bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atom‐transfer radical grafting polymerization of 2‐methacryloyloxyethyl phosphorylcholine from silicon wafer surfaces
Authors: Feng Wei , Brash John , Zhu Shiping 
Published: May 2004

Abstract2‐Methacryloyloxyethyl phosphorylcholine (MPC), a biomimetic monomer, was grafted from silicon wafer surfaces at room temperature by combining self‐assembly of initiator and surface‐initiated atom transfer radical polymerization. Two methods were used to control the grafting process. One was to add free initiator to the reaction system; the other was to add excess deactivator. The grafting densities up to 0.3 chains/nm2 were obtained. The surface thickness increased linearly with MPC conversion. The thickness depended on catalyst and monomer concentrations, as well as activator/deactivator ratio. Poly(MPC) layers of >100 nm thick were obtained by optimizing the polymerization conditions. A second block of either poly(MPC) or poly[2‐(dimethylamino)ethyl methacrylate] was also grown from the grafted poly(MPC), demonstrating the system livingness. X‐ray photoelectron spectroscopy was used to examine the surface chemical compositions showed good agreement with the theoretical values. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 2931–2942, 2004
Vibration‐induced change of crystal structure in isotactic polypropylene and its improved mechanical properties
Authors: Zhang Jie , Shen Kaizhi , Na Shun , Fu Qiang 
Published: May 2004

AbstractIn order to understand the formation of different crystal structures and improve the mechanical properties of isotactic polypropylene (iPP), melt vibration technology, which generally includes shear vibration and hydrostatic pressure vibration, was used to induce the change of crystal structure of iPP. iPP forms α crystal structure in traditional injection molding. Through melt vibration, crystal orientated and its size became smaller, and a change of crystal structure of iPP from α form to β form and γ form was achieved. Therefore, the mechanical properties of iPP were improved. At high melting temperature (230 °C), only β form can be induced. At low melting temperature (190 °C), either β form or γ form can be induced, depending on the combination of frequency and vibration pressure. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2385–2390, 2004
Characterization of epoxy resin (SU‐8) film using thickness‐shear mode (TSM) resonator under various conditions
Authors: Hossenlopp Jeanne , Jiang Lizhong , Cernosek Richard , Josse Fabien 
Published: May 2004

AbstractCharacterization of an epoxy resin film, commonly known as SU‐8, is presented using thickness shear mode (TSM) quartz resonator. The impedance‐admittance characteristics of the equivalent circuit models of the unperturbed and coated resonators are analyzed to extract the storage modulus and loss modulus (G′ andG″). Those parameters are needed to establish SU‐8 film as an effective wave‐guiding layer in the implementation of guided shear‐horizontal surface acoustic wave (SH‐SAW) sensor platforms. Both cured and uncured polymer films are studied at the fundamental and third harmonic frequencies of the TSM resonators. The storage modulus (G′) and loss modulus (G″) of the SU‐8 film approach constant values of 1.66 × 1010dyne/cm2and 6.0 × 108dyne/cm2, respectively, for relatively thicker films (>20 μm) at a relatively low frequency of 9 MHz. The most accurate values for the extracted shear moduliG(G=G′+jG″) are obtained at high thickness where the viscoelastic contribution to the TSM response is substantial. The effect of temperature on the storage and loss moduli is determined for the range of −75 to 40 °C. It is found that the polymer approaches a totally glassy state below −60 °C. Exposure to water appears to follow Fickian diffusion behavior at short times and this exposure also results in changes to bothG′ andG″. However, stability is rapidly reached with exposure to water, indicating relatively lower water absorption, consistent with the extracted diffusion coefficient. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 2373–2384, 2004
Job stress and job satisfaction of cancer care workers
Authors: Grunfeld Eva , Zitzelsberger Louise , Coristine Marjorie , Whelan Timothy J. , Aspelund Faye , Evans William K. 
Published: May 2004

AbstractBackground: There is an increasing demand for oncology care as a result of a number of trends. In combination with ongoing changes to the health‐care system, these trends have an impact on the workplace environment of systemic therapy personnel.Methods: A postal survey was sent to major providers of tertiary systemic therapy services in Ontario. Included in the survey were measures of job satisfaction and stress. In order to capture in‐depth data related to survey themes, focus groups were held with personnel at six major cancer treatment facilities. Content analysis identified major themes.Results: Analysis of focus group and survey studies showed that the greatest source of job satisfaction stemmed from patient care and contact. Manifestations of increasing workload emerged as major sources of job stress. Personnel were concerned as to what they saw as negative consequences of heavy workload—a perceived decrease in the quality of patient care and staff morale.Conclusions: The findings of this research suggest that the current workplace environment is having a negative impact on the well‐being of systemic therapy staff, and may have consequences in terms of quality of patient care. Personnel identified system changes that they felt would help alleviate workload and resulting stress. Copyright © 2004 John Wiley & Sons, Ltd.
The structural genomics experimental pipeline: Insights from global target lists
Authors: O'Toole Nicholas , Grabowski Marek , Otwinowski Zbyszek , Minor Wladek , Cygler Miroslaw 
Published: May 2004

