bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative proteome analysis of TGF‐β1‐induced fibrosis processes in normal rat kidney interstitial fibroblast cells in response to ascofuranone
Authors: Kang Jeong‐Han , Cho Hyun‐Ji , Lee In‐Seon , Kim Moonkyu , Lee In‐Kyu , Chang Young‐Chae 
Published: August 2009

AbstractTransforming growth factor‐β1 (TGF‐β1) has a wide range of biological functions such as the regulation of cell growth, differentiation, and immunological response in various types of cells. Particularly, TGF‐β1 induces plasminogen activator inhibitor‐1 (PAI‐1) as a major target protein. PAI‐1 is associated with fibrosis, thrombosis, and metabolic disorders. In this study, to identify proteins potentially involved in TGF‐β1‐induced fibrosis processes, we performed a proteomic analysis of TGF‐β1‐induced normal rat kidney cells exposed to ascofuranone (AF). In these cells, we detected 1500 proteins, with 74 differentially expressed proteins identified by MALDI‐TOF and reference to the NCBI and Swiss‐Prot databases, including PAI‐1, peroxisome prdifesator‐activated receptor, prohibitin, glutamate formyltransferase, LIM domain protein 1, LASP‐1, porphobilinogen deaminase, and peroxiredoxin 2. We also found that AF suppresses expression of profibrotic factors induced by TGF‐β in renal fibroblasts, including matrix proteins and PAI‐1. AF was also shown to inhibit selectively phosphorylation of epidermal growth factor receptor, and downstream kinases such as extracellular signal‐regulated kinase 1/2 (ERK‐1/2). Further ongoing analysis of fibrosis‐related proteins will determine AF's potential for application in fibrotic diseases and therapeutics.
TheFusarium oxysporumcell wall proteome under adhesion‐inducing conditions
Authors: Prados‐Rosales Rafael , Luque‐Garcia Jose L. , Martínez‐López Raquel , Gil Concha , Di Pietro Antonio 
Published: August 2009

AbstractFusarium oxysporumis a soilborne fungus that causes vascular wilt disease on a wide range of crops. During initial stages of infection, fungal hyphae attach firmly to roots, penetrate the cortex and colonize xylem vessels. The mechanisms underlying root attachment are poorly understood, although it was previously shown that this process depends on Fmk1, a mitogen‐activated protein kinase orthologous to the mating/filamentation mitogen‐activated protein kinases Fus3/Kss1 in yeast. We investigated the hypothesis that root adhesion is mediated by fungal cell wall proteins (CWPs). To characterize the cell wall subproteome ofF. oxysporum, we performed LC‐MS/MS analysis of tryptic digests of purified cell walls obtained from adhesion‐inducing conditions, identifying a total of 174 proteins, 19 of which contain a predicted signal peptide and 10 of which have a predicted glycosylphosphatidyl‐inositol motif. 2‐D DIGE was used to compare four different fractions of CWPs extracted from hyphae of the wild‐type strain and the Δfmk1mutant. We detected 18 proteins differing significantly in abundance between the two strains. Differential expression of five of these proteins was confirmed by RT‐PCR analysis. A significant fraction of the subproteome lacked functional information, highlighting the limitations in the current understanding of CWPs inF. oxysporum.
Proteomic analysis of changes in mitochondrial protein expression during fruit senescence
Authors: Qin Guozheng , Wang Qing , Liu Jia , Li Boqiang , Tian Shiping 
Published: August 2009

AbstractFruit senescence has been reported to be an oxidative phenomenon, but the detailed mechanisms by which ROS regulate this process remain largely unknown. Here we show that senescence process of apple fruit was concomitant with the dynamic alterations in the mitochondrial proteome. Mitochondrial proteins involved in tricarboxylic acid cycle, electron transport chain, carbon metabolism, and stress response were found to be differentially expressed during fruit senescence. Alleviating oxidative stress by lowering the ambient oxygen concentration noticeably decreased the number of changed proteins and delayed fruit senescence, indicating the involvement of ROS in this process. To further investigate the regulatory effect of ROS on senescence process, we analyzed the mitochondrial proteome variations upon exposure to high oxygen (100%), which induces oxidative stress and accelerates fruit senescence. High oxygen treatment led to a further identification of differentially expressed proteins such as mitochondrial manganese superoxide dismutase, an antioxidant scavenging superoxide radicals produced in the mitochondria. Activity of manganese superoxide dismutase was reduced after high oxygen exposure, accompanied by an increase in oxidative protein carbonylation (damaged proteins). These data suggest that ROS may regulate fruit senescence by changing expression profiles of specific mitochondrial proteins and impairing the biological function of these proteins.
Proteome reference map for the plant growth‐promoting bacterium Pseudomonas putida UW4
Authors: Cheng Zhenyu , Woody Owen Z. , Song Jiming , Glick Bernard R. , McConkey Brendan J. 
Published: August 2009

