bluuebunny/crossref_metadata_2025_split huggingface dataset:
Systematic prediction of human membrane receptor interactions
Authors: Qi Yanjun , Dhiman Harpreet K. , Bhola Neil , Budyak Ivan , Kar Siddhartha , Man David , Dutta Arpana , Tirupula Kalyan , Carr Brian I. , Grandis Jennifer , Bar‐Joseph Ziv , Klein‐Seetharaman Judith 
Published: October 2009

AbstractMembrane receptor‐activated signal transduction pathways are integral to cellular functions and disease mechanisms in humans. Identification of the full set of proteins interacting with membrane receptors by high‐throughput experimental means is difficult because methods to directly identify protein interactions are largely not applicable to membrane proteins. Unlike prior approaches that attempted to predict the global human interactome, we used a computational strategy that only focused on discovering the interacting partners of human membrane receptors leading to improved results for these proteins. We predict specific interactions based on statistical integration of biological data containing highly informative direct and indirect evidences together with feedback from experts. The predicted membrane receptor interactome provides a system‐wide view, and generates new biological hypotheses regarding interactions between membrane receptors and other proteins. We have experimentally validated a number of these interactions. The results suggest that a framework of systematically integrating computational predictions, global analyses, biological experimentation and expert feedback is a feasible strategy to study the human membrane receptor interactome.
The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3‐D cell
Authors: Widjaja Yose Y. , Pang Chi Nam Ignatius , Li Simone S. , Wilkins Marc R. , Lambert Tim D. 
Published: October 2009

AbstractHere, we describe the Interactorium, a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3‐D structures. The tool has been designed to display very complex networks of up to 40 000 proteins or 6000 multiprotein complexes and has a series of toolboxes and menus to allow real‐time data manipulation and control the manner in which data are displayed. It incorporates new algorithms that reduce the complexity of the visualisation by the generation of putative new complexes from existing data and by the reduction of edges through the use of protein “twins” when they occur in multiple locations. Since the Interactorium permits multi‐level viewing of the molecular biology of the cell, it is a considerable advance over existing approaches. We illustrate its use for Saccharomyces cerevisiae but note that it will also be useful for the analysis of data from simpler prokaryotes and higher eukaryotes, including humans. The Interactorium is available for download at http://www.interactorium.net.
A novel S3S‐TAP‐tag for the isolation of T‐cell interaction partners of adhesion and degranulation promoting adaptor protein
Authors: Lehmann Roland , Meyer Johann , Schuemann Michael , Krause Eberhard , Freund Christian 
Published: October 2009

AbstractThe identification of modular units of cellular function is a major goal for proteomic research. Protein complexes represent important building blocks defining functionality and deciphering their composition remains a major challenge. Here, we have designed a new tandem affinity purification (TAP) tag (termed S3S‐tag) for the isolation of protein complexes. Specifically, the immune cell protein ADAP that regulates integrin adhesion was fused either C‐ or N‐terminally to the S3S‐tag. After retroviral transduction of a vector containing S3S‐tagged ADAP and internal ribosomal entry site encoded enhanced green fluorescent protein (eGFP), Jurkat T cells were sorted according to eGFP expression and further selected for expression of TAP‐tagged protein close to endogenous levels. The combination of a cleavable S‐tag and a Strep‐tag II allowed for the isolation of ADAP and associated proteins. Subsequently, stable isotope labeling with amino acids in cell culture‐based mass spectrometric analysis was performed to identify potentially specific interaction partners. Co‐purification of the known interaction partner Src kinase‐associated phosphoprotein of 55 kDa indicates the validity of our approach, while the identification of the ENA/VASP family member EVL, the guanine nucleotide exchange factor GEF‐H1 and the adaptor protein DOCK2 corroborates a link between ADAP‐mediated integrin regulation and the cytoskeleton.
A proteomic view of the facultatively chemolithoautotrophic lifestyle of Ralstonia eutropha H16
Authors: Schwartz Edward , Voigt Birgit , Zühlke Daniela , Pohlmann Anne , Lenz Oliver , Albrecht Dirk , Schwarze Alexander , Kohlmann Yvonne , Krause Cornelia , Hecker Michael , Friedrich Bärbel 
Published: October 2009

