bluuebunny/crossref_metadata_2025_split huggingface dataset:
Polymer‐TiO2 Nanocomposites: A Route Towards Visually Transparent Broadband UV Filters and High Refractive Index Materials
Authors: Nussbaumer René J. , Caseri Walter R. , Smith Paul , Tervoort Theo 
Published: February 2003

AbstractColloids of TiO2, where rutile was the only crystal modification which could be detected, with ca. 2.5 nm average particle diameter were synthesized by hydrolysis of TiCl4 in acidic solutions. The as‐prepared particles were incorporated in polymers such as poly(vinyl alcohol) (PVAL), partially hydrolyzed poly(vinyl acetate) (PVAC88), polyvinylpyrrolidone, and poly(4‐vinylpyridine). Nanocomposites transparent in the visible range were obtained. The highest TiO2 contents in such materials were achieved with PVAL and PVAC88, with TiO2 contents of ca. 35 wt.‐% (i.e. 10.5 vol.‐%). In particular, the nanocomposites with TiO2 contents above 24 wt.‐% acted as efficient UV filters for radiation up to ca. 360 nm. At very low TiO2 contents, an absorption maximum of the embedded TiO2 particles was observed at 225 nm with an extinction coefficient of 140 000 cm−1 and a full width at half maximum of 45 nm, i.e. not only the absorption at the maximum at 225 nm but also at the flank of this band contributed significantly to the broadband UV absorption in the nanocomposites at higher TiO2 fractions. The incorporation of TiO2 enhanced the refractive index of the nanocomposites: for instance a refractive index of 1.609 was measured for a nanocomposite comprising 10.5 vol.‐% TiO2 in PVAL, compared with 1.521 for the pristine polymer.
TEM image of a section of a nanocomposite of poly(vinyl alcohol) and 11 wt.‐% TiO2 (appearing dark).magnified imageTEM image of a section of a nanocomposite of poly(vinyl alcohol) and 11 wt.‐% TiO2 (appearing dark).
Improvement of Flexural Strengths of Poly(L‐lactic acid) by Solid‐State Extrusion, 2. Extrusion Through Rectangular Die
Authors: Lim Jung Yul , Kim Soo Hyun , Lim Soonho , Kim Young Ha 
Published: February 2003

AbstractSolid‐state extrusion of poly (L‐lactic acid) (PLLA) through rectangular die was performed to produce high flexural strength plates that can be used as internal fixation devices. A single‐angle wedge‐shaped rectangular die was utilized having the die exit dimension of 4 mm × 1 mm. Billets were machined out from vacuum compression molded PLLA having different crystallinities to have various thicknesses and thus various imposed draw ratios. Solid‐state extrusion of billets was performed at various drawing rates at 130 °C, above glass transition and below melting temperature. Extruded plates had the width and thickness smaller than the die due to the further drawing outside the die. The decrease in width was larger than the decrease in thickness, and this became more prominent with increasing draw ratio and drawing rate, resulting in a significantly smaller aspect ratio. Contributions of die drawing and further drawing outside the die were estimated from the extruded plate dimensions, by which the drawing rate effect was attributed to the further drawing outside the die. As actual draw ratio increased, crystallinity, melting temperature, crystalline orientation factor, and birefringence increased. Throughout the whole process the decrease in molecular weight was largely suppressed to be about 10%. As billet crystallinity, draw ratio, and drawing rate increased, both flexural strength and flexural modulus increased up to the maxima of 202 MPa and 9.7 GPa, respectively. This enhancement in mechanical properties was correlated with structural developments.
Changes in flexural strength of solid‐state extruded PLLA plates as a function of draw ratio (the effect of drawing rate is co‐plotted by hollow symbols at corresponding draw ratio.).magnified imageChanges in flexural strength of solid‐state extruded PLLA plates as a function of draw ratio (the effect of drawing rate is co‐plotted by hollow symbols at corresponding draw ratio.).
Morphology and Mechanical Properties in Polymer Blends of Photocurable Polymer and Polycarbonate
Authors: Murata Kazutaka , Amamiya Akiko , Anazawa Takanori 
Published: February 2003

