WorldWideScience

Sample records for chain protein transfer

  1. Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

    International Nuclear Information System (INIS)

    The 'leading coordinate' approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information

  2. Electron transfer in proteins

    DEFF Research Database (Denmark)

    Farver, O; Pecht, I

    1991-01-01

    Electron migration between and within proteins is one of the most prevalent forms of biological energy conversion processes. Electron transfer reactions take place between active centers such as transition metal ions or organic cofactors over considerable distances at fast rates and with remarkable...... specificity. The electron transfer is attained through weak electronic interaction between the active sites, so that considerable research efforts are centered on resolving the factors that control the rates of long-distance electron transfer reactions in proteins. These factors include (in addition to the......-containing proteins. These proteins serve almost exclusively in electron transfer reactions, and as it turns out, their metal coordination sites are endowed with properties uniquely optimized for their function....

  3. Lipid-transfer proteins.

    Science.gov (United States)

    Ng, Tzi Bun; Cheung, Randy Chi Fai; Wong, Jack Ho; Ye, Xiujuan

    2012-01-01

    Lipid-transfer proteins (LTPs) are basic proteins found in abundance in higher plants. LTPs play lots of roles in plants such as participation in cutin formation, embryogenesis, defense reactions against phytopathogens, symbiosis, and the adaptation of plants to various environmental conditions. In addition, LTPs from field mustard and Chinese daffodil exhibit antiproliferative activity against human cancer cells. LTPs from chili pepper and coffee manifest inhibitory activity against fungi pathogenic to humans such as Candida species. The intent of this article is to review LTPs in the plant kingdom. PMID:23193591

  4. Modelling proton transfer in water molecule chains

    CERN Document Server

    Korzhimanov, Artem; Shutova, Tatiana; Samuelsson, Goran

    2011-01-01

    The process of protons transport in molecular water chains is of fundamental interest for many biological systems. Although many features of such systems can be analyzed using large-scale computational modeling, other features are better understood in terms of simplified model problems. Here we have tested, analytically and numerically, a model describing the classical proton hopping process in molecular water chains. In order to capture the main features of the proton hopping process in such molecular chains, we use a simplified model for our analysis. In particular, our discrete model describes a 1D chain of water molecules situated in an external protein channel structure, and each water molecule is allowed to oscillate around its equilibrium point in this system, while the protons are allowed to move along the line of neighboring oxygen atoms. The occurrence and properties of nonlinear solitary transport structures, allowing for much faster proton transport, are discussed, and the possible implications of...

  5. Electron transfer in proteins.

    Science.gov (United States)

    Gray, H B; Winkler, J R

    1996-01-01

    Electron-transfer (ET) reactions are key steps in a diverse array of biological transformations ranging from photosynthesis to aerobic respiration. A powerful theoretical formalism has been developed that describes ET rates in terms of two parameters: the nuclear reorganization energy (lambda) and the electronic-coupling strength (HAB). Studies of ET reactions in ruthenium-modified proteins have probed lambda and HAB in several metalloproteins (cytochrome c, myoglobin, azurin). This work has shown that protein reorganization energies are sensitive to the medium surrounding the redox sites and that an aqueous environment, in particular, leads to large reorganization energies. Analyses of electronic-coupling strengths suggest that the efficiency of long-range ET depends on the protein secondary structure: beta sheets appear to mediate coupling more efficiently than alpha-helical structures, and hydrogen bonds play a critical role in both. PMID:8811189

  6. Effects of medium-chain fatty acids and oleic acid on blood lipids, lipoproteins, glucose, insulin, and lipid transfer protein activities

    DEFF Research Database (Denmark)

    Tholstrup, T.; Ehnholm, C.; Jauhiainen, M.;

    2004-01-01

    cholesterol, although this claim is poorly documented. Objective: We compared the effects of a diet rich in either MCFAs or oleic acid on fasting blood lipids, lipoproteins, glucose, insulin, and lipid transfer protein activities in healthy men. Design: In a study with a double-blind, randomized, crossover...... design, 17 healthy young men replaced part of their habitual dietary fat intake with 70 g MCTs (66% 8:0 and 34% 10:0) or high-oleic sunflower oil (89.4% 18:1). Each intervention period lasted 21 d, and the 2 periods were separated by a washout period of 2 wk. Blood samples were taken before and after the...... oleic acid, MCT fat unfavorably affected lipid profiles in healthy young men by increasing plasma LDL cholesterol and triacylglycerol. No changes in the activities of phospholipid transfer protein and cholesterol ester transfer protein were evident....

  7. Excitation transfer in stacked quantum dot chains

    International Nuclear Information System (INIS)

    Stacked InAs quantum dot chains (QDCs) on InGaAs/GaAs cross-hatch pattern (CHP) templates yield a rich emission spectrum with an unusual carrier transfer characteristic compared to conventional quantum dot (QD) stacks. The photoluminescent spectra of the controlled, single QDC layer comprise multiple peaks from the orthogonal QDCs, the free-standing QDs, the CHP, the wetting layers and the GaAs substrate. When the QDC layers are stacked, employing a 10 nm GaAs spacer between adjacent QDC layers, the PL spectra are dominated by the top-most stack, indicating that the QDC layers are nominally uncoupled. Under high excitation power densities when the high-energy peaks of the top stack are saturated, however, low-energy PL peaks from the bottom stacks emerge as a result of carrier transfers across the GaAs spacers. These unique PL signatures contrast with the state-filling effects in conventional, coupled QD stacks and serve as a means to quickly assess the presence of electronic coupling in stacks of dissimilar-sized nanostructures. (paper)

  8. Inter-firm knowledge transfer in international supply chain management

    OpenAIRE

    Meyer, Geesche Anna

    2009-01-01

    OBJECTIVES OF THE STUDY The primary objective of this thesis is to assess whether, both in theory and practice, knowledge transfer can be implemented into the supply chain management context, and more practically, whether collaborative supply chain management practices can be utilized to effectuate inter-firm knowledge transfer between intermediaries in a supply chain. A secondary objective is to investigate whether knowledge transfer between autonomous companies is sought after and benefi...

  9. A lipid transfer protein that transfers lipid

    OpenAIRE

    Levine, T. P.

    2007-01-01

    Very few lipid transfer proteins (LTPs) have been caught in the act of transferring lipids in vivo from a donor membrane to an acceptor membrane. Now, two studies (Halter, D., S. Neumann, S. M. van Dijk, J. Wolthoorn, A. M. de Maziere, O.V. Vieira, P. Mattjus, J. Klumperman, G. van Meer, and H. Sprong. 2007. J. Cell Biol. 179: 101 115; D'Angelo, G., E. Polishchuk, G. D. Tullio, M. Santoro, A. D. Campli, A. Godi, G. West, J. Bielawski, C.C. Chuang, A. C. van der Spoel, et al. 2007. Nature. 449...

  10. Efficient Gene Transfer in Bacterial Cell Chains

    OpenAIRE

    Babic, Ana; Berkmen, Melanie B.; Lee, Catherine A.; Grossman, Alan D.

    2011-01-01

    Horizontal gene transfer contributes to evolution and the acquisition of new traits. In bacteria, horizontal gene transfer is often mediated by conjugative genetic elements that transfer directly from cell to cell. Integrative and conjugative elements (ICEs; also known as conjugative transposons) are mobile genetic elements that reside within a host genome but can excise to form a circle and transfer by conjugation to recipient cells. ICEs contribute to the spread of genes involved in pathoge...

  11. Effects of medium-chain fatty acids and oleic acid on blood lipids, lipoproteins, glucose, insulin, and lipid transfer protein activities

    DEFF Research Database (Denmark)

    Tholstrup, T.; Ehnholm, C.; Jauhiainen, M.; Petersen, M.; Høy, Carl-Erik; Lund, Pia; Sandstrøm, B.

    2004-01-01

    Background: Dietary medium-chain fatty acids (MCFAs) are of nutritional interest because they are more easily absorbed from dietary medium-chain triacylglycerols (MCTs) than are long-chain fatty acids from, for example, vegetable oils. It has generally been claimed that MCFAs do not increase plasma...... design, 17 healthy young men replaced part of their habitual dietary fat intake with 70 g MCTs (66% 8:0 and 34% 10:0) or high-oleic sunflower oil (89.4% 18:1). Each intervention period lasted 21 d, and the 2 periods were separated by a washout period of 2 wk. Blood samples were taken before and after the...... intervention periods. Results: Compared with the intake of high-oleic sunflower oil, MCT intake resulted in 11% higher plasma total cholesterol (P = 0.0005), 12% higher LDL cholesterol (P = 0.0001), 32% higher VLDL cholesterol (P = 0.080), a 12% higher ratio of LDL to HDL cholesterol (P = 0.002), 22% higher...

  12. Almost perfect state transfer in quantum spin chains

    CERN Document Server

    Vinet, Luc

    2012-01-01

    The natural notion of almost perfect state transfer (APST) is introduced. It is applied to the modelling of efficient quantum wires with the help of $XX$ spin chains. It is shown that APST occurs in mirror-symmetric systems, when the 1-excitation energies of the chains are linearly independent over rational numbers. This result is obtained as a corollary of the Kronecker theorem in Diophantine approximation. APST happens under much less restrictive conditions than those for perfect state transfer (PST) and moreover accommodates the unavoidable imperfection of PST devices. Some examples are discussed.

  13. Reversible addition-fragmentation chain transfer polymerization in microemulsion.

    Science.gov (United States)

    O'Donnell, Jennifer M

    2012-04-21

    This tutorial review first details the uncontrolled microemulsion polymerization mechanism, and the RAFT polymerization mechanism to provide the necessary background for examining the RAFT microemulsion polymerization mechanism. The effect of the chain transfer agent per micelle ratio and the chain transfer agent aqueous solubility on the RAFT microemulsion polymerization kinetics, polymer molecular weight and polydispersity, and polymer nanoparticle size are discussed with a focus on oil-in-water microemulsions. Modeling of RAFT microemulsion polymerization kinetics and the resulting final polymer molecular weight are presented to assist with the analysis of observed experimental trends. Lastly, the current significance of RAFT microemulsion polymerization and the future directions are discussed. PMID:22246214

  14. Controlled Quantum State Transfer in a Spin Chain

    CERN Document Server

    Gong, J; Brumer, Paul; Gong, Jiangbin

    2007-01-01

    Control of the transfer of quantum information encoded in quantum wavepackets moving along a spin chain is demonstrated. Specifically, based on a relationship with control in a paradigm of quantum chaos, it is shown that wavepackets with slow dispersion can automatically emerge from a class of initial superposition states involving only a few spins, and that arbitrary unspecified travelling wavepackets can be nondestructively stopped and later relaunched with perfection. The results establish an interesting application of quantum chaos studies in quantum information science.

  15. Quantum state transfer in a XX chain with impurities

    International Nuclear Information System (INIS)

    One spin excitation states are involved in the transmission of quantum states and entanglement through a quantum spin chain, the localization properties of these states are crucial to achieve the transfer of information from one extreme of the chain to the other. We investigate the bipartite entanglement and localization of the one excitation states in a quantum XX chain with one impurity. The bipartite entanglement is obtained using the concurrence and the localization is analyzed using the inverse participation ratio (IPR). Changing the strength of the exchange coupling of the impurity allows us to control the number of localized or extended states. The analysis of the IPR allows us to identify scenarios where the transmission of quantum states or entanglement can be achieved with a high degree of fidelity. In particular, we identify a regime where the transmission of quantum states between the extremes of the chain is executed in a short transmission time ∼N/2, where N is the number of spins in the chain, and with a large fidelity.

  16. SCit: web tools for protein side chain conformation analysis.

    Science.gov (United States)

    Gautier, R; Camproux, A-C; Tufféry, P

    2004-07-01

    SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit. PMID:15215438

  17. Electrode assemblies composed of redox cascades from microbial respiratory electron transfer chains

    Energy Technology Data Exchange (ETDEWEB)

    Gates, Andrew J. [Univ. of East Anglia, Norwich (United Kingdom); Marritt, Sophie [Univ. of East Anglia, Norwich (United Kingdom); Bradley, Justin [Univ. of East Anglia, Norwich (United Kingdom); Shi, Liang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); McMillan, Duncan G. [Univ. of Leeds (United Kingdom); Jeuken, Lars J. [Univ. of Leeds (United Kingdom); Richardson, David [Univ. of East Anglia, Norwich (United Kingdom); Butt, Julea N. [Univ. of East Anglia, Norwich (United Kingdom)

    2013-10-01

    Respiratory and photosynthetic electron transfer chains are dependent on vectorial electron transfer through a series of redox proteins. Examples include electron transfer from NapC to NapAB nitrate reductase in Paracoccus denitrificans and from CymA to Fcc3 (flavocytochrome c3) fumarate reductase in Shewanella oneidensis MR-1. In the present article, we demonstrate that graphite electrodes can serve as surfaces for the stepwise adsorption of NapC and NapAB, and the stepwise adsorption of CymA and Fcc3. Aspects of the catalytic properties of these assemblies are different from those of NapAB and Fcc3 adsorbed in isolation. We propose that this is due to the formation of NapC-NapAB and of CymA-Fcc3 complexes that are capable of supporting vectorial electron transfer.

  18. Polonium ({sup 210}Po) and lead ({sup 210}Pb) in marine organisms and their transfer in marine food chains

    Energy Technology Data Exchange (ETDEWEB)

    Carvalho, Fernando P., E-mail: carvalho@itn.p [Instituto Tecnologico e Nuclear, Departamento de Proteccao Radiologica e Seguranca Nuclear, E.N. 10, 2686-953 Sacavem (Portugal)

    2011-05-15

    The determination of {sup 210}Po and {sup 210}Pb was performed in marine organisms from the seashore to abyssal depths, encompassing a plethora of species from the microscopic plankton to the sperm whale. Concentrations of those radionuclides ranged from low values of about 5 x 10{sup -1} Bq kg{sup -1} (wet wt.) in jellyfish, to very high values of about of 3 x 10{sup 4} Bq kg{sup -1} (wet wt.) in the gut walls of sardines, with a common pattern of {sup 210}Po > {sup 210}Pb.These radionuclides are primarily absorbed from water and concentrated by phyto- and microzooplankton, and then are transferred to the next trophic level along marine food chains. Investigation in epipelagic, mesopelagic, bathypelagic and abyssobenthic organisms revealed that {sup 210}Po is transferred in the marine food webs with transfer factors ranging from 0.1 to 0.7, and numerically similar to those of the energy transfer in the marine food chains. As {sup 210}Po preferentially binds to amino acids and proteins, its transfer in food chains likely traces protein transfer and, thus, {sup 210}Po transfer factors are similar to ecotrophic coefficients. {sup 210}Pb is transferred less efficiently in marine food chains and this contributes to increased {sup 210}Po:{sup 210}Pb activity ratios in some trophic levels.

  19. ''adding'' algorithm for the Markov chain formalism for radiation transfer

    International Nuclear Information System (INIS)

    The Markov chain radiative transfer method of Esposito and House has been shown to be both efficient and accurate for calculation of the diffuse reflection from a homogeneous scattering planetary atmosphere. The use of a new algorithm similar to the ''adding'' formula of Hansen and Travis extends the application of this formalism to an arbitrarily deep atmosphere. The basic idea for this algorithm is to consider a preceding calculation as a single state of a new Markov chain. Successive application of this procedure makes calculation possible for any optical depth without increasing the size of the linear system used. The time required for the algorithm is comparable to that for a doubling calculation for a homogeneous atmosphere, but for a non-homogeneous atmosphere the new method is considerably faster than the standard ''adding'' routine. As with he standard ''adding'' method, the information on the internal radiation field is lost during the calculation. This method retains the advantage of the earlier Markov chain method that the time required is relatively insensitive to the number of illumination angles or observation angles for which the diffuse reflection is calculated. A technical write-up giving fuller details of the algorithm and a sample code are available from the author

  20. Mechanisms of Ligand Transfer by the Hepatic Tocopherol Transfer Protein*

    OpenAIRE

    Morley, Samantha; Cecchini, Matt; Zhang, Wendy; Virgulti, Alessandro; Noy, Noa; Atkinson, Jeffrey; Manor, Danny

    2008-01-01

    α-Tocopherol is a member of the vitamin E family that functions as the principal fat-soluble antioxidant in vertebrates. Body-wide distribution of tocopherol is regulated by the hepatic α-tocopherol transfer protein (αTTP), which stimulates secretion of the vitamin from hepatocytes to circulating lipoproteins. This biological activity of αTTP is thought to stem from its ability to facilitate the transfer of vitamin E between membranes, but the mechanism by which the pr...

  1. A potent antimicrobial protein from onion seeds showing sequence homology to plant lipid transfer proteins

    OpenAIRE

    Cammue, Bruno; Thevissen, Karin; Hendriks, M.; Eggermont, Kristel; Goderis, I. J.; Proost, Paul; Van Damme, Jozef; Osborn, R W; Guerbette, F.; Kader, J. C.; Broekaert, Willem

    1995-01-01

    An antimicrobial protein of about 10 kD, called Ace-AMP1, was isolated from onion (Allium cepa L.) seeds. Based on the near-complete amino acid sequence of this protein, oligonucleotides were designed for polymerase chain reaction-based cloning of the corresponding cDNA. The mature protein is homologous to plant nonspecific lipid transfer proteins (nsLTPs), but it shares only 76% of the residues that are conserved among all known plant nsLTPs and is unusually rich in arginine. Ace-AMP1 inhibi...

  2. How to construct the spin chains with perfect state transfer

    CERN Document Server

    Vinet, Luc

    2011-01-01

    It is shown how to systematically construct the $XX$ quantum spin chains with nearest-neighbor interaction that allow perfect state transfer (PST). Sets of orthogonal polynomials (OPs) are in correspondence with such systems. The key observation is that for any admissible one-excitation energy spectrum, the weight function of the associated OPs is uniquely prescribed. This entails the complete characterization of these PST models with the mirror symmetry property arising as a corollary. A simple and efficient algorithm to obtain the corresponding Hamiltonians is presented. A new model connected to a special case of the symmetric $q$-Racah polynomials is offered. It is also explained how additional models with PST can be derived from from a parent system by removing energy levels from the one-excitation spectrum of the latter. This is achieved through Christoffel transformations and is also completely constructive in regards to the Hamiltonians.

  3. Lipid transfer proteins of barley

    Czech Academy of Sciences Publication Activity Database

    Žídková, Jitka; Matejková, M.; Petry-Podgorska, Inga; Žídek, L.; Sikorová, K.; Nálezková, M.; Chmelík, Josef; Sklenář, V.

    2007-01-01

    Roč. 14, č. 1 (2007), s. 51. ISSN 1211-5894. [Discussions in Structural Molecular Biology and Bioinformatics /6./. 29.03.2007-31.03.2007, Nové Hrady] R&D Projects: GA MŠk 1M0570 Institutional research plan: CEZ:AV0Z40310501 Keywords : protein separation * barley * MALDI-TOF/TOF MS-MS Subject RIV: CB - Analytical Chemistry, Separation

  4. ELASTIC BEHAVIOR OF PROTEIN-LIKE SINGLE CHAIN

    Institute of Scientific and Technical Information of China (English)

    Wei-qi Yi; Lin-xi Zhang

    2005-01-01

    The conformational properties and elastic behaviors of protein-like single chains in the process of tensile elongation were investigated by means of Monte Carlo method. The sequences of protein-like single chains contain two types of residues: hydrophobic (H) and hydrophilic (P). The average conformations and thermodynamics statistical properties of protein-like single chains with various elongation ratio λ were calculated. It was found that the mean-square end-to-end distance r increases with elongation ratio,λ. The tensor eigenvalues ratio of : decreases with elongation ratio λ for short (HP)x protein-like polymers, however, the ratio of : increases with elongation ratioλ,especially for long (H)x sequence. Average energy per bond increases with elongation ratioλ, especially for(H)x protein-like single chains. Helmholtz free energy per bond also increases with elongation ratioλ. Elastic force (f), energy contribution to force (fU) and entropy contribution to force (fs) for different protein-like single chains were also calculated.These investigations may provide some insights into elastic behaviors of proteins.

  5. A protein-dependent side-chain rotamer library.

    KAUST Repository

    Bhuyan, M.S.

    2011-12-14

    Protein side-chain packing problem has remained one of the key open problems in bioinformatics. The three main components of protein side-chain prediction methods are a rotamer library, an energy function and a search algorithm. Rotamer libraries summarize the existing knowledge of the experimentally determined structures quantitatively. Depending on how much contextual information is encoded, there are backbone-independent rotamer libraries and backbone-dependent rotamer libraries. Backbone-independent libraries only encode sequential information, whereas backbone-dependent libraries encode both sequential and locally structural information. However, side-chain conformations are determined by spatially local information, rather than sequentially local information. Since in the side-chain prediction problem, the backbone structure is given, spatially local information should ideally be encoded into the rotamer libraries. In this paper, we propose a new type of backbone-dependent rotamer library, which encodes structural information of all the spatially neighboring residues. We call it protein-dependent rotamer libraries. Given any rotamer library and a protein backbone structure, we first model the protein structure as a Markov random field. Then the marginal distributions are estimated by the inference algorithms, without doing global optimization or search. The rotamers from the given library are then re-ranked and associated with the updated probabilities. Experimental results demonstrate that the proposed protein-dependent libraries significantly outperform the widely used backbone-dependent libraries in terms of the side-chain prediction accuracy and the rotamer ranking ability. Furthermore, without global optimization/search, the side-chain prediction power of the protein-dependent library is still comparable to the global-search-based side-chain prediction methods.

  6. Coevolution study of mitochondria respiratory chain proteins:Toward the understanding of protein-protein interaction

    Institute of Scientific and Technical Information of China (English)

    Ming Yang; Yan Ge; Jiayan Wu; Jingfa Xiao; Jun Yu

    2011-01-01

    Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein-protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein-protein interaction in intra-complex and the binary protein-protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 x 10-6). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein-protein interaction.Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study.

  7. Organic cleanliness of the Mars Science Laboratory sample transfer chain.

    Science.gov (United States)

    Blakkolb, B; Logan, C; Jandura, L; Okon, A; Anderson, M; Katz, I; Aveni, G; Brown, K; Chung, S; Ferraro, N; Limonadi, D; Melko, J; Mennella, J; Yavrouian, A

    2014-07-01

    One of the primary science goals of the Mars Science Laboratory (MSL) Rover, Curiosity, is the detection of organics in Mars rock and regolith. To achieve this, the Curiosity rover includes a robotic sampling system that acquires rock and regolith samples and delivers it to the Sample Analysis at Mars (SAM) instrument on board the rover. In order to provide confidence that any significant organics detection result was Martian and not terrestrial in origin, a requirement was levied on the flight system (i.e., all sources minus the SAM instrument) to impart no more than 36 parts per billion (ppb by weight) of total reduced carbon terrestrial contamination to any sample transferred to the SAM instrument. This very clean level was achieved by a combination of a rigorous contamination control program on the project, and then using the first collected samples for a "dilution cleaning" campaign of the sample chain prior to delivering a sample to the SAM instrument. Direct cleanliness assays of the sample-contacting and other Flight System surfaces during pre-launch processing were used as inputs to determine the number of dilution cleaning samples needed once on Mars, to enable delivery of suitably clean samples to the SAM experiment. Taking into account contaminant redistribution during launch thorough landing of the MSL on Mars, the amount of residue present on the sampling hardware prior to the time of first dilution cleaning sample acquisition was estimated to be 60 ng/cm(2) on exposed outer surfaces of the sampling hardware and 20 ng/cm(2) on internal sample contacting surfaces; residues consisting mainly of aliphatic hydrocarbons and esters. After three dilution cleaning samples, estimated in-sample contamination level for the first regolith sample delivered to the SAM instrument at the Gale Crater "Rocknest" site was bounded at ≤10 ppb total organic carbon. A Project decision to forego ejecting the dilution cleaning sample and instead transfer the first drill

  8. Microsomal triglyceride transfer protein lipidation and control of CD1d on antigen-presenting cells

    OpenAIRE

    Dougan, Stephanie K.; Salas, Azucena; Rava, Paul; Agyemang, Amma; Kaser, Arthur; Morrison, Jamin; Khurana, Archana; Kronenberg, Mitchell; Johnson, Caroline; Exley, Mark; Hussain, M. Mahmood; Blumberg, Richard S.

    2005-01-01

    Microsomal triglyceride transfer protein (MTP), an endoplasmic reticulum (ER) chaperone that loads lipids onto apolipoprotein B, also regulates CD1d presentation of glycolipid antigens in the liver and intestine. We show MTP RNA and protein in antigen-presenting cells (APCs) by reverse transcription–polymerase chain reaction and by immunoblotting of mouse liver mononuclear cells and mouse and human B cell lines. Functional MTP, demonstrated by specific triglyceride transfer activity, is prese...

  9. Plasma cholesteryl ester transfer protein mass and phospholipid transfer protein activity are associated with leptin in type 2 diabetes mellitus

    NARCIS (Netherlands)

    Dullaart, R. P. F.; de Vries, R.; Dallinga-Thie, G. M.; van Tol, A.; Sluiter, W. J.

    2007-01-01

    Adipose tissue contributes to plasma levels of lipid transfer proteins and is also the major source of plasma adipokines. We hypothesized that plasma cholesteryl ester transfer protein (CETP) mass, phospholipid transfer protein (PLTP) activity and cholesteryl ester transfer (CET, a measure of CETP a

  10. Mechanisms involved in the selective transfer of long chain polyunsaturted fatty acids to the fetus

    Directory of Open Access Journals (Sweden)

    Alfonso eGil-Sánchez

    2011-09-01

    Full Text Available The concentration of long chain polyunsaturated fatty acid (LCPUFA in the fetal brain increases dramatically from the third trimester until 18 months of life. Several studies have shown an association between the percentage of maternal plasma docosahexaenoic acid (DHA during gestation and development of the cognitive functions in the neonate. Since only very low levels of LCPUFA are synthesized in the fetus and placenta, their primary source for the fetus is that of maternal origin. Both in vitro and human in vivo studies using labelled fatty acids have shown the preferential transfer of LCPUFA from the placenta to the fetus compared with other fatty acids, although the mechanisms involved are still uncertain. The placenta takes up circulating maternal non-esterified fatty acids (NEFA and fatty acids released mainly by maternal lipoprotein lipase and endothelial lipase. These NEFA may enter the cell by passive diffusion or by means of membrane carrier proteins. Once in the cytosol, NEFA bind to cytosolic fatty acid-binding proteins for transfer to the fetal circulation or can be oxidized within the trophoblasts and even re-esterified and stored in lipid droplets (LD. Although trophoblast cells are not specialized in lipid storage, LCPUFA may up-regulate peroxisome proliferator activated receptor-γ (PPARγ and hence the gene expression of fatty acid transport carriers, fatty acid acyl-CoA synthetases and adipophilin or other enzymes related with lipolysis, modifying their rate of placental transfer and metabolization. The placental transfer of LCPUFA during pregnancy seems to be a key factor in the neurological development of the fetus. Increased knowledge on the factors that modify placental transfer of fatty acids would contribute to our understanding of this complex process.

  11. Regulation of microsomal triglyceride transfer protein

    OpenAIRE

    Hussain, M. Mahmood; Nijstad, Niels; Franceschini, Lisa

    2011-01-01

    Microsomal triglyceride transfer protein (MTP) facilitates the transport of dietary and endogenous fat by the intestine and liver by assisting in the assembly and secretion of triglyceride-rich apolipoprotein B-containing lipoproteins. Higher concentrations of apolipoprotein B lipoproteins predispose individuals to various cardiovascular and metabolic diseases such as atherosclerosis, diabetes, obesity and the metabolic syndrome. These can potentially be avoided by reducing MTP activity. In t...