AbstractRalstonia eutropha H16 is an H2‐oxidizing, facultative chemolithoautotroph. Using 2‐DE in conjunction with peptide mass spectrometry we have cataloged the soluble proteins of this bacterium during growth on different substrates: (i) H2 and CO2, (ii) succinate and (iii) glycerol. The first and second conditions represent purely lithoautotrophic and purely organoheterotrophic nutrition, respectively. The third growth regime permits formation of the H2‐oxidizing and CO2‐fixing systems concomitant to utilization of an organic substrate, thus enabling mixotrophic growth. The latter type of nutrition is probably the relevant one with respect to the situation faced by the organism in its natural habitats, i.e. soil and mud. Aside from the hydrogenase and Calvin‐cycle enzymes, the protein inventories of the H2‐CO2‐ and succinate‐grown cells did not reveal major qualitative differences. The protein complement of the glycerol‐grown cells resembled that of the lithoautotrophic cells. Phosphoenolpyruvate (PEP) carboxykinase was present under all three growth conditions, whereas PEP carboxylase was not detectable, supporting earlier findings that PEP carboxykinase is alone responsible for the anaplerotic production of oxaloacetate from PEP. The elevated levels of oxidative stress proteins in the glycerol‐grown cells point to a significant challenge by ROS under these conditions. The results reported here are in agreement with earlier physiological and enzymological studies indicating that R. eutropha H16 has a heterotrophic core metabolism onto which the functions of lithoautotrophy have been grafted.
Quantitative prediction of protein–protein binding affinity with a potential of mean force considering volume correction
Authors: Su Yu , Zhou Ao , Xia Xuefeng , Li Wen , Sun Zhirong 
Published: October 2009

AbstractQuantitative prediction of protein–protein binding affinity is essential for understanding protein–protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein–protein binding affinity. The potential is obtained by statistically analyzing X‐ray structures of protein–protein complexes in the Protein Data Bank. This approach circumvents the complicated steps of the volume correction process and is very easy to implement in practice. It can obtain more reasonable pair potential compared with traditional PMF and shows a classic picture of nonbonded atom pair interaction as Lennard‐Jones potential. To evaluate the prediction ability for protein–protein binding affinity, six test sets are examined. Sets 1–5 were used as test set in five published studies, respectively, and set 6 was the union set of sets 1–5, with a total of 86 protein–protein complexes. The correlation coefficient (R) and standard deviation (SD) of fitting predicted affinity to experimental data were calculated to compare the performance of ours with that in literature. Our predictions on sets 1–5 were as good as the best prediction reported in the published studies, and for union set 6, R = 0.76, SD = 2.24 kcal/mol. Furthermore, we found that the volume correction can significantly improve the prediction ability. This approach can also promote the research on docking and protein structure prediction.
Folding and assembly kinetics of procaspase‐3
Authors: Milam Sara L. , Clark A. Clay 
Published: October 2009

AbstractCaspases are vital to apoptosis and exist in the cell as inactive zymogens. Dimerization is central to procaspase activation because the active sites are comprised of loops from both monomers. Although initiator procaspases are stable monomers until activated on cell death scaffolds, the effector caspases, such as procaspase‐3, are stable dimers. The activation mechanisms are reasonably well understood in terms of polypeptide chain cleavage and subsequent active site rearrangements in the dimer, but the mechanisms that govern dimer assembly are not known. To further understand procaspase dimerization, we examined the folding and assembly of procaspase‐3 by fluorescence emission, circular dichroism, differential quenching by acrylamide, anisotropy, and enzyme activity assays. Single‐mixing stopped‐flow refolding studies showed a complex burst phase in which multiple monomeric species form rapidly. At longer times, the monomer folds through several intermediates, some of which appear to be off‐pathway or misfolded, before eventually forming a dimerization‐competent species. Enzyme activity studies demonstrated a slow rate of dimerization (∼70 M−1 s−1). In addition, single‐mixing stopped‐flow unfolding studies revealed a complex unfolding process with a slow rate of dimer dissociation. Interestingly, multiple dimeric species were observed in the burst phase for unfolding, suggesting that the native ensemble consists of at least two major conformations. Collectively, these results demonstrate complex folding and unfolding behavior for procaspase‐3 and suggest that slow dimerization results from the lack of stabilizing native contacts in the initial encounter complex.
Revealing the dimer dissociation and existence of a folded monomer of the mature HIV‐2 protease
Authors: Louis John M. , Ishima Rieko , Aniana Annie , Sayer Jane M. 
Published: October 2009