AbstractRelationships between the morphologies and mechanical properties of binary blends of a photocurable polymer (2‐propenoic acid, (octahydro‐4,7‐methano‐1H‐indenediyl) bis(methylene)ester; DCA) and a linear polymer (poly(4,4′‐cyclohexylidene bisphenol carbonate); PCz) have been investigated. The blend films are prepared by in situ photopolymerization of homogeneous mixtures of a DCA‐monomer and PCz. The phase structure has been converted from a semi‐interpenetrating polymer networks (semi‐IPN) structure to a bicontinuous structure by controlling the cure temperature. Bicontinuous phase‐separated structures can be obtained by curing a wide range of compositions of 17–50 wt.‐% PCz at high temperatures. Miscible semi‐IPN structures are attained by means of photopolymerization below the glass transition temperature of the homogenous mixture before performing photoirradiation, such that magnetic relaxation measurements showed the blend to be miscible in the 10 nm order. The tensile strength and modulus reached a maximum in those blends having an intermediate vague phase structure between semi‐IPN and bicontinuous structures that have a strong interfacial interaction, which leads to incomplete phase decomposition in the PCz‐rich matrix phase. The maximum strength and modulus prepared under optimum condition are inferior to those of the individual components. In contrast, the elongation and break energy are greatly improved in those blends with bicontinuous structures having a diffused phase boundary.
DCA‐rich domain size in bicontinuous structure for DCA/PCz system, as a function of cure temperature; (□) 17 wt.‐% PCz, (○) 30 wt.‐% PCz, and (⋄) 50 wt.‐% PCz.magnified imageDCA‐rich domain size in bicontinuous structure for DCA/PCz system, as a function of cure temperature; (□) 17 wt.‐% PCz, (○) 30 wt.‐% PCz, and (⋄) 50 wt.‐% PCz.
Novel Phenol‐Formaldehyde Resins, 2. Resols Prepared Using Reactive Solvents
Authors: Lubczak Renata 
Published: February 2003

AbstractNew results on the method of preparation of phenol‐formaldehyde resins from phenol and multihydroxymethyl derivatives of some ketones are presented. The latter, known as the reactive solvents of melamine, were prepared by reacting acetone and methyl ethyl ketone with excess of formaldehyde. A novel group of resins of resol type has been obtained. The structure of products is discussed and compared to that of classical resols. The fragments of ketones have been found incorporated into the structure of resins.
Temperature dependence of viscosity of a classical resol and of the resols modified with reactive solvents.magnified imageTemperature dependence of viscosity of a classical resol and of the resols modified with reactive solvents.
Proteases to Improve the Mechanical Characteristics of Durable Press Finished Cotton Fabrics
Authors: Stamenova Maria , Tzanov Tzanko , Betcheva Rossitza , Cavaco‐Paulo Artur 
Published: February 2003

AbstractN‐Methylol reagents are conventional crosslinking agents that are still widely used in textile industry to produce crease‐resistant cotton fabrics. In this work serine proteases were used to recover the strength of fabrics, cross‐linked with N‐hydroxymethylacrylamide. Nearly one half of the strength loss of crosslinked cotton fabrics could be restored after protease treatment, while the wrinkle recovery angle (WRA) decreased only slightly. The enzymatic hydrolysis of the amide cross‐links in the durable pressed cellulose was confirmed by FT‐IR analysis and dyeability with an acid dye.
Effect of protease concentration on the tensile strength recovery, WRA and acid dye dyeability at 30 min reaction time.magnified imageEffect of protease concentration on the tensile strength recovery, WRA and acid dye dyeability at 30 min reaction time.
Biomimetic Polymer Nanostructures by Injection Molding
Authors: Gadegaard Nikolaj , Mosler Stephan , Larsen Niels B. 
Published: February 2003

AbstractThe nanometer scale topography of self‐assembling structural protein complexes in animals is believed to induce favorable cell responses. An important example of such nanostructured biological complexes is fibrillar collagen that possesses a cross‐striation structure with a periodicity of 69 nm and a peak‐to‐valley distance of 4–6 nm. Bovine collagen type I was assembled into fibrillar structures in vitro and sedimented onto solid supports. Their structural motif was transferred into a nickel replica by physical vapor deposition of a small‐grained metal layer followed by galvanic plating. The resulting inverted nickel structure was found to faithfully present most of the micrometer and nanometer scale topography of the biological original. This nickel replica was used as a die for the injection molding of a range of different thermoplastic polymers. Total injection molding cycle times were in the range of 30–45 seconds. One of the polymer materials investigated, polyethylene, displayed poor replication of the biological nanotopographical motif. However, the majority of the polymers showed very high replication fidelity as witnessed by their ability to replicate the cross‐striation features of less than 5 nm height difference. The latter group of materials includes poly(propylene), poly(methyl methacrylate), poly(L‐lactic acid), polycaprolactone, and a copolymer of cyclic and linear olefins (COC). This work suggests that the current limiting factor for the injection molding of nanometer scale topography in thermoplastic polymers lies with the grain size of the initial metal coating of the mold rather than the polymers themselves.
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Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all‐atom statistical potential and the AMBER force field with the Generalized Born solvation model
Authors: de Bakker Paul I. W. , DePristo Mark A. , Burke David F. , Blundell Tom L. 
Published: February 2003