  12. Nonlinear exciton transfer in protein helices

    International Nuclear Information System (INIS)

    We study the transfer of vibronic excitation energy in helical forms of proteins. The steric structure of the helix protein is modelled by a three-dimensional network of oscillators representing peptide groups. The covalent and hydrogen bonds between the peptide groups are described by pair interaction potentials. Each peptide group possesses one internal vibrational (excitonic) degree of freedom embodying the amide-I mode. The transfer dynamics of an amide-I exciton along the helix is expressed in terms of a tight-binding system. In the first part of this paper we study a reduced system arising when the vibrations of the covalent bonds are neglected. For the resulting system consisting of the exciton coupled to the hydrogen bond vibrations oriented along the helix axis we construct polaron solutions. Subsequently we investigate the mobility of the polarons within the complete protein matrix including deformations of the covalent bonds too. In particular we show that, during a phase of adaptation going along with internal energy exchange between the exciton and the bond vibrations, a relaxation into a new steady regime takes place. The newly reached equilibrium state is characterized by a localized exciton breather and is attributed local deformations of the steric peptide cage in the form of phonobreathers. Finally, coherent motion of an exciton breather is initiated through suitable injection of kinetic energy. In this way the long-range transfer of vibronic amide-I energy in the steric protein cage is provided. Interestingly, the α-helix possesses better facilities in supporting mobile localized excitons compared to the 3-10-helix form of proteins

  13. Determination of phospholipid transfer proteins in rat tissues by immunoassays

    International Nuclear Information System (INIS)

    Several quantitative immunoassays have been developed for two phospholipid transfer proteins from rat liver, i.e. the phosphatidylcholine transfer protein and the non-specific lipid transfer protein. The development of a double-antibody radioimmunoassay for the phosphatidylcholine transfer protein is described. The transfer protein was labelled with iodine-125 by the mild glucose oxidase-lactoperoxidase method. Although less than one tyrosine residue per molecule of transfer protein was labelled, only 20% of the labelled transfer protein was immunoprecipitable. This value could be increased to 80% by purifying the labelled protein by affinity chromatography on a column of anti-phosphatidylcholine transfer protein-IgG coupled to Sepharose 4B. The radioimmunoassay was used to determine the levels of phosphatidylcholine transfer protein in homogenates and 105 000 xg supernatants from various rat tissues as well as several Morris hepatomas. An enzyme immunoassay for the non-specific lipid transfer protein is also described. The antiserum that was raised especially by the author was cross-reactive with the non-specific lipid transfer protein present in 105 000 xg supernatants from human, mouse and bovine liver. The non-specific lipid transfer protein lost its immunoreactivity upon labelling with iodine-125 using different labelling techniques. Therefore, a regular radioimmunoassay could not be developed. The results of these different assays were compared. (Auth.)

  14. [Progress in ubiquitin, ubiquitin chain and protein ubiquitination].

    Science.gov (United States)

    Lan, Qiuyan; Gao, Yuan; Li, Yanchang; Hong, Xuechuan; Xu, Ping

    2016-01-01

    Protein ubiquitination is one of the most important and widely exist protein post-translational modifications in eukaryotic cells, which takes the ubiquitin and ubiquitin chains as signal molecules to covalently modify other protein substrates. It plays an important roles in the control of almost all of the life processes, including gene transcription and translation, signal transduction and cell-cycle progression, besides classical 26S protesome degradation pathway. Varied modification sites in the same substrates as well as different types of ubiquitin linkages in the same modification sites contain different structural information, which conduct different signal or even determine the fate of the protein substrates in the cell. Any abnormalities in ubiquitin chain formation or its modification process may cause severe problem in maintaining the balance of intracellular environment and finally result in serious health problem of human being. In this review, we discussed the discovery, genetic characteristics and the crystal structure of the ubiquitin. We also emphasized the recent progresses of the assembly processes, structure and their biological function of ubiquitin chains. The relationship between the disregulation and related human diseases has also been discussed. These progress will shed light on the complexity of proteome, which may also provide tools in the new drug research and development processes. PMID:27363196

  15. Electron transfer and interfacial behavior of redox proteins

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    This paper reviews the recent progress in the electron transfer and interfacial behavior of redox proteins. Significant achievements in the relevant fields are summarized including the direct electron transfer between proteins and electrodes, the thermodynamic and kinetic properties, catalytic activities and activity regulation of the redox proteins. It has been demonstrated that the electrochemical technique is an effective tool for protein studies, especially for probing into the electron transfer and interfacial behavior of redox proteins.

  16. Enzymic construction of maltosaccharide chains on a heart protein

    International Nuclear Information System (INIS)

    The authors have reported that when 100,000 g pellets of rabbit-heart and rabbit-muscle homogenates are incubated with UDP(14C)glucose, the sugar is incorporated into a protein with Mr 40 KDa. They suggested that these in vitro observations corresponded to the initial stage in the synthesis of glycogen on a protein that they have named glycogenin and which in rabbit muscle appears to be covalently linked to the glycogen via tyrosine residues. The following new observations support the role of a protein as the precursor of glycogen and suggest that glycogen-free glycogenin is present in heart tissue. (1) The (14C)glucose residues added to the heart protein can be removed with glycogenolytic enzymes that hydrolyse 1,4-alpha-glucosidic bonds and therefore constitute synthetic maltosaccharide chains. (2) The newly added glucose residues appear to be attached to pre-existing glucose residues on the protein. Chain elongation does not proceed beyond a few glucose residues. (3) The further relevance of these observations to glycogen synthesis shown by a Western blot in which the radioglucosylated heart protein was found to cross-react with polyclonal antibody to glycogenin obtained from rabbit-muscle glycogen

  17. All Possible Coupling Schemes in XY Spin Chains for Perfect State Transfer

    CERN Document Server

    Wang, Yaoxiong; Rabitz, Herschel

    2011-01-01

    We investigate quantum state transfer in XY spin chains and propose a recursive procedure to construct the nonuniform couplings of these chains with arbitrary length to achieve perfect state transfer(PST). We show that this method is capable of finding all possible coupling schemes for PST. These schemes, without external control fields, only involve preengineered couplings but not dynamical control of them, so they can be simply realized experimentally. The analytical solutions provide all information for coupling design.

  18. Quantum error correction for state transfer in noisy spin chains

    Science.gov (United States)

    Kay, Alastair

    2016-04-01

    Can robustness against experimental imperfections and noise be embedded into a quantum simulation? In this paper, we report on a special case in which this is possible. A spin chain can be engineered such that, in the absence of imperfections and noise, an unknown quantum state is transported from one end of the chain to the other, due only to the intrinsic dynamics of the system. We show that an encoding into a standard error-correcting code (a Calderbank-Shor-Steane code) can be embedded into this simulation task such that a modified error-correction procedure on readout can recover from sufficiently low rates of noise during transport.

  19. A recombinant single chain antibody interleukin-2 fusion protein.

    OpenAIRE

    Savage, P; So, A; Spooner, R A; Epenetos, A. A.

    1993-01-01

    Recombinant interleukin-2 (rIL-2) therapy has been shown to be of value in the treatment of some cases of melanoma and renal cell carcinoma. However its use can be limited by severe systemic toxicity. Targeting rIL-2 to the tumour should improve the anti-tumour immune response and decrease the systemic toxicity. With this aim we have employed recombinant DNA techniques to construct a single chain antibody interleukin-2 fusion protein (SCA-IL-2). The protein used in this model system comprises...

  20. Beta-scission of side-chain alkoxyl radicals on peptides and proteins results in the loss of side-chains as aldehydes and ketones

    DEFF Research Database (Denmark)

    Headlam, Henrietta A; Davies, Michael Jonathan

    2002-01-01

    Exposure of proteins to radicals in the presence of O(2) results in side-chain oxidation and backbone fragmentation; the interrelationship between these processes is not fully understood. Recently, initial attack on Ala side-chains was shown to give alpha-carbon radicals (and hence backbone...... cleavage) and formaldehyde, via the formation and subsequent beta-scission, of C-3 alkoxyl radicals. We now show that this side-chain to backbone damage transfer, is a general mechanism for aliphatic side-chains. Oxidation of Val, Leu, and Asp residues by HO(*)/O(2) results in the release of a family of...... carbonyls (including formaldehyde, acetone, isobutyraldehyde, and glyoxylic acid) via the formation, and subsequent beta-scission of alkoxyl radicals. The concentration of these products increases with the HO(*) flux. The release of multiple carbonyls confirms the occurrence of oxidation at C-3 and C-4 for...

  1. Innovations and Knowledge Transfer for the Food Supply Chain Sustainability: Challenges in the Czech Dairy Industry

    OpenAIRE

    Ratinger, Tomas; Bošková, Iveta

    2013-01-01

    A mobilisation of research, knowledge transfer and innovation to deal with the current challenges as raising world food demand while protecting natural resources is a priority area of the EU. The effective knowledge transfer and innovation activities in the agri-food supply chain may push all producers in the vertical to improve their competitiveness while saving resources. In the paper we examine the current level of innovation activities and knowledge transfer in milk processing industry in...

  2. Acquisition of Triacylglycerol Transfer Activity by Microsomal Triglyceride Transfer Protein During Evolution

    OpenAIRE

    Rava, Paul; Hussain, M. Mahmood

    2007-01-01

    Microsomal triglyceride transfer protein (MTP) is essential for the assembly of neutral lipid rich apolipoprotein B (apoB)-lipoproteins. Previously we reported that the Drosophila MTP transfers phospholipids but does not transfer triglycerides. In contrast, human MTP transfers both lipids. To explore the acquisition of triglyceride transfer activity by MTP, we evaluated amino acid sequences, protein structures, as well as the biochemical and cellular properties of various MTP orthologs obtain...

  3. Radiative transfer calculated from a Markov chain formalism

    International Nuclear Information System (INIS)

    The theory of Markov chains is used to formulate the radiative transport problem in a general way by modeling the successive interactions of a photon as a stochastic process. Under the minimal requirement that the stochastic process is a Markov chain, the determination of the diffuse reflection of transmission from a scattering atmosphere is equivalent to the solution of a system of linear equations. This treatment is mathematically equivalent to and thus has many of the advantages of, Monte Carlo methods, but can be considerably more rapid than Monte Carlo algorithms for numerical calculations in particular applications. We have verified the speed and accuracy of this formalism for the stand problem of finding the intensity of scattered light from a homogeneous plane-parallel atmosphere with an arbitrary phase function for scattering. Accurate results over a wide range of parameters were obtained with computation times comparable to those of a standard ''doubling'' routine. The generality of this formalism thus allows fast, direct solutions to problems that were previously soluble only by Monte Carlo methods. Some comparisons are made with respect to integral equation methods

  4. Radiative transfer calculated from a Markov chain formalism

    Science.gov (United States)

    Esposito, L. W.; House, L. L.

    1978-01-01

    The theory of Markov chains is used to formulate the radiative transport problem in a general way by modeling the successive interactions of a photon as a stochastic process. Under the minimal requirement that the stochastic process is a Markov chain, the determination of the diffuse reflection or transmission from a scattering atmosphere is equivalent to the solution of a system of linear equations. This treatment is mathematically equivalent to, and thus has many of the advantages of, Monte Carlo methods, but can be considerably more rapid than Monte Carlo algorithms for numerical calculations in particular applications. We have verified the speed and accuracy of this formalism for the standard problem of finding the intensity of scattered light from a homogeneous plane-parallel atmosphere with an arbitrary phase function for scattering. Accurate results over a wide range of parameters were obtained with computation times comparable to those of a standard 'doubling' routine. The generality of this formalism thus allows fast, direct solutions to problems that were previously soluble only by Monte Carlo methods. Some comparisons are made with respect to integral equation methods.

  5. Spin Chains and Electron Transfer at Stepped Silicon Surfaces.

    Science.gov (United States)

    Aulbach, J; Erwin, S C; Claessen, R; Schäfer, J

    2016-04-13

    High-index surfaces of silicon with adsorbed gold can reconstruct to form highly ordered linear step arrays. These steps take the form of a narrow strip of graphitic silicon. In some cases-specifically, for Si(553)-Au and Si(557)-Au-a large fraction of the silicon atoms at the exposed edge of this strip are known to be spin-polarized and charge-ordered along the edge. The periodicity of this charge ordering is always commensurate with the structural periodicity along the step edge and hence leads to highly ordered arrays of local magnetic moments that can be regarded as "spin chains." Here, we demonstrate theoretically as well as experimentally that the closely related Si(775)-Au surface has-despite its very similar overall structure-zero spin polarization at its step edge. Using a combination of density-functional theory and scanning tunneling microscopy, we propose an electron-counting model that accounts for these differences. The model also predicts that unintentional defects and intentional dopants can create local spin moments at Si(hhk)-Au step edges. We analyze in detail one of these predictions and verify it experimentally. This finding opens the door to using techniques of surface chemistry and atom manipulation to create and control silicon spin chains. PMID:26974012

  6. Theory of quantum energy transfer in spin chains: From superexchange to ballistic motion

    OpenAIRE

    Yu, Claire X.; Wu, Lian-Ao; Segal, Dvira

    2011-01-01

    Quantum energy transfer in a chain of two-level (spin) units, connected at its ends to two thermal reservoirs, is analyzed in two limits: (i) In the off-resonance regime, when the characteristic subsystem excitation energy gaps are larger than the reservoirs frequencies, or the baths temperatures are low. (ii) In the resonance regime, when the chain excitation gaps match populated bath modes. In the latter case the model is studied using a master equation approach, showing that the dynamics i...

  7. Electrotransfer of proteins in an environmentally friendly methanol-free transfer buffer.

    Science.gov (United States)

    Villanueva, Marco A

    2008-02-15

    Western blot transfer buffer was modified to substitute the acute poison methanol, with the common rubbing alcohol, isopropanol in concentrations of as low as 5 % for protein electrotransfer. Commercially available molecular weight markers and rabbit serum were run on polyacrylamide gels and shown to be transferred adequately to both nitrocellulose and polyvinylidene difluoride membranes under either wet or semi-dry conditions with similar results in all cases. This procedure was successfully used for immunodetection of the rabbit IgG heavy chain from serum. Therefore, this represents a good alternative for less toxic and environmentally friendly conditions for western immunoblotting of proteins. PMID:17850757

  8. Bioaccumulation and food chain transfer of corrosion products from radioactive stainless steel

    International Nuclear Information System (INIS)

    Two sets of experiments were conducted to determine if corrosion products from radioactive Type 347 stainless steel could be biologically transferred from sediment through a marine food chain, and whether corrosion products dissolved in seawater could be bioaccumulated and then eliminated. Corrosion products containing 60Co and 63Ni from the radioactive stainless steel were introduced into marine sediments. Infaunal polychaete worms exposed to these sediments bioaccumulated the radionuclides. The feeding of these worms to shrimp and fish resulted in a trophic transfer of the radioactive products across a one-step food chain. The magnitude of the transfers are described in terms of transfer factors. Dissolved corrosion products as measured by the radionuclides were also bioaccumulated by shrimp and fish concentrating more than fish. Concentration factors were calculated

  9. Bioaccumulation and food chain transfer of corrosion products from radioactive stainless steel

    Energy Technology Data Exchange (ETDEWEB)

    Young, J.S.

    1986-07-01

    Two sets of experiments were conducted to determine if corrosion products from radioactive Type 347 stainless steel could be biologically transferred from sediment through a marine food chain, and whether corrosion products dissolved in seawater could be bioaccumulated and then eliminated. Corrosion products containing /sup 60/Co and /sup 63/Ni from the radioactive stainless steel were introduced into marine sediments. Infaunal polychaete worms exposed to these sediments bioaccumulated the radionuclides. The feeding of these worms to shrimp and fish resulted in a trophic transfer of the radioactive products across a one-step food chain. The magnitude of the transfers are described in terms of transfer factors. Dissolved corrosion products as measured by the radionuclides were also bioaccumulated by shrimp and fish concentrating more than fish. Concentration factors were calculated.

  10. Protein electron transfer: is biology (thermo)dynamic?

    Science.gov (United States)

    Matyushov, Dmitry V

    2015-12-01

    Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life's ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein's elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic activated

  11. Transfer of 137Cs through the food chain to man

    International Nuclear Information System (INIS)

    Deposition, concentrations in diet, and body burdens of 137Cs have been measured since 1954 at various sites throughout the world. This report is a compilation and updating of various fallout 137Cs measurements and an interpretation of transfer properties of 137Cs from deposition to diet and from diet to man. An empirical model is used to correlate deposition and diet data. Direct foliar contamination, stored food supplies, and uptake from soil contribute to the dietary levels of 137Cs. The accumulation of 137Cs by man is described by a single exponential model. The inferred biological half-times, 200 to 400 days, are somewhat greater than the half-time of about 100 days obtained from shorter term studies. Differences in body burdens due to sex, age, and weight are discussed. During the period 1954 to 1974, the internal dose from fallout 137Cs, based on average body burdens, is estimated to be 4 to 5 percent of the 21 year radiation dose from 40K

  12. Transfer of Metals in Food Chain: An Example with Copper and Lettuce

    OpenAIRE

    Vincevica-Gaile, Z; M. Klavins

    2012-01-01

    Present study investigated the possible transfer of metals in the food chain (from soil to edible plants). The experiment was done with lettuce Lactuca sativa grown in different types of soil contaminated with copper (Cu2+) in various concentrations, with or without addition of humic substances. The highest content of copper was detected in lettuce samples grown in soils with lower levels of organic matter, thus indicating the importance of soil organics in metal transfer...

  13. Long-range doublon transfer in a dimer chain induced by topology and ac fields

    Science.gov (United States)

    Bello, M.; Creffield, C. E.; Platero, G.

    2016-03-01

    The controlled transfer of particles from one site of a spatial lattice to another is essential for many tasks in quantum information processing and quantum communication. In this work we study how to induce long-range transfer between the two ends of a dimer chain, by coupling states that are localized just on the chain’s end-points. This has the appealing feature that the transfer occurs only between the end-points - the particle does not pass through the intermediate sites-making the transfer less susceptible to decoherence. We first show how a repulsively bound-pair of fermions, known as a doublon, can be transferred from one end of the chain to the other via topological edge states. We then show how non-topological surface states of the familiar Shockley or Tamm type can be used to produce a similar form of transfer under the action of a periodic driving potential. Finally we show that combining these effects can produce transfer by means of more exotic topological effects, in which the driving field can be used to switch the topological character of the edge states, as measured by the Zak phase. Our results demonstrate how to induce long range transfer of strongly correlated particles by tuning both topology and driving.

  14. Protein electron transfer: is biology (thermo)dynamic?

    Science.gov (United States)

    Matyushov, Dmitry V.

    2015-12-01

    Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life’s ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein’s elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic

  15. Protein electron transfer: is biology (thermo)dynamic?

    International Nuclear Information System (INIS)

    Simple physical mechanisms are behind the flow of energy in all forms of life. Energy comes to living systems through electrons occupying high-energy states, either from food (respiratory chains) or from light (photosynthesis). This energy is transformed into the cross-membrane proton-motive force that eventually drives all biochemistry of the cell. Life’s ability to transfer electrons over large distances with nearly zero loss of free energy is puzzling and has not been accomplished in synthetic systems. The focus of this review is on how this energetic efficiency is realized. General physical mechanisms and interactions that allow proteins to fold into compact water-soluble structures are also responsible for a rugged landscape of energy states and a broad distribution of relaxation times. Specific to a protein as a fluctuating thermal bath is the protein-water interface, which is heterogeneous both dynamically and structurally. The spectrum of interfacial fluctuations is a consequence of protein’s elastic flexibility combined with a high density of surface charges polarizing water dipoles into surface nanodomains. Electrostatics is critical to the protein function and the relevant questions are: (i) What is the spectrum of interfacial electrostatic fluctuations? (ii) Does the interfacial biological water produce electrostatic signatures specific to proteins? (iii) How is protein-mediated chemistry affected by electrostatics? These questions connect the fluctuation spectrum to the dynamical control of chemical reactivity, i.e. the dependence of the activation free energy of the reaction on the dynamics of the bath. Ergodicity is often broken in protein-driven reactions and thermodynamic free energies become irrelevant. Continuous ergodicity breaking in a dense spectrum of relaxation times requires using dynamically restricted ensembles to calculate statistical averages. When applied to the calculation of the rates, this formalism leads to the nonergodic

  16. First principles design of a core bioenergetic transmembrane electron-transfer protein.

    Science.gov (United States)

    Goparaju, Geetha; Fry, Bryan A; Chobot, Sarah E; Wiedman, Gregory; Moser, Christopher C; Dutton, P Leslie; Discher, Bohdana M

    2016-05-01

    Here we describe the design, Escherichia coli expression and characterization of a simplified, adaptable and functionally transparent single chain 4-α-helix transmembrane protein frame that binds multiple heme and light activatable porphyrins. Such man-made cofactor-binding oxidoreductases, designed from first principles with minimal reference to natural protein sequences, are known as maquettes. This design is an adaptable frame aiming to uncover core engineering principles governing bioenergetic transmembrane electron-transfer function and recapitulate protein archetypes proposed to represent the origins of photosynthesis. This article is part of a Special Issue entitled Biodesign for Bioenergetics--the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. PMID:26672896

  17. Chain-growth simulations of the HP model for proteins

    Science.gov (United States)

    Santos, Fabricio S. H.; Martins, Paulo H. L.; Bachmann, Michael

    2016-01-01

    We consider a generalized hydrophobic-polar model for proteins on square lattices. Besides the attraction between nonbonded hydrophobic monomers, the present model also takes into account an interaction between hydrophobic and polar units. By using the pruned- enriched Rosenbluth method (PERM), we investigate a specific polymer sequence composed of 42 monomers that has been proposed to simulate the physical properties of the parallel β- helix of pectate lyase C. For each temperature, the total number of generated chains varies from 106 to 107. Physical observables such as specific heat, total energy, end-to-end distance, radius of gyration, and the average number of hydrophobic-hydrophobic and hydrophobic-polar contacts are evaluated for different values of the ratio between the hydrophobic-hydrophobic and the hydrophobic-polar contact energies. Eventually, a pseudo-phase diagram in the space of temperature and the ratio of contact energy scales is constructed.

  18. Protein-protein interactions of mitochondrial-associated protein via bioluminescence resonance energy transfer

    Science.gov (United States)

    Koshiba, Takumi

    2015-01-01

    Protein-protein interactions are essential biological reactions occurring at inter- and intra-cellular levels. The analysis of their mechanism is generally required in order link to understand their various cellular functions. Bioluminescence resonance energy transfer (BRET), which is based on an enzymatic activity of luciferase, is a useful tool for investigating protein-protein interactions in live cells. The combination of the BRET system and biomolecular fluorescence complementation (BiFC) would provide us a better understanding of the hetero-oligomeric structural states of protein complexes. In this review, we discuss the application of BRET to the protein-protein interactions of mitochondrial-associated proteins and discuss its physiological relevance. PMID:27493852

  19. Dynamic modeling system for the transfer of radioactivity in terrestrial food chains

    International Nuclear Information System (INIS)

    A dynamic modeling system is described for the transfer of radionuclides in terrestrial food chains. The main features of the system are its ability to predict the time dependence of the major transfer processes and its flexibility and applicability to a range of contamination scenarios. The modeling system is regarded as a basic framework on which more realistic models can be based, given the availability of reliable environmental transfer data. An example of such a development is included for 90Sr in the pasture-cow-milk pathway. The model predicts annual average concentrations of 90Sr in milk caused by fallout in the United Kingdom to within 15% of measured values for over most of the 20-y period for which data exist. It makes possible the evaluation of the time dependence of the contributions of various transfer processes. Following acute releases to the atmosphere or releases in any other contamination scenario where direct deposition is absent, certain pathways often not considered in food-chain models, such as the external contamination of plants caused by resuspension processes or the ingestion of contaminants together with soil by grazing animals, are shown to be potentially important in the transfer of activity to man. The main application of dynamic food-chain models is the prediction of the consequences of accidental releases to the terrestrial environment. The predictions can be used in planning countermeasures and in assessing the health, economic, and social impacts of accidental release

  20. Influence of dispersants on trophic transfer of petroleum hydrocarbons in a marine food chain

    Energy Technology Data Exchange (ETDEWEB)

    Wolfe, M. F.; Schwartz, G. J. B.; Singaram, S.; Tjeerdema, R. S. [California Univ., Santa Cruz, CA (United States). Dept. of Chemistry; Mielbrecht, E. E. [California Univ., Santa Cruz, CA (United States). Inst. of Marine Sciences; Sowby, M. L. [California State Dept. of Fish and Game, Sacramento, CA (United States)

    1997-10-01

    Experiments were conducted to determine the impact of dispersing agents on petroleum hydrocarbons (PH) bioavailability and trophic transfer in primary levels of a marine food chain. Uptake, bioaccumulation and metabolic transformation of a model PH, ({sup 1}4C)naphthalene, were measured and compared with Prudhoe Bay Crude Oil (PBCO) dispersed with Corexit 9527, and undispersed preparations of PBCO. The model food chain consisted of a primary algae producer and a primary rotifer consumer. Results showed that uptake of naphthalene increased significantly in the presence of a dispersant in algae. A significant increase in uptake was also recorded in rotifers via trophic transfer. Trophic transfer played a significant, sometimes even dominant, role in uptake and bioaccumulation. 27 refs., 6 figs.

  1. Influence of dispersants on trophic transfer of petroleum hydrocarbons in a marine food chain

    International Nuclear Information System (INIS)

    Experiments were conducted to determine the impact of dispersing agents on petroleum hydrocarbons (PH) bioavailability and trophic transfer in primary levels of a marine food chain. Uptake, bioaccumulation and metabolic transformation of a model PH, (14C)naphthalene, were measured and compared with Prudhoe Bay Crude Oil (PBCO) dispersed with Corexit 9527, and undispersed preparations of PBCO. The model food chain consisted of a primary algae producer and a primary rotifer consumer. Results showed that uptake of naphthalene increased significantly in the presence of a dispersant in algae. A significant increase in uptake was also recorded in rotifers via trophic transfer. Trophic transfer played a significant, sometimes even dominant, role in uptake and bioaccumulation. 27 refs., 6 figs

  2. Screening models to predict food-chain transfer of environmental toxicants

    International Nuclear Information System (INIS)

    The objectives of the research effort were to determine transfer coefficients to milk, beef, eggs, and poultry meat of six radionuclides for which transfer coefficients were either undetermined or based upon secondary data. The radionuclides were isotopes of Tc, Mo, Te, Ba, Zr, and Nb. In addition, 131I was used in experiments with hens to determine egg and poultry meat transfer coefficients. The new information on transfer coefficients obtained during this project indicates that, in some cases, lower values are appropriate and that those currently in use may provide an overestimate of the risks to man from the animal food chain. The objective of the second phase of this research was to provide information to clarify the physiological parameters that control transfer of radionuclides to animal food products. The data from the first phase has been published but this data has not appeared in the literature and thus is presented here in some detail. 10 refs., 4 figs., 6 tabs

  3. A general model for the transfer of radioactive materials in terrestrial food chains

    International Nuclear Information System (INIS)

    A general methodology for modelling the transfer of radionuclides in the food chains to man is described. The models are dynamic in nature so that the long-term time dependence of processes in environmental materials can be represented, for example, the build-up of activity concentrations in soils during continuous deposition from atmosphere. Modules for radionuclide migration are described in well-mixed (cultivated) soil and undisturbed soil (pasture). The methods by which the transfer coefficients used in plant and animal modules are derived are also given. The foodstuffs considered are those derived from green vegetables, grain, and root vegetables together with meat and liver products from the cow and sheep and cow dairy products. The dynamic model permits the time dependence of food chain transfer processes to be represented for different land contamination scenarios; in particular, the model can be adapted to represent behaviour following a single deposit. Using the sensitivity of results to the variation of transfer parameters the model can be used to determine the parts of the food chain where improved data would be most effective in increasing the reliability of radiological assessments; a worked example is given. (author)

  4. Identification and evaluation of modularization practices in an automotive supplier: progressivity analysis of transferring activities in the supply chain

    OpenAIRE

    Evandro Prieto; Paulo A. Cauchick Miguel

    2013-01-01

    The automotive value chain has more and more been making room to a strategy of which activities of product design and production have been transferred to the module suppliers. The transfer of value-added activities occurs from assembler to the module suppliers. The former assume the role of integrators within the supply chain. The supply chain participants have started to strengths their competencies in order to obtain advantages in the economy of scale and scope. In this context, the present...

  5. Tunable self-assembled spin chains of strongly interacting cold atoms for demonstration of reliable quantum state transfer

    Science.gov (United States)

    Loft, N. J. S.; Marchukov, O. V.; Petrosyan, D.; Zinner, N. T.

