bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of temperature, pressure, and composition on DC resistivity and AC conductivity of conductive styrene–butadiene rubber–particulate metal alloy nanocomposites
Authors: Mohanraj G.T. , Dey P.K. , Chaki T.K. , Chakraborty A. , Khastgir D. 
Published: September 2007

AbstractConductive nanocomposites were prepared using styrene butadiene rubber as the polymer matrix and nanosized powder of copper–nickel (Cu–Ni) alloy as the filler. The filler loading was varied from 0 to 40 phr. The electrical conductivity of filled polymer composites is due to the formation of some continuous conductive networks in the polymer matrix. Atomic force microscopy was used to determine the particle size of the nanofiller and its nature of dispersion in the rubber matrix. The DC volume resistivity was measured against the loading of the nanofiller to check the percolation limit. The effect of temperature, applied pressure, time duration under constant compressive stress on the DC resistivity and AC conductivity of the composites with different filler loading were investigated. The change in DC resistivity and AC conductivity against temperature of these composites exhibited positive coefficient of temperature. With the change in applied pressure and time duration under constant compressive stress the DC resistivity undergoes an exponential decrease. The effect of AC field frequency on the AC conductivity was investigated. POLYM. COMPOS. 28:696–704, 2007. © 2007 Society of Plastics Engineers
Extracellular matrix regenerated: tissue engineering via electrospun biomimetic nanofibers
Authors: Sell Scott , Barnes Catherine , Smith Matthew , McClure Michael , Madurantakam Parthasarathy , Grant Joshua , McManus Michael , Bowlin Gary 
Published: September 2007

AbstractWhile electrospinning had seen intermittent use in the textile industry from the early twentieth century, it took the explosion of the field of tissue engineering, and its pursuit of biomimetic extracellular matrix (ECM) structures, to create an electrospinning renaissance. Over the past decade, a growing number of researchers in the tissue engineering community have embraced electrospinning as a polymer processing technique that effectively and routinely produces non‐woven structures of nanoscale fibers (sizes of 80 nm to 1.5 µm). These nanofibers are of physiological significance as they closely resemble the structure and size scale of the native ECM (fiber diameters of 50 to 500 nm). Attempts to replicate the many roles of native ECM have led to the electrospinning of a wide array of polymers, both synthetic (poly(glycolic acid), poly(lactic acid), polydioxanone, polycaprolactone, etc.) and natural (collagen, fibrinogen, elastin, etc.) in origin, for a multitude of different tissue applications. With various compositions, fiber dimensions and fiber orientations, the biological, chemical and mechanical properties of the electrospun materials can be tailored. In this review we highlight the role of electrospinning in the engineering of different tissues and applications (skin/wound healing, cartilage, bone, vascular tissue, urological tissues, nerve, and ligament), and discuss its potential role in future work. Copyright © 2007 Society of Chemical Industry
Apparatus for preparing electrospun nanofibers: designing an electrospinning process for nanofiber fabrication
Authors: Park SuA , Park Koeun , Yoon Hyeon , Son JoonGon , Min Teijin , Kim GeunHyung 
Published: September 2007

AbstractNanofibers are widely used in a range of material applications, such as filter media, biosensors, military protective coatings, three‐dimensional tissue scaffolds, composites, drug delivery, wound dressings and electronic devices. To fabricate nanofibers with desired physical and chemical functions, a variety of electrospinning processes have been introduced using specially designed collectors, microelectromechanical system (MEMS) nozzle tips and auxiliary electrodes to stabilize the spin jets. However, the development of new electrospinning processes continues in the search for ‘tailor‐made’ nanofibers, in which parameters such as the fiber orientation and three‐dimensional structure are ultimately controllable. This paper discusses recently suggested electrospinning methods that are designed to impart specific functionality. It also details the correlations between applied processing parameters and the obtained physical properties of electrospun fibers. Finally, future design directions are suggested for developing an electrospinning apparatus capable of producing optimally structured nanofibers. Copyright © 2007 Society of Chemical Industry
Alternative and effective proteomic analysis inArabidopsis
Authors: Espagne Christelle , Martinez Aude , Valot Benoît , Meinnel Thierry , Giglione Carmela 
Published: September 2007