AbstractA proteome reference map containing 326 2‐D gel spots representing 275 different proteins was constructed for the plant growth‐promoting bacterium Pseudomonas putida UW4. Protein identifications were obtained using Q‐TOF MS/MS spectra matching to homologous proteins from other Pseudomonas strains and confirmed by PMF analysis. This data set is accessible at http://world‐2dpage.expasy.org/repository/ and will aid in further characterization of Pseudomonas strains and interactions of plant growth‐promoting bacterium with the plant rhizosphere environment.
LC‐MS/MS as an alternative for SDS‐PAGE in blue native analysis of protein complexes
Authors: Wessels Hans J. C. T. , Vogel Rutger O. , van den Heuvel Lambert , Smeitink Jan A. , Rodenburg Richard J. , Nijtmans Leo G. , Farhoud Murtada H. 
Published: August 2009

AbstractTwo‐dimensional blue native/SDS‐PAGE is widely applied to investigate native protein–protein interactions, particularly those within membrane multi‐protein complexes. MS has enabled the application of this approach at the proteome scale, typically by analysis of picked protein spots. Here, we investigated the potential of using LC‐MS/MS as an alternative for SDS‐PAGE in blue native (BN) analysis of protein complexes. By subjecting equal slices from BN gel lanes to label‐free semi‐quantitative LC‐MS/MS, we determined an abundance profile for each protein across the BN gel, and used these profiles to identify potentially interacting proteins by protein correlation profiling. We demonstrate the feasibility of this approach by considering the oxidative phosphorylation complexes I–V in the native human embryonic kidney 293 mitochondrial fraction, showing that the method is capable of detecting both the fully assembled complexes as well as assembly/turnover intermediates of complex I (NADH:ubiquinone oxidoreductase). Using protein correlation profiling with a profile for subunits NDUFS2, 3, 7 and 8 we identified multiple proteins possibly involved in the biogenesis of complex I, including the recently implicated chaperone C6ORF66 and a novel candidate, C3ORF60.
Comparative proteome analysis of porcine follicular fluid and serum reveals that excessive α2‐macroglobulin in serum hampers successful expansion of cumulus‐oocyte complexes
Authors: Bijttebier Jo , Tilleman Kelly , Dhaenens Maarten , Deforce Dieter , Van Soom Ann , Maes Dominiek 
Published: August 2009

AbstractPorcine follicular fluid (pFF) constitutes the micro‐environment of the maturing oocyte. Although pFF is a transudate of serum, in pigs, it is superior to serum in promoting in vitro expansion of the cumulus cells, a specialized cell population surrounding the oocyte. A comparative proteome analysis of autologous serum and pFF was performed to investigate proteins involved in successful cumulus expansion of porcine oocytes. iTRAQ labeling followed by 2‐D LC ESI‐Q‐TOF MS/MS revealed 63 proteins common to both fluids of which the abundance of 13 proteins was significantly different (p<0.05). Seven proteins were more concentrated in serum whereas six proteins were more abundant in pFF. To investigate the importance of these proteins, the cumulus matrices of COCs were collected after in vitro maturation in media supplemented with either of both biologically fluids and then subjected to 2‐D PAGE analysis. α2‐Macroglobulin and CH4 and secrete domains of swine IgM, which were both less abundant in pFF, were absent from cumulus matrix extracts after in vitro maturation in pFF. Although both proteins were incorporated in the matrices of cumulus‐oocyte complexes matured in serum, depletion of α2‐macroglobulin from serum could significantly compensate for the impaired cumulus expansion of oocytes matured in serum.
Rapid selection of peptide containing fractions in off‐line 2‐D HPLC in shotgun proteome analysis by screening with MALDI TOF MS
Authors: Lasaosa Maria , Jakoby Thomas , Delmotte Nathanaël , G. Huber Christian , Heinzle Elmar , Tholey Andreas 
Published: August 2009