AbstractStructural genomics (SG) initiatives are currently attempting to achieve the high‐throughput determination of protein structures on a genome‐wide scale. Here we analyze the SG target data that have been publicly released over a period of 16 months to assess the potential of the SG initiatives. We use statistical techniques most commonly applied in epidemiology to describe the dynamics of targets through the experimental SG pipeline. There is no clear bottleneck among the key stages of cloning, expression, purification and crystallization. An SG target will progress through each of these steps with a probability of approximately 45%. Around 80% of targets with diffraction data will yield a crystal structure, and 20% of targets with HSQC spectra will yield an NMR structure. We also find the overlaps among SG targets: 61% of SG protein sequences share at least 30% sequence identity with one or more other SG targets. There is no significant difference in average structure quality among SG structures and other structures in the PDB determined by “traditional” methods, but on average SG structures are deposited to the PDB twice as quickly after X‐ray data collection. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Prediction of transmembrane regions of β‐barrel proteins using ANN‐ and SVM‐based methods
Authors: Natt Navjyot K. , Kaur Harpreet , Raghava G. P. S. 
Published: May 2004

AbstractThis article describes a method developed for predicting transmembrane β‐barrel regions in membrane proteins using machine learning techniques: artificial neural network (ANN) and support vector machine (SVM). The ANN used in this study is a feed‐forward neural network with a standard back‐propagation training algorithm. The accuracy of the ANN‐based method improved significantly, from 70.4% to 80.5%, when evolutionary information was added to a single sequence as a multiple sequence alignment obtained from PSI‐BLAST. We have also developed an SVM‐based method using a primary sequence as input and achieved an accuracy of 77.4%. The SVM model was modified by adding 36 physicochemical parameters to the amino acid sequence information. Finally, ANN‐ and SVM‐based methods were combined to utilize the full potential of both techniques. The accuracy and Matthews correlation coefficient (MCC) value of SVM, ANN, and combined method are 78.5%, 80.5%, and 81.8%, and 0.55, 0.63, and 0.64, respectively. These methods were trained and tested on a nonredundant data set of 16 proteins, and performance was evaluated using “leave one out cross‐validation” (LOOCV). Based on this study, we have developed a Web server, TBBPred, for predicting transmembrane β‐barrel regions in proteins (available at http://www.imtech.res.in/raghava/tbbpred). Proteins 2004. © 2004 Wiley‐Liss, Inc.
Predictive reconstruction of the mitochondrial iron–sulfur cluster assembly metabolism: I. The role of the protein pair ferredoxin–ferredoxin reductase (Yah1–Arh1)
Authors: Alves Rui , Herrero Enrique , Sorribas Albert 
Published: May 2004

AbstractAdrenodoxin reductase homologue (Arh1) and yeast adrenodoxin homologue (Yah1) are essential Saccharomyces cerevisiae mitochondrial proteins involved in heme A biosynthesis and in iron–sulfur cluster (FeSC) assembly. Although the role of Arh1 and Yah1 in heme A biosynthesis is fairly well established, their systemic role on FeSC synthesis is not well understood. Also, while it is thought that the reductase Arh1 provides electrons for the ferredoxin Yah1, two hybrid experiments do not show interaction between the two proteins. In the first part of this article, we use structural bioinformatics methods to evaluate the possibility of interaction between Arh1 and Yah1. Using protein model building and docking algorithms, we predict a complex between Arh1 and Yah1 that is similar to that of their bovine homologues (adrenodoxin reductase–adrenodoxin reductase), suggesting that Arh1 can indeed reduce Yah1. The predicted complex allows us to suggest point mutations to either molecule that could hinder Arh1–Yah1 interaction and test the role of Arh1 as the reductase for Yah1. In the second part of this article, we investigate the physiological role of Arh1–Yah1 on FeSC assembly by deriving alternative mathematical models of the process, based on published information. Comparing the dynamical behavior of each model with that observed in reported experiments emphasizes the importance of Arh1–Yah1 providing electrons for in situ FeSC repair. Only when this mode of action of either of the two proteins in FeSC synthesis is considered can previously reported results be reproduced. Proteins 2004; © 2004 Wiley‐Liss, Inc.
The structure of murine neuroglobin: Novel pathways for ligand migration and binding
Authors: Vallone Beatrice , Nienhaus Karin , Brunori Maurizio , Nienhaus G. Ulrich 
Published: May 2004