    2016-04-01

    We have developed an efficient computational method to treat long, one-dimensional systems of strongly interacting atoms forming self-assembled spin chains. Such systems can be used to realize many spin chain model Hamiltonians tunable by the external confining potential. As a concrete demonstration, we consider quantum state transfer in a Heisenberg spin chain and we show how to determine the confining potential in order to obtain nearly perfect state transfer.

  6. Transfer of radionuclides at the uranium and thorium decay chains in aquatic and terrestrial environments

    International Nuclear Information System (INIS)

    This report examines the transfer of radionuclides from the uranium and thorium decay chains (U-238, Ra-226, Th-232, Th-230, Po-210 and Pb-210) through the aquatic and terrestrial environment. This transfer is characterized by a transfer coefficient; environmental and experimental factors which cause this coefficient to vary are presented and discussed in this report. Furthermore, based on a literature survey, the report indicates the range of coefficients found for the aquatic sector (that is, sediment and freshwater and marine organisms) and for the terrestrial sector (that is, plants and domestic and wild animals). Afterwards, generalisations are formulated on the transfer of the different radionuclides through the multiple environmental compartments. 75 refs

  7. Universal scheme for finite-probability perfect transfer of arbitrary multispin states through spin chains

    Energy Technology Data Exchange (ETDEWEB)

    Man, Zhong-Xiao, E-mail: zxman@mail.qfnu.edu.cn [Shandong Provincial Key Laboratory of Laser Polarization and Information Technology, Department of Physics, Qufu Normal University, Qufu 273165 (China); An, Nguyen Ba, E-mail: nban@iop.vast.ac.vn [Center for Theoretical Physics, Institute of Physics, Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Cau Giay, Hanoi (Viet Nam); Xia, Yun-Jie, E-mail: yjxia@mail.qfnu.edu.cn [Shandong Provincial Key Laboratory of Laser Polarization and Information Technology, Department of Physics, Qufu Normal University, Qufu 273165 (China); Kim, Jaewan, E-mail: jaewan@kias.re.kr [School of Computational Sciences, Korea Institute for Advanced Study, Hoegiro 85, Dongdaemun-gu, Seoul 130-722 (Korea, Republic of)

    2014-12-15

    In combination with the theories of open system and quantum recovering measurement, we propose a quantum state transfer scheme using spin chains by performing two sequential operations: a projective measurement on the spins of ‘environment’ followed by suitably designed quantum recovering measurements on the spins of interest. The scheme allows perfect transfer of arbitrary multispin states through multiple parallel spin chains with finite probability. Our scheme is universal in the sense that it is state-independent and applicable to any model possessing spin–spin interactions. We also present possible methods to implement the required measurements taking into account the current experimental technologies. As applications, we consider two typical models for which the probabilities of perfect state transfer are found to be reasonably high at optimally chosen moments during the time evolution. - Highlights: • Scheme that can achieve perfect quantum state transfer is devised. • The scheme is state-independent and applicable to any spin-interaction models. • The scheme allows perfect transfer of arbitrary multispin states. • Applications to two typical models are considered in detail.

  8. Universal scheme for finite-probability perfect transfer of arbitrary multispin states through spin chains

    International Nuclear Information System (INIS)

    In combination with the theories of open system and quantum recovering measurement, we propose a quantum state transfer scheme using spin chains by performing two sequential operations: a projective measurement on the spins of ‘environment’ followed by suitably designed quantum recovering measurements on the spins of interest. The scheme allows perfect transfer of arbitrary multispin states through multiple parallel spin chains with finite probability. Our scheme is universal in the sense that it is state-independent and applicable to any model possessing spin–spin interactions. We also present possible methods to implement the required measurements taking into account the current experimental technologies. As applications, we consider two typical models for which the probabilities of perfect state transfer are found to be reasonably high at optimally chosen moments during the time evolution. - Highlights: • Scheme that can achieve perfect quantum state transfer is devised. • The scheme is state-independent and applicable to any spin-interaction models. • The scheme allows perfect transfer of arbitrary multispin states. • Applications to two typical models are considered in detail

  9. Transfer of Metals in Food Chain: An Example with Copper and Lettuce

    Science.gov (United States)

    Vincevica-Gaile, Zane; Klavins, Maris

    2012-12-01

    Present study investigated the possible transfer of metals in the food chain (from soil to edible plants). The experiment was done with lettuce Lactuca sativa grown in different types of soil contaminated with copper (Cu2+) in various concentrations, with or without addition of humic substances. The highest content of copper was detected in lettuce samples grown in soils with lower levels of organic matter, thus indicating the importance of soil organics in metal transfer routes and accumulation rates in plants. It was found that copper accumulation in lettuce grown in contaminated soils can be significantly reduced by the addition of humic substances.

  10. Volume holographic recording in nanoparticle-polymer composites doped with multifunctional chain transfer agents

    Science.gov (United States)

    Guo, Jinxin; Fujii, Ryuta; Tomita, Yasuo

    2015-10-01

    We report on an experimental investigation of the properties of volume holographic recording in photopolymerizable nanoparticle-polymer composites (NPCs) doped with chain transferring multifunctional di- and tri-thiols as chain transfer agents. It is shown that the incorporation of the multifunctional thiols into NPCs more strongly influences on volume holographic recording than that doped with mono-thiol since more chemical reactions involve in the polymer network formation. It is found that, as similar to the case of mono-thiol doping, there exist optimum concentrations of di- and tri-thiols for maximizing the saturated refractive index modulation. It is also seen that recording sensitivity monotonically decreases with an increase in multifunctional thiol concentration due to the partial inhibition of the photopolymerization event by excessive thiols.

  11. Removal of phase transfer agent leads to restricted dynamics of alkyl chains in monolayer protected clusters

    Indian Academy of Sciences (India)

    V R Rajeev Kumar; R Mukhopadhyay; T Pradeep

    2008-11-01

    The effect of phase transfer agent in the dynamics of monolayer protected gold nanoparticles has been investigated by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopies. The experiments were performed with octadecane thiol and dodecane thiol protected gold nanoparticles. The materials prepared were characterized by UV-Visible spectroscopy, transmission electron microscopy and IR spectroscopy. Repeated purification of the monolayer protected gold clusters made the alkyl chains defect-free. Such effects are reflected in the infrared spectra. Interdigitation of the monolayers that followed the purification leads to alkyl chains with limited mobility. This was reflected in 13C and 1H NMR linewidths. The NMR measurements indicate that the removal of phase transfer agent affects the dynamics of isolated clusters and those with interdigitated monolayers in different ways.

  12. Spin-state transfer in laterally coupled quantum-dot chains with disorders

    International Nuclear Information System (INIS)

    Quantum dot arrays are a promising medium for transferring quantum information between two distant points without resorting to mobile qubits. Here we study the two most common disorders, namely hyperfine interaction and exchange coupling fluctuations, in quantum dot arrays and their effects on quantum communication through these chains. Our results show that the hyperfine interaction is more destructive than the exchange coupling fluctuations. The average optimal time for communication is not affected by any disorder in the system and our simulations show that antiferromagnetic chains are much more resistive than the ferromagnetic ones against both kind of disorders. Even when time modulation of a coupling and optimal control is employed to improve the transmission, the antiferromagnetic chain performs much better. We have assumed the quasistatic approximation for hyperfine interaction and time-dependent fluctuations in the exchange couplings. Particularly for studying exchange coupling fluctuations we have considered the static disorder, white noise, and 1/f noise.

  13. Ultrafast energy transfer from rigid, branched side-chains into a conjugated, alternating copolymer

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, Graham B.; Rolczynski, Brian S.; Linkin, Alexander; McGillicuddy, Ryan D.; Engel, Gregory S., E-mail: gsengel@uchicago.edu [Department of Chemistry, The James Franck Institute, Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637 (United States); Lundin, Pamela M. [Department of Chemical Engineering, Stanford University, Stauffer III, 381 North-South Mall, Stanford, California 94305 (United States); A. R. Smith Department of Chemistry, Appalachian State University, 417 CAP Building, 525 Rivers Street, Boone, North Carolina 28608 (United States); Bao, Zhenan [Department of Chemical Engineering, Stanford University, Stauffer III, 381 North-South Mall, Stanford, California 94305 (United States)

    2014-01-21

    We present the synthesis and characterization of a benzodithiophene/thiophene alternating copolymer decorated with rigid, singly branched pendant side chains. We characterize exciton migration and recombination dynamics in these molecules in tetrahydrofuran solution, using a combination of static and time-resolved spectroscopies. As control experiments, we also measure electronic relaxation dynamics in isolated molecular analogues of both the side chain and polymer moieties. We employ semi-empirical and time-dependent density functional theory calculations to show that photoexcitation of the decorated copolymer using 395 nm laser pulses results in excited states primarily localized on the pendant side chains. We use ultrafast transient absorption spectroscopy to show that excitations are transferred to the polymer backbone faster than the instrumental response function, ∼250 fs.

  14. Modelling of radiocesium transfer in the lichen-reindeer/caribou-wolf food chain

    Directory of Open Access Journals (Sweden)

    D. F. Holleman

    1990-09-01

    Full Text Available The environmental contaminate radiocesium (cesium-137 has been shown to be of value as a marker in food selection and intake studies. Its greatest potential value as a food marker is in the subarctic/arctic regions, particularly in the lichen to reindeer/caribou to wolf food chain. A kinetic model describing the movement of radiocesium through the food chain has been developed using the SAAM computer program and is presented here. The program has been written so that the various paramenters affecting the transfer of radiocesium in the food chain can be altered more realistically to describe the system being modeled. The values of the parameters as given in this example are realistic for interior Alaska, however caution should be exercised in the application of the present results to regions that may be vastly different from the Alaskan interior without first evaluating the parameters and assumptions of the model.

  15. Technology Transfer in the Global Automotive Value Chain. Lessons from the Turkish Automotive Industry

    OpenAIRE

    M. Teoman Pamukçu; Alper Sönmez

    2011-01-01

    The automotive industry is one of the main contributors to value added, employment and exports of the Turkish economy and it has undergone major changes since the mid-nineties. Most of the automotive manufacturers in Turkey are either joint ventures or wholly-owned affiliates of multinational companies. Literature on global value chains point to the possibility of technology transfer occurring through backward linkages from automotive manufacturers to their suppliers. We test for the existenc...

  16. Dynamical response of a disordered ferromagnetic chain: alloy transfer matrix approximation

    International Nuclear Information System (INIS)

    The alloy transfer matrix approximation is used to study the uniform dynamic susceptibility of a disordered ferromagnetic chain. The approximation allows for a consistent treatment of diagonal and off- diagonal disorder. The results, in the limit of low concentrations, are in agreement with the exact single impurity ones. Intensities and lineshapes for infrared absorption are calculated for finite impurity concentrations and different values of the relative anisotropy parameter of a model alloy. (Author)

  17. A model for the chain-to-plane charge transfer in YBa2Cu3O6+x

    Institute of Scientific and Technical Information of China (English)

    V.M.Matic; N.Dj.Lazarov; M.Milic

    2012-01-01

    A model for the chain-to-plane charge transfer is proposed to account for the two plateaus,at 60 K and at 90 K,of the Tc(x) characteristics of the YBa2Cu3O6+x high-Tc superconductor.It is assumed that the number of holes transferred from a CuO chain of length l to two nearby CuO2 sheets is proportional to l (that is,to the number of oxygen atoms in the chain),if the chain length is greater than,or equal to,a certain critical chain length,lcr,that is required to trigger the charge transfer process.No holes are assumed to have been transferred from chains of length l < lcr.The calculated Tc(x) dependence is found to be in excellent agreement with the experimentally reported Tc(x).The critical chain length parameter is estimated to be equal to lcr =11 (eleven oxygen atoms in a chain),which is a greater value than that obtained in the previously proposed model for the chain-to plane charge transfer (lcr =4).The results obtained out of the proposed model are briefly discussed.

  18. Alpha-Tocopherol Transfer Protein (α-TTP): Insights from Alpha-Tocopherol Transfer Protein Knockout Mice

    OpenAIRE

    Lim, Yunsook; Traber, Maret G.

    2007-01-01

    Alpha-tocopherol transfer protein (α-TTP) is a liver cytosolic transport protein that faciliates α-tocopherol (α-T) transfer into liver secreted plasma lipoproteins. Genetic defects in α-TTP, like dietary vitamin E deficiency, are associated with infertility, muscular weakness and neurological disorders. Both human and α-TTP deficient (α-TTP-/-) mice exhibit severe plasma and tissue vitamin E deficiency that can be attenuated by sufficient dietary α-T supplementations. In this review, we summ...

  19. Transfer coefficient study of Sr-90 in the soil-grass-milk chain for Cuba

    International Nuclear Information System (INIS)

    One of the most important problems in modern radioecology is the lack of able information about the features of radionuclide migration in tropical and subtropical environment. The development of nuclear energy and the enhancing in the applications of nuclear techniques in those latitudes indicate that studies in this area are necessary. Cuba is carrying out studies on radioecological characterization of the principal food chains in the country. One of the objectives of these studies is to define the values of the transfer coefficients to be used in the evaluation programs for the assessment of the radiological impact of practices which involve ionizing radiation. This paper shows the results obtained in the determination of Sr-90 transfer coefficients in soil-grass-milk food chain in 'La Quebrada', a place near the Havana City where an important part of the milk that the citizens consume is produced. Transfer coefficients for Sr-90 were calculated on the basis of data collected during 5 years in the region. Soil-grass transfer coefficients are in the range 0.18-5 while grass-milk coefficients are in the range of 1.2x10-4 - 6x10-3 day/L. These values are in accordance with values reported by other authors in the literature. (authors). 4 refs., 2 tabs

  20. How does a protein reach its binding locus: sliding along DNA chain or not?

    CERN Document Server

    Li, Jingwei

    2016-01-01

    In gene expression, various kinds of proteins need to bind to specific locus of DNA. It is still not clear how these proteins find their target locus. In this study, the mean first-passage time (FPT) of protein binding to its target locus on DNA chain is discussed by a chain-space coupled model. Our results show that the 1-dimensional diffusion constant has a critical value, with which the mean time spent by a protein to find its target locus is almost independent of the binding rate of protein to DNA chain and the detachment rate from DNA chain. Which implies that, the frequency of protein binding to DNA and the sliding time on DNA chain have little influence on the search efficiency, and therefore whether or not the 1-dimensional sliding on DNA chain increases the search efficiency depends on the 1-dimensional diffusion constant of the protein on DNA chain. This study also finds that only protein bindings to DNA loci which are close to the target locus help to increase the search efficiency, while bindings ...

  1. iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition

    OpenAIRE

    Peng, Jian; Hosur, Raghavendra; Berger, Bonnie; Xu, Jinbo

    2015-01-01

    Protein side-chain packing is a critical component in obtaining the 3D coordinates of a structure and drug discovery. Single-domain protein side-chain packing has been thoroughly studied. A major challenge in generalizing these methods to protein complexes is that they, unlike monomers, often have very large treewidth, and thus algorithms such as TreePack cannot be directly applied. To address this issue, SCWRL4 treats the complex effectively as a monomer, heuristically excluding weak interac...

  2. RADAL: a dynamic model for the transfer of radionuclides through agricultural food chains

    International Nuclear Information System (INIS)

    The contamination of agricultural products by radionuclides is a mechanism which results in radiation dose commitment to the population, following fallout deposits from the atmosphere to the landscape. This paper describes the structure of the dynamic food chain model RADAL. This model simulates an acute environmental transport of fallout radionuclides through agricultural food chains to man and estimates the levels of radiation doses resulting from consumption of contaminated food. The development of RADAL was based on different existing models. For mathematical representation the transport of radionuclides was modeled through compartments representing environmental elements and/or food products. The model solves a set of linear, first-order, differential equations to estimate the concentrations of radionuclides in soil, vegetation, animal tissues and animal products as a function of time following their deposition. Dynamic physico-chemical processes of the model include the following: deposition and foliar interception, weathering, foliar absorption, soil resuspension, transfer from soil surface to the root zone, absorption by plant roots, transfer to deep soil, transfer to animal products, and human consumption of agricultural products. A parameter sensitivity analyses, performed for the main parameters of the model, showed that the foliar interception constant and resuspension factor are the most influential parameters over the radiation doses / model output. (author)

  3. Natural ligand binding and transfer from liver fatty acid binding protein (LFABP) to membranes.

    Science.gov (United States)

    De Gerónimo, Eduardo; Hagan, Robert M; Wilton, David C; Córsico, Betina

    2010-09-01

    Liver fatty acid-binding protein (LFABP) is distinctive among fatty acid-binding proteins because it binds more than one molecule of long-chain fatty acid and a variety of diverse ligands. Also, the transfer of fluorescent fatty acid analogues to model membranes under physiological ionic strength follows a different mechanism compared to most of the members of this family of intracellular lipid binding proteins. Tryptophan insertion mutants sensitive to ligand binding have allowed us to directly measure the binding affinity, ligand partitioning and transfer to model membranes of natural ligands. Binding of fatty acids shows a cooperative mechanism, while acyl-CoAs binding presents a hyperbolic behavior. Saturated fatty acids seem to have a stronger partition to protein vs. membranes, compared to unsaturated fatty acids. Natural ligand transfer rates are more than 200-fold higher compared to fluorescently-labeled analogues. Interestingly, oleoyl-CoA presents a markedly different transfer behavior compared to the rest of the ligands tested, probably indicating the possibility of specific targeting of ligands to different metabolic fates. PMID:20541621

  4. Quantum correlation transfer through two parallel XXZ spin chains with phase shift control

    International Nuclear Information System (INIS)

    Transmitting quantum states and entanglement through quantum channels is one of the key requirements for the development of quantum computation. Quantum discord has received much attention in quantum computation. We transfer quantum discord through two parallel XXZ spin chains with phase shift. The maximum discord can be enhanced by the phase shift. It will take more time to obtain an enhanced maximum discord in some cases, but for other cases, both the maximum and speed are enhanced by the phase shift. In the thermodynamic limit, the effect of the phase shift disappears and the maximum discord exponentially decays with increasing of the receiving position. Our results on spin chains are generalized to a family of linear Hamiltonians.

  5. Quantum correlation transfer through two parallel XXZ spin chains with phase shift control

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Jian [Department of Chemistry, School of Sciences, Beijing Institute of Technology, Beijing 100081 (China); Shao Bin; Liu Benqiong; Zou Jian [Key Laboratory of Cluster Science of Ministry of Education and Department of Physics, School of Sciences, Beijing Institute of Technology, Beijing 100081 (China); Li Qianshu [Center for Computational Quantum Chemistry, South China Normal University, Guangzhou 510631 (China); Institute of Chemical Physics, Beijing Institute of Technology, Beijing 100081 (China); Wu Lianao [Department of Theoretical Physics and History of Science, University of the Basque Country, Post Office Box 644, 48080 Bilbao (Spain); IKERBASQUE, Basque Foundation for Science, 48011 Bilbao (Spain)

    2011-07-15

    Transmitting quantum states and entanglement through quantum channels is one of the key requirements for the development of quantum computation. Quantum discord has received much attention in quantum computation. We transfer quantum discord through two parallel XXZ spin chains with phase shift. The maximum discord can be enhanced by the phase shift. It will take more time to obtain an enhanced maximum discord in some cases, but for other cases, both the maximum and speed are enhanced by the phase shift. In the thermodynamic limit, the effect of the phase shift disappears and the maximum discord exponentially decays with increasing of the receiving position. Our results on spin chains are generalized to a family of linear Hamiltonians.

  6. Neutral-lipid transfers and cholesteryl ester transfer protein in hemodialyzed patients.

    Science.gov (United States)

    Reade, V; Mezdour, H; Reade, R; Kandoussi, M; Dracon, M; Fruchart, J C; Cachera, C

    1996-01-01

    Abnormalities in cholesteryl ester transfers may play a role in the development of atherosclerosis observed in patients with end-stage renal failure treated by chronic hemodialysis. Net neutral-lipid transfers and cholesteryl ester transfer protein activity and mass were investigated in 20 hemodialyzed patients, arbitrarily divided into two groups based on fasting triglyceride levels, and compared to triglyceride-matched control groups. In the hypertriglyceridemic subjects (plasma triglyceride values > 150 mg/dl), high-density lipoprotein cholesterol was decreased, and the net cholesteryl ester transfer rates were significantly higher than the rates in normolipidemic subjects. The comparison of subjects matched for plasma triglyceride and cholesterol levels showed no significant difference in cholesteryl ester or triglyceride transfer rates between patients and controls. Our results suggest that normal or elevated net neutral-lipid transfers are not related to the renal status of the subjects, but rather to their plasma triglyceride levels. PMID:8886176

  7. Surfactant Protein A Enhances Constitutive Immune Functions of Clathrin Heavy Chain and Clathrin Adaptor Protein 2.

    Science.gov (United States)

    Moulakakis, Christina; Steinhäuser, Christine; Biedziak, Dominika; Freundt, Katja; Reiling, Norbert; Stamme, Cordula

    2016-07-01

    NF-κB transcription factors are key regulators of pulmonary inflammatory disorders and repair. Constitutive lung cell type- and microenvironment-specific NF-κB/inhibitor κBα (IκB-α) regulation, however, is poorly understood. Surfactant protein (SP)-A provides both a critical homeostatic and lung defense control, in part by immune instruction of alveolar macrophages (AMs) via clathrin-mediated endocytosis. The central endocytic proteins, clathrin heavy chain (CHC) and the clathrin adaptor protein (AP) complex AP2, have pivotal alternative roles in cellular homeostasis that are endocytosis independent. Here, we dissect endocytic from alternative functions of CHC, the α-subunit of AP2, and dynamin in basal and SP-A-modified LPS signaling of macrophages. As revealed by pharmacological inhibition and RNA interference in primary AMs and RAW264.7 macrophages, respectively, CHC and α-adaptin, but not dynamin, prevent IκB-α degradation and TNF-α release, independent of their canonical role in membrane trafficking. Kinetics studies employing confocal microscopy, Western analysis, and immunomagnetic sorting revealed that SP-A transiently enhances the basal protein expression of CHC and α-adaptin, depending on early activation of protein kinase CK2 (former casein kinase II) and Akt1 in primary AMs from rats, SP-A(+/+), and SP-A(-/-) mice, as well as in vivo when intratracheally administered to SP-A(+/+) mice. Constitutive immunomodulation by SP-A, but not SP-A-mediated inhibition of LPS-induced NF-κB activity and TNF-α release, requires CHC, α-adaptin, and dynamin. Our data demonstrate that endocytic proteins constitutively restrict NF-κB activity in macrophages and provide evidence that SP-A enhances the immune regulatory capacity of these proteins, revealing a previously unknown pathway of microenvironment-specific NF-κB regulation in the lung. PMID:26771574

  8. One-step copolymerization modified magnetic nanoparticles via surface chain transfer free radical polymerization

    International Nuclear Information System (INIS)

    Copolymer brushes growing onto magnetic nanoparticles were prepared by surface chain transfer free radical polymerization. Block copolymer brushes (P(PEGMA)-co-PNIPAAm) consist of poly(ethylene glycol) monomethacrylate (PEGMA) and N-isopropylacrylamide monomer. X-ray photoelectron spectroscopy (XPS) characterized the chemical composition of copolymer. Thermogravimetric analysis (TGA) suggested that the amount of copolymer on magnetic nanoparticles decreased with increasing azodiisobutyronitrile (AIBN). The saturation magnetization decreased significantly with increasing P(PEGMA)-co-PNIPAAm. The thermosensitive point is about 43 deg. C for magnetic nanoparticles with 33.8% P(PEGMA)-co-PNIPAAm

  9. Non-specific lipid transfer proteins in maize

    OpenAIRE

    Wei, Kaifa; Zhong, Xiaojun

    2014-01-01

    Background In plant, non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that have been reported to be involved in numerous biological processes such as transfer of phospholipids, reproductive development, pathogen defence and abiotic stress response. To date, only a tiny fraction of plant nsLTPs have been functionally identified, and even fewer have been identified in maize [Zea mays (Zm)]. Results In this study, we carried out a genome-wide analysis of nsLTP gene family ...

  10. Protein dynamics modulated electron transfer kinetics in early stage photosynthesis.

    Science.gov (United States)

    Kundu, Prasanta; Dua, Arti

    2013-01-28

    A recent experiment has probed the electron transfer kinetics in the early stage of photosynthesis in Rhodobacter sphaeroides for the reaction center of wild type and different mutants [Science 316, 747 (2007)]. By monitoring the changes in the transient absorption of the donor-acceptor pair at 280 and 930 nm, both of which show non-exponential temporal decay, the experiment has provided a strong evidence that the initial electron transfer kinetics is modulated by the dynamics of protein backbone. In this work, we present a model where the electron transfer kinetics of the donor-acceptor pair is described along the reaction coordinate associated with the distance fluctuations in a protein backbone. The stochastic evolution of the reaction coordinate is described in terms of a non-Markovian generalized Langevin equation with a memory kernel and Gaussian colored noise, both of which are completely described in terms of the microscopics of the protein normal modes. This model provides excellent fits to the transient absorption signals at 280 and 930 nm associated with protein distance fluctuations and protein dynamics modulated electron transfer reaction, respectively. In contrast to previous models, the present work explains the microscopic origins of the non-exponential decay of the transient absorption curve at 280 nm in terms of multiple time scales of relaxation of the protein normal modes. Dynamic disorder in the reaction pathway due to protein conformational fluctuations which occur on time scales slower than or comparable to the electron transfer kinetics explains the microscopic origin of the non-exponential nature of the transient absorption decay at 930 nm. The theoretical estimates for the relative driving force for five different mutants are in close agreement with the experimental estimates obtained using electrochemical measurements. PMID:23387626

  11. Assessment of Protein Side-Chain Conformation Prediction Methods in Different Residue Environments

    Science.gov (United States)

    Peterson, Lenna X.; Kang, Xuejiao; Kihara, Daisuke

    2016-01-01

    Computational prediction of side-chain conformation is an important component of protein structure prediction. Accurate side-chain prediction is crucial for practical applications of protein structure models that need atomic detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side-chain prediction methods in reproducing the side-chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane-spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side-chains at protein interfaces and membrane-spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane-spanning regions as for modeling monomers. PMID:24619909

  12. Improvement of entanglement transfer by weak measurement and quantum measurement reversal in two parallel Heisenberg spin chains

    International Nuclear Information System (INIS)

    The effect of weak measurement (WM) and quantum measurement reversal (QMR) on the entanglement transfer in two parallel Heisenberg spin chains is investigated. We find that the entanglement transfer can be enhanced by the WM and QMR control for different N (N is the length of each spin chain) and m (m denotes the mth spin pair). More interestingly, we also find that, in the thermodynamic limit where the so-called phase-shift control is invalid, the WM and QMR control is instead very effective. So this investigation indicates that the WM and QMR approach has potential applications in quantum information processing based on the spin chain. (paper)

  13. Recombinant production and solution structure of lipid transfer protein from lentil Lens culinaris

    International Nuclear Information System (INIS)

    Highlights: •Lipid transfer protein from lentil seeds (Lc-LTP2) was overexpressed in E. coli. •Antimicrobial activity and spatial structure of the recombinant Lc-LTP2 were examined. •Internal tunnel-like lipid-binding cavity occupies ∼7% of the total Lc-LTP2 volume. •Binding of DMPG lipid induces moderate rearrangements in the Lc-LTP2 structure. •Lc-LTP2/DMPG complex has limited lifetime and dissociates within tens of hours. -- Abstract: Lipid transfer protein, designated as Lc-LTP2, was isolated from seeds of the lentil Lens culinaris. The protein has molecular mass 9282.7 Da, consists of 93 amino acid residues including 8 cysteines forming 4 disulfide bonds. Lc-LTP2 and its stable isotope labeled analogues were overexpressed in Escherichia coli and purified. Antimicrobial activity of the recombinant protein was examined, and its spatial structure was studied by NMR spectroscopy. The polypeptide chain of Lc-LTP2 forms four α-helices (Cys4-Leu18, Pro26-Ala37, Thr42-Ala56, Thr64-Lys73) and a long C-terminal tail without regular secondary structure. Side chains of the hydrophobic residues form a relatively large internal tunnel-like lipid-binding cavity (van der Waals volume comes up to ∼600 Å3). The side-chains of Arg45, Pro79, and Tyr80 are located near an assumed mouth of the cavity. Titration with dimyristoyl phosphatidylglycerol (DMPG) revealed formation of the Lc-LTP2/lipid non-covalent complex accompanied by rearrangements in the protein spatial structure and expansion of the internal cavity. The resultant Lc-LTP2/DMPG complex demonstrates limited lifetime and dissociates within tens of hours

  14. Recombinant production and solution structure of lipid transfer protein from lentil Lens culinaris

    Energy Technology Data Exchange (ETDEWEB)

    Gizatullina, Albina K. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700, Dolgoprudny, Moscow Region (Russian Federation); Finkina, Ekaterina I.; Mineev, Konstantin S.; Melnikova, Daria N.; Bogdanov, Ivan V. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow (Russian Federation); Telezhinskaya, Irina N.; Balandin, Sergey V. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700, Dolgoprudny, Moscow Region (Russian Federation); Shenkarev, Zakhar O. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow (Russian Federation); Arseniev, Alexander S. [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700, Dolgoprudny, Moscow Region (Russian Federation); Ovchinnikova, Tatiana V., E-mail: ovch@ibch.ru [Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str., 16/10, 117997 Moscow (Russian Federation); Moscow Institute of Physics and Technology (State University), Department of Physicochemical Biology and Biotechnology, Institutskii per., 9, 141700, Dolgoprudny, Moscow Region (Russian Federation)

    2013-10-04

    Highlights: •Lipid transfer protein from lentil seeds (Lc-LTP2) was overexpressed in E. coli. •Antimicrobial activity and spatial structure of the recombinant Lc-LTP2 were examined. •Internal tunnel-like lipid-binding cavity occupies ∼7% of the total Lc-LTP2 volume. •Binding of DMPG lipid induces moderate rearrangements in the Lc-LTP2 structure. •Lc-LTP2/DMPG complex has limited lifetime and dissociates within tens of hours. -- Abstract: Lipid transfer protein, designated as Lc-LTP2, was isolated from seeds of the lentil Lens culinaris. The protein has molecular mass 9282.7 Da, consists of 93 amino acid residues including 8 cysteines forming 4 disulfide bonds. Lc-LTP2 and its stable isotope labeled analogues were overexpressed in Escherichia coli and purified. Antimicrobial activity of the recombinant protein was examined, and its spatial structure was studied by NMR spectroscopy. The polypeptide chain of Lc-LTP2 forms four α-helices (Cys4-Leu18, Pro26-Ala37, Thr42-Ala56, Thr64-Lys73) and a long C-terminal tail without regular secondary structure. Side chains of the hydrophobic residues form a relatively large internal tunnel-like lipid-binding cavity (van der Waals volume comes up to ∼600 Å{sup 3}). The side-chains of Arg45, Pro79, and Tyr80 are located near an assumed mouth of the cavity. Titration with dimyristoyl phosphatidylglycerol (DMPG) revealed formation of the Lc-LTP2/lipid non-covalent complex accompanied by rearrangements in the protein spatial structure and expansion of the internal cavity. The resultant Lc-LTP2/DMPG complex demonstrates limited lifetime and dissociates within tens of hours.

