bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact‐modified polypropylene/vermiculite nanocomposites
Authors: Tjong S. C. , Meng Y. Z. 
Published: August 2003

AbstractImpact‐modified polypropylene (PP)/vermiculite (VMT) nanocomposites toughened with maleated styrene–ethylene butylene–styrene (SEBS‐g‐MA) were compounded in a twin‐screw extruder and injection‐molded. VMT was treated with maleic anhydride, which acted both as a compatibilizer for the polymeric matrices and as a swelling agent for VMT in the nanocomposites. The effects of the impact modifier on the morphology and the impact, static, and dynamic mechanical properties of the PP/VMT nanocomposites were investigated. Transmission electron microscopy revealed that an exfoliated VMT silicate layer structure was formed in ternary (PP–SEBS‐g‐MA)/VMT nanocomposites. Tensile tests showed that the styrene–ethylene butylene–styrene additions improved the tensile ductility of the (PP–SEBS‐g‐MA)/VMT ternary nanocomposites at the expense of their tensile stiffness and strength. Moreover, Izod impact measurements indicated that the SEBS‐g‐MA addition led to a significant improvement in the impact strength of the nanocomposites. The SEBS‐g‐MA elastomer was found to be very effective at converting brittle PP/VMT organoclay composites into tough nanocomposites. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2332–2341, 2003
Effect of a silicate filler on the crystal morphology of poly(trimethylene terephthalate)/clay nanocomposites
Authors: Hu Xianbo , Lesser Alan J. 
Published: August 2003

AbstractA series of intercalated poly(trimethylene terephthalate) (PTT)/clay nanocomposites were prepared in a twin‐screw extruder by the melt mixing of PTT with either quaternary or ternary ammonium salt‐modified clays. The morphology and structure, along with the crystallization and melting behavior, and the dynamic mechanical behavior of the composites were characterized by X‐ray diffraction, transmission electron microscopy, differential scanning calorimetry, and dynamic mechanical thermal analysis. The results showed that the PTT chains could undergo center‐mass transport from the polymer melt into the silicate galleries successfully during the blending and extrusion process. More coherent stacking of the silicate layers was reserved at higher clay concentrations and shorter blend times. Compared with conventionally compounded composites, the nanoscale‐dispersed organophilic clays were more effective as crystal nucleation agents. The influence of the nanosilicates on the crystallization and melting behavior of PTT became distinct when the concentration of clay was around 3 wt %. The changes in the crystallization behavior of the polymer/clay nanocomposites depended not only on the size of the silicates but also on the intrinsic crystallization characteristics of the polymers. The resulting nanocomposites showed an increase in the dynamic modulus of PTT and a decrease in the relaxation intensity (both in loss modulus and loss tangent magnitude). © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2275–2289, 2003
Wetting and dynamics of structured liquid films
Authors: Green Peter F. 
Published: August 2003

AbstractThe stability of a sufficiently thin, supported, homopolymer film against the development of local thickness fluctuations which can become amplified, eventually leading to structural destabilization of the film, is typically determined by long and short‐range intermolecular forces. In A‐B diblock copolymers, the connectivity between the blocks, the preferential attraction of one block to an external interface, combined with an incompatibility between the A‐B segments, the situation is very different. Two cases, largely dictated by χN, wher χ is the Flory‐Huggins interaction parameter andNis the degree of polymerization, can arise in thin copolyme films. When χNis large, thin films exhibit comparatively stable topographical structures, where the dimensions of the topographies normal to the substrate reflect a natural length‐scale associated with phase separation in the material. In the other situation, where χNis sufficiently small, the copolymer bulk structure is homogeneous. An ordered structure can be induced into the otherwise compositionally homogeneous structure in the vicinity of a substrate. Here, depending on film thickness, a series of transient and stable topographies can develop. Wetting, early stage structural destabilization dynamics leading to the formation of droplets, and late stage coarsening of the droplets are discussed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2219–2235, 2003
Prostate‐specific antigen‐derived epitopes capable of inducing cellular and humoral responses in HLA‐A24+ prostate cancer patients
Authors: Harada Mamoru , Kobayashi Kazuhiko , Matsueda Satoko , Nakagawa Masami , Noguchi Masanori , Itoh Kyogo 
Published: August 2003

