bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of Mechanical Properties of Thermoplastics Suitable for Micro Systems
Authors: Haberstroh Edmund , Brandt Marcel
Published: February 2003

Aircraft and aerospace industry as well as medical and automotive engineering continuously develop smaller and lighter system components. Therefore it is not only important to be able to produce micro parts but also to provide properties for dimensioning and design. This paper explains to what extent mechanical properties from the macro‐range are also valid for micro structures. Thereby the modulus of elasticity as well as stress and strain at the yield point are regarded as relevant properties for the part dimensioning. Systematic investigations with tensile bars of different size show that the geometry‐dependent property changes are obviously not specific for the material classes of amorphous or semi‐crystalline thermoplastics, respectively. That is why a single material testing of micro samples is necessary to determine valid properties for this range. On the other hand the determination known from the classic materials science of plastics that lower temperatures as well as higher loading rates lead to a stiffer material behaviour, is also appropriate for the micro range. The measurements prove that the influence of temperature is much higher than the one of deformation rate. The influence of the production conditions on the mechanical behaviour of test specimen made of semi‐crystalline thermoplastics is demonstrated by using a varied cooling process. The correlation between the resulting different morphological structures and the changes in the mechanical properties is pointed up on the basis of microscopic views.

Micro tensile testing machine at the IKV.

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Micro tensile testing machine at the IKV.
Micro‐ and Nanoscale Evaluation of Scratch Damage in Poly(propylene)s
Authors: Dasari A. , Rohrmann J. , Misra R. D. K.
Published: February 2003

The technique of atomic force microscopy (AFM) has been used to obtain comparative evaluation of scratch damage in polymeric materials (low‐ and high‐crystallinity poly(propylene)s and ethylene‐propylene diblock copolymers) and examine the surface deformation processes. A comparative assessment of scratch damage is made in terms of average surface height of the plastically deformed region, and the depth, thickness, and density of the scratch tracks. The resistance to scratch deformation under identical conditions of scratch test follows the sequence: high‐crystallinity poly(propylene)s > low‐crystallinity poly(propylene)s > ethylene‐propylene diblock copolymers. Additionally, short‐chain polymers are characterized by a greater resistance to mechanical deformation than their respective long‐chain polymers. The scratch tracks in low‐ and high‐crystallinity poly(propylene)s are zig‐zag in shape, while in ethylene‐propylene diblock copolymers they are parabolic with localized plastic flow involving voids. The AFM observations suggest that higher tensile modulus and higher yield stress are key factors responsible for superior resistance to mechanically induced deformation in high‐crystallinity poly(propylene)s.

Low magnification SEM micrographs of the scratch deformed regions of long‐chain EP‐L (e) and short‐chain EP‐S (f).

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Low magnification SEM micrographs of the scratch deformed regions of long‐chain EP‐L (e) and short‐chain EP‐S (f).
1,8‐Naphthalimides as Blue Emitting Fluorophores for Polymer Materials
Authors: Grabchev Ivo , Petkov Christo , Bojinov Vladimir
Published: February 2003

The copolymerization of 1,8‐naphthalimide derivatives (as fluorophore) with acrylonitrile has been investigated. The photophysical characteristics of monomeric and polymeric fluorophores in N,N‐dimethylformamide solution have been determined and discussed. During copolymerization, no changes in the chromophoric systems of the fluorophore occur. The influence of the studied monomeric 1,8‐naphthalimide fluorophores upon the structurally bleached polyacrylonitrile has been determined. Infrared absorption characteristics of the polymerizable 4‐alkoxy‐ and 4‐allyloxy‐N‐substituted‐1,8‐naphthalimides have been measured and discussed. The effect of the substituents upon the vibration frequencies of the carbonyl and allylic groups has been established.

Blue fluorescent polyacrylonitrile copolymers with 1,8‐naphthalimides side‐group.