AbstractA simple and fast screening method for the selection of fractions of first dimension separation to be analyzed in second dimension‐MS/MS experiments in offline multidimensional liquid chromatographic separation schemes for shotgun proteome analysis was developed. The method is based on the measurement of total peptide content of the first dimension fractions by MALDI MS and was established using a tryptic digest of a bacterial proteome. The results of the screening process were in good agreement with those obtained in a detailed proteome analysis performed by RP×ion‐pair RP‐MALDI TOF/TOF MS analysis. The method supports a straightforward planning of experiments, also enabling a reduction of overall measurement time in shotgun proteome analysis.
Spectroscopic (FT‐IR, FT‐Raman, UV, 1H, and 13C NMR) and theoretical studies of m‐anisic acid and lithium, sodium, potassium, rubidium, and caesium m‐anisates
Authors: Kalinowska M. , Świsłocka R. , Rzączyńska Z. , Sienkiewicz J. , Lewandowski W. 
Published: August 2009

AbstractIn order to understand the nature of the interactions of biologically important ligands, it is necessary to carry out the physico‐chemical studies of these compounds with their biological targets (e.g., receptors in the cell or important cell components). Results of this study make it possible to predict some properties of a molecule, such as its reactivity, durability of complex compounds, and kinship to enzymes. In this paper the effect of alkali metal cations (Li, Na, K, Rb, and Cs) on the electronic structure of m‐methoxybenzoic acid (m‐anisic acid) was studied. The experimental IR (in solid state and solution), Raman, UV (in solid state and solution), 1H, and 13C NMR spectra of m‐methoxybenzoic acid, and its salts were registered, assigned, and analyzed. Some of the obtained results were compared with published data for o‐anisic acid and o‐anisates. The structures of anisic acid and Li, Na, and K m‐anisates were optimized at the B3LYP/6‐311++G** level. The IR, 1H, and 13C NMR spectra and NPA, ChelpG, and MK atomic charges were calculated. The change of metal along with the series: Li → Na → K → Rb → Cs caused: (1) the change in the electronic charge distribution in anisate anion that is seen via the occurrence of the systematic shifts of several bands in the experimental and theoretical IR and Raman spectra of anisates; (2) systematic 1H and 13C NMR chemical shifts; (3) hypsochromic shifts in UV spectra of salts as compared to ligands. Copyright © 2009 John Wiley & Sons, Ltd.
Conformations and enthalpies of formation of methylenecyclohexane, 1,4‐dimethylenecyclohexane, cyclohexanone, 4‐methylenecyclohexanone, 1,4‐cyclohexanedione, and their mono‐ and dioxa derivatives by G3(MP2)//B3LYP calculations
Authors: Taskinen Esko 
Published: August 2009

AbstractA computational study of the stable conformations and gas‐phase enthalpies of formation at 25 °C of the title compounds has been carried out by G3(MP2)//B3LYP calculations. The work stems from our early observations on the thermodynamic and NMR spectroscopic properties of 2‐methylenetetrahydropyran and related compounds suggesting a dominating chair conformation, with poor p–π overlap in the OCC moiety, for these compounds. Besides computational verification of the chair conformation of 2‐methylenetetrahydropyran, the work was extended to find out the stable conformations of a number of other related compounds and to evaluate the relative stabilities of the various conformers. Another important goal of the work was the estimation of the gas‐phase enthalpies of formation of the present compounds, for which such literature data are scarce. A significant error in the literature value of the enthalpy of formation of methylenecyclohexane was found. Finally, the relative enthalpy levels of the isomeric compounds of this work are discussed. The high thermodynamic stability of the compounds containing an ester functional group, OCO, relative to the stability of isomeric compounds with an OCC moiety in place of the ester function, is demonstrated. Copyright © 2009 John Wiley & Sons, Ltd.
DFT study of the 1,3‐dipolar cycloaddition of azomethine ylides with maleimide, maleic anhydride, methylacrylate and some simple substituted alkenes
Authors: Das Tapas Kumar , Banerjee Manas 
Published: August 2009