AbstractNeuroglobin, a recently discovered globin predominantly expressed in neuronal tissue of vertebrates, binds small, gaseous ligands at the sixth coordination position of the heme iron. In the absence of an exogenous ligand, the distal histidine (His64) binds to the heme iron in the ferrous and ferric states. The crystal structure of murine ferric (met) neuroglobin at 1.5 Å reveals interesting features relevant to the ligand binding mechanism. Only weak selectivity is observed for the two possible heme orientations, the occupancy ratio being 70:30. Two small internal cavities are present on the heme distal side, which enable the His64(E7) side chain to move out of the way upon exogenous ligand binding. Moreover, a third, huge cavity (volume approximately 290 Å3) connecting both sides of the heme, is open towards the exterior and provides a potential passageway for ligands. The CD and EF corners exhibit substantial flexibility, which may assist ligands in entering the protein and accessing the active site. Based on this high‐resolution structure, further structure‐function studies can be planned to elucidate the role of neuroglobin in physiological responses to hypoxia. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Strategy for supplementing structure calculations using limited data with hydrophobic distance restraints
Authors: Alexandrescu Andrei T. 
Published: May 2004

AbstractIntroductory biochemistry texts often note that the fold of a protein is completely defined when the dihedral angles ϕ and ψ are known for each amino acid. This assertion was examined with torsion angle dynamics and simulated annealing (TAD/SA) calculations of protein G using only dihedral angle restraints. When all dihedral angles were restrained to within 1° of the values of the X‐ray structure, the TAD/SA structures gave a backbone root mean square deviation to the target of 4 Å. Factors that contributed to divergence from the correct solution include deviations of peptide bonds from planarity, internal conflicts resulting from the nonuniform energies of different ϕ, ψ combinations, and relaxation to extended conformations in the absence of long‐range constraints. Simulations including hydrogen‐bond restraints showed that even a few long‐range contacts constrain the fold better than a complete set of accurate dihedral restraints. A procedure is described for TAD/SA calculations using hydrogen‐bond restraints, idealized dihedral restraints for residues in regular secondary structures, and “hydrophobic distance restraints” derived from the positions of hydrophobic residues in the amino acid sequence. The hydrogen‐bond restraints are treated as inviolable, whereas violated hydrophobic restraints are removed following reduction of restraint upper bounds from 2 to 1 times the predicted radius of gyration. The strategy was tested with simulated restraints from X‐ray structures of proteins from different fold classes and NMR data for cold shock protein A that included only backbone chemical shifts and hydrogen bonds obtained from a long‐range HNCO experiment. Proteins 2004. © 2004 Wiley‐Liss, Inc.
The SHS2 module is a common structural theme in functionally diverse protein groups, like Rpb7p, FtsA, GyrI, and MTH1598/TM1083 superfamilies
Authors: Anantharaman V. , Aravind L. 
Published: May 2004

AbstractUsing structural comparisons, we identified a novel domain with a simple fold in the bacterial cell division ATPase FtsA, the archaeo‐eukaryotic RNA polymerase subunit Rpb7p, the GyrI superfamily, and the uncharacterized MTH1598/Tm1083‐like proteins. The fold contains a core of 3 strands, forming a curved sheet, and a single helix in a strand–helix–strand–strand (SHS2) configuration. The SHS2 domain may exist either in single or duplicate copies within the same polypeptide. The single‐copy versions of the domain in FtsA and Rbp7p are most closely related, and appear to mediate protein–protein interactions by means of strand 1, and the loop between strand 2 and strand 3 of the domain. We predict that the interactions between FtsA and its functional partners in bacterial cell division are likely to be similar to the interactions of Rbp7p in the archaeo‐eukaryotic RNA polymerase complex. The dimeric versions typified by the GyrI superfamily appear to have been adapted for small‐molecule binding. Sequence profiles searches helped us to identify several new versions of the GyrI superfamily, including a family of secreted forms that is found only in animals and the bacterial pathogen Leptospira. Through sequence–structure comparisons, we predict the positions that are likely to be important for ligand specificity in the GyrI superfamily. In the MTH1598/Tm1083‐like proteins, a SHS2 domain is inserted into the loop between strand 1 and helix 1 of another SHS2 domain. This has resulted in a structure that has convergent similarities with the Hsp33 and green fluorescent protein folds. The sequence conservation pattern and its phyletic profile suggest that it might function as an enzyme in some conserved aspect of nucleic acid metabolism. Thus, the SHS2 domain is an example of a simple module that has been adapted to perform an entire spectrum of functions ranging from protein–protein interactions to small‐molecule recognition and catalysis. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Designing proteins from the inside out
Authors: Ventura Salvador , Serrano Luis 
Published: May 2004