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Blue fluorescent polyacrylonitrile copolymers with 1,8‐naphthalimides side‐group.
Controlled Swelling of Poly(hydroxyethyl methacrylate) Hydrogels by Photochemical Grafting of Hydrophobic Acrylates
Authors: Campan Rozenn , Cazaux Frédéric , Coqueret Xavier
Published: February 2003

The photochemically induced grafting polymerization of various alkyl acrylates onto cross‐linked poly(hydroxyethyl methacrylate) (PHEMA) was performed to reduce the hydrophilicity of the swellable network. Butyl, 2‐ethylhexyl and lauryl acrylate were used as monofunctional monomers for increasing the hydrophobic character, whereas hexanediol diacrylate was used as a multifunctional monomer with the additional feature of forming networks. The various steps of the grafting procedure were examined sequentially so as to optimize the overall hydrophobing effect. The grafting yield was shown to depend primarily of PHEMA swelling in the considered ethanol/monomer mixture. In spite of their high specific hydrophobic character, alkyl monoacrylates were shown to be less efficient because of lower grafting yield. Grafting initiation by hydrogen abstraction with benzophenone or by homolytic cleavage of a hydroxyalkyl‐phenone resulted in comparable grafting yields even with monofunctional monomers. The hardness measured for the water swollen rubbery materials correlated well to the equilibrium water content.

Shore A hardness as a function of the swelling ratio in water at T = 22 °C for grafted and ungrafted PHEMA hydrogels (same samples as those described in Table 5).

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Shore A hardness as a function of the swelling ratio in water at T = 22 °C for grafted and ungrafted PHEMA hydrogels (same samples as those described in Table 5).
Thermal Imidization of the Precursor of a Liquid Crystalline Polyimide
Authors: Pramoda Kumari P. , Liu Songlin , Chung Tai‐Shung
Published: February 2003

Imidization of the precursor of a liquid crystalline polyimide was investigated using modulated differential scanning calorimetry (MDSC), Fourier transform infrared (FTIR) spectroscopy, X‐ray photoelectron spectroscopy (XPS), and thermogravimetric analyzer (TGA) coupled to FTIR (TG‐IR). The FTIR study revealed that the rate and degree of imidization are functions of curing temperature and time. Imidization proceeds in two stages under isothermal condition. The initial weight loss up to 250 °C as observed from TGA was due to thermal cyclization, i.e., imidization process. The XPS analysis shows that the poly(amic acid) has two nitrogen 1s species at 400.3 and 399.2 eV possibly due to the isomerism of the dianhydride carbonyl, while liquid crystalline polyimide shows only a single nitrogen 1s species at 400.8 eV due to imide species.

PLM micrograph of PAA (at 280 °C) after imidization.

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PLM micrograph of PAA (at 280 °C) after imidization.
Novel Poly(N‐isopropylacrylamide)‐graft‐poly(vinylidene fluoride) Copolymers for Temperature‐Sensitive Microfiltration Membranes
Authors: Ying Lei , Kang En T. , Neoh Koon G. , Kato Koichi , Iwata Hiroo
Published: February 2003

In the present work, we report on the synthesis and characterization of poly(vinylidene fluoride) (PVDF) with N‐isopropylacrylamide (NIPAAM) polymer side chains from molecular graft copolymerization in solution. The copolymer can be readily cast into temperature‐sensitive microfiltration (MF) membranes by the phase inversion technique. The copolymer approach to membrane fabrication allows a much better control of the physicochemical nature of the membrane pores through the variation in graft concentration, membrane casting temperature and concentration of the membrane casting solution.