AbstractVarious functional genomics platforms are required to define the phenotype associated with a mutant. Global protein analyses may be included in any study. We describe here a rapid method of protein sample preparation and analysis, suitable for all laboratories and usingArabidopsisplantlets as the starting material. This reliable and reproducible method for high yield protein extraction from small amounts of material can be used on even the most recalcitrant tissues. The proteins extracted are suitable for many types of protein analysis, including nondenaturing investigations. This method was validated by a rigorous 2‐DE approach, coupled with unambiguous LC‐MS/MS identifications featuring strong sequence coverage (average of 26% with eight different peptides/spot protein). The reproducibility of the method was demonstrated by multiple protein identifications from identical series of spots. An interactive map (http://www.isv.cnrsgif.fr/gel2d/), including 435 protein variants showed that (i) 38% of the proteins were yet unreported, (ii) reduced subfractionation, (iii) had frequent protein modifications (average of two spots/protein entry), and (iv) underwent no major proteolytic events other than leader peptide cleavage. Finally, a simple mobility shift method for the large subunit of RuBisCo (LS) in the first dimension made it possible to characterize previously masked protein spots.
Analysis of membrane microdomain‐associated proteins in the insular cortex of post‐mortem human brain
Authors: Behan Áine T. , Foy Martina , Wynne Kieran , Clarke Michael , Sullivan Matthew , Cotter David R. , Maguire Patricia B. 
Published: September 2007

AbstractMembrane microdomains (MM) are membrane rafts within the cell membrane enriched in cholesterol and glycosphingolipids that have been implicated in the trafficking and sorting of membrane proteins, secretory and endocytotic pathways, and signal transduction. To date, MM have not been characterised in the human brain. We reason that by identifying MM in the normal human cortex, we may better understand the molecular mechanisms of human brain dysfunction. To characterize the protein composition of MM in the human brain, we have carried out a comprehensive proteomic analysis of detergent resistant membranes (DRMs) associated proteins derived from human postmortem insular cortex using 1‐DE separation prior to LC coupled to MS/MS or GeLC‐MS/MS. Eighty five proteins were identified including 57 unique to human brain cortex DRMs (by comparison with DRM proteins reported in other cell types). High levels of signal transduction, cell adhesion, cell transport and cell trafficking proteins were identified including synaptic proteins such as synapsin II and synaptic vesicle membrane protein, mitochondrial proteins such as ATPase subunits and metabolic enzymes such as malate dehydrogenase. This data will facilitate our understanding of protein expression changes within membranes in candidate brain regions in human brain diseases such as schizophrenia, bipolar disorder and other psychiatric and neurodegenerative disorders.
Markers of breast and gynecological malignancies: The clinical approach of proteomics‐based studies
Authors: Lomnytska Marta , Souchelnytskyi Serhiy 
Published: September 2007

AbstractBreast, ovarian, endometrial and cervical cancers are diseases with a relatively high lethal outcome, despite recent development of surgical, chemotherapeutic, radiotherapeutic and anti‐hormonal treatments. The mortality of women with breast cancer is at the level of 20%, while for ovarian cancer it is up to 75%. For cervical cancer it is 38% and for endometrial cancer 17%. To enhance survival of patients, better diagnostics of these cancers in early and non‐invasive stages is essential. Proteomics allows a comprehensive analysis of hundreds of proteins in clinical samples. Studies of tissue samples and body fluids, e.g., blood and plasma, have shown their usefulness in discovery of markers of cancers at early stages. Searches for markers of breast and ovarian cancers have been performed with promising results. Studies of endometrial and cervical cancer markers have been less extensive. This review describes recent reports of markers for early detection of breast, ovarian, endometrial and cervical cancers. A clinical evaluation of the markers discovered with the use of proteomics techniques is discussed.
Towards stable diagnostic setups in clinical proteomics: Absolute quantitation of peptide biomarkers using MALDI‐TOF‐MS
Authors: Baechle Daniel , Sparbier Katrin , Dihazi Hassan , Blaschke Sabine , Mueller Gerhard‐Anton , Kostrzewa Markus , Flad Thomas 
Published: September 2007