AbstractBACKGROUNDWe tried to identify prostate‐specific antigen (PSA)‐derived epitopes immunogenic in HLA‐A24+ prostate cancer patients.METHODSPeripheral blood mononuclear cells (PBMCs) were in vitro stimulated with each of four different PSA peptides carrying the HLA‐A24 binding motif, and their HLA‐A24‐restricted anti‐tumor responses were examined using a parental HLA‐A24‐negative prostate cancer cell line (PC93) and its HLA‐A24‐expressing transfectant line (PC93‐A24). Serum levels of immunoglobulin G (IgG) against PSA peptides were measured by enzyme‐linked immunosorbent assay (ELISA).RESULTSPBMCs, which were in vitro stimulated with either the PSA152–160 or PSA248–257 peptide, showed higher levels of IFN‐γ production and cytotoxicity against the PC93‐A24 than against the PC93. IgG against the PSA248–257 peptide was detected in half of the prostate cancer patients tested.CONCLUSIONSThe PSA152–160 and PSA248–257 peptides could be appropriate target molecules in use for specific immunotherapy of HLA‐A24+ prostate cancer patients. Prostate 57: 152–159, 2003. © 2003 Wiley‐Liss, Inc.
Transgenic mouse with high cre recombinase activity in all prostate lobes, seminal vesicle, and ductus deferens
Authors: Jin Chengliu , McKeehan Kerstin , Wang Fen 
Published: August 2003

AbstractBACKGROUNDProstate‐specific gene ablation provides a powerful tool for functional characterization of genes that have impact on embryonic development or on other organs, specifically in the prostate. Uniform expression of Cre with high recombinase activity in the prostate is needed for prostate‐specific gene ablation based on Cre‐loxP recombinations. Currently, available strains of Cre transgenic mice only express Cre recombinase adequately in certain lobes of the prostate. In other lobes, the expression is low and mosaic. Additional strains of transgenic mice expressing high levels of prostate‐specific Cre in all prostate lobes would be useful to study the impact of genome manipulation in all prostate lobes.METHODSThe ARR2PB composite promoter with improved capacity to drive androgen‐responsive gene expression was used to initiate expression of a transgene bearing the cDNA encoding a recently modified Cre recombinase with improved recombination activity. In addition, an insulator element from the chicken globin locus that minimized negative effect on transcription of the transgene imposed by chromosome structure was employed. The derived transgenic founders were crossed with the Z/AP reporter mouse and Fgfr2f/f mice bearing loxP flanking the FGFR2 locus. Immunochemical and mRNA analyses were employed to test expression and efficacy of the Cre recombinase in the prostate and other tissues.RESULTSThe ARR2PBi‐Cre transgenic mouse specifically and uniformly expressed Cre recombinase in the dorsal, lateral, ventral, and anterior lobes of the prostate, seminal vesicles, and ductus deferens. The Cre recombinase in these tissues effectively excised loxP flanked DNA fragments in the Z/AP reporter that triggered expression of β‐galactosidase, and the loxP–flanked FGFR2f/f locus resulting in specific ablation of FGFR2 in the prostate.CONCLUSIONSCompared with the currently available prostate‐specific Cre strains, the new ARR2PBi‐Cre strain exhibited higher and more uniform expression of Cre recombinase in the prostate as well as in seminal vesicles and ductus deferens. This provides an additional tool for efficient hormone‐dependent gene targeting in epithelial cells of all lobes of the adult prostate, seminal vesicle, and ductus deferens. Prostate 57: 160–164, 2003. © 2003 Wiley‐Liss, Inc.
Laterally directed biopsies detect more clinically threatening prostate cancer: Computer simulated results
Authors: Kawata Nozomu , Miller Gary J. , Crawford E. David , Torkko Kathleen C. , Stewart J. Scott , Lucia M. Scott , Miller Heidi L. , Hirano Daisaku , Werahera Priya N. 
Published: August 2003

