bluuebunny/crossref_metadata_2025_split huggingface dataset:
New super‐tough poly(butylene terephthalate) materials based on compatibilized blends with metallocenic poly(ethylene‐octene) copolymer
Authors: Aróstegui A. , Nazábal J. 
Published: June 2003

AbstractNew super‐tough poly(butylene terephthalate) (PBT)/poly(ethylene‐octene) copolymer (PEO) blends containing 2 wt% poly(ethylene‐co‐glycidyl methacrylate) (EGMA) as a compatibilizer were obtained by extrusion and injection molding. The blends comprised of an amorphous PBT‐rich phase with some miscibilized EGMA, a pure PEO amorphous phase, and a crystalline PBT phase that was not influenced by the presence of either PEO or EGMA. The blends showed a fine particle size up to 20 wt% PEO content. Super‐tough blends were obtained with PEO contents equal to or higher than 10%. The maximum toughness was very high (above 710 J/m) and was attained with 20% PEO without chemical modification of the commercial components used. Copyright © 2003 John Wiley & Sons, Ltd.
Surface functionalization of styrene/butyl acrylate latex with a water‐soluble monosaccharide monomer. Synthesis and morphology of the polymer particles
Authors: Deppe O. , Subat M. , Yaacoub E.‐J. 
Published: June 2003

AbstractNew polymer latexes bearing saccharide moieties on the particle surface were synthesized by using a water‐soluble sugar monomer, such as 1‐deoxy‐1‐methacryl‐amido‐D‐glucitol, (MAG). All the latexes were prepared by a two‐stage emulsion polymerization technique. In the first step, the core was prepared with butyl acrylate (BA) and styrene (St). In the second step, the seed latex was polymerized with ethyl acrylate (EA) and MAG. The influence of a bifunctional monomer such as allyl methacrylate (ALMA), introduced at various concentrations, on the final latexes morphologies and properties was investigated. It was found that the latex particles exhibit a core‐shell structure. The mass balance of MAG showed that the main part of the sugar moiety is on the shell layer. The molecular properties, such as structure, composition, and molecular weight, were determined by elemental analysis,
1H‐ and
13C‐NMR spectroscopy. Colloidal (particle size and their distributions), thermal, and rheological properties were also studied. Copyright © 2003 John Wiley & Sons, Ltd.
Properties of low temperature swelling hydrogels prepared with partially saponified PVA and drug release using the hydrogels
Authors: Horiike Satoshi , Yumoto Kyoji , Matsuzawa Shuji , Yamaura Kazuo 
Published: June 2003

AbstractThe hydrogels prepared by the crosslinking of partially saponified poly(vinyl alcohol) (PVA) which has low critical solution temperature (LCST) in water showed characteristics of swelling at low temperature and shrinkage at high temperature. The hydrogels showed repeatable swelling–shrinking behavior. The hydrogels containing release substances such as cyanocobalamin, p‐acetamidophenol, insulin and ovalbumin were prepared by dipping these aqueous solutions and the release substances were studied. Insulin and ovalbumin were not absorbed by the hydrogels when the use of partially PVA with the degrees of polymerization (DPs) of 540 were prepared, but absorbed by the hydrogels with DPs of 1860. The size of the polymer network prepared with a higher DP was suitable for the absorption of insulin and ovalbumin. In accordance with release substances, the release patterns were different. In this way, the polymer network sizes and their swelling behaviors of partially saponified PVAs were estimated. Copyright © 2003 John Wiley & Sons, Ltd.
Preparation of inclusion complex between polyaniline and β‐cyclodextrin in aqueous solution
Authors: Yuan Guo‐Li , Kuramoto Noriyuki , Takeishi Makoto 
Published: June 2003

AbstractTwo routes have been developed inorder to prepare an inclusion complex of polyaniline (PANI) and β‐cyclodextrin (βCyD). The first route was to in situ polymerize N‐phenyl‐1,4‐phenylenediamine (PPD) which was encapsulated in βCyD in advance. The formation of an inclusion complex was confirmed by UV‐vis, circular dichroism (CD), and NMR spectra. It was found that the synthesized complex was readily dissolved in a range of solvents due to the solubility of βCyD. In these solvents, PANI was well encapsulated by βCyD with some conformation change in the chain of PANI, which was proved by the CD spectra of PANI. The second route involved preparing the inclusion complex by post‐encapsulation of PANI emeraldine base (EB) into βCyD in aqueous solution at room temperature. The encapsulation of EB into βCyD was confirmed by FT‐IR and UV‐vis spectra. The band shift in UV‐vis spectra indicated that the inclusion complexation was a gradual process, and the change in the chain conformation of PANI was also observed after it was encapsulated into βCyD. Copyright © 2003 John Wiley & Sons, Ltd.
Effect of molecular weight on gas selectivity of oriented thin polyimide membrane
Authors: Nakajima K. , Nagaoka S. , Kawakami H. 
Published: June 2003