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Dual‐Curing of Waterborne Urethane‐Acrylate Coatings by UV and Thermal Processing
Authors: Decker Christian , Masson Frédéric , Schwalm Reinhold
Published: February 2003

A waterbased dual‐cure urethane‐acrylate oligomer has been synthesized by polycondensation of monomers bearing hydroxyl, isocyanate and acrylate groups. To obtain a stable aqueous dispersion, carboxylate groups were grafted on the oligomer chain and the isocyanate groups were protected by a blocking agent. After water release by a brief heating, the dry films were cured either by a short UV exposure in the presence of a photoinitiator to induce the polymerization of the acrylate double bonds, or by heating up to 150 °C to release the isocyanates and promote the polycondensation by reaction with the hydroxyl groups, but mainly by a combination of UV and thermal cure. Both processes have been followed quantitatively by infrared spectroscopy to evaluate the influence of the temperature on the reaction rate and on the cure extent. The newly developed waterbased dual‐cure coatings were found to be quite resistant to accelerated weathering because of their aliphatic structure and their high crosslink density. Their light stability was substantially improved by the addition of a hydroxyphenyltriazine UV absorber and a hindered amine radical scavenger.

Thermal curing of the dual‐cure waterborne PUA formulation at a temperature of 150 °C.

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Thermal curing of the dual‐cure waterborne PUA formulation at a temperature of 150 °C.
Near Infrared Reflection Spectroscopy: A Versatile Tool for Rapid Characterization of Olefin Copolymers and High‐Throughput Experiments
Authors: Tuchbreiter Arno , Kappler Bernd , Stockmann Roger , Mülhaupt Rolf , Honerkamp Josef
Published: February 2003

Near infrared (NIR) spectroscopy was developed as a rapid analytical method for the determination of the composition of olefin copolymers obtained in high‐throughput screening. NIR spectra of ethene/propene and ethene/1‐hexene copolymers, also characterized by means of 13C NMR spectroscopy, were recorded and used to design multivariate calibration models. Different methods for the preprocessing of the spectra, including the linearization by non‐linear transformations, were compared. Optimal methods and error estimates were established using crossvalidation. This technique is of particular interest for the rapid on‐line analysis of high‐throughput experiments in the field of polymer and catalyst design employing methods from combinatorial chemistry.

Predicted versus true value of the propene incorporation and standard deviation for ethene/propene copolymers.

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Predicted versus true value of the propene incorporation and standard deviation for ethene/propene copolymers.
Biocomposites Made from Short Abaca Fiber and Biodegradable Polyesters
Authors: Shibata Mitsuhiro , Ozawa Koichi , Teramoto Naozumi , Yosomiya Ryutoku , Takeishi Hiroyuku
Published: February 2003

Natural fiber‐reinforced biodegradable polyester composites were prepared from biodegradable polyesters and surface‐untreated or ‐treated abaca fibers (length ca. 5 mm) by melt mixing and subsequent injection molding. Poly(butylene succinate)(PBS), polyestercarbonate (PEC)/poly(lactic acid)(PLA) blend, and PLA were used as biodegradable polyesters. Esterifications using acetic anhydride and butyric anhydride, alkali treatment, and cyanoethylation were performed as surface treatments on the fiber. The flexural moduli of all the fiber‐reinforced composites increased with fiber content. The effect of the surface treatment on the flexural modulus of the fiber‐reinforced composites was not so pronounced. The flexural strength of PBS composites increased with fiber content, and esterification of the fiber by butyric anhydride gave the best result. For the PEC/PLA composites, flexural strength increased slightly with increased fiber content (0–20 wt.‐%) in the case of using untreated fiber, while it increased considerably in the case of using the fiber esterified by butyric anhydride. For the PLA composite, flexural strength did not increase with the fiber reinforcement. The result of soil‐burial tests showed that the composites using untreated fiber have a higher weight loss than both the neat resin and the composites made using acetylated fiber.

Flexural modulus of PBS composites as a function of fiber content.

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Flexural modulus of PBS composites as a function of fiber content.
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

Colloids 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).

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TEM 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

Solid‐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.).

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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.).
Morphology and Mechanical Properties in Polymer Blends of Photocurable Polymer and Polycarbonate
Authors: Murata Kazutaka , Amamiya Akiko , Anazawa Takanori
Published: February 2003

Relationships 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.

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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.
Novel Phenol‐Formaldehyde Resins, 2. Resols Prepared Using Reactive Solvents
Authors: Lubczak Renata
Published: February 2003

New 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.