AbstractBACKGROUNDThe purpose of this study was to determine, whether a modified fan‐shaped biopsy (MFSB) technique which utilizes six laterally directed biopsies would lead to higher detection rates of clinically threatening prostatic carcinoma than the six random systematic core biopsy (SRSCB) method.METHODSWe reconstructed 3‐dimensional solid computer models of 86 autopsy prostates and 40 radical prostatatectomy specimens. Simulations of SRSCB and MFSB were then performed using the same biopsy sites except that the biopsy probe was rotated 45° toward posterolateral peripheral zone for MFSB. When the Gleason sum was less than 7, clinically threatening cancers were defined as having a tumor volume ≥0.25 cc or ≥0.5 cc.RESULTSWhen the cut off volume was 0.25 cc, MFSB detected significantly more threatening carcinomas in autopsy prostates than did SRSCB (P < 0.0082). This was also true for the surgical prostates (P < 0.0047) as well as for a sub‐group of non‐palpable carcinomas (P < 0.0047). When the cut off volume was increased to 0.5 cc, MFSB detected significantly more threatening carcinomas in the radical series (P < 0.0047) and for the non‐palpable carcinomas (P < 0.0082), but not in the autopsy series.CONCLUSIONSThe MFSB technique, which utilizes laterally directed biopsies, appears to be an effective approach to improve the detection of clinically threatening prostatic carcinoma. Prostate 57: 118–128, 2003. © 2003 Wiley‐Liss, Inc.
The origin and extent of coarse‐grained regularities in protein internal packing
Authors: Bagci Zerrin , Kloczkowski Andrzej , Jernigan Robert L. , Bahar Ivet 
Published: August 2003

AbstractDespite the suitability of various lattice geometries for coarse‐grained modeling of proteins, the actual packing geometry of residues in folded structures has remained largely unexplored. A strong tendency to assume a regular packing geometry is shown here by optimally reorienting and superimposing clusters of neighboring residues from databank structures examined on a coarse‐grained (single‐site‐per‐residue) scale. The orientation function (or order parameter) of the examined coordination clusters with respect to fcc lattice directions is found to be 0.82. The observed geometry, which may be termed an incomplete distorted face‐centered cubic (fcc) packing, is apparently favored by the drive to maximize packing density, in a fashion analogous to the way identical spheres pack densely and follow fcc geometry. About 2/3 of all residues obey this packing geometry, while the remainder occupy other context‐dependent positions. The preferred coordination directions show relatively small variations over the various amino acid types, consistent with uniform residue viewpoint. Both the extremes of solvent‐exposed and completely buried residue neighborhoods approximate the same generic packing, the only difference being in the numbers (and not the orientations) of coordination sites that are occupied (or left void for solvent occupancy). We observe the prevalence of a rather uniform (tight) residue packing density throughout the structure, including even the residues packed near solvent‐exposed regions. The observed orientation distribution reveals an underlying, intrinsic orientation lattice for proteins. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Anatomy of specific interactions between λ repressor and operator DNA
Authors: Oobatake Motohisa , Kono Hidetoshi , Wang Yifei , Sarai Akinori 
Published: August 2003

AbstractRecognition of specific DNA sequences by proteins is essential for regulation of gene expression. To fully understand the recognition mechanism, it is necessary to understand not only the structure of the specific protein–DNA interactions but also the energetics. We therefore performed a computer analysis in which a phage DNA‐binding protein, λ repressor, was used to examine the changes in binding free energy (ΔΔG) and its energy components caused by single base mutations. We then determined which of the calculated energy components best correlated with the experimental data. The experimental ΔΔG values were well reproduced by the calculations. Component analysis revealed that the electrostatic and hydrogen bond energies were most strongly correlated with the experimental data. Among the 51 single base‐substitution mutants examined, positive ΔΔG values, corresponding to weakened binding, were caused by the loss of favorable electrostatic interactions and hydrogen bonds, the introduction of steric collisions and electrostatic repulsion, the loss of favorable interactions with a thymine methyl group, and the increase of unfavorable hydration energy from isolated DNA. This analysis also showed distinct patterns of recognition at A‐T and G‐C positions, as different combinations of energy components were involved in ΔΔG caused by the two substitution types. We have thus been able to identify the energy components that most strongly correlate with sequence‐dependent ΔΔG and determine their contribution to the specificity of DNA sequence recognition by the λ repressor. Application of this method to other systems should provide additional insight into the molecular mechanism of protein–DNA recognition. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Evolutionary analysis reveals collective properties and specificity in the C‐type lectin and lectin‐like domain superfamily
Authors: Ebner Sharon , Sharon Nathan , Ben‐Tal Nir 
Published: August 2003