AbstractThe accuracy of model selection from decoy ensembles of protein loop conformations was explored by comparing the performance of the Samudrala–Moult all‐atom statistical potential (RAPDF) and the AMBER molecular mechanics force field, including the Generalized Born/surface area solvation model. Large ensembles of consistent loop conformations, represented at atomic detail with idealized geometry, were generated for a large test set of protein loops of 2 to 12 residues long by a novel ab initio method called RAPPER that relies on fine‐grained residue‐specific phi/psi propensity tables for conformational sampling. Ranking the conformers on the basis of RAPDF scores resulted in selected conformers that had an average global, non‐superimposed RMSD for all heavy mainchain atoms ranging from 1.2 Å for 4‐mers to 2.9 Å for 8‐mers to 6.2 Å for 12‐mers. After filtering on the basis of anchor geometry and RAPDF scores, ranking by energy minimization of the AMBER/GBSA potential energy function selected conformers that had global RMSD values of 0.5 Å for 4‐mers, 2.3 Å for 8‐mers, and 5.0 Å for 12‐mers. Minimized fragments had, on average, consistently lower RMSD values (by 0.1 Å) than their initial conformations. The importance of the Generalized Born solvation energy term is reflected by the observation that the average RMSD accuracy for all loop lengths was worse when this term is omitted. There are, however, still many cases where the AMBER gas‐phase minimization selected conformers of lower RMSD than the AMBER/GBSA minimization. The AMBER/GBSA energy function had better correlation with RMSD to native than the RAPDF. When the ensembles were supplemented with conformations extracted from experimental structures, a dramatic improvement in selection accuracy was observed at longer lengths (average RMSD of 1.3 Å for 8‐mers) when scoring with the AMBER/GBSA force field. This work provides the basis for a promising hybrid approach of ab initio and knowledge‐based methods for loop modeling. Proteins 2003;51:21–40. © 2003 Wiley‐Liss, Inc.
Ab initio construction of polypeptide fragments: Efficient generation of accurate, representative ensembles
Authors: DePristo Mark A. , de Bakker Paul I. W. , Lovell Simon C. , Blundell Tom L. 
Published: February 2003

AbstractWe describe a novel method to generate ensembles of conformations of the main‐chain atoms {N, Cα, C, O, Cβ} for a sequence of amino acids within the context of a fixed protein framework. Each conformation satisfies fundamental stereo‐chemical restraints such as idealized geometry, favorable ϕ/ψ angles, and excluded volume. The ensembles include conformations both near and far from the native structure. Algorithms for effective conformational sampling and constant time overlap detection permit the generation of thousands of distinct conformations in minutes. Unlike previous approaches, our method samples dihedral angles from fine‐grained ϕ/ψ state sets, which we demonstrate is superior to exhaustive enumeration from coarse ϕ/ψ sets. Applied to a large set of loop structures, our method samples consistently near‐native conformations, averaging 0.4, 1.1, and 2.2 Å main‐chain root‐mean‐square deviations for four, eight, and twelve residue long loops, respectively. The ensembles make ideal decoy sets to assess the discriminatory power of a selection method. Using these decoy sets, we conclude that quality of anchor geometry cannot reliably identify near‐native conformations, though the selection results are comparable to previous loop prediction methods. In a subsequent study (de Bakker et al.: Proteins 2003;51:21–40), we demonstrate that the AMBER forcefield with the Generalized Born solvation model identifies near‐native conformations significantly better than previous methods. Proteins 2003;51:41–55. © 2003 Wiley‐Liss, Inc.
Consistency matrices: Quantified structure alignments for sets of related proteins
Authors: Van Walle Ivo , Lasters Ignace , Wyns Lode 
Published: February 2003