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Temperature 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

N‐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.

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Effect 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

The 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

The 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

We 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

Comparing 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

The 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

Aligned 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

Multiple 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

The 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

Polyglutamine 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.
Hidden order in the GroEL‐GroES‐(ADP)7 chaperonin: Forms, folding, and ADP‐binding sites
Authors: Janner A.
Published: February 2003

A molecular crystallography approach reveals the existence of a hidden order in GroEL‐GroES‐(ADP)7. The new crystallographic symmetry concepts required are first illustrated for a hypothetical planar molecule. Their application to the chaperonin complex leads to molecular forms with vertices having integral coordinates (the indices) with respect to a symmetry‐adapted basis and to folding points approximated by ideal Cα positions with rational indices connected by integral scale‐rotations, just as for the vertices of the molecular forms. The Mg+2‐ions at nucleotide binding sites are symmetry‐related in a similar way to Cα's folding points. Proteins 2003;51:126–136. © 2003 Wiley‐Liss, Inc.
Efficient identification of side‐chain patterns using a multidimensional index tree
Authors: Hamelryck Thomas
Published: February 2003

Convergent evolution often produces similar functional sites in nonhomologous proteins. The identification of these sites can make it possible to infer function from structure, to pinpoint the location of a functional site, to identify enzymes with similar enzymatic mechanisms, or to discover putative functional sites. In this article, a novel method is presented that (a) queries a database of protein structures for the occurrence of a given side chain pattern and (b) identifies interesting side‐chain patterns in a given structure. For efficiency and to make a robust statistical evaluation of the significance of a similarity possible, patterns of three residues (or triads) are considered. Each triad is encoded as a high‐dimensional vector and stored in an SR (Sphere/Rectangle) tree, an efficient multidimensional index tree. Identifying similar triads can then be reformulated as identifying neighboring vectors. The method deals with many features that otherwise complicate the identification of meaningful patterns: shifted backbone positions, conservative substitutions, various atom label ambiguities and mirror imaged geometries. The combined treatment of these features leads to the identification of previously unidentified patterns. In particular, the identification of mirror imaged side‐chain patterns is unique to the here‐described method. Interesting triads in a given structure can be identified by extracting all triads and comparing them with a database of triads involved in ligand binding. The approach was tested by an all‐against‐all comparison of unique representatives of all SCOP superfamilies. New findings include mirror imaged metal binding and active sites, and a putative active site in bacterial luciferase. Proteins 2003;51:96–108. © 2003 Wiley‐Liss, Inc.
Prediction of folding rates and transition‐state placement from native‐state geometry
Authors: Micheletti Cristian
Published: February 2003

A variety of experimental and theoretical studies have established that the folding process of monomeric proteins is strongly influenced by the topology of the native state. In particular, folding times have been shown to correlate well with the contact order, a measure of contact locality. Our investigation focuses on identifying additional topologic properties that correlate with experimentally measurable quantities, such as folding rates and transition‐state placement, for both two‐ and three‐state folders. The validation against data from 40 experiments shows that a particular topological property that measures the interdependence of contacts, termed cliquishness or clustering coefficient, can account with statistically significant accuracy both for the transition state placement and especially for folding rates. The observed correlations can be further improved by optimally combining the distinct topological information captured by cliquishness and contact order. Proteins 2003;51:74–84. © 2003 Wiley‐Liss, Inc.
Characterization of the electrophile binding site and substrate binding mode of the 26‐kDa glutathione S‐transferase from Schistosoma japonicum
Authors: Cardoso Rosa M.F. , Daniels Douglas S. , Bruns Christopher M. , Tainer John A.
Published: February 2003