  15. Transfer data for radio-cesium in the food chain feed/meat

    International Nuclear Information System (INIS)

    It is necessary to have some knowledge of the behaviour of radioactive material in the food chain to be able to assess the radiation exposure of humans via the ingestion path way. The transfer factor has to be defined precisely because there is a linear dependence of the radiation dose on the transfer factor in the mathematical models for calculating the annual radiation doses. Knowledge of the animal-specific cesium retention, of the biological half-life as well as of the distribution system is required for an accurate calculation of the transfer-data of the particularly important radionuclide cesium 137. After having studied the original literature thoroughly the following transfer factors have been found as an average: cattle 0.03 +- 0.02, calf 0.43 +- 0.06, goat 0.20, sheep 0.11 +- 0.02, swine 0.26 +- 0.01, chicken 3.23 +- 1.41, reindeer 0.31 +- 0.07. (MG)

  16. Transfer of some Chernobyl fallout nuclides in the animal-product food chain

    International Nuclear Information System (INIS)

    One of the most important tasks after the Chernobyl accident was the tracing of radionuclides into the food chain because of the acute interest in view of radiation protection considerations and of the fundamental significance to extend the knowledge on consequences of an accidental release. In this context five experiments have been performed during the last two years to investigate the transfer of radiocesium from grass into milk and meat of dairy cows. The first experiment, which was started immediately after the accident, involved 10 stable-kept cows fed with the freshly contaminated grass. Cs-transfer from grass into milk was found to be considerably lower than expected. After the starting phase of one week the mean transfer factor milk/grass for Cs-134 and Cs-137 leveled at 3.2.10-3 d/kg during the second week. This interesting result gave rise to four additional experiments, to study the Cs-transfer during the following feeding periods applying grass of fallout and root-uptake contamination

  17. Simulation of radioactive cesium transfer in the southern Fukushima coastal biota using a dynamic food chain transfer model

    International Nuclear Information System (INIS)

    The Fukushima Dai-ichi Nuclear Power Plant (1F NPP) accident occurred on 11 March 2011. The accident introduced 137Cs into the coastal waters which was subsequently transferred to the local coastal biota thereby elevating the concentration of this radionuclide in coastal organisms. In this study, the radioactive cesium levels in coastal biota from the southern Fukushima area were simulated using a dynamic biological compartment model. The simulation derived the possible maximum radioactive cesium levels in organisms, indicating that the maximum 137Cs concentrations in invertebrates, benthic fish and predator fish occurred during late April, late May and late July, respectively in the studied area where the source was mainly the direct leakage of 137Cs effluent from the 1F NPP. The delay of a 137Cs increase in fish was explained by the gradual food chain transfer of 137Cs introduced to the ecosystem from the initial contamination of the seawater. The model also provided the degree of radionuclide depuration in organisms, and it demonstrated the latest start of the decontamination phase in benthic fish. The ecological half-lives, derived both from model simulation and observation, were 1–4 months in invertebrates, and 2–9 months in plankton feeding fish and coastal predator fish from the studied area. In contrast, it was not possible to similarly calculate these parameters in benthic fish because of an unidentified additional radionuclide source which was deduced from the biological compartment model. To adequately reconstruct the in-situ depuration of radiocesium in benthic fish in the natural ecosystem, a contamination source associated with the bottom sediments is necessary. -- Highlights: • Cs-137 in the southern Fukushima coastal biota were simulated using a dynamic biological compartment model. • Simulation derived contamination phase of marine biota was completed until late April to July 2011. • The delay of Cs-137 concentration increase in fish was

  18. Entanglement Transfer and Periodic Sudden Death Phenomenon in Two Parallel 1D Spin Chains of Quantum Spin Network

    Institute of Scientific and Technical Information of China (English)

    WANG Zhao-Ming; SHAO Bin; ZOU Jian

    2007-01-01

    We investigate the entanglement transfer in two parallel 1D spin chains of a quantum spin network,and show that the perfect entanglement transfer can be realized at some special times.In addition,the so-called 'sudden death' phenomenon of entanglement is found in the spin network system.

  19. Beyond rotamers: a generative, probabilistic model of side chains in proteins

    DEFF Research Database (Denmark)

    Harder, Tim; Boomsma, Wouter; Paluszewski, Martin; Frellsen, Jes; Johansson, Kristoffer Enøe; Hamelryck, Thomas

    2010-01-01

    collections of side chain conformations derived from experimentally determined protein structures. The discretization can be exploited to efficiently search the conformational space. However, discretizing this naturally continuous space comes at the cost of losing detailed information that is crucial for...

  20. Investigating Protein-protein Interactions in Live Cells Using Bioluminescence Resonance Energy Transfer

    Science.gov (United States)

    Estruch, Sara B.; Fisher, Simon E.

    2014-01-01

    Assays based on Bioluminescence Resonance Energy Transfer (BRET) provide a sensitive and reliable means to monitor protein-protein interactions in live cells. BRET is the non-radiative transfer of energy from a 'donor' luciferase enzyme to an 'acceptor' fluorescent protein. In the most common configuration of this assay, the donor is Renilla reniformis luciferase and the acceptor is Yellow Fluorescent Protein (YFP). Because the efficiency of energy transfer is strongly distance-dependent, observation of the BRET phenomenon requires that the donor and acceptor be in close proximity. To test for an interaction between two proteins of interest in cultured mammalian cells, one protein is expressed as a fusion with luciferase and the second as a fusion with YFP. An interaction between the two proteins of interest may bring the donor and acceptor sufficiently close for energy transfer to occur. Compared to other techniques for investigating protein-protein interactions, the BRET assay is sensitive, requires little hands-on time and few reagents, and is able to detect interactions which are weak, transient, or dependent on the biochemical environment found within a live cell. It is therefore an ideal approach for confirming putative interactions suggested by yeast two-hybrid or mass spectrometry proteomics studies, and in addition it is well-suited for mapping interacting regions, assessing the effect of post-translational modifications on protein-protein interactions, and evaluating the impact of mutations identified in patient DNA. PMID:24893771

  1. Ballistic quantum state transfer in spin chains: General theory for quasi-free models and arbitrary initial states

    Science.gov (United States)

    Banchi, Leonardo

    2013-11-01

    Ballistic quantum information transfer through spin chains is based on the idea of making the spin dynamics ruled by collective excitations with linear dispersion relation. Unlike perfect state transfer schemes, a ballistic transmission requires only a minimal engineering of the interactions; in fact, for most practical purposes, the optimization of the couplings to the ends of the chain is sufficient to obtain an almost perfect transmission. In this work we review different ballistic quantum state transfer protocols based on the dynamics of quasi-free spin chains, and further generalize them both at zero and finite temperature. In particular, besides presenting novel analytical results for XX, XY, and Ising spin models, it is shown how, via a complete control on the first and last two qubits of the chain, destructive thermal effects can be cancelled, leading to a high-quality state transmission irrespective of the temperature.

  2. Carrier transfer in vertically stacked quantum ring-quantum dot chains

    Energy Technology Data Exchange (ETDEWEB)

    Mazur, Yu. I., E-mail: ymazur@uark.edu; Dorogan, V. G.; Benamara, M.; Salamo, G. J. [Arkansas Institute for Nanoscale Materials Science and Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States); Lopes-Oliveira, V.; Lopez-Richard, V.; Teodoro, M. D.; Marques, G. E. [Departamento de Fisica, Universidade Federal de São Carlos, 13565-905 São Carlos, São Paulo (Brazil); Souza, L. D. de [Departamento de Fisica, Universidade Federal de São Carlos, 13565-905 São Carlos, São Paulo (Brazil); Arkansas Institute for Nanoscale Materials Science and Engineering, University of Arkansas, Fayetteville, Arkansas 72701 (United States); Wu, J.; Wang, Z. M. [State Key Laboratory of Electronic Thin Film and Integrated Devices, University of Electronic Science and Technology of China, Chengdu (China); Tarasov, G. G. [Institute of Semiconductor Physics, National Academy of Sciences, pr. Nauki 45, Kiev 03028 (Ukraine); Marega, E. [Instituto de Fisica de São Carlos, Universidade de São Paulo, 13.566-590 São Carlos, São Paulo (Brazil)

    2015-04-21

    The interplay between structural properties and charge transfer in self-assembled quantum ring (QR) chains grown by molecular beam epitaxy on top of an InGaAs/GaAs quantum dot (QD) superlattice template is analyzed and characterized. The QDs and QRs are vertically stacked and laterally coupled as well as aligned within each layer due to the strain field distributions that governs the ordering. The strong interdot coupling influences the carrier transfer both along as well as between chains in the ring layer and dot template structures. A qualitative contrast between different dynamic models has been developed. By combining temperature and excitation intensity effects, the tuning of the photoluminescence gain for either the QR or the QD mode is attained. The information obtained here about relaxation parameters, energy scheme, interlayer and interdot coupling resulting in creation of 1D structures is very important for the usage of such specific QR–QD systems for applied purposes such as lasing, detection, and energy-harvesting technology of future solar panels.

  3. Copolymerization of Styrene and Methacrylates in the presence of Catalytic Chain Transfer Agents (Cacti's)

    International Nuclear Information System (INIS)

    The present paper focuses on the use of a Co (II) complex, [Co(afdo-H)] as a catalytic chain transfer agent (CCTA) for controlling molecular weight in copolymerization of styrene (STY) with butyl methacrylate (BMA) and methylmethacrylate (MMA). The catalyst is structurally similar to [co(dmg-H) (BF)] patented by Du Pont as a CCTA. Average catalytic chain transfer constant, C8 of [co(afdo-H) (BF)] for coplymerization of STY with BMA and MMA determined from Maya plot, was found to be in the range of 10-10.This value is lower than the value reported for the [Co(dmg-H)(BF)). In the case of STY-BMA or STY-MMA copolymerization, a considerable reduction in the viscosity average molecular weights (Mv) was observed in the copolymers. The average molecular weight of poly (MMA-BMA) was reduced by a factor of ten compared to the reduction in poly (STY-MMA) and poly (STY-BMA) for the same concentration of the CCTA. (author)

  4. Preparation of polystyrene brush film by radical chain-transfer polymerization and micromechanical properties

    Science.gov (United States)

    Zhao, Jing; Chen, Miao; An, Yanqing; Liu, Jianxi; Yan, Fengyuan

    2008-12-01

    A radical chain-transfer polymerization technique has been applied to graft-polymerize brushes of polystyrene (PSt) on single-crystal silicon substrates. 3-Mercapto-propyltrimethoxysilane (MPTMS), as a chain-transfer agent for grafting, was immobilized on the silicon surface by a self-assembling process. The structure and morphology of the graft-functionalized silicon surfaces were characterized by the means of contact-angle measurement, ellipsometric thickness measurement, Fourier transformation infrared (FTIR) spectroscopy, and atomic force microscopy (AFM). The nanotribological and micromechanical properties of the as-prepared polymer brush films were investigated by frictional force microscopy (FFM), force-volume analysis and scratch test. The results indicate that the friction properties of the grafted polymer films can be improved significantly by the treatment of toluene, and the chemically bonded polystyrene film exhibits superior scratch resistance behavior compared with the spin-coated polystyrene film. The resultant polystyrene brush film is expected to develop as a potential lubrication coating for microelectromechanical systems (MEMS).

  5. Carrier transfer in vertically stacked quantum ring-quantum dot chains

    International Nuclear Information System (INIS)

    The interplay between structural properties and charge transfer in self-assembled quantum ring (QR) chains grown by molecular beam epitaxy on top of an InGaAs/GaAs quantum dot (QD) superlattice template is analyzed and characterized. The QDs and QRs are vertically stacked and laterally coupled as well as aligned within each layer due to the strain field distributions that governs the ordering. The strong interdot coupling influences the carrier transfer both along as well as between chains in the ring layer and dot template structures. A qualitative contrast between different dynamic models has been developed. By combining temperature and excitation intensity effects, the tuning of the photoluminescence gain for either the QR or the QD mode is attained. The information obtained here about relaxation parameters, energy scheme, interlayer and interdot coupling resulting in creation of 1D structures is very important for the usage of such specific QR–QD systems for applied purposes such as lasing, detection, and energy-harvesting technology of future solar panels

  6. Impairment of electron transfer chain induced by acute carnosine administration in skeletal muscle of young rats.

    Science.gov (United States)

    Macarini, José Roberto; Maravai, Soliany Grassi; Cararo, José Henrique; Dimer, Nádia Webber; Gonçalves, Cinara Ludvig; Kist, Luiza Wilges; Bogo, Mauricio Reis; Schuck, Patrícia Fernanda; Streck, Emilio Luiz; Ferreira, Gustavo Costa

    2014-01-01

    Serum carnosinase deficiency is an inherited disorder that leads to an accumulation of carnosine in the brain tissue, cerebrospinal fluid, skeletal muscle, and other tissues of affected patients. Considering that high levels of carnosine are associated with neurological dysfunction and that the pathophysiological mechanisms involved in serum carnosinase deficiency remain poorly understood, we investigated the in vivo effects of carnosine on bioenergetics parameters, namely, respiratory chain complexes (I-III, II, and II-III), malate dehydrogenase, succinate dehydrogenase, and creatine kinase activities and the expression of mitochondrial-specific transcription factors (NRF-1, PGC-1α , and TFAM) in skeletal muscle of young Wistar rats. We observed a significant decrease of complexes I-III and II activities in animals receiving carnosine acutely, as compared to control group. However, no significant alterations in respiratory chain complexes, citric acid cycle enzymes, and creatine kinase activities were found between rats receiving carnosine chronically and control group animals. As compared to control group, mRNA levels of NRF-1, PGC-1α , and TFAM were unchanged. The present findings indicate that electron transfer through the respiratory chain is impaired in skeletal muscle of rats receiving carnosine acutely. In case these findings are confirmed by further studies and ATP depletion is also observed, impairment of bioenergetics could be considered a putative mechanism responsible for the muscle damage observed in serum carnosinase-deficient patients. PMID:24877122

  7. Impairment of Electron Transfer Chain Induced by Acute Carnosine Administration in Skeletal Muscle of Young Rats

    Directory of Open Access Journals (Sweden)

    José Roberto Macarini

    2014-01-01

    Full Text Available Serum carnosinase deficiency is an inherited disorder that leads to an accumulation of carnosine in the brain tissue, cerebrospinal fluid, skeletal muscle, and other tissues of affected patients. Considering that high levels of carnosine are associated with neurological dysfunction and that the pathophysiological mechanisms involved in serum carnosinase deficiency remain poorly understood, we investigated the in vivo effects of carnosine on bioenergetics parameters, namely, respiratory chain complexes (I–III, II, and II-III, malate dehydrogenase, succinate dehydrogenase, and creatine kinase activities and the expression of mitochondrial-specific transcription factors (NRF-1, PGC-1α, and TFAM in skeletal muscle of young Wistar rats. We observed a significant decrease of complexes I–III and II activities in animals receiving carnosine acutely, as compared to control group. However, no significant alterations in respiratory chain complexes, citric acid cycle enzymes, and creatine kinase activities were found between rats receiving carnosine chronically and control group animals. As compared to control group, mRNA levels of NRF-1, PGC-1α, and TFAM were unchanged. The present findings indicate that electron transfer through the respiratory chain is impaired in skeletal muscle of rats receiving carnosine acutely. In case these findings are confirmed by further studies and ATP depletion is also observed, impairment of bioenergetics could be considered a putative mechanism responsible for the muscle damage observed in serum carnosinase-deficient patients.

  8. Interaction of the anaphase-promoting complex/cyclosome and proteasome protein complexes with multiubiquitin chain-binding proteins

    DEFF Research Database (Denmark)

    Seeger, Michael; Hartmann-Petersen, Rasmus; Wilkinson, Caroline R M; Wallace, Mairi; Samejima, Itaru; Taylor, Martin S; Gordon, Colin

    2003-01-01

    Fission yeast Rhp23 and Pus1 represent two families of multiubiquitin chain-binding proteins that associate with the proteasome. We show that both proteins bind to different regions of the proteasome subunit Mts4. The binding site for Pus1 was mapped to a cluster of repetitive sequences also foun...

  9. Regulation of secretory transport by protein kinase D–mediated phosphorylation of the ceramide transfer protein

    OpenAIRE

    Fugmann, Tim; Hausser, Angelika; Schöffler, Patrik; Schmid, Simone; Pfizenmaier, Klaus; Olayioye, Monilola A.

    2007-01-01

    Protein kinase D (PKD) has been identified as a crucial regulator of secretory transport at the trans-Golgi network (TGN). Recruitment and activation of PKD at the TGN is mediated by the lipid diacylglycerol, a pool of which is generated by sphingomyelin synthase from ceramide and phosphatidylcholine. The nonvesicular transfer of ceramide from the endoplasmic reticulum to the Golgi complex is mediated by the lipid transfer protein CERT (ceramide transport). In this study, we identify CERT as ...

  10. The Role of Dietary Protein Intake and Resistance Training on Myosin Heavy Chain Expression

    Directory of Open Access Journals (Sweden)

    Willoughby Darryn S

    2004-12-01

    Full Text Available Abstract During resistance training the muscle undergoes many changes. Possibly the most profound and significant changes are those that occur in the muscles contractile proteins. Increases in these contractile proteins are one of the primary factors contributing to myofibrillar hypertrophy. The most abundant muscle protein is myosin, which comprises 25% of the total muscle protein. Due to the large amount of skeletal muscle that is composed of myosin, changes in this fiber may have profound effects on skeletal muscle size and strength. The myosin molecule is made up of 6 subunits, 2 very large heavy chains, and 4 smaller light chains. The myosin heavy chain (MHC accounts for 25–30% of all muscle proteins making its size an important factor in skeletal muscle growth. In conjunction with resistance training, dietary protein intake must be adequate to illicit positive adaptations. Although many studies have evaluated the role of dietary protein intake on skeletal muscle changes, few have evaluated the MHC specifically. Research has clearly defined the need for dietary protein and resistance training to facilitate positive changes in skeletal muscle. The purpose of this review was to evaluate the current literature on the effects of dietary protein and resistance training on the expression of the myosin heavy chain.

  11. Gene ontology based transfer learning for protein subcellular localization

    Directory of Open Access Journals (Sweden)

    Zhou Shuigeng

    2011-02-01

    Full Text Available Abstract Background Prediction of protein subcellular localization generally involves many complex factors, and using only one or two aspects of data information may not tell the true story. For this reason, some recent predictive models are deliberately designed to integrate multiple heterogeneous data sources for exploiting multi-aspect protein feature information. Gene ontology, hereinafter referred to as GO, uses a controlled vocabulary to depict biological molecules or gene products in terms of biological process, molecular function and cellular component. With the rapid expansion of annotated protein sequences, gene ontology has become a general protein feature that can be used to construct predictive models in computational biology. Existing models generally either concatenated the GO terms into a flat binary vector or applied majority-vote based ensemble learning for protein subcellular localization, both of which can not estimate the individual discriminative abilities of the three aspects of gene ontology. Results In this paper, we propose a Gene Ontology Based Transfer Learning Model (GO-TLM for large-scale protein subcellular localization. The model transfers the signature-based homologous GO terms to the target proteins, and further constructs a reliable learning system to reduce the adverse affect of the potential false GO terms that are resulted from evolutionary divergence. We derive three GO kernels from the three aspects of gene ontology to measure the GO similarity of two proteins, and derive two other spectrum kernels to measure the similarity of two protein sequences. We use simple non-parametric cross validation to explicitly weigh the discriminative abilities of the five kernels, such that the time & space computational complexities are greatly reduced when compared to the complicated semi-definite programming and semi-indefinite linear programming. The five kernels are then linearly merged into one single kernel for

  12. Concerted actions of cholesteryl ester transfer protein and phospholipid transfer protein in type 2 diabetes : effects of apolipoproteins

    NARCIS (Netherlands)

    Dallinga-Thie, Geesje M.; Dullaart, Robin P. F.; van Tol, Arie

    2007-01-01

    Purpose of review Type 2 diabetes frequently coincides with dyslipidemia, characterized by elevated plasma triglycerides, low high-density lipoprotein cholesterol levels and the presence of small dense low-density lipoprotein particles. Plasma lipid transfer proteins play an essential role in lipopr

  13. Simulation of radioactive cesium transfer in the southern Fukushima coastal biota using a dynamic food chain transfer model.

    Science.gov (United States)

    Tateda, Yutaka; Tsumune, Daisuke; Tsubono, Takaki

    2013-10-01

    The Fukushima Dai-ichi Nuclear Power Plant (1F NPP) accident occurred on 11 March 2011. The accident introduced (137)Cs into the coastal waters which was subsequently transferred to the local coastal biota thereby elevating the concentration of this radionuclide in coastal organisms. In this study, the radioactive cesium levels in coastal biota from the southern Fukushima area were simulated using a dynamic biological compartment model. The simulation derived the possible maximum radioactive cesium levels in organisms, indicating that the maximum (137)Cs concentrations in invertebrates, benthic fish and predator fish occurred during late April, late May and late July, respectively in the studied area where the source was mainly the direct leakage of (137)Cs effluent from the 1F NPP. The delay of a (137)Cs increase in fish was explained by the gradual food chain transfer of (137)Cs introduced to the ecosystem from the initial contamination of the seawater. The model also provided the degree of radionuclide depuration in organisms, and it demonstrated the latest start of the decontamination phase in benthic fish. The ecological half-lives, derived both from model simulation and observation, were 1-4 months in invertebrates, and 2-9 months in plankton feeding fish and coastal predator fish from the studied area. In contrast, it was not possible to similarly calculate these parameters in benthic fish because of an unidentified additional radionuclide source which was deduced from the biological compartment model. To adequately reconstruct the in-situ depuration of radiocesium in benthic fish in the natural ecosystem, a contamination source associated with the bottom sediments is necessary. PMID:23639689

  14. Plant lipid transfer proteins : Evolution, expression and function

    OpenAIRE

    Edstam, Monika

    2013-01-01

    The plant non-specific lipid transfer proteins (nsLTPs) are known for the ability to transfer different lipids in vitro, but their in vivo functions have not yet been elucidated. They seem to play a role in the defense against biotic and abiotic stresses; the gene expression of nsLTPs is often upregulated when exposed to stresses. Further, two different nsLTPs have been shown to affect the lipid composition of the plant cuticle, a structure acting as a protective barrier. However, more eviden...

  15. Proteins containing the UBA domain are able to bind to multi-ubiquitin chains

    DEFF Research Database (Denmark)

    Wilkinson, C R; Seeger, M; Hartmann-Petersen, R; Stone, M; Wallace, M; Semple, C; Gordon, C

    2001-01-01

    The UBA domain is a motif found in a variety of proteins, some of which are associated with the ubiquitin-proteasome system. We describe the isolation of a fission-yeast gene, mud1+, which encodes a UBA domain containing protein that is able to bind multi-ubiquitin chains. We show that the UBA do...

  16. Improved Side Chain Dynamics in MARTINI Simulations of Protein-Lipid Interfaces.

    Science.gov (United States)

    Herzog, Florian A; Braun, Lukas; Schoen, Ingmar; Vogel, Viola

    2016-05-10

    Specific interactions of protein side chains and lipid membranes regulate the localization, orientation, and activity of many peripheral proteins. Here, we introduce a modification of the coarse-grained MARTINI protein model, called 'side chain fix' (scFix), that was necessary and sufficient to correctly sample the side chain dynamics of β-strands in several globular proteins. When compared to μs long atomistic simulations or previous experimental findings, scFix MARTINI simulations reproduced all key interactions between the well-studied PLC-δ1 pleckstrin homology domain and a phosphatidylinositol-4,5-bisphosphate (PIP2) containing lipid membrane. Moreover, the extended runtime and higher sampling speed enabled the systematic mapping of the protein's rolling motion at the membrane, the identification of short-lived and stable binding orientations, as well as the verification and prediction of already known and of novel transient PIP2 binding sites. scFix also showed promise to maintain proper side chain orientation in other secondary structural motifs of the α-spectrin SH3 domain, the B1 domain of protein G, and the villin headpiece. This suggests that scFix improves on the predictive power of MARTINI simulations regarding protein-lipid and protein-ligand interactions. PMID:27042944

  17. Conformational Dependence of a Protein Kinase Phosphate Transfer Reaction

    CERN Document Server

    Henkelman, Graeme; Tung, Chang-Shung; Fenimore,, P W; McMahon, Benjamin H

    2004-01-01

    Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase (PKA) are calculated by plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In the TC, we calculate that the reactants and products are nearly isoenergetic with a 0.2 eV barrier; while phosphate transfer is unfavorable by over 1.2 eV in the RC, with an even higher barrier. With the protein in the TC, the motions involved in reaction are small, with only P$_\\gamma$ and the catalytic proton moving more than 0.5 \\AA. Examination of the structures reveals that in the RC the active site cleft is not completely closed and there is insufficient space for the phosphorylated serine residue in the product state. Together, these observations imply that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by...