AbstractComparing two remotely similar structures is a difficult problem: more often than not, resulting structure alignments will show ambiguities and a unique answer usually does not even exist. In addition, alignments in general have a limited information content because every aligned residue is considered equally important. To solve these issues to a certain extent, one can take the perspective of a whole group of similar structures and then evaluate common structural features. Here, we describe a consistency approach that, although not actually performing a multiple structure alignment, does produce the information that one would conceivably want from such an experiment: the key structural features of the group, e.g., a fold, which in this case are projected onto either a pair of proteins or a single protein. Both representations are useful for a number of applications, ranging from the detection of (partially) wrong structure alignments to protein structure classification and fold recognition. To demonstrate some of these applications, the procedure was applied to 195 SCOP folds containing a total of 1802 domains sharing very low sequence similarity. Proteins 2003;51:1–9. © 2003 Wiley‐Liss, Inc.
Time scale of protein aggregation dictated by liquid‐liquid demixing
Authors: Vaiana S.M. , Palma‐Vittorelli M.B. , Palma M.U. 
Published: February 2003

AbstractThe growing impact of protein aggregation pathologies, together with the current high need for extensive information on protein structures are focusing much interest on the physics underlying the nucleation and growth of protein aggregates and crystals. Sickle Cell Hemoglobin (HbS), a point‐mutant form of normal human Hemoglobin (HbA), is the first recognized and best‐studied case of pathologically aggregating protein. Here we reanalyze kinetic data on nucleation of deoxy‐HbS aggregates by referring them to the (concentration‐dependent) temperature Ts characterizing the occurrence of the phase transition of liquid‐liquid demixing (LLD) of the solution. In this way, and by appropriate scaling of kinetic data at different concentrations, so as to normalize their spans, the apparently disparate sets of data are seen to fall on a master curve. Expressing the master curve vs. the parameter ϵ = (T − Ts) / Ts, familiar from phase transition theory, allows eliciting the role of anomalously large concentration fluctuations associated with the LLD phase transition and also allows decoupling quantitatively the role of such fluctuations from that of microscopic, inter‐protein interactions leading to nucleation. Referring to ϵ shows how in a narrow temperature span, that is at T≈Ts, nucleation kinetics can undergo orders‐of‐magnitude changes, unexpected in terms of ordinary chemical kinetics. The same is true for similarly small changes of other parameters (pH, salts, precipitants), capable of altering Ts and consequently ϵ. This offers the rationale for understanding how apparently minor changes of parameters can dramatically affect protein aggregation and related diseases. Proteins 2003;51:147–153. © 2003 Wiley‐Liss, Inc.
BATMAS30: Amino acid substitution matrix for alignment of bacterial transporters
Authors: Sutormin Roman A. , Rakhmaninova Aleksandra B. , Gelfand Mikhail S. 
Published: February 2003

AbstractAligned amino acid sequences of three functionally independent samples of transmembrane (TM) transport proteins have been analyzed. The concept of TM‐kernel is proposed as the most probable transmembrane region of a sequence. The average amino acid composition of TM‐kernels differs from the published amino acid composition of transmembrane segments. TM‐kernels contain more alanines, glycines, and less polar, charged, and aromatic residues in contrast to non‐TM‐proteins. There are also differences between TM‐kernels of bacterial and eukaryotic proteins. We have constructed amino acid substitution matrices for bacterial TM‐kernels, named the BATMAS (BActerial Transmembrane MAtrix of Substitutions) series. In TM‐kernels, polar and charged residues, as well as proline and tyrosine, are highly conserved, whereas there are more substitutions within the group of hydrophobic residues, in contrast to non‐TM‐proteins that have fewer, relatively more conserved, hydrophobic residues. These results demonstrate that alignment of transmembrane proteins should be based on at least two amino acid substitution matrices, one for loops (e.g., the BLOSUM series) and one for TM‐segments (the BATMAS series), and the choice of the TM‐matrix should be different for eukaryotic and bacterial proteins. Proteins 2003;51:85–95. © 2003 Wiley‐Liss, Inc.
Dynamic fluorescence studies of β‐glycosidase mutants from Sulfolobus solfataricus: Effects of single mutations on protein thermostability
Authors: Bismuto Ettore , Febbraio Ferdinando , Limongelli Simona , Briante Raffaella , Nucci Roberto 
Published: February 2003