AbstractMembers of the C‐type lectin/C‐type lectin‐like domain (CTL/CTLD) superfamily share a common fold and are involved in a variety of functions, such as generalized defense mechanisms against foreign agents, discrimination between healthy and pathogen‐infected cells, and endocytosis and blood coagulation. In this work we used ConSurf, a computer program recently developed in our lab, to perform an evolutionary analysis of this superfamily in order to further identify characteristics of all or part of its members. Given a set of homologous proteins in the form of multiple sequence alignment (MSA) and an inferred phylogenetic tree, ConSurf calculates the conservation score in every alignment position, taking into account the relationships between the sequences and the physicochemical similarity between the amino acids. The scores are then color‐coded onto the three‐dimensional structure of one of the homologous proteins. We provide here and at http://ashtoret.tau.ac.il/∼sharon a detailed analysis of the conservation pattern obtained for the entire superfamily and for two subgroups of proteins: (a) 21 CTLs and (b) 11 heterodimeric CTLD toxins. We show that, in general, proteins of the superfamily have one face that is constructed mostly of conserved residues and another that is not, and we suggest that the former face is involved in binding to other proteins or domains. In the CTLs examined we detected a region of highly conserved residues, corresponding to the known calcium‐ and carbohydrate‐binding site of the family, which is not conserved throughout the entire superfamily, and in the CTLD toxins we found a patch of highly conserved residues, corresponding to the known dimerization region of these proteins. Our analysis also detected patches of conserved residues with yet unknown function(s). Proteins 2003. © 2003 Wiley‐Liss, Inc.
An improved protein decoy set for testing energy functions for protein structure prediction
Authors: Tsai Jerry , Bonneau Richard , Morozov Alexandre V. , Kuhlman Brian , Rohl Carol A. , Baker David 
Published: August 2003

AbstractWe have improved the original Rosetta centroid/backbone decoy set by increasing the number of proteins and frequency of near native models and by building on sidechains and minimizing clashes. The new set consists of 1,400 model structures for 78 different and diverse protein targets and provides a challenging set for the testing and evaluation of scoring functions. We evaluated the extent to which a variety of all‐atom energy functions could identify the native and close‐to‐native structures in the new decoy sets. Of various implicit solvent models, we found that a solvent‐accessible surface area–based solvation provided the best enrichment and discrimination of close‐to‐native decoys. The combination of this solvation treatment with Lennard Jones terms and the original Rosetta energy provided better enrichment and discrimination than any of the individual terms. The results also highlight the differences in accuracy of NMR and X‐ray crystal structures: a large energy gap was observed between native and non‐native conformations for X‐ray structures but not for NMR structures. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Subtle functional collective motions in pancreatic‐like ribonucleases: From ribonuclease A to angiogenin
Authors: Merlino Antonello , Vitagliano Luigi , Ceruso Marc Antoine , Mazzarella Lelio 
Published: August 2003

AbstractThe analysis of the dynamic behavior of enzymes is fundamental to structural biology. A direct relationship between protein flexibility and biological function has been shown for bovine pancreatic ribonuclease (RNase A) (Rasmussen et al., Nature 1992;357:423–424). More recently, crystallographic studies have shown that functional motions in RNase A involve the enzyme β‐sheet regions that move concertedly on substrate binding and release (Vitagliano et al., Proteins 2002;46:97–104). These motions have been shown to correspond to intrinsic dynamic properties of the native enzyme by molecular dynamics (MD) simulations. To unveil the occurrence of these collective motions in other members of pancreatic‐like superfamily, we carried out MD simulations on human angiogenin (Ang). Essential dynamics (ED) analyses performed on the trajectories reveal that Ang exhibits collective motions similar to RNase A, despite the limited sequence identity (33%) of the two proteins. Furthermore, we show that these collective motions are also present in ensembles of experimentally determined structures of both Ang and RNase A. Finally, these subtle concerted β‐sheet motions were also observed for other two members of the pancreatic‐like superfamily by comparing the ligand‐bound and ligand‐free structures of these enzymes. Taken together, these findings suggest that pancreatic‐like ribonucleases share an evolutionary conserved dynamic behavior consisting of subtle β‐sheet motions, which are essential for substrate binding and release. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Host‐guest scale of left‐handed polyproline II helix formation
Authors: Rucker Adam L. , Pager Cara T. , Campbell Margaret N. , Qualls Joseph E. , Creamer Trevor P. 
Published: August 2003