AbstractIn this study, we focused on effect of the molecular weight of polyimide on the gas selectivity of the asymmetric membrane with an oriented surface skin layer prepared at different shear stresses. Asymmetric polyimide membranes, which have a defect‐free surface skin layer supported by a porous substructure, were prepared by a dry/wet phase inversion process. The structures of the asymmetric polyimides consisted of a thin skin layer and a porous substructure characterized by the presence of finger‐voids. The gas selectivities of the asymmetric polyimide membranes increased with an increase in the shear rate or a decrease in the molecular weight, indicating that the oriented polyimide structure in the surface skin layer provided a high size and shape discrimination between the gas molecules. The selectivity values of (O2/N2) and (CO2/CH4) in the asymmetric polyimide membrane prepared from the 7.2 × 104 molecular weight material at 1000 sec−1 shear rate were 12 and 143, respectively. Copyright © 2003 John Wiley & Sons, Ltd.
Data mining crystallization databases: Knowledge‐based approaches to optimize protein crystal screens
Authors: Kimber Matthew S. , Vallee François , Houston Simon , Nečakov Alexander , Skarina Tatiana , Evdokimova Elena , Beasley Steven , Christendat Dinesh , Savchenko Alexei , Arrowsmith Cheryl H. , Vedadi Masoud , Gerstein Mark , Edwards Aled M. 
Published: May 2003

AbstractProtein crystallization is a major bottleneck in protein X‐ray crystallography, the workhorse of most structural proteomics projects. Because the principles that govern protein crystallization are too poorly understood to allow them to be used in a strongly predictive sense, the most common crystallization strategy entails screening a wide variety of solution conditions to identify the small subset that will support crystal nucleation and growth. We tested the hypothesis that more efficient crystallization strategies could be formulated by extracting useful patterns and correlations from the large data sets of crystallization trials created in structural proteomics projects. A database of crystallization conditions was constructed for 755 different proteins purified and crystallized under uniform conditions. Forty‐five percent of the proteins formed crystals. Data mining identified the conditions that crystallize the most proteins, revealed that many conditions are highly correlated in their behavior, and showed that the crystallization success rate is markedly dependent on the organism from which proteins derive. Of the proteins that crystallized in a 48‐condition experiment, 60% could be crystallized in as few as 6 conditions and 94% in 24 conditions. Consideration of the full range of information coming from crystal screening trials allows one to design screens that are maximally productive while consuming minimal resources, and also suggests further useful conditions for extending existing screens. Proteins 2003;51:562–568. © 2003 Wiley‐Liss, Inc.
Scaling law in sizes of protein sequence families: From super‐families to orphan genes
Authors: Unger Ron , Uliel Shai , Havlin Shlomo 
Published: May 2003

AbstractIt has been observed that the size of protein sequence families is unevenly distributed, with few super families with a large number of members and many “orphan” proteins that do not belong to any family. Here it is shown that the distribution of sizes of protein families in different databases and classifications (Protomap, Prodom, Cog) follows a power‐law behavior with similar scaling exponents, which is characteristic of self‐organizing systems. Since large databases are used in this study, a more detailed analysis of the data than in previous studies was possible. Hence, it is shown that the size distribution is governed by two exponents, different for the super families and the orphan proteins. A simple model of protein evolution is proposed, in which proteins are dynamically generated and clustered into families. The model yields a scaling behavior very similar to the distribution observed in the actual sequence databases, including the two distinct regimes for the large and small families, and thus suggests that the existence of “super families” of proteins and “orphan” proteins are two manifestations of the same evolutionary process. Proteins 2003;51:569–576. © 2003 Wiley‐Liss, Inc.
Generation of accurate protein loop conformations through low‐barrier molecular dynamics
Authors: Hornak Viktor , Simmerling Carlos 
Published: May 2003