  18. Effects of intersegmental transfers on target location by proteins

    CERN Document Server

    Sheinman, Michael

    2008-01-01

    We study a model for a protein searching for a target, using facilitated diffusion, on a DNA molecule confined in a finite volume. The model includes three distinct pathways for facilitated diffusion: (a) sliding - in which the protein diffuses along the contour of the DNA (b) jumping - where the protein travels between two sites along the DNA by three-dimensional diffusion, and finally (c) intersegmental transfer - which allows the protein to move from one site to another by transiently binding both at the same time. The typical search time is calculated using scaling arguments which are verified numerically. Our results suggest that the inclusion of intersegmental transfer (i) decreases the search time considerably (ii) makes the search time much more robust to variations in the parameters of the model and (iii) that the optimal search time occurs in a regime very different than that found for models which ignore intersegmental transfers. The behavior we find is rich and shows surprising dependencies, for e...

  19. Absolute rate constants for the reaction of hypochlorous acid with protein side chains and peptide bonds

    DEFF Research Database (Denmark)

    Pattison, D I; Davies, Michael Jonathan

    2001-01-01

    , absolute second-order rate constants for the reactions of HOCl with protein side chains, model compounds, and backbone amide (peptide) bonds have been determined at physiological pH values. The reactivity of HOCl with potential reactive sites in proteins is summarized by the series: Met (3.8 x 10(7) M(-1....... Proteins are major targets for this oxidant, and such reaction results in side-chain modification, backbone fragmentation, and cross-linking. Despite a wealth of qualitative data for such reactions, little absolute kinetic data is available to rationalize the in vitro and in vivo data. In this study...

  20. Evaluation of the clenbuterol imprinted monolithic column prepared by reversible addition-fragmentation chain transfer polymerization

    Institute of Scientific and Technical Information of China (English)

    Mamat Turson; Xiao Lei Zhuang; Hui Na Liu; Ping Jiang; Xiang Chao Dong

    2009-01-01

    To make more homogenous organic monolithic structure,reversible addition-fragmentation chain transfer(RAFT)process was employed in the synthesis of the clenbuterol imprinted polymer.In the synthesis,the influence of synthetic conditions on the polymer structure and separation efficiency was studied.The result demonstrated that the imprinted columns prepared with RAFT process have higher column efficiency and selectivity than the columns prepared with conventional polymerization in the present study,which may result from the higher surface area,smaller pore size and the narrower globule size distribution in their structures.The result indicated that RAFT polymerization provided better conditions for the clenbuterol imprinted monolithic polymer preparation.

  1. Influence of dispersants on trophic transfer of petroleum hydrocarbons in a marine food chain

    Energy Technology Data Exchange (ETDEWEB)

    Wolfe, M.; Tjeerdema, R. [Univ. of California, Santa Cruz, CA (United States). Dept. of Chemistry and Biochemistry; Sowby, M. [California Dept. of Fish and Game, Sacramento, CA (United States)

    1995-12-31

    When crude oil is accidentally released into the ocean, it threatens many levels of marine life. Intervention, in the form of chemical dispersing agents, alters the normal behavior of petroleum hydrocarbons (PH) by increasing their functional water solubility and the extent of their exposure to sub-surface organisms. Dispersing agents may modify bioavailability as a result of altered interactions between dispersed PH droplets and organismal cell membranes.The objective of this research was to determine the impact of dispersing agents on PH bioavailability and trophic transfer in primary levels of a marine food chain. Uptake, bioaccumulation, depuration, and metabolic transformation of a model PH, {sup 14}C-naphthalene, were measured and compared for Prudhoe Bay Crude Oil (PBCO) dispersed with Corexit 9527 and undispersed preparations of the water-accommodated fractions (WAF) of PBCO at two salinities and temperatures. The model food chain consisted of Isochrysis galbana and Brachionus plicatilis. Direct aqueous exposure was compared with combined aqueous and dietary exposure. Fractionation and identification of metabolites was done by HPLC co-chromatography with analytical standards, and quantitation was done by liquid scintillation counting. GC-FID characterization of WAF and dispersed oil (DO) preparations shows higher concentrations of petroleum hydrocarbons and a greater number of individual constituents in the dispersed oil preparations.

  2. Transfer of selenium from prey to predators in a simulated terrestrial food chain

    International Nuclear Information System (INIS)

    Little is known about the accumulation and effects of selenium in reptiles. We developed a simplified laboratory food chain where we fed commercial feed laden with seleno-D,L-methionine (30 μg/g dry mass) to crickets (Acheta domestica) for 5-7 d. Se-enriched crickets (∼15 μg/g Se [dry mass]) were fed to juvenile male and female lizards (Sceloporus occidentalis) for 98 d while conspecifics were fed uncontaminated crickets. Lizards fed contaminated prey accumulated Se concentrations ranging from 9.3 (in female carcass) to 14.1 (in female gonad) μg/g compared to <1.5 μg/g in tissues of controls. Female gonad concentrations approached the highest of thresholds for reproductive toxicity in oviparous vertebrates. However, we observed no consistent effect of dietary treatment on sublethal parameters or survival. Our simplified food chain proved to be an ecologically relevant method of exposing lizards to Se, and forms the foundation for future studies on maternal transfer and teratogenicity of Se. - Partitioning of selenium among tissues differs between male and female lizards

  3. Influence of dispersants on trophic transfer of petroleum hydrocarbons in a marine food chain

    International Nuclear Information System (INIS)

    When crude oil is accidentally released into the ocean, it threatens many levels of marine life. Intervention, in the form of chemical dispersing agents, alters the normal behavior of petroleum hydrocarbons (PH) by increasing their functional water solubility and the extent of their exposure to sub-surface organisms. Dispersing agents may modify bioavailability as a result of altered interactions between dispersed PH droplets and organismal cell membranes.The objective of this research was to determine the impact of dispersing agents on PH bioavailability and trophic transfer in primary levels of a marine food chain. Uptake, bioaccumulation, depuration, and metabolic transformation of a model PH, 14C-naphthalene, were measured and compared for Prudhoe Bay Crude Oil (PBCO) dispersed with Corexit 9527 and undispersed preparations of the water-accommodated fractions (WAF) of PBCO at two salinities and temperatures. The model food chain consisted of Isochrysis galbana and Brachionus plicatilis. Direct aqueous exposure was compared with combined aqueous and dietary exposure. Fractionation and identification of metabolites was done by HPLC co-chromatography with analytical standards, and quantitation was done by liquid scintillation counting. GC-FID characterization of WAF and dispersed oil (DO) preparations shows higher concentrations of petroleum hydrocarbons and a greater number of individual constituents in the dispersed oil preparations

  4. Transfer of selenium from prey to predators in a simulated terrestrial food chain

    Energy Technology Data Exchange (ETDEWEB)

    Hopkins, William A. [Wildlife Ecotoxicology and Physiological Ecology Program, Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29801 (United States)]. E-mail: hopkins@srel.edu; Staub, Brandon P. [Wildlife Ecotoxicology and Physiological Ecology Program, Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29801 (United States); Baionno, Jennifer A. [Wildlife Ecotoxicology and Physiological Ecology Program, Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29801 (United States); Jackson, Brian P. [Wildlife Ecotoxicology and Physiological Ecology Program, Savannah River Ecology Laboratory, University of Georgia, Drawer E, Aiken, SC 29801 (United States); Talent, Larry G. [Department of Zoology, Oklahoma State University, Stillwater, OK 74078 (United States)

    2005-04-01

    Little is known about the accumulation and effects of selenium in reptiles. We developed a simplified laboratory food chain where we fed commercial feed laden with seleno-D,L-methionine (30 {mu}g/g dry mass) to crickets (Acheta domestica) for 5-7 d. Se-enriched crickets ({approx}15 {mu}g/g Se [dry mass]) were fed to juvenile male and female lizards (Sceloporus occidentalis) for 98 d while conspecifics were fed uncontaminated crickets. Lizards fed contaminated prey accumulated Se concentrations ranging from 9.3 (in female carcass) to 14.1 (in female gonad) {mu}g/g compared to <1.5 {mu}g/g in tissues of controls. Female gonad concentrations approached the highest of thresholds for reproductive toxicity in oviparous vertebrates. However, we observed no consistent effect of dietary treatment on sublethal parameters or survival. Our simplified food chain proved to be an ecologically relevant method of exposing lizards to Se, and forms the foundation for future studies on maternal transfer and teratogenicity of Se. - Partitioning of selenium among tissues differs between male and female lizards.

  5. Simulation of a Heisenberg XY- chain and realization of a perfect state transfer algorithm using liquid nuclear magnetic resonance

    CERN Document Server

    Zhang, J; Zhang, W; Deng, Z; Liu, W; Lü, Z; Zhang, Jingfu; Long, Gui Lu; Zhang, Wei; Deng, Zhiwei; Liu, Wenzhang; Lu, Zhiheng

    2005-01-01

    The three- spin chain with Heisenberg XY- interaction is simulated in a three- qubit nuclear magnetic resonance (NMR) quantum computer. The evolution caused by the XY- interaction is decomposed into a series of single- spin rotations and the $J$- coupling evolutions between the neighboring spins. The perfect state transfer (PST) algorithm proposed by M. Christandl et al [Phys. Rev. Lett, 92, 187902(2004)] is realized in the XY- chain.

  6. Biotransformation and Incorporation into Proteins along a Simulated Terrestrial Food Chain

    Energy Technology Data Exchange (ETDEWEB)

    Unrine, J.M., B.P. Jackson and W.A. Hopkins

    2007-01-01

    Selenium is an essential trace element in vertebrates, but there is a narrow concentration range between dietary requirement and toxicity threshold. Although a great deal is known about the biochemistry of Se from a nutritional perspective, considerably less attention has been focused on the specific biochemistry of Se as an environmental toxicant. Recent advances in hyphenated analytical techniques have provided the capability of quantifying specific chemical forms of Se in biological tissues as well as the distribution of Se among macromolecules. We applied liquid chromatography coupled to inductively coupled plasma mass spectrometry to investigate biotransformations of selenomethionine along a simulated terrestrial food chain consisting of selenomethionine exposed crickets (Acheta domesticus) fed to western fence lizards (Sceloporus occidentalis). Evidence was obtained for selenomethionine biotransformation as well as for sex-specific differences in the metabolism of Se compounds and their subsequent incorporation into proteins in the lizard. The results demonstrate the complexities involved in trophic transfer of Se due to the potential for extensive biotransformation and the species- and even sex-specific nature of these biotransformations.

  7. Bioaccumulative and conchological assessment of heavy metal transfer in a soil-plant-snail food chain

    Directory of Open Access Journals (Sweden)

    Nica Dragos V

    2012-06-01

    Full Text Available Abstract Background Copper (Cu, zinc (Zn, cadmium (Cd, and lead (Pb can pose serious threats to environmental health because they tend to bioaccumulate in terrestrial ecosystems. We investigated under field conditions the transfer of these heavy metals in a soil-plant-snail food chain in Banat area, Romania. The main goal of this paper was to assess the Roman snail (Helix pomatia usefulness in environmental monitoring as bioindicator of heavy metal accumulation. Eight sampling sites, selected by different history of heavy metal (HM exposure, were chosen to be sampled for soil, nettle leaves, and newly matured snails. This study also aimed to identify the putative effects of HM accumulation in the environment on phenotypic variability in selected shell features, which included shell height (SH, relative shell height (RSH, and whorl number (WN. Results Significantly higher amounts of HMs were accumulated in snail hepatopancreas and not in foot. Cu, Zn, and Cd have biomagnified in the snail body, particularly in the hepatopancreas. In contrast, Pb decreased when going up into the food chain. Zn, Cd, and Pb correlated highly with each other at all levels of the investigated food chain. Zn and Pb exhibited an effective soil–plant transfer, whereas in the snail body only foot Cu concentration was correlated with that in soil. There were significant differences among sampling sites for WN, SH, and RSH when compared with reference snails. WN was strongly correlated with Cd and Pb concentrations in nettle leaves but not with Cu and Zn. SH was independent of HM concentrations in soil, snail hepatopancreas, and foot. However, SH correlated negatively with nettle leaves concentrations for each HM except Cu. In contrast, RSH correlated significantly only with Pb concentration in hepatopancreas. Conclusions The snail hepatopancreas accumulates high amounts of HMs, and therefore, this organ can function as a reliable biomarker for tracking HM bioavailability

  8. PRIMO: A Transferable Coarse-grained Force Field for Proteins

    OpenAIRE

    Kar, Parimal; Gopal, Srinivasa Murthy; Cheng, Yi-Ming; Predeus, Alexander; Feig, Michael

    2013-01-01

    We describe here the PRIMO (PRotein Intermediate Model) force field, a physics-based fully transferable additive coarse-grained potential energy function that is compatible with an all-atom force field for multi-scale simulations. The energy function consists of standard molecular dynamics energy terms plus a hydrogen-bonding potential term and is mainly parameterized based on the CHARMM22/CMAP force field in a bottom-up fashion. The solvent is treated implicitly via the generalized Born mode...

  9. Electrochemical studies of a reconstituted photosynthetic electron-transfer chain or towards a biomimetic photoproduction of hydrogen

    International Nuclear Information System (INIS)

    The aim of this work is to find an efficient process to convert solar energy into hydrogen. The electrons transfers in reconstituted photosynthetic chains have been particularly studied with the aims 1)in one hand, to better understand the interactions of the different molecules of the photosynthetic chain in order to optimize the changes of the entire organisms for hydrogen production 2)in another hand, to insert the hydrogenases in a photosynthetic chain and then to photo reduce them in order to obtain kinetic data to better understand how it works. (O.M.)

  10. Kinetic modelling of radionuclide transfer in northern European marine food chains

    International Nuclear Information System (INIS)

    A biokinetic modelling approach with allometric considerations has been used to estimate the trophic transfer of 137Cs and 239Pu in a marine foodchain consisting of 4 trophic levels including phytoplankton, zooplankton, polar cod, and with harp seal as a top predator. The time-dependent transfer of radionuclides within the foodchain is defined by uptake rates, assimilation efficiencies and egestion/excretion rates and can be described by a system of linear 1st order differential equations. The Matlab based software ECOLEGO was used to solve the equation system numerically, and the activity concentration for animals in each trophic level was found as a function of time. For the simulation concerning 137Cs, the preliminary results suggest that equilibrium is not attained for higher trophic levels, i.e. polar cod and harp seal, before time > 2000 days. Biomagnification appears to occur for the lower trophic levels but is not occurring at the highest trophic level, i.e. seal. For 239Pu, transfer to successively higher trophic levels is low - there is a fall of several orders of magnitude between primary producers, represented by phytoplankton, and polar cod representing trophic level 3-4. However, the model predicts that this decreasing trend in activity concentrations along the food-chain is reversed for the highest trophic level, represented by seal. The simulated results for seal display equilibrium activity concentrations about 2 orders of magnitude higher than those observed for polar cod (one of its prey species). However equilibrium (165 years) is not reached during the life span of a seal. The equilibrium 137Cs CFs are approximately 50, 130 and 70 ml/g for zooplankton, polar cod and seal respectively. The predicted equilibrium 239Pu CFs for zooplankton and polar cod are 2.5x103 and 25 ml/g. For seal, following a 1 year equilibration period, a CF of approximately 75 ml/g is predicted. (author)

  11. Recent developments in atom transfer radical polymerization initiators for development of polymer-protein bioconjugates

    Directory of Open Access Journals (Sweden)

    AKHILESH KUMAR SHAKYA

    2013-01-01

    Full Text Available One of the major challenges in modern synthetic polymer chemistry is to synthesize end defined polymers of different end functionality with predetermined uniform molecular weight. End functionalized polymers/copolymers basically in block and grafting form are having several potential applications in biomedical areas in the form of surface modifications, coatings, adhesives, and in order to increase the biocompatibility of polymeric blends. Among the existing controlled radical polymerization (CRP methods for synthesis of these functional polymers, the atom transfer radical polymerization (ATRP is one of the powerful techniques. The functional groups in these polymers can be easily introduced at the chain ends through functionalized ATRP initiators. A number of ATRP initiators have been developed in polymer science to develop defined polymer-protein bioconjugates. This critical review basically focuses on different types of ATRP initiators and their mechanisms used in the synthesis of polymer-protein bioconjugates.

  12. Controlling time scales for electron transfer through proteins

    Directory of Open Access Journals (Sweden)

    Scot Wherland

    2015-12-01

    Full Text Available Electron transfer processes within proteins constitute key elements in biological energy conversion processes as well as in a wide variety of biochemical transformations. Pursuit of the parameters that control the rates of these processes is driven by the great interest in the latter reactions. Here, we review a considerable body of results emerging from investigation of intramolecular electron transfer (ET reactions in two types of proteins, all done by the use of the pulse-radiolysis method: first are described results of extensive studies of a model system, the bacterial electron mediating protein azurin, where an internal ET between the disulfide radical ion and the Cu(II is induced. Impact of specific structural changes introduced into azurin on the reaction rates and the parameters controlling it are discussed. Then, the presentation is extended to results of investigations of intra-protein ET reactions that are part of catalytic cycles of multi-copper containing enzymes. Again, the rates and the parameters controlling them are presented and discussed in the context of their efficacy and possible constraints set on their evolution.

  13. An Exact Algorithm for Side-Chain Placement in Protein Design

    CERN Document Server

    Canzar, Stefan; Klau, Gunnar W

    2011-01-01

    Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combinatorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting overall energy is minimum. The choice of the side-chain then also determines the amino acid for this position. Many algorithms for this NP-hard problem have been proposed in the context of homology modeling, which, however, reach their limits when faced with large protein design instances. In this paper, we propose a new exact method for the side-chain placement problem that works well even for large instance sizes as they appear in protein design. Our main contribution is a dedicated branch-and-bound algorithm that combines tight upper and lower bounds resulting from a novel Lagrangian relaxation approach for side-chain placement. Our experimental results show...

  14. Regulation of secretory transport by protein kinase D–mediated phosphorylation of the ceramide transfer protein

    Science.gov (United States)

    Fugmann, Tim; Hausser, Angelika; Schöffler, Patrik; Schmid, Simone; Pfizenmaier, Klaus; Olayioye, Monilola A.

    2007-01-01

    Protein kinase D (PKD) has been identified as a crucial regulator of secretory transport at the trans-Golgi network (TGN). Recruitment and activation of PKD at the TGN is mediated by the lipid diacylglycerol, a pool of which is generated by sphingomyelin synthase from ceramide and phosphatidylcholine. The nonvesicular transfer of ceramide from the endoplasmic reticulum to the Golgi complex is mediated by the lipid transfer protein CERT (ceramide transport). In this study, we identify CERT as a novel in vivo PKD substrate. Phosphorylation on serine 132 by PKD decreases the affinity of CERT toward its lipid target phosphatidylinositol 4-phosphate at Golgi membranes and reduces ceramide transfer activity, identifying PKD as a regulator of lipid homeostasis. We also show that CERT, in turn, is critical for PKD activation and PKD-dependent protein cargo transport to the plasma membrane. Thus, the interdependence of PKD and CERT is key to the maintenance of Golgi membrane integrity and secretory transport. PMID:17591919

  15. Regulation of secretory transport by protein kinase D-mediated phosphorylation of the ceramide transfer protein.

    Science.gov (United States)

    Fugmann, Tim; Hausser, Angelika; Schöffler, Patrik; Schmid, Simone; Pfizenmaier, Klaus; Olayioye, Monilola A

    2007-07-01

    Protein kinase D (PKD) has been identified as a crucial regulator of secretory transport at the trans-Golgi network (TGN). Recruitment and activation of PKD at the TGN is mediated by the lipid diacylglycerol, a pool of which is generated by sphingomyelin synthase from ceramide and phosphatidylcholine. The nonvesicular transfer of ceramide from the endoplasmic reticulum to the Golgi complex is mediated by the lipid transfer protein CERT (ceramide transport). In this study, we identify CERT as a novel in vivo PKD substrate. Phosphorylation on serine 132 by PKD decreases the affinity of CERT toward its lipid target phosphatidylinositol 4-phosphate at Golgi membranes and reduces ceramide transfer activity, identifying PKD as a regulator of lipid homeostasis. We also show that CERT, in turn, is critical for PKD activation and PKD-dependent protein cargo transport to the plasma membrane. Thus, the interdependence of PKD and CERT is key to the maintenance of Golgi membrane integrity and secretory transport. PMID:17591919

  16. Porcine circovirus type 2 ORF4 protein binds heavy chain ferritin

    Indian Academy of Sciences (India)

    Qizhuang Lv; Kangkang Guo; Tao Wang; Chengcheng Zhang; Yanming Zhang

    2015-09-01

    Porcine circovirus type 2 (PCV2) is the primary infectious agent of PCV-associated disease (PCVAD) in swine. ORF4 protein is a newly identified viral protein of PCV2 and is involved in virus-induced apoptosis. However, the molecular mechanisms of ORF4 protein regulation of apoptosis remain unclear, especially given there is no information regarding any cellular partners of the ORF4 protein. Here, we have utilized the yeast two-hybrid assay and identified four host proteins (FHC, SNRPN, COX8A and Lamin C) interacting with the ORF4 protein. Specially, FHC was chosen for further characterization due to its important role in apoptosis. GST pull-down, subcellular co-location and co-immunoprecipitation assays confirmed that the PCV2 ORF4 protein indeed interacted with the heavy-chain ferritin, which is an interesting clue that will allow us to determine the role of the ORF4 protein in apoptosis.

  17. Optimisation of recombinant protein production in Pichia pastoris:single-chain antibody fragment model protein

    OpenAIRE

    Khatri, N. K. (Narendar Kumar)

    2011-01-01

    Abstract Potential lethal diarrhoea caused by enterotoxigenic Escherichia coli strains is one of the most common diseases in young pigs. It can be cured by single-chain antibody fragments (scFv), which can be produced in recombinant microorganisms. Pichia pastoris, a methylotrophic yeast, is generally considered an interesting production system candidate, as it can secrete properly folded proteins. These proteins accumulate in high concentrations during fermentation, reducing the cost for...

  18. Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

    Directory of Open Access Journals (Sweden)

    Noah Ollikainen

    Full Text Available Interactions between small molecules and proteins play critical roles in regulating and facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, in addition to inaccuracies in energy functions, is the exquisite sensitivity of protein-ligand interactions to subtle conformational changes, coupled with the computational problem of sampling the large conformational search space of degrees of freedom of ligands, amino acid side chains, and the protein backbone. Here, we describe two benchmarks for evaluating the accuracy of computational approaches for re-engineering protein-ligand interactions: (i prediction of enzyme specificity altering mutations and (ii prediction of sequence tolerance in ligand binding sites. After finding that current state-of-the-art "fixed backbone" design methods perform poorly on these tests, we develop a new "coupled moves" design method in the program Rosetta that couples changes to protein sequence with alterations in both protein side-chain and protein backbone conformations, and allows for changes in ligand rigid-body and torsion degrees of freedom. We show significantly increased accuracy in both predicting ligand specificity altering mutations and binding site sequences. These methodological improvements should be useful for many applications of protein-ligand design. The approach also provides insights into the role of subtle conformational adjustments that enable functional changes not only in engineering applications but also in natural protein evolution.

  19. Trophic transfer of naturally produced brominated aromatic compounds in a Baltic Sea food chain.

    Science.gov (United States)

    Dahlgren, Elin; Lindqvist, Dennis; Dahlgren, Henrik; Asplund, Lillemor; Lehtilä, Kari

    2016-02-01

    Brominated aromatic compounds (BACs) are widely distributed in the marine environment. Some of these compounds are highly toxic, such as certain hydroxylated polybrominated diphenyl ethers (OH-PBDEs). In addition to anthropogenic emissions through use of BACs as e.g. flame retardants, BACs are natural products formed by marine organisms such as algae, sponges, and cyanobacteria. Little is known of the transfer of BACs from natural producers and further up in the trophic food chain. In this study it was observed that total sum of methoxylated polybrominated diphenyl ethers (MeO-PBDEs) and OH-PBDEs increased in concentration from the filamentous red alga Ceramium tenuicorne, via Gammarus sp. and three-spined stickleback (Gasterosteus aculeatus) to perch (Perca fluviatilis). The MeO-PBDEs, which were expected to bioaccumulate, increased in concentration accordingly up to perch, where the levels suddenly dropped dramatically. The opposite pattern was observed for OH-PBDEs, where the concentration exhibited a general trend of decline up the food web, but increased in perch, indicating metabolic demethylation of MeO-PBDEs. Debromination was also indicated to occur when progressing through the food chain resulting in high levels of tetra-brominated MeO-PBDE and OH-PBDE congeners in fish, while some penta- and hexa-brominated congeners were observed to be the dominant products in the alga. As it has been shown that OH-PBDEs are potent disruptors of oxidative phosphorylation and that mixtures of different congener may act synergistically in terms of this toxic mode of action, the high levels of OH-PBDEs detected in perch in this study warrants further investigation into potential effects of these compounds on Baltic wildlife, and monitoring of their levels. PMID:26517387

  20. Identification and evaluation of modularization practices in an automotive supplier: progressivity analysis of transferring activities in the supply chain

    Directory of Open Access Journals (Sweden)

    Evandro Prieto

    2013-08-01

    Full Text Available The automotive value chain has more and more been making room to a strategy of which activities of product design and production have been transferred to the module suppliers. The transfer of value-added activities occurs from assembler to the module suppliers. The former assume the role of integrators within the supply chain. The supply chain participants have started to strengths their competencies in order to obtain advantages in the economy of scale and scope. In this context, the present work aims at investigating the valued-added transfer between first and second tiers of automotive supply chain in new product development and production. The work was carried out from an evaluation of a supplier with regard to modularization. The theoretical background considers the concepts of integrated and modular architecture as well as the progressiveness of competencies among suppliers. It adopts single cased as the research methodological approach. The literature points out that the process of modularization either in product development or in production offer benefits for both sides: assemblers and suppliers. The results from the investigated supplier shows inherent benefits due to the acquisition of new technologies that enable an increase of technical and management learning in projects of new products. Therefore, it demonstrates that in this modularity environment, the potential of value-added transfer is associated to the level of progressiveness of competencies that are incorporated to deliver module solutions to assemblers; the investigated supplier can be categorized in an “embrionary” stage.

  1. Transfer and accumulation of metals in a soil-diet-wood mouse food chain along a metal pollution gradient

    International Nuclear Information System (INIS)

    We studied the accumulation and transfer of As, Cd, Cu, Pb and Zn in the compartments of a soil-diet-wood mouse (Apodemus sylvaticus) food chain at five sites located along a metal pollution gradient. We observed a clear gradient in metal exposure at increasing distance from the smelter in all compartments of the food chain for the non-essential metals. The gradient was less clear or absent for the essential metals in acorn and mice target tissues. Regression analysis showed overall strong relationships within the soil-diet and diet-wood mouse compartments for the non-essential metals, while relationships for the essential metals were weak or absent. Total metal in soil appeared as a better predictor for the diet metal content than the available metal fraction. Our results suggest a more important transfer of non-essential elements through the food chain than essential elements, which is probably a consequence of homeostatic control of the latter group. - Non-essential metal transfer through a soil-diet-wood mouse food chain is more important than essential metal transfer

  2. Transfer of Paralytic Shellfish Toxins via Marine Food Chains:A Simulated Experiment

    Institute of Scientific and Technical Information of China (English)

    ZHI-JUN TAN; TIAN YAN; PEN-CHENG YU; MING-JIANG ZHOU

    2007-01-01

    Objective To study the transfer of paralytic shellfish toxins(PST)using four simulated marine food chains:d8noflagellate Alexandrium tamarense→Artemia Anemia salina→Mysid shrimp Neomysis awatschensis;A.tamarense→N.awatschensis:A.tamarense→A.salina→Perch Lateolabrax japonicus;and A.tamarenae→L. japonicus. Methods The ingestion of A.tamarenge.a producer of PST, by L. japonicus,N.awatschensis,and A.salina was first confirmed by microscopic observation of A.tamarense cells in the intestine samples of the three different organisms,and by the analysis of Chl.a levels in the samples.Toxin accumulation in L.japonicus and N.awatschensis directly from the feeding on A.tamarense 8r indirectly through the vector of A.salina was then studied.The toxicity of samples was measured using the AOAC mouse bioassay method,and the toxin content and profile of A.tamarense were analyzed by the HPLC method.Results Both A.salina and N.nwatschensis could ingest A.tamarense cells.However,the ingestion capability of A.salina exceeded that of N.L. japonicus.N.awatschensis and A.salina by microscopic observation.Therefore,the three organisms could ingest A.tamarense cells directly.A.salina could accumulate high content of PST,and the toxicity of A.salina in samples collected on of tested mice within 7 minutes,and the toxin content in artemia sample collected on the lst day was estimated to be 1.65×10-5 μg STX equal/individual.Toxin accumulation in L.japonicus and N.awatschensis directly from the feeding on A.tamarense or indirectly from the vector of A.salina was also studied.The mice injected with extracts from L.japonicus and N. awatschensis samples that accumulated PST either directly or indirectly showed PST intoxication symptoms,indicating that low levels of PST existed in these samples Conclusion Paralytic shellfish toxins can be transferred to L.japonicus,N.awatschensis,and A.salina from A.tamarense directly or indirectly via the food chains.