AbstractIn routine clinical diagnostics, peptide biomarkers are most commonly quantified using immunological techniques but these methods often lack sensitivity and/or specificity. Hence, quantitative mass spectrometry detection is desirable as an alternative diagnostic tool. To date, quantitative mass spectrometry is mostly based on ESI‐MS coupled to LC, requiring highly sophisticated instrumentation and knowledge and is time consuming and expensive. In contrast, MALDI‐TOF‐MS is a very simple, sensitive and rapid method for the detection of peptide biomarkers. However, the infeasibility of absolute quantification has been a tremendous handicap to the use of MS in stable clinical diagnostics. Here, we describe the development of a technical platform based on ClinProt particles and heavy‐isotope internal peptide standards for the fast and reliable preparation of samples. This combines the advantages of MALDI‐TOF as a read‐out system with absolute quantitation of peptide biomarkers. As a proof‐of‐concept, this platform was successfully employed for the absolute determination of the concentration of the highly abundant serum peptide des‐Ala‐Fibrinopeptide A in 45 serum samples from healthy donors. Such technology essentially contributes to the development of a stable MALDI‐TOF‐MS‐based clinical assay.
Epitope mapping and structural analysis of an anti‐ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism
Authors: Hu Siyi , Zhu Zhiqiang , Li Liangwei , Chang Liang , Li Weifang , Cheng Liansheng , Teng Maikun , Liu Jing 
Published: September 2007

AbstractAnti‐ErbB2 antibodies targeting distinct epitopes can have different biological functions on cancer cells. A21 prepared by surface epitope masking (SEM) method is a tumor‐inhibitory anti‐ErbB2 monoclonal antibody. Previously we engineered a single chain chimeric antibody chA21 with potential for therapy of ErbB2‐overexpressing tumors. Here, we mapped the A21 epitope on ErbB2 extracellular domain (ECD) by screening a combinatorial phage display peptide library, serial subdomain deletion, and mutagenesis scanning. X‐ray crystal structure of the A21 scFv fragment at 2.1 Å resolution was also determined. A molecular model of Ag‐Ab complex was then constructed based on the crystal structures of the A21 scFv and ErbB2 ECD. Some of biological functions of the A21 mAb and its derivative antibodies including their tumor cell growth inhibition and effects on the expression, internalization, and phosphorylation of ErbB2 receptor were also investigated. The results showed that A21 recognized a conformational epitope comprising a large region mostly from ErbB2 extracellular subdomain I with several surface‐exposed residues important for the binding affinity. These data provide unique functional properties of A21 that are quite different from two broadly used anti‐ErbB2 mAbs, Herceptin and 2C4. It suggested that the A21 epitope may be another valuable target for designing new anti‐ErbB2 therapeutics. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Distance dependent centroid to centroid force fields using high resolution decoys
Authors: Rajgaria R. , McAllister S. R. , Floudas C. A. 
Published: September 2007