The 26‐kDa glutathione S‐transferase from Schistosoma japonicum (Sj26GST), a helminth worm that causes schistosomiasis, catalyzes the conjugation of glutathione with toxic secondary products of membrane lipid peroxidation. Crystal structures of Sj26GST in complex with glutathione sulfonate (Sj26GSTSLF), S‐hexyl glutathione (Sj26GSTHEX), and S‐2‐iodobenzyl glutathione (Sj26GSTIBZ) allow characterization of the electrophile binding site (H site) of Sj26GST. The S‐hexyl and S‐2‐iodobenzyl moieties of these product analogs bind in a pocket defined by side‐chains from the β1‐α1 loop (Tyr7, Trp8, Ile10, Gly12, Leu13), helix α4 (Arg103, Tyr104, Ser107, Tyr111), and the C‐terminal coil (Gln204, Gly205, Trp206, Gln207). Changes in the Ser107 and Gln204 dihedral angles make the H site more hydrophobic in the Sj26GSTHEX complex relative to the ligand‐free structure. These structures, together with docking studies, indicate a possible binding mode of Sj26GST to its physiologic substrates 4‐hydroxynon‐2‐enal (4HNE), trans‐non‐2‐enal (NE), and ethacrynic acid (EA). In this binding mode, hydrogen bonds of Tyr111 and Gln207 to the carbonyl oxygen atoms of 4HNE, NE, and EA could orient the substrates and enhance their electrophilicity to promote conjugation with glutathione. Proteins 2003;51:137–146. © 2003 Wiley‐Liss, Inc.
Influence of Nd3+ concentration on its optical absorption and luminescence properties in potassium borate glass
Authors: Ratnakaram Y. C. , Abdul Altaf Md. , Chakradhar R. P. S. , Rao J. L. , Ramakrishna J.
Published: February 2003

Spectroscopic and laser properties of Nd3+ doped potassium borate glass have been studied for different Nd3+ concentrations ranging from 0.5 to 2.0 mol%. From the absorption spectra, optical band gaps (Eopt) and various spectroscopic parameters (E1, E2, E3, ξ4f and α) are determined. Using Judd‐Ofelt intensity parameters Ω2, Ω4 and Ω6, radiative lifetimes (τR), branching ratios (β) and integrated absorption cross sections (Σ) have been calculated for certain excited states of Nd3+ for all the Nd3+ concentrations. From the spectral profiles of the hypersensitive transition, it is observed that there is slight change in the environment of Nd3+ ion in different concentrations of Nd3+ doped potassium borate glass. The radiative lifetimes (τR) for certain excited levels are minimum when the concentration is high. From the emission spectra, peak wavelengths (λp), effective line widths (Δλeff) and stimulated emission cross‐sections (σp) have been obtained for the three transitions 4F3/2 → 4I9/2, 4F3/2 → 4I11/2 and 4F3/2 → 4I13/2 of Nd3+ and are compared for different concentrations.
Structural properties and ionic conductivities of CuCr1–xVxS2 solid solutions
Authors: Almukhametov R. F. , Yakshibayev R. A. , Gabitov E. V. , Abdullin A. R. , Kutusheva R. M.
Published: February 2003

In the Cu(1 – x)CrxVS system CuCr1–xVxS2 solid solutions isostructural with CuCrS2 and Cu3VS4 were found by replacement of Cr by V up to x = 0.20. The oxidation states of Cr and V were determined from structural data and paramagnetic susceptibility measurements. The CuCr1–xVxS2 solid solutions were found to have mixed electronic and Cu+‐cationic conductivity. Copper cationic conductivity increases with increasing unit cell size.
Quantum and thermodynamic properties of proton transfer in hydrogen‐bonded systems
Authors: Xiao‐Feng Pang
Published: February 2003

The quantum and thermodynamic properties of proton transfer along hydrogen‐bonded molecular systems have been studied by our model at zero temperature and finite temperature, respectively. The dynamic equations of the proton transfer along the molecular chains have been obtained using the quantum‐mechanical method. Some quantum features of the proton–soliton are given. We also give the specific heats, resulting from the motion of the solitons in the systems with finite temperature, and find the critical temperature of the soliton in the protein molecules by quantum mechanics. The critical temperatures are in the region of 310.73–328.51 K for different helix‐type protein molecules with three channels. This shows that the solitons in these biopolymers are stable at biological temperatures.
F centers in LiF: A nuclear magnetic resonance study
Authors: Klempt T. , Kanert O. , Suter D.
Published: February 2003