  3. Protein side-chain packing problem: a maximum edge-weight clique algorithmic approach.

    Science.gov (United States)

    Dukka Bahadur, K C; Tomita, Etsuji; Suzuki, Jun'ichi; Akutsu, Tatsuya

    2005-02-01

    "Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard. In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution. We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction. PMID:15751115

  4. Some observations on plutonium transfers in human and animal food-chains and Gi tract: plutonium complexation parameters

    International Nuclear Information System (INIS)

    Although many data have been accumulated concerning the distribution of Pu in waters, soils, and foodchains, recent studies have raised the question of the Pu physico-chemical species and their differential availability. Accordingly, we reviewed published data on the transfer of Pu in foodchains and in the gastrointestinal tracts. Dietetic, physico-chemical, biochemical and microbiological parameters have been studied and their incidence on the intestinal transfer factor f1 of Pu in man briefly discussed: the transfer in the trophic chains often increases Pu mobility and perhaps f1. Experimental research is needed to obtain quantitative data

  5. Simultaneous NMR assignment of backbone and side chain amides in large proteins with IS-TROSY

    International Nuclear Information System (INIS)

    A new strategy for the simultaneous NMR assignment of both backbone and side chain amides in large proteins with isotopomer-selective transverse-relaxation-optimized spectroscopy (IS-TROSY) is reported. The method considers aspects of both the NMR sample preparation and the experimental design. First, the protein is dissolved in a buffer with 50%H2O/50%D2O in order to promote the population of semideuterated NHD isotopomers in side chain amides of Asn/Gln residues. Second, a 13C'-coupled 2D 15N-1H IS-TROSY spectrum provides a stereospecific distinction between the geminal protons in the E and Z configurations of the carboxyamide group. Third, a suite of IS-TROSY-based triple-resonance NMR experiments, e.g. 3D IS-TROSY-HNCA and 3D IS-TROSY-HNCACB, are designed to correlate aliphatic carbon atoms with backbone amides and, for Asn/Gln residues, at the same time with side chain amides. The NMR assignment procedure is similar to that for small proteins using conventional 3D HNCA/3D HNCACB spectra, in which, however, signals from NH2 groups are often very weak or even missing due to the use of broad-band proton decoupling schemes and NOE data have to be used as a remedy. For large proteins, the use of conventional TROSY experiments makes resonances of side chain amides not observable at all. The application of IS-TROSY experiments to the 35-kDa yeast cytosine deaminase has established a complete resonance assignment for the backbone and stereospecific assignment for side chain amides, which otherwise could not be achieved with existing NMR experiments. Thus, the development of IS-TROSY-based method provides new opportunities for the NMR study of important structural and biological roles of carboxyamides and side chain moieties of arginine and lysine residues in large proteins as well as amino moieties in nucleic acids

  6. The impact of amino acid side chain mutations in conformational design of peptides and proteins

    OpenAIRE

    Laufer, B.; Frank, A.O.; Chatterjee, J; Neubauer, T; Mas Moruno, Carlos; Kummerlöwe, G.; Kessler, H.

    2010-01-01

    Local energetic effects of amino acid replacements are often considered to have only a moderate influence on the backbone conformation of proteins or peptides. As these effects are difficult to determine experimentally, no comparison has yet been performed. However, knowledge of the influence of side chain mutations is essential in protein homology modeling and in optimizing biologically active peptide ligands in medicinal chemistry. Furthermore, the tool of N-methylation of peptides is of in...

  7. Post-Translational Decrease in Respiratory Chain Proteins in the Polg Mutator Mouse Brain

    OpenAIRE

    Hauser, David N.; Dillman, Allissa A.; Ding, Jinhui; LI Yan; Cookson, Mark R.

    2014-01-01

    Mitochondrial DNA damage is thought to be a causal contributor to aging as mice with inactivating mutations in polymerase gamma (Polg) develop a progeroid phenotype. To further understand the molecular mechanisms underlying this phenotype, we used iTRAQ and RNA-Seq to determine differences in protein and mRNA abundance respectively in the brains of one year old Polg mutator mice compared to control animals. We found that mitochondrial respiratory chain proteins are specifically decreased in a...

  8. The establishment of a human myeloma cell line elaborating lambda-light chain protein.

    Science.gov (United States)

    Niho, Y; Shibuya, T; Yamasaki, K; Kimura, N

    1984-05-01

    A human myeloma cell line (KMM-56) producing lambda-light chain protein was established in vitro by cultivation of the cells in the pleural effusion obtained from a patient with IgD-lambda-myeloma. The cells proliferate in suspension and do not aggregate or attach to the culture dish. Surface marker analysis revealed that the cells were negative for E-rosette, and surface immunoglobulin. Immunoelectrophoresis, immunodiffusion, and immunofluorescence with various antibodies demonstrated no heavy chains, while lambda-light chains were detected in the cytoplasm of the cells. Using the immunodiffusion technique, only lambda-light chains were detected in the frozen and thawed cell extract, the concentrated supernatant of the cell culture, and the urine of the patient. Electron microscopic examination revealed the plasmablastoid appearance of the cells. This cell line may be useful for future studies of human immunoglobulin genes and for the material of human-human hybridoma, which could produce monoclonal human immunoglobulin. PMID:6429256

  9. How Chain Length and Charge Affect Surfactant Denaturation of Acyl Coenzyme A Binding Protein (ACBP)

    DEFF Research Database (Denmark)

    Andersen, Kell Kleiner; Otzen, Daniel

    2009-01-01

    Using intrinsic tryptophan fluorescence, equilibria and kinetics of unfolding of acyl coenzyme A binding protein (ACBP) have been investigated in sodium alkyl sulfate surfactants of different chain length (8-16 carbon atoms) and with different proportions of the nonionic surfactant dodecyl maltos...

  10. Nonspecific lipid-transfer protein genes expression in grape (vitis sp.) Cells in response to fungal elicitor treatments

    OpenAIRE

    Gomès, Eric; Sagot, Emeric; Gaillard, Cécile; Laquitaine, Laurent; Poinssot, Benoît; Sanejouand, Yves-Henri; Delrot, Serge; Coutos-Thévenot, Pierre

    2003-01-01

    Nonspecific lipid transfer proteins (nsLTPs) are small, basic cystein-rich proteins believed to be involved in plant defense mechanisms. Three cDNAs coding nsLTPs from grape (Vitis vinifera sp.) were cloned by reverse-transcriptase-polymerase chain reaction (RT-PCR) and PCR. The expression of nsLTP genes was investigated in 41B-rootstock grape cell suspension, in response to various defense-related signal molecules. Ergosterol (a fungi-specific sterol) and a proteinaceous elicitor puri...

  11. Acute and chronic effects of a 24-hour intravenous triglyceride emulsion challenge on plasma lecithin : cholesterol acyltransferase, phospholipid transfer protein, and cholesteryl ester transfer protein activities

    NARCIS (Netherlands)

    Riemens, SC; Van Tol, A; Sluiter, WJ; Dullaart, RPF

    1999-01-01

    Lecithin:cholesterol acyltransferase (LCAT), phospholipid transfer protein (PLTP), and cholesteryl ester transfer protein (CETP) are key factors in remodeling of high density lipoproteins (HDL) and triglyceride-rich lipoproteins. We examined the effect of a large, 24 h intravenous fat load on plasma

  12. L-alpha-glycerylphosphorylcholine inhibits the transfer function of phosphatidylinositol transfer protein alpha.

    Science.gov (United States)

    Komatsu, Hiroaki; Westerman, Jan; Snoek, Gerry T; Taraschi, Theodore F; Janes, Nathan

    2003-12-30

    Phosphatidylinositol transfer protein alpha (PITP-alpha) is a bifunctional phospholipid transfer protein that is highly selective for phosphatidylinositol (PtdIns) and phosphatidylcholine (PtdCho). Polar lipid metabolites, including L-alpha-glycerylphosphorylcholine (GroPCho), increasingly have been linked to changes in cellular function and to disease. In this study, polar lipid metabolites of PtdIns and PtdCho were tested for their ability to influence PITP-alpha activity. GroPCho inhibited the ability of PITP-alpha to transfer PtdIns or PtdCho between liposomes. The IC(50) of both processes was dependent on membrane composition. D-myo-inositol 1-phosphate and glycerylphosphorylinositol modestly enhanced PITP-alpha-mediated phospholipid transfer. Choline, phosphorylcholine (PCho), CDP-choline, glyceryl-3-phosphate, myo-inositol and D-myo-inositol 1,4,5-trisphosphate had little effect. Membrane surface charge was a strong determinant of the GroPCho inhibition with the inhibition being greatest for highly anionic membranes. GroPCho was shown to enhance the binding of PITP-alpha to anionic vesicles. In membranes of low surface charge, phosphatidylethanolamine (PtdEtn) was a determinant enabling the GroPCho inhibition. Anionic charge and PtdEtn content appeared to increase the strength of PITP-alpha-membrane interactions. The GroPCho-enhanced PITP-alpha-membrane binding was sufficient to cause inhibition, but not sufficient to account for the extent of inhibition observed. Processes associated with strengthened PITP-alpha-membrane binding in the presence of GroPCho appeared to impair the phospholipid insertion/extraction process. PMID:14729069

  13. Elucidating the design principles of photosynthetic electron-transfer proteins by site-directed spin labeling EPR spectroscopy.

    Science.gov (United States)

    Ishara Silva, K; Jagannathan, Bharat; Golbeck, John H; Lakshmi, K V

    2016-05-01

    Site-directed spin labeling electron paramagnetic resonance (SDSL EPR) spectroscopy is a powerful tool to determine solvent accessibility, side-chain dynamics, and inter-spin distances at specific sites in biological macromolecules. This information provides important insights into the structure and dynamics of both natural and designed proteins and protein complexes. Here, we discuss the application of SDSL EPR spectroscopy in probing the charge-transfer cofactors in photosynthetic reaction centers (RC) such as photosystem I (PSI) and the bacterial reaction center (bRC). Photosynthetic RCs are large multi-subunit proteins (molecular weight≥300kDa) that perform light-driven charge transfer reactions in photosynthesis. These reactions are carried out by cofactors that are paramagnetic in one of their oxidation states. This renders the RCs unsuitable for conventional nuclear magnetic resonance spectroscopy investigations. However, the presence of native paramagnetic centers and the ability to covalently attach site-directed spin labels in RCs makes them ideally suited for the application of SDSL EPR spectroscopy. The paramagnetic centers serve as probes of conformational changes, dynamics of subunit assembly, and the relative motion of cofactors and peptide subunits. In this review, we describe novel applications of SDSL EPR spectroscopy for elucidating the effects of local structure and dynamics on the electron-transfer cofactors of photosynthetic RCs. Because SDSL EPR Spectroscopy is uniquely suited to provide dynamic information on protein motion, it is a particularly useful method in the engineering and analysis of designed electron transfer proteins and protein networks. This article is part of a Special Issue entitled Biodesign for Bioenergetics - the design and engineering of electronic transfer cofactors, proteins and protein networks, edited by Ronald L. Koder and J.L. Ross Anderson. PMID:26334844

  14. Haptoglobin inhibits phospholipid transfer protein activity in hyperlipidemic human plasma

    Directory of Open Access Journals (Sweden)

    Leon Carlos G

    2009-07-01

    Full Text Available Abstract Background Haptoglobin is a plasma protein that scavenges haemoglobin during haemolysis. Phospholipid Transfer Protein (PLTP transfers lipids from Low Density Lipoproteins (LDL to High Density Lipoproteins (HDL. PLTP is involved in the pathogenesis of atherosclerosis which causes coronary artery disease, the leading cause of death in North America. It has been shown that Apolipoprotein-A1 (Apo-A1 binds and regulates PLTP activity. Haptoglobin can also bind to Apo-A1, affecting the ability of Apo-A1 to induce enzymatic activities. Thus we hypothesize that haptoglobin inhibits PLTP activity. This work tested the effect of Haptoglobin and Apo-A1 addition on PLTP activity in human plasma samples. The results will contribute to our understanding of the role of haptoglobin on modulating reverse cholesterol transport. Results We analyzed the PLTP activity and Apo-A1 and Haptoglobin content in six hyperlipidemic and six normolipidemic plasmas. We found that Apo-A1 levels are proportional to PLTP activity in hyperlipidemic (R2 = 0.66, p 2 = 0.57, p > 0.05. When the PLTP activity was graphed versus the Hp/Apo-A1 ratio in hyperlipidemic plasma there was a significant correlation (R2 = 0.69, p Conclusion These findings suggest an inhibitory effect of Haptoglobin over PLTP activity in hyperlipidemic plasma that may contribute to the regulation of reverse cholesterol transport.

  15. Resonant energy transfer based biosensor for detection of multivalent proteins.

    Energy Technology Data Exchange (ETDEWEB)

    Song, X. (Xuedong); Swanson, Basil I.

    2001-01-01

    We have developed a new fluorescence-based biosensor for sensitive detection of species involved in a multivslent interaction. The biosensor system utilizes specific interactions between proteins and cell surface receptors, which trigger a receptor aggregation process. Distance-dependent fluorescence self-quenching and resonant energy transfer mechanisms were coupled with a multivalent interaction to probe the receptor aggregation process, providing a sensitive and specific signal transduction method for such a binding event. The fluorescence change induced by the aggregation process can be monitored by different instrument platforms, e.g. fluorimetry and flow cytometry. In this article, a sensitive detection of pentavalent cholera toxin which recognizes ganglioside GM1 has been demonstrated through the resonant energy transfer scheme, which can achieve a double color change simultaneously. A detection sensitivity as high as 10 pM has been achieved within a few minutes (c.a. 5 minutes). The simultaneous double color change (an increase of acceptor fluorescence and a decrease of donor fluorescence intensity) of two similar fluorescent probes provides particularly high detection reliability owing to the fact that they act as each other's internal reference. Any external perturbation such as environmental temperature change causes no significant change in signal generation. Besides the application for biological sensing, the method also provides a useful tool for investigation of kinetics and thermodynamics of a multivalent interaction. Keywords: Biosensor, Fluorescence resonant energy transfer, Multivalent interaction, Cholera Toxin, Ganglioside GM1, Signal Transduction

  16. Transfer of fall-out plutonium in the food-chain lichen→reindeer→man

    International Nuclear Information System (INIS)

    Fall-out of 239Pu and 238Pu was investigated by studying samples of lichen collected during 1947-1961 at different places in Scandinavia and between 1961-1972 at Lake Rogen in Sweden, which lies 62.30N, 12.40E. The maximum 239Pu level in the lichen carpet, which occurred in 1963, was about 300 pCi per kg dry weight and decreased to about 200 pCi per kg dry weight in 1970. The 238Pu concentration showed a maximum value during 1963 corresponding to about 12pCi per kg dry weight. This concentration decreased to about 7 pCi per kg dry weight in 1967. During 1966-1970 the 238Pu concentration increased and resulted in an increase in the 238Pu/239Pu activity ratio from 0.026 to 0.046. The activity concentration of 239Pu has been studied in the bone, liver, kidney and flesh of reindeer slaughtered in 1964-1974. The average concentrations found in cortical bone were 0.4 pCi/kg fresh weight, in trabecular bone 0.8 pCi/kg, in liver 5.2 pCi/kg, in kidneys 0.6 pCi/kg and in flesh 0.04 pCi/kg. A study of the transfer of 239Pu through the food-chain has been performed by using a simple compartment model. The average values of fsub(a), the estimated fraction of ingested activity retained, were in cortical bone 4.6x10-6, in trabecular bone 2.7x10-6, in liver 14x10-6 and in flesh 2.5x10-6. The maximum mean residence times were estimated to be about 11 a, 14 a, 8 a and 5 a, respectively. On the basis of reindeer meat consumption and the estimated fractional residence time, tau'=fsub(a)xtau, the 239Pu content of Lapps due to this food-chain was estimated to be about 0.1 fCi/kg in bone and 1 fCi/kg in liver. (author)

  17. Origin of the red sites and energy transfer rates in single MEH-PPV chains at low temperature.

    Science.gov (United States)

    Feist, Florian A; Zickler, Martin F; Basché, Thomas

    2011-06-01

    Single poly[2-methoxy-5-(2'-ethyl-hexyloxy)-1,4-phenylene vinylene] (MEH-PPV) molecules dispersed in thin poly(methylmethacrylate) films have been investigated by fluorescence emission, excitation and time-resolved spectroscopy at 1.2 K. For the molecular weight studied (∼200 kDa) a bimodal distribution of emission maxima is observed. Based on a comparison of the spectroscopic properties of blue and red sites and on polarisation-resolved measurements, we argue in agreement with recent quantum-chemical calculations that the red subpopulation most probably does not arise from interchromophoric excitation delocalisation but is to be attributed to longer chromophoric units originating from ordered regions of a polymer chain, where due to constraints on the chain conformation larger conjugation lengths can be realised. In excitation spectra within the red spectral region we can identify multiple chromophoric units, among them chromophores without correspondence in the emission spectrum-donors of the intramolecular energy transfer. Zero-phonon lines of donor chromophores proved to be significantly broadened, indicating fast excited-state population decay due to energy transfer. Thus, a distribution of energy transfer times within MEH-PPV chains could be determined from donor zero-phonon line widths, with an average value of 3.9 ps. Our study represents the first direct measurement of energy transfer times in conjugated polymers, parameters that are crucial for the performance of many technical applications based on this class of material. PMID:21472962

  18. On correlation between protein secondary structure, backbone bond angles, and side-chain orientations

    CERN Document Server

    Lundgren, Martin

    2012-01-01

    We investigate the fine structure of the sp3 hybridized covalent bond geometry that governs the tetrahedral architecture around the central C$_\\alpha$ carbon of a protein backbone, and for this we develop new visualization techniques to analyze high resolution X-ray structures in Protein Data Bank. We observe that there is a correlation between the deformations of the ideal tetrahedral symmetry and the local secondary structure of the protein. We propose a universal coarse grained energy function to describe the ensuing side-chain geometry in terms of the C$_\\beta$ carbon orientations. The energy function can model the side-chain geometry with a sub-atomic precision. As an example we construct the C$_\\alpha$-C$_\\beta$ structure of HP35 chicken villin headpiece. We obtain a configuration that deviates less than 0.4 \\.A in root-mean-square distance from the experimental X-ray structure.

  19. Transfer of mercury and methylmercury along macroinvertebrate food chains in a floodplain lake of the Beni River, Bolivian Amazonia

    International Nuclear Information System (INIS)

    We have evaluated the mercury and methylmercury transfers to and within the macroinvertebrate communities of a floodplain lake of the Beni River basin, Bolivia, during three hydrological seasons and in two habitats (open water and vegetation belt). Using the stable isotopes δ13C and δ15N, six trophic chains were identified during a previous study. Four are based on only one source: seston, organic matter from the bottom sediment, periphyton and macrophytes. Two are based on mixed sources (seston and periphyton in one case, periphyton and macrophytes in the other). During sampling, we found only one taxon that had surface sediment organic matter as food source and very few taxa whose trophic source was constituted by macrophytes. The periphyton was the most important source during all seasons; it produced the longest chain, with three trophic positions. Whatever the season and trophic source, all collected macroinvertebrates contained methyl mercury and the latter was biomagnified in all trophic chains that we identified. The biomagnification of methylmercury through invertebrate trophic chains accurately reflected the existence and length of these chains. Biomagnification was virtually non-existent in the sediment-based chain, low and restricted to the dry season in the macrophyte-based chain. It was significant in the seston-based chain, but limited by the existence of only two trophic levels and restricted to the wet season. Finally, it was very effective in the periphyton-based chain, which offers the highest rate of contamination of the source but, above all, the largest number of trophic levels.

  20. Transfer of mercury and methylmercury along macroinvertebrate food chains in a floodplain lake of the Beni River, Bolivian Amazonia

    Energy Technology Data Exchange (ETDEWEB)

    Molina, Carlos Israel, E-mail: camoar6088@gmail.com [Instituto de Ecologia, Unidad de Limnologia, UMSA, Casilla postal 10077, La Paz (Bolivia, Plurinational State of); Institut de Recherche pour le Developpement IRD, Casilla postal 9214, La Paz (Bolivia, Plurinational State of); CONICET-Facultad de Ciencias Naturales, Universidad Nacional de Tucuman, Miguel Lillo 205, 4 000, Tucuman (Argentina); Gibon, Francois-Marie [Institut de Recherche pour le Developpement IRD, Casilla postal 9214, La Paz (Bolivia, Plurinational State of); IRD, UMR BOREA, Museum national d' Histoire Naturelle MNHN, Case postale 26, 75231, Paris cedex 05 (France); Duprey, Jean-Louis [Institut de Recherche pour le Developpement IRD, Casilla postal 9214, La Paz (Bolivia, Plurinational State of); Dominguez, Eduardo [CONICET-Facultad de Ciencias Naturales, Universidad Nacional de Tucuman, Miguel Lillo 205, 4 000, Tucuman (Argentina); Guimaraes, Jean-Remy D. [Instituto de Biofisica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Bloco G-CCS, Rio de Janeiro, CEP 21949-900 (Brazil); Roulet, Marc [Institut de Recherche pour le Developpement IRD, Casilla postal 9214, La Paz (Bolivia, Plurinational State of)

    2010-07-15

    We have evaluated the mercury and methylmercury transfers to and within the macroinvertebrate communities of a floodplain lake of the Beni River basin, Bolivia, during three hydrological seasons and in two habitats (open water and vegetation belt). Using the stable isotopes {delta}{sup 13}C and {delta}{sup 15}N, six trophic chains were identified during a previous study. Four are based on only one source: seston, organic matter from the bottom sediment, periphyton and macrophytes. Two are based on mixed sources (seston and periphyton in one case, periphyton and macrophytes in the other). During sampling, we found only one taxon that had surface sediment organic matter as food source and very few taxa whose trophic source was constituted by macrophytes. The periphyton was the most important source during all seasons; it produced the longest chain, with three trophic positions. Whatever the season and trophic source, all collected macroinvertebrates contained methyl mercury and the latter was biomagnified in all trophic chains that we identified. The biomagnification of methylmercury through invertebrate trophic chains accurately reflected the existence and length of these chains. Biomagnification was virtually non-existent in the sediment-based chain, low and restricted to the dry season in the macrophyte-based chain. It was significant in the seston-based chain, but limited by the existence of only two trophic levels and restricted to the wet season. Finally, it was very effective in the periphyton-based chain, which offers the highest rate of contamination of the source but, above all, the largest number of trophic levels.

  1. A case study of apple seed and grape allergy with sensitisation to nonspecific lipid transfer protein.

    Science.gov (United States)

    Murad, Ari; Katelaris, Constance H; Baumgart, Karl

    2016-04-01

    Lipid transfer proteins can be an important cause of allergy given their stability and high degree of protein sequence homology. We describe the case of a child who developed two separate episodes of anaphylaxis after consuming apple seed and grape, with evidence that nonspecific lipid transfer proteins may have been responsible for these reactions. Lipid transfer protein allergy should be considered when anaphylaxis is inconsistent, such as in patients who can tolerate fruit pulp but react to fresh whole fruit juices. PMID:27141487

  2. A case study of apple seed and grape allergy with sensitisation to nonspecific lipid transfer protein

    Science.gov (United States)

    Katelaris, Constance H; Baumgart, Karl

    2016-01-01

    Lipid transfer proteins can be an important cause of allergy given their stability and high degree of protein sequence homology. We describe the case of a child who developed two separate episodes of anaphylaxis after consuming apple seed and grape, with evidence that nonspecific lipid transfer proteins may have been responsible for these reactions. Lipid transfer protein allergy should be considered when anaphylaxis is inconsistent, such as in patients who can tolerate fruit pulp but react to fresh whole fruit juices. PMID:27141487

  3. SDRL: a sequence-dependent protein side-chain rotamer library.

    Science.gov (United States)

    Taghizadeh, Mohammad; Goliaei, Bahram; Madadkar-Sobhani, Armin

    2015-07-01

    Since the introduction of the first protein side-chain rotamer library (RL) almost half a century ago, RLs have been components of many programs and algorithms in structural bioinformatics. Based on the dependence of side-chain dihedral angles on the local backbone, three types of RLs have been identified: backbone-independent, secondary-structure-dependent and backbone-dependent. In all previous studies, the effect of sequence specificity on side-chain conformational preferences was neglected. In the effort to develop a new class of RLs, we considered that the side-chain conformation of the central residue in each triplet on a protein backbone depends on the sequence of the triplet; therefore, we developed a sequence-dependent rotamer library (SDRL). To accomplish this, 400 possible triplet sequences for 18 natural amino acids as the central residue, which corresponds to 7200 triplet sequences in total, were considered. Searching the set of 11 546 selected PDB entries for the 7200 triplet sequences resulted in 2 364 541 instances occurring for 18 amino acids. Our results show that Leu and Val experience minimal impact from the adjacent residues in adopting side-chain conformations. Cys, Ile, Trp, His, Asp, Met, Glu, Gln, Arg and Lys, on the other hand, adopt their side-chain conformations mostly based on the adjacent residues on the backbone. The remaining residue types were moderately dependent on the adjacent residues. Using the new library, side-chain repacking algorithms can find preferred conformations of each residue more easily than with other backbone-independent RLs. PMID:25953624

  4. Detection of κ and λ Light Chain Monoclonal Proteins in Human Serum: Automated Immunoassay versus Immunofixation Electrophoresis

    OpenAIRE

    Jaskowski, Troy D; Litwin, Christine M.; Hill, Harry R.

    2006-01-01

    Recently, turbidimetric immunoassays for detecting and quantifying κ and λ free light chains (FLC) have become available and are promoted as being more sensitive than immunofixation electrophoresis (IFE) in detecting FLC monoclonal proteins. In this study, we assessed the ability of these turbidimetric assays to detect serum monoclonal proteins involving both free and heavy-chain-bound κ and λ light chains compared to standard immunofixation electrophoresis. Sera demonstrating a restricted ba...

