrained outer vestibule in which the aromatic residues Phe266 and Tyr294 may stabilize binding of IbTX and ChTX by π–π stacking with the aromatic residues Trp14 and Tyr36 of the peptides. This study also suggests that the extra net negative charge of IbTX is not related to the selectivity of this peptide for the Maxi‐K channel. Proteins 2003;52:146–154. © 2003 Wiley‐Liss, Inc.
Conserved residue clustering and protein structure prediction
Authors: Schueler‐Furman Ora , Baker David 
Published: June 2003

AbstractProtein residues that are critical for structure and function are expected to be conserved throughout evolution. Here, we investigate the extent to which these conserved residues are clustered in three‐dimensional protein structures. In 92% of the proteins in a data set of 79 proteins, the most conserved positions in multiple sequence alignments are significantly more clustered than randomly selected sets of positions. The comparison to random subsets is not necessarily appropriate, however, because the signal could be the result of differences in the amino acid composition of sets of conserved residues compared to random subsets (hydrophobic residues tend to be close together in the protein core), or differences in sequence separation of the residues in the different sets. In order to overcome these limits, we compare the degree of clustering of the conserved positions on the native structure and on alternative conformations generated by the de novo structure prediction method Rosetta. For 65% of the 79 proteins, the conserved residues are significantly more clustered in the native structure than in the alternative conformations, indicating that the clustering of conserved residues in protein structures goes beyond that expected purely from sequence locality and composition effects. The differences in the spatial distribution of conserved residues can be utilized in de novo protein structure prediction: We find that for 79% of the proteins, selection of the Rosetta generated conformations with the greatest clustering of the conserved residues significantly enriches the fraction of close‐to‐native structures. Proteins 2003;52:225–235. © 2003 Wiley‐Liss, Inc.
Electrostatic properties in the catalytic site of papain: A possible regulatory mechanism for the reactivity of the ion pair
Authors: Dardenne Laurent E. , Werneck Araken S. , de Oliveira Neto Marçal , Bisch Paulo M. 
Published: June 2003

AbstractWe present an analysis of the electrostatic properties in the catalytic site of papain (EC 3.4.22.2), an archetype enzyme of the C1 cysteine proteinase family, and we investigate their possible role in the formation, stabilization and regulation of the Cys25(−)…His159(+) catalytic ion pair. The electrostatic properties were computed using a reassociation method based in multicentered multipolar expansions obtained from ab initio quantum calculations of overlapping protein fragments. Solvent effects were introduced by coupling the use of multicentered multipolar expansions to two continuum boundary element methods to solve the Poisson and the linearized Poisson‐Boltzmann equations. The electrostatic profile found in the proton transfer region of papain showed that this enzyme has a well‐defined electrostatic environment to favor the formation and stabilization of the catalytic ion pair. The papain catalytic site electrostatic profile can be considered as an electrostatic fingerprint of the papain family with the following characteristics: (i) the presence of a net electric field highly aligned in the (Cys25)‐SG→(His159)‐ND1 direction; (ii) the electrostatic profile has a saddle‐point character; (iii) it is basically a local environmental effect. Furthermore, our analysis describes a possible regulatory mechanism (the ESG→ND1 attenuation effect) controlling the ion pair reactivity and permits to infer the Asp57 acidic residue as the most probable candidate to act as the electrostatic modulator. Proteins 2003;52:236–253. © 2003 Wiley‐Liss, Inc.
Assembly of protein tertiary structures from secondary structures using optimized potentials
Authors: Hoang Trinh Xuan , Seno Flavio , Banavar Jayanth R. , Cieplak Marek , Maritan Amos 
Published: June 2003

AbstractWe present a simulated annealing‐based method for the prediction of the tertiary structures of proteins given knowledge of the secondary structure associated with each amino acid in the sequence. The backbone is represented in a detailed fashion whereas the sidechains and pairwise interactions are modeled in a simplified way, following the LINUS model of Srinivasan and Rose. A perceptron‐based technique is used to optimize the interaction potentials for a training set of three proteins. For these proteins, the procedure is able to reproduce the tertiary structures to below 3 Å in root mean square deviation (rmsd) from the PDB targets. We present the results of tests on twelve other proteins. For half of these, the lowest energy decoy has a rmsd from the native state below 6 Å and, in 9 out of 12 cases, we obtain decoys whose rmsd from the native states are also well below 5 Å. Proteins 2003;52:155–165. © 2003 Wiley‐Liss, Inc.
Molecular dynamics simulations of a helicase
Authors: Cox Katherine , Watson Tim , Soultanas Panos , Hirst Jonathan D. 
Published: June 2003

AbstractHelicases are ubiquitous enzymes involved in nucleic acid metabolism. The PcrA DNA helicase is an essential bacterial protein involved in rolling circle plasmid replication and DNA repair. Recent crystal structures of PcrA bound to DNA indicate that a flexible loop mediates a functionally important rigid‐body‐domain rotation. In this study, we report stochastic boundary molecular dynamics simulations focused on this region for wild‐type and mutants designed to increase the rigidity of the region. Residues in the region that were helix‐disfavoring, such as glycine, threonine, and others, were mutated to alanine. The simulated dynamics, analyzed with a variety of measures of structure and mobility, indicate that a few point mutations will substantially increase helix formation in this region. Subnanosecond stochastic boundary molecular dynamics simulations at several temperatures offer a rapid protocol for assessing large numbers of mutants and provides a novel strategy for the design of experiments to test the role of this flexible loop region in the function of PcrA. Proteins 2003;52:254–262. © 2003 Wiley‐Liss, Inc.