AbstractDespite the clear importance of the left‐handed polyproline II (PPII) helical conformation in many physiologically important processes as well as its potential significance in protein unfolded states, little is known about the physical determinants of this conformation. We present here a scale of relative PPII helix‐forming propensities measured for all residues, except tyrosine and tryptophan, in a proline‐based host peptide system. Proline has the highest measured propensity in this system, a result of strong steric interactions that occur between adjacent prolyl rings. The other measured propensities are consistent with backbone solvation being an important component in PPII helix formation. Side chain to backbone hydrogen bonding may also play a role in stabilizing this conformation. The PPII helix‐forming propensity scale will prove useful in future studies of the conformational properties of proline‐rich sequences as well as provide insights into the prevalence of PPII helices in protein unfolded states. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Conformational interconversion in compstatin probed with molecular dynamics simulations
Authors: Mallik Buddhadeb , Lambris John D. , Morikis Dimitrios 
Published: August 2003

AbstractCompstatin is a 13‐residue cyclic peptide that has the potential to become a therapeutic agent against unregulated complement activation. In our effort to understand the structural and dynamic characteristics of compstatin that form the basis for rational and combinatorial optimization of structure and activity, we performed 1‐ns molecular dynamics (MD) simulations. We used as input in the MD simulations the ensemble of 21 lowest energy NMR structures, the average minimized structure, and a global optimization structure. At the end of the MD simulations we identified five conformations, with populations ranging between 9% and 44%. These conformations are as follows: 1) coil with αR‐αR β‐turn, as was the conformation of the initial ensemble of NMR structures; 2) β‐hairpin with ϵ‐αR β‐turn; 3) β‐hairpin with αR‐αR β‐turn; 4) β‐hairpin with αR‐β β‐turn; and 5) α‐helical. Conformational switch was possible with small amplitude backbone motions of the order of 0.1–0.4 Å and free energy barrier crossing of 2–11 kcal/mol. All of the 21 MD structures corresponding to the NMR ensemble possessed a β‐turn, with 14 structures retaining the αR‐αR β‐turn type, but the average minimized structure and the global optimization structures were converted to α‐helical conformations. Overall, the MD simulations have aided to gain insight into the conformational space sampled by compstatin and have provided a measure of conformational interconversion. The calculated conformers will be useful as structural and possibly dynamic templates for optimization in the design of compstatin using structure‐activity relations (SAR) or dynamics‐activity relations (DAR). Proteins 2003. © 2003 Wiley‐Liss, Inc.
Relationship between protein structures and disulfide‐bonding patterns
Authors: Chuang Chao‐Chun , Chen Chun‐Yin , Yang Jinn‐Moon , Lyu Ping‐Chiang , Hwang Jenn‐Kang 
Published: August 2003

AbstractWe found that that disulfide‐bonding patterns can be used to discriminate structure similarity. Our method, based on the hierarchical clustering scheme, is applicable to proteins with two or more disulfide bonds and is able to detect the structural similarities of proteins of low sequence identities (<25%). Our results show the surprisingly close relationship between disulfide‐bonding patterns and proteins structures. Our findings should be useful in protein structure modeling. Proteins 2003. © 2003 Wiley‐Liss, Inc.
Relative stability of protein structures determined by X‐ray crystallography or NMR spectroscopy: A molecular dynamics simulation study
Authors: Fan Hao , Mark Alan E. 
Published: August 2003

AbstractThe relative stability of protein structures determined by either X‐ray crystallography or nuclear magnetic resonance (NMR) spectroscopy has been investigated by using molecular dynamics simulation techniques. Published structures of 34 proteins containing between 50 and 100 residues have been evaluated. The proteins selected represent a mixture of secondary structure types including all α, all β, and α/β. The proteins selected do not contain cysteine–cysteine bridges. In addition, any crystallographic waters, metal ions, cofactors, or bound ligands were removed before the systems were simulated. The stability of the structures was evaluated by simulating, under identical conditions, each of the proteins for at least 5 ns in explicit solvent. It is found that not only do NMR‐derived structures have, on average, higher internal strain than structures determined by X‐ray crystallography but that a significant proportion of the structures are unstable and rapidly diverge in simulations. Proteins 2003. © 2003 Wiley‐Liss, Inc.