AbstractPurification and in vitro protein‐folding schemes were developed to produce monodisperse samples of the mature wild‐type HIV‐2 protease (PR2), enabling a comprehensive set of biochemical and biophysical studies to assess the dissociation of the dimeric protease. An E37K substitution in PR2 significantly retards autoproteolytic cleavage during expression. Furthermore, it permits convenient measurement of the dimer dissociation of PR2E37K (elevated Kd ∼20 nM) by enzyme kinetics. Differential scanning calorimetry reveals a Tm of 60.5 for PR2 as compared with 65.7°C for HIV‐1 protease (PR1). Consistent with weaker binding of the clinical inhibitor darunavir (DRV) to PR2, the Tm of PR2 increases by 14.8°C in the presence of DRV as compared with 22.4°C for PR1. Dimer interface mutations, such as a T26A substitution in the active site (PR2T26A) or a deletion of the C‐terminal residues 96–99 (PR21–95), drastically increase the Kd (>105‐fold). PR2T26A and PR21–95 consist predominantly of folded monomers, as determined by nuclear magnetic resonance (NMR) and size‐exclusion chromatography coupled with multiangle light scattering and refractive index measurements (SMR), whereas wild‐type PR2 and its active‐site mutant PR2D25N are folded dimers. Addition of twofold excess active‐site inhibitor promotes dimerization of PR2T26A but not of PR21–95, indicating that subunit interactions involving the C‐terminal residues are crucial for dimer formation. Use of SMR and NMR with PR2 facilitates probing for potential inhibitors that restrict protein folding and/or dimerization and, thus, may provide insights for the future design of inhibitors to circumvent drug resistance.
Efficacy and attractiveness of zinc phosphide bait in common voles (Microtus arvalis)
Authors: Jacob Jens , Budde Mechthild , Leukers Angela 
Published: October 2009

AbstractBACKGROUND: Minimising the concentration of active ingredient in rodenticide bait is desirable economically and for the protection of the agroecosystem. This study aimed to identify a zinc phosphide concentration that balances palatability and efficacy for common vole (Microtus arvalis Pall.) management and to compare the attractiveness of two bait carriers.RESULTS: Bait uptake of voles was reduced by 87–98% compared with plain bait when bait contained 0.4–3.2% zinc phosphide. There was an almost 50% decrease in the uptake of zinc phosphide when the zinc phosphide concentration of bait was doubled. Red dye used in commercially available bait decreased bait consumption by 10%. Daily consumption of zinc phosphide bait on days 2 to 5 was half the consumption on the first day of exposure. In bait choice tests, wheat kernels were preferred initially, but within 12 h similar amounts of wheat‐based pellets and wheat kernels were eaten.CONCLUSIONS: According to the results from the laboratory trial, a zinc phosphide concentration of 2.1% seemed to balance uptake/efficacy best and may be most appropriate for the management of common vole populations. This concentration is substantially lower than the concentration used in many registered products. A reduced concentration of active ingredient and the use of pellet bait instead of wheat which is highly attractive for birds may have advantages for agroecosystem health when applying zinc phosphide for rodent control. © Jens Jacob, Mechthild Budde and Angela Leukers, employees of the Federal Research Centre for Cultivated Plants, Germany. Printed with permission.
QSAR modeling of photosynthesis‐inhibiting nostoclide derivatives
Authors: Teixeira Róbson Ricardo , Pinheiro Patrícia F , Barbosa Luiz Cláudio de Almeida , Carneiro José Walkimar de M , Forlani Giuseppe 
Published: October 2009