AbstractGlobular proteins are characterized by the specific and tight packing of hydrophobic side‐chains in the so‐called “hydrophobic core.” Formation of the core is key in folding, stabilization, and conformational specificity. The critical role of hydrophobic cores in maintaining the highly ordered structures present in natural proteins justifies the tremendous efforts devoted to their redesign. Both experimental and computational combinatorial‐based approaches have been reported in the last years as powerful protein design tools. These manage to explore large regions of the sequence/conformational space, allowing the search for alternative protein core arrangements displaying native‐like properties. The overall results obtained from core design projects have contributed significantly to our present knowledge of protein folding and function. In addition, core design has worked as a benchmark for the development of ambitious protein design projects that nowadays are allowing the de novo design of novel protein structures and functions. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Hydrophobic complementarity in protein–protein docking
Authors: Berchanski Alexander , Shapira Boaz , Eisenstein Miriam 
Published: May 2004

AbstractFormation of hydrophobic contacts across a newly formed interface is energetically favorable. Based on this observation we developed a geometric–hydrophobic docking algorithm that estimates quantitatively the hydrophobic complementarity at protein–protein interfaces. Each molecule to be docked is represented as a grid of complex numbers, storing information regarding the shape of the molecule in the real part and information regarding the hydropathy of the surface in the imaginary part. The grid representations are correlated using fast Fourier transformations. The algorithm is used to compare the extent of hydrophobic complementarity in oligomers (represented by D2tetramers) and in hetero‐dimers of soluble proteins (complexes). We also test the implication of hydrophobic complementarity in distinguishing correct from false docking solutions. We find that hydrophobic complementarity at the interface exists in oligomers and in complexes, and in both groups the extent of such complementarity depends on the size of the interface. Thus, the non‐polar portions of large interfaces are more often juxtaposed than non‐polar portions of small interfaces. Next we find that hydrophobic complementarity helps to point out correct docking solutions. In oligomers it significantly improves the ranks of nearly correct reassembled and modeled tetramers. Combining geometric, electrostatic and hydrophobic complementarity for complexes gives excellent results, ranking a nearly correct solution < 10 for 5 of 23 tested systems, < 100 for 8 systems and < 1000 for 19 systems. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Towards a MIP‐based alignment and docking in computer‐aided drug design
Authors: Barbany Montserrat , Terán Hugo Gutiérrez‐de‐ , Sanz Ferran , Villà‐Freixa Jordi 
Published: May 2004

AbstractStructural alignment of ligands in their biological conformation is a crucial step in the building of pharmacophoric models in structure‐based drug design. In addition, docking algorithms are limited in some cases by the quality of the scoring functions and the limited flexibility of the environment that the different programs allow. On the other hand, GRID molecular interaction potentials (MIPs) have been used for a long time in 3D‐QSAR studies. However, in most of these studies the alignment of the molecules is performed on the basis of geometrical or physico‐chemical criteria that differ from the MIPs used in the partial least squares statistical analysis. We have previously developed a method to use the same scoring function for the molecular alignment and for 3D‐QSAR studies. This methodology, based on the use of GRID potentials, consists in the weighted averaging of similarities of the relevant MIPs of the molecules to be aligned. Here we present a method to obtain the weights for the different GRID probes in the average based on the structural information on protein‐ligand complexes for relevant systems. The method, implemented in MIPSIM, is shown to yield good accuracy in the prediction of the alignments for two systems: a set of three inhibitors of dihydrofolate reductase and a set of fifteen non‐nucleoside HIV‐1 reverse transcriptase inhibitors (NNRTIs). The smooth GRID potentials are shown to capture the flexible character of the active site, as opposed to traditional docking scoring energy functions. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Folding thermodynamics of three β‐sheet peptides: A model study
Authors: Irbäck Anders , Sjunnesson Fredrik 
Published: May 2004

AbstractWe study the folding thermodynamics of a β‐hairpin and two three‐stranded β‐sheet peptides using a simplified sequence‐based all‐atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic attraction. The native populations obtained for these three sequences are in good agreement with experimental data. We also show that the apparent native population depends on which observable is studied; the hydrophobicity energy and the number of native hydrogen bonds give different results. The magnitude of this dependence matches well with the results obtained in two different experiments on the β‐hairpin. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Study of local lattice relaxation of substitutional impurities in silicon and germanium
Authors: Sasireka D. , Palaniyandi E. , Iyakutti K. 
Published: May 2004

AbstractLocal lattice relaxation of substitutional donors in silicon investigated using self‐consistent multiple scattering Xα (MSXα) method within the framework of the standard muffin‐tin potential approximation is extended to substitutional donors in germanium and substitutional acceptors in both silicon and germanium. Incorporating the effect of lattice relaxation surrounding the impurity makes the model suitable for both shallow and deep levels. Chemical trends of some aspects of impurity states, such as local lattice relaxation and charge transfer, of the impurities both in silicon and germanium are inferred. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004