Ionizing radiation like γ‐rays, electrons, or swift heavy ions create a variety of point defects in dielectric materials. The largest fraction of the defects consists of the paramagnetic F centers. Here, we study those F centers in LiF by nuclear magnetic resonance. Nuclear spin relaxation (T1) measurements serve as a probe for the F centers offering the possibility to investigate their dynamics as a function of temperature and irradiation dose. Moreover, one is able to estimate the content of the paramagnetic defects from the T1‐data over a wide range of concentration. We further observed and analyzed radiation annealing occurring at temperatures above 360 K.
Alloy‐disorder‐scattering‐limited mobility of electrons in cylindrical quantum well wires
Authors: Ibragimov G. B.
Published: February 2003

We study the effect of the alloy‐disorder‐scattering on the electron transport in a quasi‐one‐dimensional semiconductor. Analytical calculations of the alloy‐disorder‐limited momentum relaxation time for carrier scattering in a cylindrical quantum wire using an infinite well model. The transverse part of the carrier wave function is taken to be a Bessel function. It is found that the one‐dimensional mobility is significantly greater than two‐dimensional mobility. It is shown that the alloy‐disorder‐scattering‐limited mobility increases with increasing wire radius and increases with increasing temperature. We compare our results with different scattering mechanisms for one‐dimensional systems. Results are also included for the alloy composition dependence of the mobility.
Diffusion, surface alloy formation, and spin alignment in Fe/Cr(001) systems and superlattices
Authors: Kellou A. , Aourag H.
Published: February 2003

We present first principle calculations, based on the generalized gradient approximation (GGA), of Fe/Cr(001) layered structures and superlattices. The energetics of ferromagnetic overlayer (Fe) deposition on antiferromagnetic substrate (Cr(001)) is investigated. We have found that Cr layers prefer antiferromagnetic (af) coupling in Cr(001) thin films. The same coupling is found between Fe and Cr layers in Fe/Cr (001) systems. The last Fe and Cr layers are more or less af coupled in Fen/Crn(001) superlattices. The deposition of Fe overlayer on Cr(001) favors bilayer rather than monolayer formation, which leads to an ordered surface alloy formation. More detailed investigations have confirmed that surface alloy formation is possible for Fe50Cr50/3Cr(001), in agreement with ultra‐high vacuum scanning tunneling microscope observations, which confirm that Fe atoms incorporate into the Cr surface, forming a well‐ordered surface alloy of Fe50Cr50.
Correlation between the structural and antiferromagnetic phase transitions in ZnCr2Se4
Authors: Hidaka M. , Tokiwa N. , Fujii M. , Watanabe S. , Akimitsu J.
Published: February 2003

Structural properties of normal‐type spinel ZnCr2Se4 have been studied as a function of temperature by means of neutron diffraction. It is found that the structural phase transition (TC) from a cubic to orthorhombic symmetry simultaneously occurs at the antiferromagnetic phase transition temperature (TN ∼ 21 K), where the cubic and orthorhombic symmetry is 7Oh‐Fd3m and 24D2h‐Fddd, respectively. The structural phase transition is mainly characterized by the cooperative displacements of Se2– ions, which are induced by a magnetostriction resulting from the magnetic interaction of Cr3+ ions in CrSe4 chains along [110]. The antiferromagnetic magnetic structure below TN is made by a spiral magnetic coupling between the ferromagnetic CrSe4 chains around crystallographic screw axes, which are parallel to an orthorhombic C axis. The spiral long‐range order of the spins of Cr3+ is incommensurate and its periodicity of q along a reciprocal lattice axis C* shows temperature dependence from about 0.47 (2.5 K) to 0.43 (18 K). The spiral periodicity of the spin order along the C axis shows a first order transition at about 21 K.