AbstractBACKGROUND: A statistical model, built using the CODESSA software package, was developed to describe the relationship between the structure of nostoclide derivatives and their ability to interfere with the electron transport chain in the Hill reaction.RESULTS: A QSAR treatment was carried out on a series of compounds designed using the naturally occurring toxin nostoclides to correlate molecular descriptors with their in vitro biological activity (the ability to interfere with light‐driven reduction of ferricyanide by isolated spinach chloroplast thylakoid membranes). The treatment using the CODESSA software package resulted in a three‐parameter model with n = 19, R2 = 0.83, F = 23.8 and R2cv = 0.72. In the proposed model, the Image of Onsager Kirkwood solvation energy, which gives a measure of the polarity of a given compound, is the most important descriptor. The model was internally validated.CONCLUSIONS: The results obtained in this study indicate that polarity, as expressed by the dipole moment, is the most relevant molecular property determining efficiency of photosynthetic inhibitory activity. Copyright © 2009 Society of Chemical Industry
Non‐local electron‐positron correlation effects for SiC
Authors: Rubaszek Anna 
Published: October 2009

AbstractIn the present work we study the influence of the electron‐positron (e‐p) interaction on the resulting e‐p momentum density and positron lifetime for a perfect SiC of 3C cubic structure. Results obtained within the independent particle model (IPM) and the local density approximation (LDA) are compared with their counterparts calculated beyond the local approach, within the weighted density approximation (WDA) (Rubaszek et al., Phys. Rev. B 58, 11285 (1998); Rubaszek et al., Phys. Rev. B 61, 10100 (2000) [1]). It is shown that the positron annihilation characteristics, calculated within various approximations to the e‐p correlation functions, are very sensitive to the approach. Non‐locality of the e‐p interaction is of vital importance for core electrons and has less influence on the valence electrons contribution to the e‐p momentum density and positron lifetime. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation lifetime data and actual porosity of polymers
Authors: Shantarovich Victor , Gustov Vadim , Polyakova Aleksandra , Belousova Eleonora , Filimonov Mikhail , Yampolskii Yurii 
Published: October 2009

AbstractApplication of the three‐component LT9.0 analyses and discrete four‐component PATFIT analysis to PAL distribution in some porous polymers, such as PIM‐1, AF2400, AF1600, PTMSP, give practically the same good fitting. In the conditions of this uncertainty, some additional experiments (thermomechanical tests, NMR on the protons of the absorbed water, thermo‐stimulated luminescence TSL, low temperature gas sorption BET, mathematic molecular‐dynamic simulation) give some arguments in favour of non‐Gaussian distribution of elementary free volumes EFV in some porous polymers and their possible heterogeneity. Furthermore, a comparison of PAL and TSL data confirm the idea on the interconnection between the rigidity of the polymer chains and effective size of the EFV. This interconnection is illustrated by the correlation of the o ‐Ps lifetime and intensity of the high‐temperature peak in the TSL glow curve. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrogen sorption kinetics in Nb doped Mg: role of Nb clustering and open volume defects formation
Authors: Toniutti L. , Checchetto R. , Mengucci P. , Miotello A. , Brusa R. S. 
Published: October 2009

AbstractMg and Nb‐doped Mg films were grown by rf magnetron sputtering and their structure was studied as a function of the hydrogen sorption‐desorption cycles. The Nb doping improves the H desorption kinetics: anyway the characteristic desorption time increases in the first eight cycles until the desorption kinetics attain a stationary condition. The as grown Mg films are found to be rich of vacancies, while in the as grown Nb doped Mg films small vacancy clusters are present. After eight cycles the dispersed Nb agglomerates forming clusters of few nanometers. The evolution, under H cycling, of the detected vacancies and vacancy clusters is found to be very different in the Mg and in the Nb‐doped Mg films. The results are discussed and correlated to the desorption kinetics of the two systems. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positronium formation in a liquid phase: Influence of intratrack reactions and temperature
Authors: Stepanov Sergey V. , Byakov Vsevolod M. , Duplâtre Gilles , Zvezhinskiy Dmitriy S. , Lomachuk Yuri V. 
Published: October 2009