AbstractMultiple sequence alignment on 73 proteins belonging to glycosyl hydrolase family 1 reveals the occurrence of a segment (83–124) in the enzyme sequences from hyperthermophilic archaea bacteria, which is absent in all the mesophilic members of the family. The alignment of the known three‐dimensional structures of hyperthermophilic glycosidases with the known ones from mesophilic organisms shows a similar spatial organizations of β‐glycosidases except for this sequence segment whose structure is located on the external surface of each of four identical subunits, where it overlaps two α‐helices. Site‐directed mutagenesis substituting N97 or S101 with a cysteine residue in the sequence of β‐glycosidase from hyperthermophilic archaeon Sulfolobus solfataricus caused some changes in the structural and dynamic properties as observed by circular dichroism in far‐ and near‐UV light, as well as by frequency domain fluorometry, with a simultaneous loss of thermostability. The results led us to hypothesize an important role of the sequence segment present only in hyperthermophilic β‐glycosidases, in the thermal adaptation of archaea β‐glycosidases. The thermostabilization mechanism could occur as a consequence of numerous favorable ionic interactions of the 83–124 sequence with the other part of protein matrix that becomes more rigid and less accessible to the insult of thermal‐activated solvent molecules. Proteins 2003;51:10–20. © 2003 Wiley‐Liss, Inc.
Structure of the YibK methyltransferase from Haemophilus influenzae (HI0766): A cofactor bound at a site formed by a knot
Authors: Lim Kap , Zhang Hong , Tempczyk Aleksandra , Krajewski Wojciech , Bonander Nicklas , Toedt John , Howard Andrew , Eisenstein Edward , Herzberg Osnat 
Published: February 2003

AbstractThe crystal structures of YibK from Haemophilus influenzae (HI0766) have been determined with and without bound cofactor product S‐adenosylhomocysteine (AdoHcy) at 1.7 and 2.0 Å resolution, respectively. The molecule adopts an α/β fold, with a topology that differs from that of the classical methyltransferases. Most notably, HI0766 contains a striking knot that forms the binding crevice for the cofactor. The knot formation is correlated with an alternative arrangement of the secondary structure units compared with the classical methyltransferases. Two loop regions undergo conformational changes upon AdoHcy binding. In contrast to the extended conformation of the cofactor seen in the classical methyltransferase structures, AdoHcy binds to HI0766 in a bent conformation. HI0766 and its close sequence relatives are all shorter versions of the more remotely related rRNA/tRNA methyltransferases of the spoU sequence family. We propose that the spoU sequence family contains the same core domain for cofactor binding as HI0766 but has an additional domain for substrate binding. The substrate‐binding domain is absent in HI0766 sequence family and may be provided by another Haemophilus influenzae partner protein, which is yet to be identified. Proteins 2003;51:56–67. © 2003 Wiley‐Liss, Inc.
Local protein unfolding and pathogenesis of polyglutamine‐expansion diseases
Authors: Chen Yu Wai 
Published: February 2003

AbstractPolyglutamine expansion diseases are caused by the abnormal lengthening of a glutamine repeat in the respective protein and are believed to progress via a common mechanism. Here a hypothesis based on protein unfolding is formulated to enhance understanding of the pathogenesis of these diseases. Nine disease proteins of this family were investigated with an unfolding prediction protocol based on calculating the net charge and the overall hydrophobicity from the primary sequence. These protein sequences were analysed with and without their respective nonpathogenic glutamine repeats. When full‐length protein sequences were studied, the calculations suggest that unexpanded polyglutamine repeats have a minimal effect on the global folding state of the parent proteins. When confined to a local context approximating the size of a single‐protein domain, the calculations suggest that all nine sequences including a normal‐length polyglutamine repeat correspond to the unfolded state. The unfolding predictions were applied to two model systems and were found to be consistent with published experimental data. Despite its simplicity, this analysis can be extended to simulate repeat length‐dependent protein unfolding, an event speculated to precede aggregation and disease progression. This work highlights the correlation between glutamine repeats and protein unfolding and provides insight into the as yet unknown polyglutamine expansion pathogenic mechanism. Proteins 2003;51:68–73. © 2003 Wiley‐Liss, Inc.