AbstractPrediction and refinement of protein loop structures are important and challenging tasks for which no general solution has been found. In addition to the accuracy of scoring functions, the main problems reside in (1) insufficient statistical sampling and (2) crossing energy barriers that impede conformational rearrangements of the loop. We approach these two issues by using “low‐barrier molecular dynamics,” a combination of energy smoothing techniques. To address statistical sampling, locally enhanced sampling (LES) is used to produce multiple copies of the loop, thus improving statistics and reducing energy barriers. We introduce a novel extension of LES that can improve local sampling even further through hierarchical subdivision of copies. Even though LES reduces energy barriers, it cannot provide for crossing infinite barriers, which can be problematic when substantial rearrangement of residues is necessary. To permit this kind of loop residue repacking, a “soft‐core” potential energy function is introduced, so that atomic overlaps are temporarily allowed. We tested this new combined methodology to a loop in anti‐influenza antibody Fab 17/9 (7 residues long) and to another loop in the antiprogesterone antibody DB3 (8 residues). In both cases, starting from random conformations, we were able to locate correct loop structures (including sidechain orientations) with heavy‐atom root‐mean‐square deviation (fit to the nonloop region) of ∼1.1 Å in Fab 17/9 and ∼1.8 Å in DB3. We show that the combination of LES and soft‐core potential substantially improves sampling compared to regular molecular dynamics. Moreover, the sampling improvement obtained with this combined approach is significantly better than that provided by either of the two methods alone. Proteins 2003;51:577–590. © 2003 Wiley‐Liss, Inc.
Hidden Markov models that use predicted local structure for fold recognition: Alphabets of backbone geometry
Authors: Karchin Rachel , Cline Melissa , Mandel‐Gutfreund Yael , Karplus Kevin 
Published: May 2003

AbstractAn important problem in computational biology is predicting the structure of the large number of putative proteins discovered by genome sequencing projects. Fold‐recognition methods attempt to solve the problem by relating the target proteins to known structures, searching for template proteins homologous to the target. Remote homologs that may have significant structural similarity are often not detectable by sequence similarities alone. To address this, we incorporated predicted local structure, a generalization of secondary structure, into two‐track profile hidden Markov models (HMMs). We did not rely on a simple helix‐strand‐coil definition of secondary structure, but experimented with a variety of local structure descriptions, following a principled protocol to establish which descriptions are most useful for improving fold recognition and alignment quality. On a test set of 1298 nonhomologous proteins, HMMs incorporating a 3‐letter STRIDE alphabet improved fold recognition accuracy by 15% over amino‐acid‐only HMMs and 23% over PSI‐BLAST, measured by ROC‐65 numbers. We compared two‐track HMMs to amino‐acid‐only HMMs on a difficult alignment test set of 200 protein pairs (structurally similar with 3–24% sequence identity). HMMs with a 6‐letter STRIDE secondary track improved alignment quality by 62%, relative to DALI structural alignments, while HMMs with an STR track (an expanded DSSP alphabet that subdivides strands into six states) improved by 40% relative to CE. Proteins 2003;51:504–514. © 2003 Wiley‐Liss, Inc.
Ultraviolet illumination‐induced reduction of α‐lactalbumin disulfide bridges
Authors: Permyakov Eugene A. , Permyakov Serge E. , Deikus Gintaras Y. , Morozova‐Roche Ludmila A. , Grishchenko Valery M. , Kalinichenko Lina P. , Uversky Vladimir N. 
Published: May 2003

AbstractProlonged exposure of Ca2+‐loaded or Ca2+‐depleted human α‐lactalbumin to ultraviolet light (270–290 nm, 1 mW/cm2, for 2 to 4 h) results in a 10‐nm red shift of its tryptophan fluorescence spectrum. Gel chromatography of the UV‐illuminated samples reveals two non‐native protein forms: (1) a component with a red‐shifted tryptophan fluorescence spectrum; and (2) a component with kynurenine‐like fluorescent properties. The first component has from 0.6 to 0.9 free DTNB‐reactive SH groups per protein molecule, which are absent in the native protein and is characterized by slightly lowered Ca2+‐affinity (2 × 108 M−1 versus 8 × 108 M−1 for the native protein) and absence of observable thermal transition. The second component corresponds to the protein with photochemically modified tryptophan residues. It is assumed that the UV excitation of tryptophan residue(s) in α‐lactalbumin is followed by a transfer of electrons to the SS bonds, resulting in their reduction. Mass spectrometry data obtained for trypsin‐fragmented UV‐illuminated α‐lactalbumin with acrylodan‐modified free thiol groups reveal the reduction of the 61–77 and 73–91 disulfide bridges. The effect observed has to be taken into account in any UV‐region spectral studies of α‐lactalbumin. Proteins 2003;51:498–503. © 2003 Wiley‐Liss, Inc.
The nature of the turn in omega loops of proteins
Authors: Pal Manoj , Dasgupta Swagata 
Published: May 2003