AbstractThis work clarifies some discrepancies between conventional models, used in positron annihilation lifetime (PAL) spectroscopy, and experimental data. The importance of taking into account Ps interactions with primary intratrack radiolytic products is demonstrated, for example, for PAL data in water. We examine the applicability of a nonhomogeneous chemical kinetics approach and of a well‐known expression for the reaction rate constants to describe intratrack processes, and show that the prescribed diffusion approximation (PDA) is a reasonable model for this. Moreover, we have derived an analytical expression for the time‐dependent reaction rate coefficient, which previously entered PDA as an external parameter. Preliminary fittings of the PAL spectra in H2O over a wide temperature range indicate that Ps reactions in intratrack processes are diffusion controlled (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron source based on the 48V isotope dedicated to positron lifetime spectroscopy
Authors: Dryzek Jerzy 
Published: October 2009

AbstractIn the paper we consider application of the 48V isotope as a source in the positron lifetime spectroscopy. The isotope was produced in the 48Ti(p,n)48V reaction using 15 MeV proton beam. As a target the natural titanium thin plate was used. The measurements using the typical positron lifetime spectrometer have shown the usefulness of the source obtained for this application. Due to its properties, the source may be used for measurements of positron annihilation characteristics in high temperature or aggressive environments. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation study of ion‐exchanged forms of Nafion® membrane
Authors: Mohamed Hamdy F. M. , Kobayashi Y. , Kuroda C. S. , Ohira A. 
Published: October 2009

AbstractPositron annihilation lifetime and oxygen permeability in ion‐exchanged forms (H+‐, Na+‐, K+‐, Cu2+‐, Ni2+‐, and Fe3+‐forms) of Nafion® membranes for polymer electrolyte fuel cells (PEFC's) have been investigated as a function of temperature. Exchange of H+ with Cu2+, Ni2+, or Fe3+ in Nafion® decreases both the o ‐Ps lifetime and its intensity, being interpreted as the result of inhibition and quenching of Ps. For the H+‐, Na+‐, and K+‐forms good correlations were observed between the logarithm of the O2 permeability and o ‐Ps lifetime (free volume size) at different temperatures indicating the important role played by the free volume in O2 permeation. Considerable downward deviation of the correlations for the Na+‐ and K+‐forms from the H+‐form revealed the importance of polymer stiffening in O2 permeation. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Positron annihilation studies on 9Cr reduced activation ferritic/martensitic steels
Authors: Ragunanthan V. , Babu S. Hari , Chirayath Varghese Anto , Rajaraman R. , Amarendra G. , Saroja S. , Sundar C. S. , Alamo Ana , Raj Baldev 
Published: October 2009

AbstractPositron annihilation, microstructural and hardness studies were carried out in a 9Cr reduced activation ferrtic ‐ martensitic steel (9%Cr‐1%W‐0.1%C) subjected to isochronal annealing in the temperature range of 300 to 1273 K. The measured lifetime in the ‘as‐received’ (normalized and tempered) condition was 147 ps, which exhibited considerable reduction around 670 K, indicating the annealing out of small vacancy‐defects in the matrix or matrix‐precipitate interfaces. The observed positron lifetime exhibited a broad maximum between 670 K and 1070 K, indicating the existence of second annealing stage. Between 1070 K and 1270 K, a sharp maxium is exhibited in lifetime as third annealing stage. Doppler S‐parameter has also exhibited similar annealing stages. Ab‐intio positron lifetime calculations for various defect‐impurity cluster configurations in ferritic‐matrix based Fe system are reported to understand the experimental results. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quenched‐in vacancies in Fe‐Al alloys
Authors: Melikhova Oksana , Cizek Jakub , Prochazka Ivan , Kuriplach Jan , Lukac Frantisek , Cieslar Miroslav , Brauer Gerhard , Anwand Wolfgang 
Published: October 2009

AbstractQuenched‐in vacancies in Fe3Al‐based intermetallics were studied in this work. A stoichiometric Fe3Al alloy was compared with non‐stoichiometric specimens either with a deficiency or with an excess in Al content. Vacancies in specimens quenched from the disordered A2 phase were investigated by three independent techniques of positron annihilation spectroscopy: positron lifetime (LT) studies, slow positron implantation spectroscopy (SPIS) with a continuous slow positron beam, and coincidence Doppler broadening (CDB). It was found that the combination of LT and SPIS enables to determine reliably even very high concentrations of vacancies. Infor‐mation about the local chemical environment of quenched‐in vacancies was obtained from CDB measurements. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)