AbstractDFT calculations involving the B3LYP functional and 6‐31G(d) basis set have been performed to rationalize the reactivity, regioselectivity, enantioselectivity and diasteriofacial selectivity in the context of 1,3‐dipolar cycloaddition (13DC) reactions of a few acyclic and two cyclic azomethine ylides (AY) leading to enantiomeric/ diasteriomeric excess of the products. In particular, N‐substituted and C‐substituted AYs have been considered for reactions with the substituted ethylenes, maleimide, maleic anhydride and methyl acrylate. From an analysis of the results of calculation for the selected reactions, the regio‐ and exo/endo‐stereoselectivity have been explained. Reactions were followed through transition state (TS) structure optimization, calculation of IRC and activation energies. A rationalization of the trends in regioselectivity and enantioselectivity was attempted with the help of HOMO–LUMO energies, electrophilicity differences (Δω) and an analysis of Pauling's bond order (PBO) in the TS. Copyright © 2009 John Wiley & Sons, Ltd.
‘Locking and unlocking control’ of photochromism of naphthopyran derivative
Authors: Guo Kunpeng , Chen Yi 
Published: August 2009

AbstractA ‘locking and unlocking control’ for a photochromic molecular system has been developed by using a photochromic naphthopyran derivative 1a as the model compound. With UV light irradiation, the colorless solution of 1a underwent ring‐opening photoisomerization and converted to a purple solution 1b, which quickly faded back to a colorless solution with visible light (λ ≥ 480 nm) irradiation or in the dark. Addition of boron trifluoride diethyl etherate to the solution of 1b produced a complex compound 2b, accompanying the color change from purple to blue. It was found that 2b remained photochemically inactive. With the addition of diethanolamine, however, the ‘locked’ photoreaction of 2b could be unlocked and converted back to 1b, in which the photochromism was recovered. Copyright © 2009 John Wiley & Sons, Ltd.
BuildBeta—A system for automatically constructing beta sheets
Authors: Max Nelson , Hu ChengCheng , Kreylos Oliver , Crivelli Silvia 
Published: August 2009

AbstractWe describe a method that can thoroughly sample a protein conformational space given the protein primary sequence of amino acids and secondary structure predictions. Specifically, we target proteins with β‐sheets because they are particularly challenging forab initioprotein structure prediction because of the complexity of sampling long‐range strand pairings. Using some basic packing principles, inverse kinematics (IK), and β‐pairing scores, this method creates all possible β‐sheet arrangements including those that have the correct packing of β‐strands. It uses the IK algorithms of ProteinShop to move α‐helices and β‐strands as rigid bodies by rotating the dihedral angles in the coil regions. Our results show that our approach produces structures that are within 4–6 Å RMSD of the native one regardless of the protein size and β‐sheet topology although this number may increase if the protein has long loops or complex α‐helical regions. Proteins 2010. © Published 2009 Wiley‐Liss, Inc.
Comparative binding energy analysis for binding affinity and target selectivity prediction
Authors: Henrich Stefan , Feierberg Isabella , Wang Ting , Blomberg Niklas , Wade Rebecca C. 
Published: August 2009

AbstractA major challenge in drug design is to obtain compounds that bind selectively to their target receptors and do not cause side‐effects by binding to other similar receptors. Here, we investigate strategies for applying COMBINE (COMparative BINding Energy) analysis, in conjunction with PIPSA (Protein Interaction Property Similarity Analysis) and ligand docking methods, to address this problem. We evaluate these approaches by application to diverse sets of inhibitors of three structurally related serine proteases of medical relevance: thrombin, trypsin, and urokinase‐type plasminogen activator (uPA). We generated target‐specific scoring functions (COMBINE models) for the three targets using training sets of ligands with known inhibition constants and structures of their receptor‐ligand complexes. These COMBINE models were compared with the PIPSA results and experimental data on receptor selectivity. These scoring functions highlight the ligand‐receptor interactions that are particularly important for binding specificity for the different targets. To predict target selectivity in virtual screening, compounds were docked into the three protein binding sites using the program GOLD and the docking solutions were re‐ranked with the target‐specific scoring functions and computed electrostatic binding free energies. Limits in the accuracy of some of the docking solutions and difficulties in scoring them adversely affected the predictive ability of the target specific scoring functions. Nevertheless, the target‐specific scoring functions enabled the selectivity of ligands to thrombin versus trypsin and uPA to be predicted. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Plasmodium falciparum acyl carrier protein crystal structures in disulfide‐linked and reduced states and their prevalence during blood stage growth
Authors: Gallagher John R. , Prigge Sean T. 
Published: August 2009