AbstractSimplified force fields play an important role in protein structure prediction and de novo protein design by requiring less computational effort than detailed atomistic potentials. A side chain centroid based, distance dependent pairwise interaction potential has been developed. A linear programming based formulation was used in which non‐native “decoy” conformers are forced to take a higher energy compared with the corresponding native structure. This model was trained on an enhanced and diverse protein set. High quality decoy structures were generated for ∼1400 nonhomologous proteins using torsion angle dynamics along with restricted variations of the hydrophobic cores of the native structure. The resulting decoy set was used to train the model yielding two different side chain centroid based force fields that differ in the way distance dependence has been used to calculate energy parameters. These force fields were tested on an independent set of 148 test proteins with 500 decoy structures for each protein. The side chain centroid force fields were successful in correctly identifying ∼86% native structures. The Z‐scores produced by the proposed centroid–centroid distance dependent force fields improved compared with other distance dependent Cα‐Cα or side chain based force fields. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Water penetration in the low and high pressure native states of ubiquitin
Authors: Day Ryan , García Angel E. 
Published: September 2007

AbstractTheoretical studies on the solvation of methane molecules in water have shown that the effect of increased pressure is to stabilize solvent separated contacts relative to direct contacts. This suggests that high pressure stabilizes waters that have penetrated into a protein's core, indicating a mechanism for the high pressure denaturation of proteins. We test this theory on a folded protein by studying the penetration of water into the native state of ubiquitin at low and high pressures, using molecular dynamics. An ensemble of conformations sampled in the folded state of ubiquitin has been determined by NMR at two pressures below the protein's denaturation pressure, 30 atm and 3000 atm. We find that 1–5 more waters penetrate the high pressure conformations than the low pressure conformations. Low volume configurations of the system are favored at high pressures, but different components of the system may experience increases or decreases in their specific volumes. We find that penetrating waters have a higher volume per water than bulk waters, but that the volume per protein residue may be lowered by solvation. Furthermore, we find that penetration of the protein by water at high pressures is driven by the difference in the pressure dependence of the probability of cavity opening in the protein and pressure dependence of the probability of cavity opening in the bulk solvent. The volume changes associated with cavity opening and closing indicate that each penetrating water reduces the volume of the system by about 12 mL/mol. The experimental volume change going from the low pressure to the high pressure native state of ubiquitin is 24 mL/mol. Our results indicate that this volume change can be explained by penetration of the protein by two water molecules. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Kinetic analysis of molecular dynamics simulations reveals changes in the denatured state and switch of folding pathways upon single‐point mutation of a β‐sheet miniprotein
Authors: Muff Stefanie , Caflisch Amedeo 
Published: September 2007

AbstractThe effects of a single‐point mutation on folding thermodynamics and kinetics are usually interpreted by focusing on the native structure and the transition state. Here, the entire conformational spaces of a 20‐residue three‐stranded antiparallel β‐sheet peptide (double hairpin) and of its single‐point mutant W10V are sampled close to the melting temperature by equilibrium folding–unfolding molecular dynamics simulations for a total of 40 μs. The folded state as well as the most populated free energy basins in the denatured state are isolated by grouping conformations according to fast relaxation at equilibrium. Such kinetic analysis provides more detailed and useful information than a simple projection of the free energy. The W10V mutant has the same native structure as the wild type peptide, and similar folding rate and stability. In the denatured state, the N‐terminal hairpin is about 20% more structured in W10V than the wild type mainly because of van der Waals interactions. Notably, the W10V mutation influences also the van der Waals energy at the transition state ensemble causing a shift in the ratio of fluxes between two different transition state regions on parallel folding pathways corresponding to nucleation at either of the two β‐hairpins. Previous experimental studies have focused on the effects of denaturant‐dependent or temperature‐dependent changes in the structure of the denatured state. The atomistic simulations show that a single‐point mutation in the central strand of a β‐sheet peptide results in remarkable changes in the topography of the denatured state ensemble. These changes modulate the relative accessibility of parallel folding pathways because of kinetic partitioning of the denatured state. Therefore, the observed dependence of the folding process on the starting ensemble raises questions on the biological significance of in vitro folding studies under strongly denaturing conditions. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Predicting transmembrane helix pair configurations with knowledge‐based distance‐dependent pair potentials
Authors: Wendel Christina , Gohlke Holger 
Published: September 2007