AbstractAn analysis of Ω loops in a nonredundant set of protein stuctures from the Protein Data Bank has been carried out to determine the nature of the “turn elements” present. Because Ω loops essentially reverse their direction in three‐dimensional space, this analysis was made with respect to four turn elements identified as (1) Gly; (2) Pro; (3) a residue with α‐helical ϕ,ψ angles, termed a helical residue; and (4) a cis peptide. A set of 1079 Ω loops from a set of 680 proteins were used for the analysis. Apart from other criteria that define Ω loops, the selection of an Ω loop from a cluster of loops is based on an exposure index. In this study, analyses have been made with two sets of data: (1) Ω loops arising from a minimum exposure index indicative of a less exposed loop (xmin set) and (2) Ω loops with a maximum exposure index indicative of a relatively exposed loop (xmax set). Overall residue preferences and positional preferences have been examined. Positions of the turn elements for Ω loops of varying length have also been studied. Specific positional preferences are observed for particular turn elements with regard to the length of Ω loops. Analysis in terms of the turn elements can provide guidelines for modeling of loops in proteins. Apart from Pro, which has the natural tendency to form cis peptide bonds, a higher occurrence of non‐Pro cis peptide bonds is observed. Torsion angles in Ω loops also indicate the occurrence of a large number of residues with helical ϕ,ψ angles, necessary for the turn in the loop structures. Proteins 2003;51:591–606. © 2003 Wiley‐Liss, Inc.
Static and dynamic water molecules in Cu,Zn superoxide dismutase
Authors: Falconi M. , Brunelli M. , Pesce A. , Ferrario M. , Bolognesi M. , Desideri A. 
Published: May 2003

AbstractUnderstanding protein hydration is a crucial, and often underestimated issue, in unraveling protein function. Molecular dynamics (MD) computer simulation can provide a microscopic description of the water behavior. We have applied such a simulative approach to dimeric Photobacterium leiognathi Cu,Zn superoxide dismutase, comparing the water molecule sites determined using 1.0 ns MD simulation with those detected by X‐ray crystallography. Of the water molecules detected by the two techniques, 20% fall at common sites. These are evenly distributed over the protein surface and located around crevices, which represent the preferred hydration sites. The water mean residence time, estimated by means of a survival probability function on a given protein hydration shell, is relatively short and increases for low accessibility sites constituted by polar atoms. Water molecules trapped in the dimeric protein intersubunit cavity, as identified in the crystal structure, display a trajectory mainly confined within the cavity. The simulation shows that these water molecules are characterized by relatively short residence times, because they continuously change from one site to another within the cavity, thus hinting at the absence of any relationship between spatial and temporal order for solvent molecules in proximity of protein surface. Proteins 2003;51:607–615. © 2003 Wiley‐Liss, Inc.
Analysis of the differences in the folding kinetics of structurally homologous proteins based on predictions of the gross features of residue contacts
Authors: Ichimaru Takehiro , Kikuchi Takeshi 
Published: May 2003

AbstractIt is a general notion that proteins with very similar three‐dimensional structures would show very similar folding kinetics. However, recent studies reveal that the folding kinetic properties of some proteins contradict this thought (i.e., the members in a same protein family fold through different pathways). For example, it has been reported that some β‐proteins in the intracellular lipid‐binding protein family fold through quite different pathways (Burns et al., Proteins 1998;33:107–118). Similar differences in folding kinetics are also observed in the members of the globin family (Nishimura et al., Nat Struct Biol 2000;7:679–686). In our study, we examine the possibility of predicting qualitative differences in folding kinetics of the intracellular lipid‐binding proteins and two globin proteins (i.e., myoglobin and leghemoglobin). The problem is tackled by means of a contact map based on the average distance statistics between residues, the Average Distance Map (ADM), as constructed from sequence. The ADMs for the three proteins show overall similarity, but some local differences among maps are also observed. Our results demonstrate that some properties of the protein folding kinetics are consistent with local differences in the ADMs. We also discuss the general possibility of predicting folding kinetics from sequence information. Proteins 2003;51:515–530. © 2003 Wiley‐Liss, Inc.
Guided docking: First step to locate potential binding sites
Authors: Fitzjohn Paul W. , Bates Paul A. 
Published: May 2003