AbstractAcyl Carrier Protein (ACP) has a single reactive sulfhydryl necessary for function in covalently binding nascent fatty acids during biosynthesis. In Plasmodium falciparum, the causative agent of the most lethal form of malaria, fatty acid biosynthesis occurs in the apicoplast organelle during the liver stage of the parasite life cycle. During the blood stage, fatty acid biosynthesis is inactive and the redox state of the apicoplast has not been determined. We solved the crystal structure of ACP from P. falciparum in reduced and disulfide‐linked forms, and observe the surprising result that the disulfide in the PfACP cross‐linked dimer is sequestered from bulk solvent in a tight molecular interface. We assessed solvent accessibility of the disulfide with small molecule reducing agents and found that the disulfide is protected from BME but less so for other common reducing agents. We examined cultured P. falciparum parasites to determine which form of PfACP is prevalent during the blood stages. We readily detected monomeric PfACP in parasite lysate, but do not observe the disulfide‐linked form, even under conditions of oxidative stress. To demonstrate that PfACP contains a free sulfhydryl and is not acylated or in the apo state, we treated blood stage parasites with the disulfide forming reagent diamide. We found that the effects of diamide are reversed with reducing agent. Together, these results suggest that the apicoplast is a reducing compartment, as suggested by models of P. falciparum metabolism, and that PfACP is maintained in a reduced state during blood stage growth. Proteins 2010. © 2009 Wiley‐Liss, Inc.
Validation of spring operated pressure relief valve time‐to‐failure
Authors: Harris Stephen P. , Gross Robert E. 
Published: August 2009

AbstractThe Savannah River Site operates a relief valve repair shop certified by the National Board of Pressure Vessel Inspectors. Local maintenance forces perform inspection, testing, and repair of ∼1,200 spring‐operated relief valves each year as the valves are cycled in from the field.The Site now has over 7,000 certified test records in the Computerized Maintenance Management System; a summary of that data is presented in this article. In previous articles, several statistical techniques were used to investigate failure on demand and failure rates including a quantal response method for predicting the probability of failure. The nonconservative failure mode is commonly termed “stuck shut”; industry defined as the valve opening at greater than or equal to 1.5 times the cold set pressure. Actual time‐to‐failure is typically not known, only that failure occurred some time since the last proof test.The resulting Monte Carlo simulation in this article shows that previous conclusions on the statistical lifetime predictions and failure studies were not as conservative as initially thought. Our simulations use an aging model for lift pressure increase as a function of set pressure, valve manufacturer, and time. This article attempts to answer two questions: (a) what is the predicted failure rate over the chosen maintenance/inspection interval, and (b) do we understand aging and variability sufficiently to estimate risk when basing proof test intervals on proof test results? © 2009 American Institute of Chemical Engineers Process Saf Prog 2010
Flammability characteristics of HFO‐1234yf
Authors: Minor Barbara H. , Herrmann David , Gravell Robert 
Published: August 2009

AbstractA new low global warming refrigerant, CF3CF=CH2(HFO‐1234yf), has been developed to replace HFC‐134a in automotive air conditioning systems. HFC‐134a is being phased out in the European Union due to high global warming potential. HFO‐1234yf is highly energy efficient, exhibits low toxicity, and can potentially be used in systems currently designed for refrigerant HFC‐134a with minimal modifications. Significant work has been completed to assess the flammability characteristics of HFO‐1234yf. Though it is flammable per ASTM E‐681, it is significantly less so than HFC‐152a which has also been considered as an HFC‐134a alternative. HFO‐1234yf has a relatively high lower flammability limit at 6.2 vol% in air. Computational Fluid Dynamics (CFD) modeling has shown it is very unlikely the lower flammability limit will be reached when the refrigerant is leaked into the passenger compartment of a vehicle. HFO‐1234yf also has a high minimum ignition energy (MIE) from 5,000 to 10,000 mJ which indicates there may be very few potential ignition sources in a vehicle. It also has very low burning velocity at 1.5 cm/sec indicating low potential for damage should an ignition occur. Several automotive industry groups have completed extensive risk assessments which have concluded HFO‐1234yf is safe to use as a refrigerant in vehicles. This article will review flammability test results and challenges that were overcome to measure flammability of a mildly flammable refrigerant as well as CFD modeling work for vehicle leakage scenarios. © 2009 American Institute of Chemical Engineers Process Saf Prog, 2010