AbstractAs a first step toward a novel de novo structure prediction approach for α‐helical membrane proteins, we developed coarse‐grained knowledge‐based potentials to score the mutual configuration of transmembrane (TM) helices. Using a comprehensive database of 71 known membrane protein structures, pairwise potentials depending solely on amino acid types and distances between Cα‐atoms were derived. To evaluate the potentials, they were used as an objective function for the rigid docking of 442 TM helix pairs. This is by far the largest test data set reported to date for that purpose. After clustering 500 docking runs for each pair and considering the largest cluster, we found solutions with a root mean squared (RMS) deviation <2 Å for about 30% of all helix pairs. Encouragingly, if only clusters that contain at least 20% of all decoys are considered, a success rate >71% (with a RMS deviation <2 Å) is obtained. The cluster size thus serves as a measure of significance to identify good docking solutions. In a leave‐one‐protein‐family‐out cross‐validation study, more than 2/3 of the helix pairs were still predicted with an RMS deviation <2.5 Å (if only clusters that contain at least 20% of all decoys are considered). This demonstrates the predictive power of the potentials in general, although it is advisable to further extend the knowledge base to derive more robust potentials in the future. When compared to the scoring function of Fleishman and Ben‐Tal, a comparable performance is found by our cross‐validated potentials. Finally, well‐predicted “anchor helix pairs” can be reliably identified for most of the proteins of the test data set. This is important for an extension of the approach towards TM helix bundles because these anchor pairs will act as “nucleation sites” to which more helices will be added subsequently, which alleviates the sampling problem. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Protonless 13C direct detection NMR: Characterization of the 37 kDa trimeric protein CutA1
Authors: Bertini Ivano , Jiménez Beatriz , Pierattelli Roberta , Wedd Anthony G. , Xiao Zhiguang 
Published: September 2007

AbstractThe major limitation of nuclear magnetic resonance spectroscopy arises from the increase of nuclear transverse relaxation rates with increasing molecular mass. This causes reduction in spectral resolution and coherence transfer efficiency. The use of 2H‐labeling to eliminate 1H‐mediated relaxation pathways and the constructive use of cross correlation effects (TROSY, CRINEPT) alleviate the phenomenon. An alternative approach is to use direct detection of heteronuclei. Specifically designed 13C direct detection experiments can complement the set of 1H‐based NMR experiments commonly used for structure determination providing an additional source of information less affected by the detrimental transverse relaxation effect. We applied this novel methodology to the study of the CutA1 protein (12.3 kDa) from E. coli that forms a homotrimer in solution with a total molecular mass of 37 kDa. In this work we demonstrate that the information available from 13C direct detection experiments makes it possible to completely assign the NMR resonances of the backbone of this 37 kDa trimeric protein without the need of deuteration. The structural and dynamical knowledge obtained for this system may contribute to understand its biological role. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Proton pathways in a [NiFe]‐hydrogenase: A theoretical study
Authors: Teixeira Vitor H. , Soares Cláudio M. , Baptista António M. 
Published: September 2007

AbstractWe present here a theoretical study to investigate possible proton pathways in the [NiFe]‐hydrogenase from Desulfovibrio gigas. The approach used in this study consists of a combination of Poisson–Boltzmann and Monte Carlo simulations together with a distance‐based network analysis to find possible groups involved in the proton transfer. Results obtained at different pH values show a reasonable number of proton active residues distributed by the protein interior and surface, with a concentration around the metal centres. The electrostatic interactions in this protein are strong, as shown by the unusual shape of the titration curves of several sites. Some residue pairs show strongly correlated protonations, indicating the sharing and probably exchange of a proton between them. The conjugation of the PB and MC simulations with the distance‐based analysis allows a detailed characterization of the possible proton pathways. We discuss previous suggestions and propose a new complete pathway for the proton transfer between the active site and the surface. This pathway is mainly composed of histidines and glutamic acid residues. Proteins 2008. © 2007 Wiley‐Liss, Inc.