AbstractThe long‐range electrostatic forces of the targets in round 2 of the Critical Assessment of PRediction of Interactions (CAPRI) experiment were examined and a simple guided docking method, based on these forces, was applied. The method described consists of calculating an initial rigid body trajectory and an optional final, fully flexible refinement stage. Although only limited success was found in predicting the final complexes, some interesting information was discovered. In particular, the long‐range forces seem to give some insight into the unusual binding mode of target 4 while raising some questions about target 7, which warrant further investigation. Proteins 2003;52:28–32. © 2003 Wiley‐Liss, Inc.
CAPRI: A Critical Assessment of PRedicted Interactions
Authors: Janin Joël , Henrick Kim , Moult John , Eyck Lynn Ten , Sternberg Michael J. E. , Vajda Sandor , Vakser Ilya , Wodak Shoshana J. 
Published: May 2003

AbstractCAPRI is a communitywide experiment to assess the capacity of protein‐docking methods to predict protein–protein interactions. Nineteen groups participated in rounds 1 and 2 of CAPRI and submitted blind structure predictions for seven protein–protein complexes based on the known structure of the component proteins. The predictions were compared to the unpublished X‐ray structures of the complexes. We describe here the motivations for launching CAPRI, the rules that we applied to select targets and run the experiment, and some conclusions that can already be drawn. The results stress the need for new scoring functions and for methods handling the conformation changes that were observed in some of the target systems. CAPRI has already been a powerful drive for the community of computational biologists who development docking algorithms. We hope that this issue of Proteins will also be of interest to the community of structural biologists, which we call upon to provide new targets for future rounds of CAPRI, and to all molecular biologists who view protein–protein recognition as an essential process. Proteins 2003;52:2–9. © 2003 Wiley‐Liss, Inc.
ICM‐DISCO docking by global energy optimization with fully flexible side‐chains
Authors: Fernández‐Recio Juan , Totrov Maxim , Abagyan Ruben 
Published: May 2003

AbstractThe ICM‐DISCO (Docking and Interface Side‐Chain Optimization) protein–protein‐docking method is a direct stochastic global energy optimization from multiple starting positions of the ligand. The first step is performed by docking of a rigid all‐atom ligand molecule to a set of soft receptor potentials precalculated on a 0.5 Å grid from realistic solvent‐corrected force‐field energies. This step finds the correct solution as the lowest energy conformation in almost 100% of the cases in which interfaces do not change on binding. The second step is needed to deal with the induced changes and includes the global optimization of the interface side‐chains of up to 400 best solutions. The CAPRI predictions were performed fully automatically with this method. Available experimental information was included as a filtering step to favor expected docking surfaces. In three of the seven proposed targets, the ICM‐DISCO method found a good solution (>50% of correct contacts) within the five submitted models. The procedure is global and fully automated. We demonstrate that the algorithm handles the induced changes of surface side‐chains but is less successful if the backbone undergoes large‐scale rearrangements. Proteins 2003;52:113–117. © 2003 Wiley‐Liss, Inc.
Evaluation of the third solvent clusters fitting procedure for the prediction of protein–protein interactions based on the results at the CAPRI blind docking study
Authors: Komatsu Katsuichiro , Kurihara Youji , Iwadate Mitsuo , Takeda‐Shitaka Mayuko , Umeyama Hideaki 
Published: May 2003

AbstractTo predict protein–protein interactions, rough or coarse handling for the induced fit problem is proposed. Our method involves the overlap of two hydrophobic interactions as “third solvent clusters fitting.” Predictions for binding sites and geometric centers were acceptable, but those of the binding axes were poor. In this study, only the largest benzene cluster was used for the third solvent clusters fitting. For the next CAPRI targets, we must perform protein–protein interaction analyses, which include other smaller benzene clusters. Proteins 2003;52:15–18. © 2003 Wiley‐Liss, Inc.