  5. Characterization of a new antifungal lipid transfer protein from wheat.

    Science.gov (United States)

    Kirubakaran, S Isaac; Begum, S Mubarak; Ulaganathan, K; Sakthivel, N

    2008-10-01

    Lipid transfer proteins (LTPs) are members of the family of pathogenesis-related proteins (PR-14) that are believed to be involved in plant defense responses. In this study, a novel gene Ltp 3F1 encoding an antifungal protein from wheat (Sumai 3) was subcloned, overexpressed in Escherichia coli BL-21 (DE3) and enriched using ammonium sulfate fractionation followed by gel permeation chromatography. Molecular phylogeny analyses of wheat Ltp 3F1 gene showed a strong identity to other plant LTPs. Predicted three-dimensional structural model showed the presence of 6 alpha-helices and 9 loop turns. The active site catalytic residues Gly30, Pro50, Ala52 and Cys55 may be suggested for catalyzing the reaction involved in lipid binding. SDS-PAGE analysis confirmed the production of recombinant fusion protein. The LTP fusion protein exhibited a broad-spectrum antifungal activity against Alternaria sp., Rhizoctonia solani, Curvularia lunata, Bipolaris oryzae, Cylindrocladium scoparium, Botrytis cinerea and Sarocladium oryzae. Gene cassette with cyanamide hydratase (cah) marker and Ltp 3F1 gene was constructed for genetic transformation in tobacco. Efficient regeneration was achieved in selective media amended with cyanamide. Transgenic plants with normal phenotype were obtained. Results of PCR and Southern, Northern and Western hybridization analyses confirmed the integration and expression of genes in transgenic plants. Experiments with detached leaves from transgenic tobacco expressing Ltp 3F1 gene showed fungal resistance. Due to the innate potential of broad-spectrum antifungal activity, wheat Ltp 3F1 gene can be used to enhance resistance against fungi in crop plants. PMID:18595724

  6. Electron transfer, decoherence, and protein dynamics: insights from atomistic simulations.

    Science.gov (United States)

    Narth, Christophe; Gillet, Natacha; Cailliez, Fabien; Lévy, Bernard; de la Lande, Aurélien

    2015-04-21

    Electron transfer in biological systems drives the processes of life. From cellular respiration to photosynthesis and enzymatic catalysis, electron transfers (ET) are chemical processes on which essential biological functions rely. Over the last 40 years, scientists have sought understanding of how these essential processes function in biology. One important breakthrough was the discovery that Marcus theory (MT) of electron transfer is applicable to biological systems. Chemists have experimentally collected both the reorganization energies (λ) and the driving forces (ΔG°), two parameters of Marcus theory, for a large variety of ET processes in proteins. At the same time, theoretical chemists have developed computational approaches that rely on molecular dynamics and quantum chemistry calculations to access numerical estimates of λ and ΔG°. Yet another crucial piece in determining the rate of an electron transfer is the electronic coupling between the initial and final electronic wave functions. This is an important prefactor in the nonadiabatic rate expression, since it reflects the probability that an electron tunnels from the electron donor to the acceptor through the intervening medium. The fact that a protein matrix supports electron tunneling much more efficiently than vacuum is now well documented, both experimentally and theoretically. Meanwhile, many chemists have provided examples of the rich physical chemistry that can be induced by protein dynamics. This Account describes our studies of the dynamical effects on electron tunneling. We present our analysis of two examples of natural biological systems through MD simulations and tunneling pathway analyses. Through these examples, we show that protein dynamics sustain efficient tunneling. Second, we introduce two time scales: τcoh and τFC. The former characterizes how fast the electronic coupling varies with nuclear vibrations (which cause dephasing). The latter reflects the time taken by the system

  7. Effect of the alkyl chain length of secondary amines on the phase transfer of gold nanoparticles from water to toluene.

    Science.gov (United States)

    Soliwoda, Katarzyna; Tomaszewska, Emilia; Tkacz-Szczesna, Beata; Mackiewicz, Ewelina; Rosowski, Marcin; Bald, Adam; Blanck, Christian; Schmutz, Marc; Novák, Jiří; Schreiber, Frank; Celichowski, Grzegorz; Grobelny, Jaroslaw

    2014-06-17

    In the present paper we describe a phase transfer of aqueous synthesized gold nanoparticles (AuNPs) from water to toluene using secondary amines: dioctylamine, didodecylamine, and dioctadecylamine. The effect of the hydrocarbon chain length and amount of amines on the transfer efficiency were investigated in the case of nanoparticles (NPs) with three different sizes: 5, 9, and 13 nm. Aqueous colloids were precisely characterized before the transfer process using UV-vis spectroscopy, dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), and transmission electron microscopy (TEM). Nanoparticles were next transferred to toluene and characterized using UV-vis and DLS techniques. It was found that dioctadecylamine provides the most effective transfer of nanoparticles. No time-dependent changes in the NP size were observed after 12 days, showing that the dioctadecylamine-stabilized nanoparticles dispersed in toluene were stable. This indicates that long hydrocarbon chains of dioctadecylamine exhibit sufficiently hydrophobic properties of nanoparticles and consequently their good dispersibility in nonpolar solvent. PMID:24893068

  8. In vivo visual evaluation of nanoparticle transfer in a three-species terrestrial food chain.

    Science.gov (United States)

    Chae, Yooeun; Kim, Shin Woong; An, Youn-Joo

    2016-05-01

    Nanoparticles (NPs) are increasingly being used, and they present the risk of being introduced into food webs. Numerous studies have been conducted to evaluate the toxicological effects of NPs in the aquatic and freshwater environments and their transfer to upper-level trophic organisms. However, information on the transfer and consequent effects of NPs on soil invertebrates is still limited. In this study, we assessed the transfer of quantum dots (QDs) through a three-species terrestrial food chain that consisted of the yeast Saccharomyces cerevisiae, the collembolan Folsomia candida, and the pill bug Armadillidium vulgare, as well as their biodistribution in vital organs using fluorescence analytical techniques. To visualize QD incorporation and biodistribution in F. candida, longitudinal and transversal sections were observed after short-term (3 d) and long-term (12 d) feeding with QD-treated yeast. QDs were located only in the intestine of F. candida and excreted within 1-2 d. QDs were also transferred to the pill bug by feeding, and remained in its intestine. This study showed the transfer of NPs through a model terrestrial food chain and indicated the potential hazards of released NPs for organisms at different trophic levels. PMID:26933900

  9. Surface modification of carbon nanotubes via combination of mussel inspired chemistry and chain transfer free radical polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Wan, Qing; Tian, Jianwen; Liu, Meiying; Zeng, Guangjian; Huang, Qiang [Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031 (China); Wang, Ke; Zhang, Qingsong [Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing, 100084 (China); Deng, Fengjie, E-mail: fengjiedeng@aliyun.com [Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031 (China); Zhang, Xiaoyong, E-mail: xiaoyongzhang1980@gmail.com [Department of Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang, 330031 (China); Wei, Yen, E-mail: weiyen@tsinghua.edu.cn [Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing, 100084 (China)

    2015-08-15

    Graphical abstract: A novel strategy combination of mussel inspired chemistry and chain transfer free radical polymerization has been developed for surface modification of carbon nanotubes with polymers for the first time. - Highlights: • Surface modification of CNTs via mussel inspired chemistry. • Preparation of aminated polymers through free radical polymerization. • Functionalized CNTs with aminated polymers via Michael addition reaction. • Highly dispersed CNTs in organic and aqueous solution. - Abstract: In this work, a novel strategy for surface modification of carbon nanotubes (CNTs) was developed via combination of mussel inspired chemistry and chain transfer free radical polymerization. First, pristine CNTs were functionalized with polydopamine (PDA), which is formed via self-polymerization of dopamine in alkaline conditions. These PDA functionalized CNTs can be further reacted with amino-terminated polymers (named as PDMC), which was synthesized through chain transfer free radical polymerization using cysteamine hydrochloride as chain transfer agent and methacryloxyethyltrimethyl ammonium chloride as the monomer. PDMC perfectly conjugated with CNT-PDA was ascertained by a series of characterization techniques including transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS). The dispersibility of obtained CNT nanocomposites (named as CNT-PDA-PDMC) was further examined. Results showed that the dispersibility of CNT-PDA-PDMC in aqueous and organic solutions was obviously enhanced. Apart from PDMC, many other amino-terminated polymers can also be used to functionalization of CNTs via similar strategy. Therefore, the method described in this work should be a general strategy for fabrication various polymer nanocomposites.

  10. A new look at kinetic modeling of nonlinear free radical polymerizations with terminal branching and chain transfer to polymer

    OpenAIRE

    Dias, Rolando; Costa, Mário Rui

    2003-01-01

    The authors' previously developed method for the general kinetic analysis of nonlinear irreversible polymerizations based on moment generating functions is used for simulating free radical polymerization systems in which terminal branching and chain transfer to polymer are present, leading possibly to gel formation. The numerical solution of the equations needed for postgel predictions of sol fraction and average molecular weights (a major difficulty) is discussed with some detail. Finally, s...

  11. Molecular imprinting in hydrogels using reversible addition-fragmentation chain transfer polymerization and continuous flow micro-reactor

    OpenAIRE

    Kadhirvel, Porkodi; Machado, Carla; Freitas, Ana; Oliveira, Tânia; Dias, Rolando; Costa, Mário

    2015-01-01

    Abstract BACKGROUND Stimuli responsive imprinted hydrogel micro-particles were prepared using reversible addition-fragmentation chain transfer polymerization for targeting genotoxic impurity aminopyridine in aqueous environment using a continuous flow micro-reactor. RESULTS The feasibility of operation with a continuous flow micro-reactor for particles production was demonstrated. A comparative evaluation was carried out between batch and micro-reactor produced imprinted and non...

  12. Surface modification of carbon nanotubes via combination of mussel inspired chemistry and chain transfer free radical polymerization

    International Nuclear Information System (INIS)

    Graphical abstract: A novel strategy combination of mussel inspired chemistry and chain transfer free radical polymerization has been developed for surface modification of carbon nanotubes with polymers for the first time. - Highlights: • Surface modification of CNTs via mussel inspired chemistry. • Preparation of aminated polymers through free radical polymerization. • Functionalized CNTs with aminated polymers via Michael addition reaction. • Highly dispersed CNTs in organic and aqueous solution. - Abstract: In this work, a novel strategy for surface modification of carbon nanotubes (CNTs) was developed via combination of mussel inspired chemistry and chain transfer free radical polymerization. First, pristine CNTs were functionalized with polydopamine (PDA), which is formed via self-polymerization of dopamine in alkaline conditions. These PDA functionalized CNTs can be further reacted with amino-terminated polymers (named as PDMC), which was synthesized through chain transfer free radical polymerization using cysteamine hydrochloride as chain transfer agent and methacryloxyethyltrimethyl ammonium chloride as the monomer. PDMC perfectly conjugated with CNT-PDA was ascertained by a series of characterization techniques including transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), thermal gravimetric analysis (TGA) and X-ray photoelectron spectroscopy (XPS). The dispersibility of obtained CNT nanocomposites (named as CNT-PDA-PDMC) was further examined. Results showed that the dispersibility of CNT-PDA-PDMC in aqueous and organic solutions was obviously enhanced. Apart from PDMC, many other amino-terminated polymers can also be used to functionalization of CNTs via similar strategy. Therefore, the method described in this work should be a general strategy for fabrication various polymer nanocomposites

  13. Stress relaxation via addition-fragmentation chain transfer in high Tg, high conversion methacrylate-based systems

    OpenAIRE

    Park, Hee Young; Kloxin, Christopher J.; Abuelyaman, Ahmed S.; Oxman, Joe D.; Bowman, Christopher N.

    2012-01-01

    To reduce shrinkage stress which arises during the polymerization of crosslinked polymers, allyl sulfide functional groups were incorporated into methacrylate polymerizations to determine their effect on stress relaxation via addition-fragmentation chain transfer (AFCT). Additionally, stoichiometrically balanced thiol and allyl sulfide-containing norbornene monomers were incorporated into the methacrylate resin to maximize the overall functional group conversion and promote AFCT while also en...

  14. Stress Reduction and Tg Enhancement in Ternary Thiol-Yne-Methacrylate Systems via Addition-fragmentation Chain Transfer

    OpenAIRE

    Park, Hee Young; Kloxin, Christopher J.; Fordney, Mark F.; Bowman, Christopher N.

    2012-01-01

    Since polymerization-induced shrinkage stress is detrimental in many applications, addition-fragmentation chain transfer (AFCT) was employed to induce network relaxation and adaptation that mitigate the shrinkage stress. Here, to form high glass transition temperature, high modulus polymers while still minimizing stress, multifunctional methacrylate monomers were incorporated into allyl sulfide-containing thiol-yne resins to provide simultaneously high glass transition temperatures and a faci...

  15. Intra-chain 3D segment swapping spawns the evolution of new multidomain protein architectures.

    Science.gov (United States)

    Szilágyi, András; Zhang, Yang; Závodszky, Péter

    2012-01-01

    Multidomain proteins form in evolution through the concatenation of domains, but structural domains may comprise multiple segments of the chain. In this work, we demonstrate that new multidomain architectures can evolve by an apparent three-dimensional swap of segments between structurally similar domains within a single-chain monomer. By a comprehensive structural search of the current Protein Data Bank (PDB), we identified 32 well-defined segment-swapped proteins (SSPs) belonging to 18 structural families. Nearly 13% of all multidomain proteins in the PDB may have a segment-swapped evolutionary precursor as estimated by more permissive searching criteria. The formation of SSPs can be explained by two principal evolutionary mechanisms: (i) domain swapping and fusion (DSF) and (ii) circular permutation (CP). By large-scale comparative analyses using structural alignment and hidden Markov model methods, it was found that the majority of SSPs have evolved via the DSF mechanism, and a much smaller fraction, via CP. Functional analyses further revealed that segment swapping, which results in two linkers connecting the domains, may impart directed flexibility to multidomain proteins and contributes to the development of new functions. Thus, inter-domain segment swapping represents a novel general mechanism by which new protein folds and multidomain architectures arise in evolution, and SSPs have structural and functional properties that make them worth defining as a separate group. PMID:22079367

  16. Proton transfer and water exchange in the green fluorescent protein

    Science.gov (United States)

    Agmon, Noam

    2014-03-01

    The green fluorescent protein (GFP) is the only naturally occurring protein in which excited-state proton-transfer has been identified. Upon excitation, a proton is ejected from its chromophore, travelling through the ``privileged water molecule'' (PWM) and Ser205 to Glu222, on a 10 ps timescale or faster. However, time-resolved fluorescence from the chromophore exhibits a t-α power-law decay extending into the ns regime. With increasing temperature, α switches from 1/2 (below 230 K) to 3/2 (above it). This has been interpreted as pseudo one-dimensional proton hopping along an internal ``proton wire,'' with an activated process that opens a ``doorway'' for proton escape to solution at the higher temperatures. To identify such putative pathways, we have developed a computer code mapping all ``proton wires'' within a protein structure. Applying it to a X-ray GFP structure of 0.9 Angstrom resolution, a proton wire indeed continues from Glu222 along the axis of the GFP ``barrel,'' connecting to a negatively charged surface patch (a ``proton collecting antenna''?). This might explain the t- 1 / 2 behavior. However, a direct escape pathway opening from the chromophore to solution is not readily identified in the X-ray structure. Here we report molecular dynamics results showing that the PWM escapes to solution on the 100 ps timescale. This occurs by fluctuations of the beta-sheet, creating an opening through which water molecules can leave and enter the protein. The exact pathway of the PWM on its way in and out has been identified, as well as the water-exchange kinetics that follows a stretched-exponential time behavior. This research was supported by the ISRAEL SCIENCE FOUNDATION grant No. 766/12.

  17. Intercellular Protein Transfer from Thymocytes to Thymic Epithelial Cells

    Science.gov (United States)

    Wang, Hong-Xia; Qiu, Yu-Rong; Zhong, Xiao-Ping

    2016-01-01

    Promiscuous expression of tissue restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs) is crucial for negative selection of self-reactive T cells to establish central tolerance. Intercellular transfer of self-peptide-MHC complexes from mTECs to thymic dendritic cells (DCs) allows DCs to acquire TRAs, which in turn contributes to negative selection and regulatory T cell generation. However, mTECs are unlikely to express all TRAs, such as immunoglobulins generated only in B cells after somatic recombination, hyper-mutation, or class-switches. We report here that both mTECs and cortical TECs can efficiently acquire not only cell surface but also intracellular proteins from thymocytes. This reveals a previously unappreciated intercellular sharing of molecules from thymocytes to TECs, which may broaden the TRA inventory in mTECs for establishing a full spectrum of central tolerance. PMID:27022746

  18. New horizons for cholesterol ester transfer protein inhibitors.

    Science.gov (United States)

    Schwartz, Gregory G

    2012-02-01

    High-density lipoprotein (HDL) cholesterol levels bear an inverse relationship to cardiovascular risk. To date, however, no intervention specifically targeting HDL has been demonstrated to reduce cardiovascular risk. Cholesterol ester transfer protein (CETP) mediates transfer of cholesterol ester from HDL to apolipoprotein B-containing particles. Most, but not all observational cohort studies indicate that genetic polymorphisms of CETP associated with reduced activity and higher HDL cholesterol levels are also associated with reduced cardiovascular risk. Some, but not all studies indicate that CETP inhibition in rabbits retards atherosclerosis, whereas transgenic CETP expression in mice promotes atherosclerosis. Torcetrapib, the first CETP inhibitor to reach phase III clinical development, was abandoned due to excess mortality associated with increases in aldosterone and blood pressure. Two other CETP inhibitors have entered phase III clinical development. Anacetrapib is a potent inhibitor of CETP that produces very large increases in HDL cholesterol and large reductions in low-density lipoprotein (LDL) cholesterol, beyond those achieved with statins. Dalcetrapib is a less potent CETP inhibitor that produces smaller increases in HDL cholesterol with minimal effect on LDL cholesterol. Both agents appear to allow efflux of cholesterol from macrophages to HDL in vitro, and neither agent affects blood pressure or aldosterone in vivo. Two large cardiovascular outcomes trials, one with anacetrapib and one with dalcetrapib, should provide a conclusive test of the hypothesis that inhibition of CETP decreases cardiovascular risk. PMID:22083134

  19. Purification, characterization and substrate specificity of rabbit lung phospholipid transfer proteins.

    Science.gov (United States)

    Tsao, F H; Tian, Q; Strickland, M S

    1992-05-01

    Three phospholipid transfer proteins, namely proteins I, II and III, were purified from the rabbit lung cytosolic fraction. The molecular masses of phospholipid transfer proteins I, II and III are 32 kilodaltons (kDa), 22 kDa and 32 kDa, respectively; their isoelectric point values are 6.5, 7.0 and 6.8, respectively. Phospholipid transfer proteins I and III transferred phosphatidylcholine (PC) and phosphatidylinositol (PI) from donor unilamellar liposomes to acceptor multilamellar liposomes; protein II transferred PC but not PI. All the three phospholipid transfer proteins transferred phosphatidylethanolamine poorly and showed no tendency to transfer triolein. The transfer of [14C]PC from unilamellar liposomes to multilamellar liposomes facilitated by each protein was affected differently by the presence of acidic phospholipids in the PC unilamellar liposomes. In an equal molar ratio of acidic phospholipid and PC, phosphatidylglycerol (PG) reduced the activities of proteins I and III by 70% (P = 0.0004 and 0.0032, respectively) whereas PI and phosphatidylserine (PS) had an insignificant effect. In contrast, the protein II activity was stimulated 2-3-times more by either PG (P = 0.0024), PI (P = 0.0006) or PS (P = 0.0038). In addition, protein II transferred dioleoylPC (DOPC) about 2-times more effectively than dipalmitoylPC (DPPC) (P = 0.0002), whereas proteins I and III transferred DPPC 20-40% more effectively than DOPC but this was statistically insignificant. The markedly different substrate specificities of the three lung phospholipid transfer proteins suggest that these proteins may play an important role in sorting intracellular membrane phospholipids, possibly including lung surfactant phospholipids. PMID:1596521

  20. Protein structure modelling and evaluation based on a 4-distance description of side-chain interactions

    Directory of Open Access Journals (Sweden)

    Inbar Yuval

    2010-07-01

    Full Text Available Abstract Background Accurate evaluation and modelling of residue-residue interactions within and between proteins is a key aspect of computational structure prediction including homology modelling, protein-protein docking, refinement of low-resolution structures, and computational protein design. Results Here we introduce a method for accurate protein structure modelling and evaluation based on a novel 4-distance description of residue-residue interaction geometry. Statistical 4-distance preferences were extracted from high-resolution protein structures and were used as a basis for a knowledge-based potential, called Hunter. We demonstrate that 4-distance description of side chain interactions can be used reliably to discriminate the native structure from a set of decoys. Hunter ranked the native structure as the top one in 217 out of 220 high-resolution decoy sets, in 25 out of 28 "Decoys 'R' Us" decoy sets and in 24 out of 27 high-resolution CASP7/8 decoy sets. The same concept was applied to side chain modelling in protein structures. On a set of very high-resolution protein structures the average RMSD was 1.47 Å for all residues and 0.73 Å for buried residues, which is in the range of attainable accuracy for a model. Finally, we show that Hunter performs as good or better than other top methods in homology modelling based on results from the CASP7 experiment. The supporting web site http://bioinfo.weizmann.ac.il/hunter/ was developed to enable the use of Hunter and for visualization and interactive exploration of 4-distance distributions. Conclusions Our results suggest that Hunter can be used as a tool for evaluation and for accurate modelling of residue-residue interactions in protein structures. The same methodology is applicable to other areas involving high-resolution modelling of biomolecules.

  1. Effect of medium chain triglycerides (MCT) on jejunal mucosa mass and protein synthesis.

    OpenAIRE

    Schwartz, S.; M. Farriol; Garcia-Arumi, E.; Andreu, A. L.; López Hellín, J; Arbós, M A

    1994-01-01

    The effects of medium chain triglycerides (MCT) on jejunal mucosa mass and protein synthesis were compared with results from previous experiments with rats fed by parenteral nutrition or enteral nutrition. Other published studies have also been analysed. Three experimental models were studied. In the traumatic model, production of a femoral fracture was followed by Kirschner pin insertion into the medullary canal of both fragments at reduction. (Forty ras were fed enteral nutrition and 93 wer...

  2. Utility of a fluorescent vitamin E analog as a probe for tocopherol transfer protein activity

    OpenAIRE

    Morley, Samantha; Cross, Valerie; Cecchini, Matt; Nava, Phil; Atkinson, Jeffrey; Manor, Danny

    2006-01-01

    The tocopherol transfer protein (TTP1) is a member of the CRAL-TRIO family of lipid binding proteins that facilitates vitamin E transfer between membrane vesicles in vitro. In cultured hepatocytes, TTP enhances the secretion of tocopherol to the media; presumably, tocopherol transfer is at the basis of this biological activity. The mechanism underlying ligand transfer by TTP is presently unknown, and available tools for monitoring this activity suffer from complicated assay procedure and poor...

  3. Optimising methods for the preservation, capture and identification of ubiquitin chains and ubiquitylated proteins by immunoblotting.

    Science.gov (United States)

    Emmerich, Christoph H; Cohen, Philip

    2015-10-01

    Immunoblotting is a powerful technique for the semi-quantitative analysis of ubiquitylation events, and remains the most commonly used method to study this process due to its high specificity, speed, sensitivity and relatively low cost. However, the ubiquitylation of proteins is complex and, when the analysis is performed in an inappropriate manner, it can lead to the misinterpretation of results and to erroneous conclusions being reached. Here we discuss the advantages and disadvantages of the methods currently in use to analyse ubiquitin chains and protein ubiquitylation, and describe the procedures that we have found to be most useful for optimising the quality and reliability of the data that we have generated. We also highlight commonly encountered problems and the pitfalls inherent in some of these methods. Finally, we introduce a set of recommendations to help researchers obtain high quality data, especially those new to the field of ubiquitin signalling. The specific topics addressed in this article include sample preparation, the separation, detection and identification of particular ubiquitin chains by immunoblotting, and the analysis of ubiquitin chain topology through the combined use of ubiquitin-binding proteins and ubiquitin linkage-specific deubiquitylases. PMID:26325464

  4. Fusion protein of single-chain variable domain fragments for treatment of myasthenia gravis

    Institute of Scientific and Technical Information of China (English)

    Fangfang Li; Fanping Meng; Quanxin Jin; Changyuan Sun; Yingxin Li; Honghua Li; Songzhu Jin

    2014-01-01

    Single-chain variable domain fragment (scFv) 637 is an antigen-specific scFv of myasthenia gravis. In this study, scFv and human serum albumin genes were conjugated and the fusion pro-tein was expressed in Pichia pastoris. The afifnity of scFv-human serum albumin fusion protein to bind to acetylcholine receptor at the neuromuscular junction of human intercostal muscles was detected by immunolfuorescence staining. The ability of the fusion protein to block myas-thenia gravis patient sera binding to acetylcholine receptors and its stability in healthy serum were measured by competitive ELISA. The results showed that the inhibition rate was 2.0-77.4%, and the stability of fusion protein in static healthy sera was about 3 days. This approach suggests the scFv-human serum albumin is a potential candidate for speciifc immunosuppressive therapy of myasthenia gravis.

  5. Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data

    Energy Technology Data Exchange (ETDEWEB)

    Zeng Jianyang [Duke University, Department of Computer Science (United States); Zhou Pei [Duke University Medical Center, Department of Biochemistry (United States); Donald, Bruce Randall [Duke University, Department of Computer Science (United States)

    2011-08-15

    One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY experiments perform poorly on large proteins. To overcome this deficiency, we present a novel algorithm, called Nasca (NOE Assignment and Side-Chain Assignment), to automate both side-chain resonance and NOE assignments and to perform high-resolution protein structure determination in the absence of any explicit through-bond experiment to facilitate side-chain resonance assignment, such as HCCH-TOCSY. After casting the assignment problem into a Markov Random Field (MRF), Nasca extends and applies combinatorial protein design algorithms to compute optimal assignments that best interpret the NMR data. The MRF captures the contact map information of the protein derived from NOESY spectra, exploits the backbone structural information determined by RDCs, and considers all possible side-chain rotamers. The complexity of the combinatorial search is reduced by using a dead-end elimination (DEE) algorithm, which prunes side-chain resonance assignments that are provably not part of the optimal solution. Then an A* search algorithm is employed to find a set of optimal side-chain resonance assignments that best fit the NMR data. These side-chain resonance assignments are then used to resolve the NOE assignment ambiguity and compute high-resolution protein structures. Tests on five proteins show that Nasca assigns resonances for more than 90% of side-chain protons, and achieves about 80% correct assignments. The final structures computed using the NOE distance restraints assigned by Nasca have backbone RMSD 0

  6. Breeding bread wheat cultivars for high protein content by transfer of protein genes from Triticum dicoccoides

    International Nuclear Information System (INIS)

    Triticum dicoccoides sel. G-25, a selection of wild emmer with a protein content of 20.5% and a kernel weight of 31.5 mg, was used as the donor of protein genes. Since this selection is highly resistant to stripe rust, the object of the crossing programme was to transfer this resistance, together with the high protein potential, to durum and bread wheat cultivars susceptible to the disease. In the tetraploid lines obtained from the T. dicoccoides/T. durum cross, the protein values ranged from 17 to 22%. These lines had resistance to stripe rust from the wild emmer and to stem rust from the durum. After two further crosses between these tetraploid lines and T. aestivum cultivars, several lines were selected which combined good yield, high protein level and resistance to rust diseases. These lines attained protein levels of 14 to 19% in the whole grain and 14 to 17% in the flour, combined with yields of 4.5 to 6.0 t/ha. They had also inherited resistance to stem rust, and in some instances also to leaf rust, from the cultivated wheat parental lines. (author)

  7. Reversible and Irreversible Aggregation of Proteins from the FET Family: Influence of Repeats in Protein Chain on Its Aggregation Capacity.

    Science.gov (United States)

    Galzitskaya, Oxana V

    2016-01-01

    The discovery of protein chain regions responsible for protein aggregation is an important result of studying of the molecular mechanisms of prion diseases and different proteinopathies associated with the formation of pathological aggregations through the prion mechanism. The ability to control aggregation of proteins could be an important tool in the arsenal of the drug development. Here we demonstrate, on an example of RNA-binding proteins of the FET family from six animal species (human, gorilla, pig, mouse, chicken, zebra fish), the possible role of repeats within the disordered regions. For these proteins, different repeats are revealed in the prion-like (N-terminal disordered) domains, and in the C-terminal disordered regions, predicted using bioinformatics methods. Moreover, we have found that in more complex organisms the number of repeats is increased. It can be hypothesized that the presence of a large number of repeats in the disordered regions in the proteins of the FET-family could both modulate and accelerate the formation of a dynamic cross-beta structure, and pathological aggregates. PMID:26100283

  8. In silico allergenicity prediction of several lipid transfer proteins.

    Science.gov (United States)

    Garino, Cristiano; Coïsson, Jean Daniel; Arlorio, Marco

    2016-02-01

    Non-specific lipid transfer proteins (nsLTPs) are common allergens and they are particularly widespread within the plant kingdom. They have a highly conserved three-dimensional structure that generate a strong cross-reactivity among the members of this family. In the last years several web tools for the prediction of allergenicity of new molecules based on their homology with known allergens have been released, and guidelines to assess potential allergenicity of proteins through bioinformatics have been established. Even if such tools are only partially reliable yet, they can provide important indications when other kinds of molecular characterization are lacking. The potential allergenicity of 28 amino acid sequences of LTPs homologs, either retrieved from the UniProt database or in silico deduced from the corresponding EST coding sequence, was predicted using 7 publicly available web tools. Moreover, their similarity degree to their closest known LTP allergens was calculated, in order to evaluate their potential cross-reactivity. Finally, all sequences were studied for their identity degree with the peach allergen Pru p 3, considering the regions involved in the formation of its known conformational IgE-binding epitope. Most of the analyzed sequences displayed a high probability to be allergenic according to all the software employed. The analyzed LTPs from bell pepper, cassava, mango, mungbean and soybean showed high homology (>70%) with some known allergenic LTPs, suggesting a potential risk of cross-reactivity for sensitized individuals. Other LTPs, like for example those from canola, cassava, mango, mungbean, papaya or persimmon, displayed a high degree of identity with Pru p 3 within the consensus sequence responsible for the formation, at three-dimensional level, of its major conformational epitope. Since recent studies highlighted how in patients mono-sensitized to peach LTP the levels of IgE seem directly proportional to the chance of developing cross

  9. Terrestrial model food chain and environmental chemicals. I. Transfer of sodium [14C]pentachlorophenate between springtails and carabids

    International Nuclear Information System (INIS)

    A model soil food chain of a ruderal ecosystem has been constructed in order to study the uptake, transfer, and accumulation of [14C]pentachlorophenate (PCP-Na). The model was based on three food levels, viz. baker's yeast, collembola, and carabid beetles, and the contaminant chemical introduced was via initial food. Continuous exposure of the organisms to the test chemical resulted in a significant uptake and transfer of radiocarbon into the food chain elements. Bioaccumulation of radiocarbon in the body tissues of the organisms was low, as large amounts taken up were quickly eliminated through the excrements. The radiocarbon level of prey animals was about 100 times higher than that of their predators, but there was only small difference in concentration between collembolas and yeast. This was probably because of a faster excretion of the chemical by the beetles than by the collembolas. During the test period no conversion of [14C]PCP-Na took place in the yeast, but the collembolas and beetles metabolized 50 and 59%, respectively. Criteria are proposed for successful implementation of food chain models

  10. Lysophosphatidylcholine as an adjuvant for lentiviral vector mediated gene transfer to airway epithelium: effect of acyl chain length

    Directory of Open Access Journals (Sweden)

    Anson Don S

    2010-06-01

    Full Text Available Abstract Background Poor gene transfer efficiency has been a major problem in developing an effective gene therapy for cystic fibrosis (CF airway disease. Lysophosphatidylcholine (LPC, a natural airway surfactant, can enhance viral gene transfer in animal models. We examined the electrophysiological and physical effect of airway pre-treatment with variants of LPC on lentiviral (LV vector gene transfer efficiency in murine nasal airways in vivo. Methods Gene transfer was assessed after 1 week following nasal instillations of a VSV-G pseudotype LV vector pre-treated with a low and high dose of LPC variants. The electrophysiological effects of a range of LPC variants were assessed by nasal transepithelial potential difference measurements (TPD to determine tight junction permeability. Any physical changes to the epithelium from administration of the LPC variants were noted by histological methods in airway tissue harvested after 1 hour. Results Gene transduction was significantly greater compared to control (PBS for our standard LPC (palmitoyl/stearoyl mixture treatment and for the majority of the other LPC variants with longer acyl chain lengths. The LPC variant heptadecanoyl also produced significantly greater LV gene transfer compared to our standard LPC mixture. LV gene transfer and the transepithelial depolarization produced by the 0.1% LPC variants at 1 hour were strongly correlated (r2 = 0.94, but at the 1% concentration the correlation was less strong (r2 = 0.59. LPC variants that displayed minor to moderate levels of disruption to the airway epithelium were clearly associated with higher LV gene transfer. Conclusions These findings show the LPC variants effect on airway barrier function and their correlation to the effectiveness of gene expression. The enhanced expression produced by a number of LPC variants should provide new options for preclinical development of efficient airway gene transfer techniques.

  11. Transfer of Ho Endonuclease and Ufo1 to the Proteasome by the UbL-UbA Shuttle Protein, Ddi1, Analysed by Complex Formation In Vitro

    OpenAIRE

    Voloshin, Olga; Bakhrat, Anya; Herrmann, Sharon; Raveh, Dina

    2012-01-01

    The F-box protein, Ufo1, recruits Ho endonuclease to the SCFUfo1 complex for ubiquitylation. Both ubiquitylated Ho and Ufo1 are transferred by the UbL-UbA protein, Ddi1, to the 19S Regulatory Particle (RP) of the proteasome for degradation. The Ddi1-UbL domain binds Rpn1 of the 19S RP, the Ddi1-UbA domain binds ubiquitin chains on the degradation substrate. Here we used complex reconstitution in vitro to identify stages in the transfer of Ho and Ufo1 from the SCFUfo1 complex to the proteasome...

  12. Transfer of Ho Endonuclease and Ufo1 to the Proteasome by the UbL-UbA Shuttle Protein, Ddi1, Analysed by Complex Formation In Vitro

    OpenAIRE

    Olga Voloshin; Anya Bakhrat; Sharon Herrmann; Dina Raveh

    2012-01-01

    The F-box protein, Ufo1, recruits Ho endonuclease to the SCF(Ufo1) complex for ubiquitylation. Both ubiquitylated Ho and Ufo1 are transferred by the UbL-UbA protein, Ddi1, to the 19S Regulatory Particle (RP) of the proteasome for degradation. The Ddi1-UbL domain binds Rpn1 of the 19S RP, the Ddi1-UbA domain binds ubiquitin chains on the degradation substrate. Here we used complex reconstitution in vitro to identify stages in the transfer of Ho and Ufo1 from the SCF(Ufo1) complex to the protea...

  13. Effects of conformational ordering on protein/polyelectrolyte electrostatic complexation: ionic binding and chain stiffening

    Science.gov (United States)

    Cao, Yiping; Fang, Yapeng; Nishinari, Katsuyoshi; Phillips, Glyn O.

    2016-01-01

    Coupling of electrostatic complexation with conformational transition is rather general in protein/polyelectrolyte interaction and has important implications in many biological processes and practical applications. This work studied the electrostatic complexation between κ-carrageenan (κ-car) and type B gelatin, and analyzed the effects of the conformational ordering of κ-car induced upon cooling in the presence of potassium chloride (KCl) or tetramethylammonium iodide (Me4NI). Experimental results showed that the effects of conformational ordering on protein/polyelectrolyte electrostatic complexation can be decomposed into ionic binding and chain stiffening. At the initial stage of conformational ordering, electrostatic complexation can be either suppressed or enhanced due to the ionic bindings of K+ and I− ions, which significantly alter the charge density of κ-car or occupy the binding sites of gelatin. Beyond a certain stage of conformational ordering, i.e., helix content θ > 0.30, the effect of chain stiffening, accompanied with a rapid increase in helix length ζ, becomes dominant and tends to dissociate the electrostatic complexation. The effect of chain stiffening can be theoretically interpreted in terms of double helix association. PMID:27030165

  14. Effects of conformational ordering on protein/polyelectrolyte electrostatic complexation: ionic binding and chain stiffening

    Science.gov (United States)

    Cao, Yiping; Fang, Yapeng; Nishinari, Katsuyoshi; Phillips, Glyn O.

    2016-03-01

    Coupling of electrostatic complexation with conformational transition is rather general in protein/polyelectrolyte interaction and has important implications in many biological processes and practical applications. This work studied the electrostatic complexation between κ-carrageenan (κ-car) and type B gelatin, and analyzed the effects of the conformational ordering of κ-car induced upon cooling in the presence of potassium chloride (KCl) or tetramethylammonium iodide (Me4NI). Experimental results showed that the effects of conformational ordering on protein/polyelectrolyte electrostatic complexation can be decomposed into ionic binding and chain stiffening. At the initial stage of conformational ordering, electrostatic complexation can be either suppressed or enhanced due to the ionic bindings of K+ and I‑ ions, which significantly alter the charge density of κ-car or occupy the binding sites of gelatin. Beyond a certain stage of conformational ordering, i.e., helix content θ > 0.30, the effect of chain stiffening, accompanied with a rapid increase in helix length ζ, becomes dominant and tends to dissociate the electrostatic complexation. The effect of chain stiffening can be theoretically interpreted in terms of double helix association.

  15. Structural Origins of Nitroxide Side Chain Dynamics on Membrane Protein [alpha]-Helical Sites

    Energy Technology Data Exchange (ETDEWEB)

    Kroncke, Brett M.; Horanyi, Peter S.; Columbus, Linda (UV)

    2010-12-07

    Understanding the structure and dynamics of membrane proteins in their native, hydrophobic environment is important to understanding how these proteins function. EPR spectroscopy in combination with site-directed spin labeling (SDSL) can measure dynamics and structure of membrane proteins in their native lipid environment; however, until now the dynamics measured have been qualitative due to limited knowledge of the nitroxide spin label's intramolecular motion in the hydrophobic environment. Although several studies have elucidated the structural origins of EPR line shapes of water-soluble proteins, EPR spectra of nitroxide spin-labeled proteins in detergents or lipids have characteristic differences from their water-soluble counterparts, suggesting significant differences in the underlying molecular motion of the spin label between the two environments. To elucidate these differences, membrane-exposed {alpha}-helical sites of the leucine transporter, LeuT, from Aquifex aeolicus, were investigated using X-ray crystallography, mutational analysis, nitroxide side chain derivatives, and spectral simulations in order to obtain a motional model of the nitroxide. For each crystal structure, the nitroxide ring of a disulfide-linked spin label side chain (R1) is resolved and makes contacts with hydrophobic residues on the protein surface. The spin label at site I204 on LeuT makes a nontraditional hydrogen bond with the ortho-hydrogen on its nearest neighbor F208, whereas the spin label at site F177 makes multiple van der Waals contacts with a hydrophobic pocket formed with an adjacent helix. These results coupled with the spectral effect of mutating the i {+-} 3, 4 residues suggest that the spin label has a greater affinity for its local protein environment in the low dielectric than on a water-soluble protein surface. The simulations of the EPR spectra presented here suggest the spin label oscillates about the terminal bond nearest the ring while maintaining weak

  16. Radiation and environment. Study of uranium transfer to humans by the food chain: experiment design and first results

    International Nuclear Information System (INIS)

    During years, scientific assessments had considered plants, animal and other living organism as part of the environment in which radionuclides become dispersed. They were further seen as resources which, when contaminated, may contribute to human radiation exposure since some plants and animals are elements of food chains and represent pathways for the transfer of radionuclides to humans. Today, the assessments are development reflected the generally accepted position that priority should be given to evaluating the potential consequences for humans, which are among the most radiosensitive mammalian species. The transfer of radioisotopes from food to humans is still a well debated issue, because experimental results are even scarce. As a contribution to this issue, the Linear Accelerator Laboratory of the Physics Institute at the Sao Paulo University jointed to other institute of Brazil and Cuba development a project for study of uranium in the food-chain: food-animal/vegetables-human. This project involves experimentation with mammalians (wistar rats and beagles dogs), fishes and vegetables, plus extrapolation to humans by means of the General Multiple-Compartments Model. The pilot experiments in animal and vegetables are well described in the paper. As first results were obtained the transfer coefficients of uranium to the organs of animals as a function of the uranium concentration present in the administered food and the transfer coefficients of uranium for each part of the plant, as function of both growing time and uranium concentration in the nutrients solution. With this data it would be possible to evaluate the uranium ingestion by humans from animal products and plants, given their dietary habits, to infer human absorption of uranium associated with prolonged intake of uranium contained in food and estimates the content of uranium transferred to humans organs, thus allowing the evaluation of internally localized doses and the radiobiological damage and

  17. Effect of charge transfer on chain dimension in trans-polyacetylene

    Science.gov (United States)

    Murthy, N. S.; Shacklette, L. W.; Baughman, R. H.

    1987-08-01

    X-ray diffraction measurements on all-trans-polyacetylene are consistent with a chain-axis length elongation upon donor doping (+0.026 Å for lithium and +0.04 Å for potassium) and a chain-axis length contraction upon acceptor doping (-0.010 Å for iodine), where the changes refer to the length L of a C2H2 unit (2.457 Å in the undoped polymer). These new experimentally derived results for heavily doped compositions, which ignore possible corrections for cell nonorthogonality in the lithium and iodine complexes, are similar to experimental results for graphite intercalation complexes and are consistent with theoretical predictions for doped polyacetylene. The meridional diffraction lines observed at L and L/2 for potassium-doped polyacetylene indicate that there is no lattice symmetry element which includes a translation operation of L/2 in the chain-axis direction. The observations are consistent with a structural model in which alkali-metal ions with an intracolumn spacing of 4.96 Å are commensurate with the polymer chains for the composition (CHM0.125)x. The likely polymer chain-axis repeat length is 2L (i.e., C4H4) and a lattice symmetry element which includes a translation of L is expected.

  18. Elucidation and Control of an Intramolecular Charge Transfer Property of Fucoxanthin by a Modification of Its Polyene Chain Length.

    Science.gov (United States)

    Kosumi, Daisuke; Kajikawa, Takayuki; Okumura, Satoshi; Sugisaki, Mitsuru; Sakaguchi, Kazuhiko; Katsumura, Shigeo; Hashimoto, Hideki

    2014-03-01

    Fucoxanthin is an essential pigment for the highly efficient light-harvesting function of marine algal photosynthesis. It exhibits excited state properties attributed to intramolecular charge transfer (ICT) in polar environments due to the presence of the carbonyl group in its polyene backbone. This report describes the excited state properties of fucoxanthin homologues with four to eight conjugated double bonds in various solvents using the femtosecond pump-probe technique. The results clarified that fucoxanthin homologues with longer polyene chains did not possess pronounced ICT spectroscopic signatures, while the shorter fucoxanthin homologues had a strong ICT character, even in a nonpolar solvent. On the basis of the observations, we quantitatively correlated the ICT character in the excited state to the conjugated polyene chain lengths of fucoxanthin molecules. PMID:26274069

  19. Developing a Taxonomy and Model to Transfer and Assess Best Practices for Supply Chain Management

    Science.gov (United States)

    Flores, Myrna; Mendoza, Ana; Lavin, Victor; Flores, Benito

    Supply Chain Management can be briefly defined as the orchestration of a network of entities such as suppliers, distributors and clients to achieve a common goal: delivering cost efficient products and services exceeding customers’ expectations. Therefore, firms should consider all those End-to-End processes enabling an efficient integration and interoperability of partners collaborating in such Supply Chain when designing their Business Process Architecture (BPA). One key enabler to accomplish this goal is the identification, documentation and sharing of best practices. This paper describes the outcomes of a collaborative project carried out by CEMEX Research Group and the Universidad de Monterrey (UDEM), which focused on developing taxonomy to document best practices for the supply chain management together with a generic model to evaluate their level of implementation.

  20. Trophic transfer of aluminium through an aquatic grazer-omnivore food chain

    International Nuclear Information System (INIS)

    The potential for trophic transfer of aluminium (Al) was investigated using a grazing detritivore, the freshwater snail Lymnaea stagnalis, and a predator, the signal crayfish Pacifastacus leniusculus. Snails were exposed to either aqueous Al (500 μg l-1) in the presence or absence of an inorganic ligand (phosphate (+P); 500 μg l-1) for 30 days, or kept as unexposed controls. Subcellular partitioning of Al in the snail tissues was characterised using ultracentrifugation. Al content in the soft tissues and the subcellular fractions was measured using inductively coupled plasma atomic emission spectroscopy. Exposed and control snails were fed to individually housed crayfish (n = 6 per group) over 40 days. Water samples, uneaten snail tissue and faeces were collected throughout the experiment in order to assess the fate of Al. Behavioural toxicity to the crayfish was assessed at four time points, and tissue accumulation of Al in soft tissues was measured following a 2-day depuration period. Snails exposed to Al + P accumulated more Al per snail than those exposed to Al only (291 μg vs 206 μg), and also contained a higher proportion of detoxified Al (in inorganic granules and associated with heat stable proteins) (39% vs 26%). There were no significant differences in behavioural activity between the different groups of crayfish at any time point. Crayfish fed snails exposed to only Al accumulated significant levels of Al in their total soft tissues, compared to controls; crayfish fed Al + P-exposed snails did not, even though concentrations of Al in these snails were higher. The highest concentrations of Al were found in the green gland in both crayfish feeding groups, and the gut and hepatopancreas in crayfish fed Al only exposed snails; all of these were significantly higher than in crayfish fed control snails. There was no significant accumulation of Al in the gills or flexor muscle in any group. At least 17% of trophically available Al in the snail tissues was

  1. A non-linear approach to the structure-mobility relationship in protein main chains

    International Nuclear Information System (INIS)

    A correlation investigation was carried out on the series of atomic coordinates (MPV) and temperature factor (T f), respectively for human hemoglobin and HIV-1 protease protein main chains. The MPV series revealed resemblances to the corresponding T f series. Each minor or major peak in a series had a corresponding peak in the related series. This brings a qualitative evidence for the connection of the two parameters. The series were further subjected to spectral and detrended fluctuation analysis which all revealed long-range correlation properties. This combined analysis revealed that the data were controlled both by the correlation of stationary fluctuation and trends or non-stationary contribution to correlation. The correlation of all MPV series was found to be much less sensitive to ligand binding than the corresponding T f series. Thus the long-range correlation properties of the protein main chain structure and mobility revealed two complementary properties of protein molecules. While structure imparts constancy to the system, the atomic mobility represents function yet they are intimately connected

  2. Detection of kappa and lambda light chain monoclonal proteins in human serum: automated immunoassay versus immunofixation electrophoresis.

    Science.gov (United States)

    Jaskowski, Troy D; Litwin, Christine M; Hill, Harry R

    2006-02-01

    Recently, turbidimetric immunoassays for detecting and quantifying kappa and lambda free light chains (FLC) have become available and are promoted as being more sensitive than immunofixation electrophoresis (IFE) in detecting FLC monoclonal proteins. In this study, we assessed the ability of these turbidimetric assays to detect serum monoclonal proteins involving both free and heavy-chain-bound kappa and lambda light chains compared to standard immunofixation electrophoresis. Sera demonstrating a restricted band of protein migration (other than a definite M spike) by serum protein electrophoresis (SPE), which may represent early monoclonal proteins, were also examined. When compared to IFE, percent agreement, sensitivity, and specificity for the kappa-FLC and lambda-FLC were 94.6, 72.9, and 99.5% and 98.5, 91.4, and 99.7%, respectively, in detecting monoclonal proteins involving free and heavy-chain-bound light chains. The majority of sera (73.7%) demonstrating a restricted band of protein migration on SPE demonstrated abnormal IFE patterns suggestive of multiple myeloma or monoclonal gammopathy of unknown significance, but gave normal kappa/lambda FLC ratios using the turbidimetric immunoassays. In conclusion, the kappa and lambda FLC assays are significantly less sensitive (72.9 to 91.4%) than IFE, but specific in detecting serum monoclonal proteins. Moreover, the kappa/lambda ratio has little value in routine screening since the majority of sera with abnormal IFE patterns had normal kappa/lambda FLC ratios. PMID:16467338

  3. The transfer of titanium dioxide nanoparticles from the host plant to butterfly larvae through a food chain

    OpenAIRE

    Miyoko Kubo-Irie; Masaaki Yokoyama; Yusuke Shinkai; Rikio Niki; Ken Takeda; Masaru Irie

    2016-01-01

    This study aimed to examine the transfer of nanoparticles within a terrestrial food chain. Oviposited eggs of the swallowtail butterfly (Atrophaneura alcinous) were hatched on the leaves of the host plant (Aristolochia debilis), and the root stock and root hairs were submerged in a suspension of 10 μg/ml titanium dioxide nanoparticles (TiO2-NPs) in a 100 ml bottle. The presence of TiO2-NPs in the veins of the leaves was confirmed by X-ray analytical microscopy (X-ray AM). The hatched 1st inst...

  4. Enhancing Chinese Agribusiness Supply Chains with Internet Technologies: A Transnational Knowledge Transfer Approach

    Science.gov (United States)

    Duan, Yanqing; Bentley, Yongmei; Fu, Zetian; Zografos, Konstantinos; Bemeleit, Boris

    2008-01-01

    This paper reports research findings from a project funded by the European Commission. The research used case studies and surveys to identify gaps between Europe and China in the level of Internet adoption in fresh-produce supply chains. The project reveals barriers to Internet adoption in China in this industry, and employs a transnational…

  5. Transfer and effects of 1,2,3,5,7-pentachloronaphthalene in an experimental food chain

    DEFF Research Database (Denmark)

    Slootweg, Tineke; Segner, Helmut; Mayer, Philipp;

    2015-01-01

    of this study was to gain insights into the biomagnification and effects of 1,2,3,5,7-pentachloronaphthalene (PeCN52) in an experimental food chain consisting of benthic worms and juvenile rainbow trout. Worms were contaminated with PeCN52 by passive dosing from polydimethylsiloxane silicone. The...

  6. Construction and analysis of a plant non-specific lipid transfer protein database (nsLTPDB)

    OpenAIRE

    Wang Nai-Jyuan; Lee Chi-Ching; Cheng Chao-Sheng; Lo Wei-Cheng; Yang Ya-Fen; Chen Ming-Nan; Lyu Ping-Chiang

    2012-01-01

    Abstract Background Plant non-specific lipid transfer proteins (nsLTPs) are small and basic proteins. Recently, nsLTPs have been reported involved in many physiological functions such as mediating phospholipid transfer, participating in plant defence activity against bacterial and fungal pathogens, and enhancing cell wall extension in tobacco. However, the lipid transfer mechanism of nsLTPs is still unclear, and comprehensive information of nsLTPs is difficult to obtain. Methods In this study...

  7. Probing Membrane Protein Structure Using Water Polarization Transfer Solid-State NMR

    OpenAIRE

    Williams, Jonathan K.; Hong, Mei

    2014-01-01

    Water plays an essential role in the structure and function of proteins, lipid membranes and other biological macromolecules. Solid-state NMR heteronuclear-detected 1H polarization transfer from water to biomolecules is a versatile approach for studying water-protein, water-membrane, and water-carbohydrate interactions in biology. We review radiofrequency pulse sequences for measuring water polarization transfer to biomolecules, the mechanisms of polarization transfer, and the application of ...

  8. Mirage, a food chain transfer and dosimetric impact code in relation with atmospheric and liquid dispersion codes

    International Nuclear Information System (INIS)

    Full text: The numerical code M.I.R.A.G.E. (Module of Radiological impact calculations on the Environment due to accidental or chronic nuclear releases through Aqueous and Gas media) has been developed to simulate the radionuclides transfer in the biosphere and food chains, as well as the dosimetric impact on man, after accidental or chronic releases in the environment by nuclear installations. The originality of M.I.R.A.G.E. is to propose a single tool chained downstream with various atmospheric and liquid dispersion codes. The code M.I.R.A.G.E. is a series of modules which makes it possible to carry out evaluations on the transfers in food chains and human dose impact. Currently, M.I.R.A.G.E. is chained with a Gaussian atmospheric dispersion code H.A.R.M.A.T.T.A.N. (Cea), a 3 D atmospheric dispersion code with Lagrangian model named M.I.N.E.R.V.E.-S.P.R.A.Y. (Aria Technology) and a 3 D groundwater transfer code named M.A.R.T.H.E. (B.R.G.M.). M.I.R.A.G.E. uses concentration or activity result files as initial data input for its calculations. The application initially calculates the concentrations in the various compartments of the environment (soils, plants, animals). The results are given in the shape of concentration and dose maps and also on a particular place called a reference group for dosimetric impact (like a village or a specific population group located around a nuclear installation). The input and output data of M.I.R.A.G.E. can have geographic coordinates and thus readable by a G.I.S. M.I.R.A.G. E.is an opened system with which it is easy to chain other codes of dispersion that those currently used. The calculations uncoupled with dispersion calculations are also possible by manual seizure of the dispersion data (contamination of a tablecloth, particular value in a point, etc.). M.I.R.A.G.E. takes into account soil deposits and resuspension phenomenon, transfers in plants and animals (choice of agricultural parameters, types of plants and animals, etc

  9. Transfer of 226Ra, 228Ra, 210Pb and 210Po in aquatic organisms and food chain

    International Nuclear Information System (INIS)

    Objective: To find out the transfer regularities of 226Ra, 228Ra, 210Pb and 210Po, which are natural radionuclides in the aquatic organisms and food chain. Methods: Large amount of breed of representative aquatic products and their living waters and sediments were collected and treated according to routine experimental procedures. The contents of 226Ra, 228Ra, 210Pb and 210Po were detected in each sample. Measured data were analyzed statistically and pairwise comparisons were made to determine the differences between groups. Results: 226Ra, 228Ra and 210Pb were mainly deposited in the bones (or shells), their concentration factors (CF) ranged from 102 to 103; the CF ranged only from 100 to 102 in the flesh. 210Po was mainly deposited in the soft tissues, CF ranged from 102 to 104; especially in the stomachs and intestines of fishes, the value reached 104. The cooking process did not impinge significantly on the transfer of 226Ra, 228Ra and 210Pb in the food chain (P>0.05), but did significantly influence the transfer of 210Po, especially in the freshwater fishes and shrimps. Paired comparison test of the activities between raw flesh and cooked flesh showed very significant difference (P226Ra, 228Ra, 210Pb and 210Po. Even though the bones (or shells) of aquatic organisms contained relatively higher levels of 226Ra, 228Ra and 210Pb, the cooking process does not significantly increase the radioactive contents in the foodstuffs. However, the cooking process does significantly influence the transfer of 210Po. It does significantly increase the content of 210Po in foodstuffs

  10. Evaluation of data on the transfer of radionuclides in the food chain post-Chernobyl action

    International Nuclear Information System (INIS)

    During the accident at Chernobyl large amounts of radioactive materials were released into the atmosphere and distributed all over Europe. Depending on the trajectories of the radioactive clouds and the large variation of rainfall during its passage through, large local and regional differences in deposition were observed, leading to an enhanced contamination of soil and plants. Consequently, the radionuclides entered the foodchain by several pathways. The radiological consequences of radionuclides discharged from nuclear installations usually are evaluated using doses assessment models. In these models the passage from one compartment into another, e.g. the transfer from soil into plants, from plants into milk or meat is defined by transfer factors, which are influenced by various parameters. From the long term point of view only the long-lived nuclides like 134/137Cs are important for long term radiation risk assessment after the Chernobyl accident. In this accident the release of radioactive materials took place over a longer time period and varied in rate and radionuclide composition. Some regions of Europe were contaminated several times. To improve radiation dose prediction the CEC has initiated the Post-Chernobyl radiation protection programme 'Evaluation of Data on the Transfer of Radionuclides in the Foodchain' including five main items to be studied by different laboratories: 1. Impact of chemical speciation on the radionuclide transfer in terrestrial ecosystems after a core disruptive accident, especially in soils and plants. 2. Transfer paths of radionuclides in seminatural and natural ecosystems and their role in contaminating the foodchain. 3. Validation of soil-to-plant parameters. 4. Transfer of radionuclides to animals and animal products. 5. Transfer paths in aquatic systems and their importance for the contamination of the foodchain

  11. Sphingolipid metabolism and interorganellar transport: localization of sphingolipid enzymes and lipid transfer proteins.

    Science.gov (United States)

    Yamaji, Toshiyuki; Hanada, Kentaro

    2015-02-01

    In recent decades, many sphingolipid enzymes, sphingolipid-metabolism regulators and sphingolipid transfer proteins have been isolated and characterized. This review will provide an overview of the intracellular localization and topology of sphingolipid enzymes in mammalian cells to highlight the locations where respective sphingolipid species are produced. Interestingly, three sphingolipids that reside or are synthesized in cytosolic leaflets of membranes (ceramide, glucosylceramide and ceramide-1-phosphate) all have cytosolic lipid transfer proteins (LTPs). These LTPs consist of ceramide transfer protein (CERT), four-phosphate adaptor protein 2 (FAPP2) and ceramide-1-phosphate transfer protein (CPTP), respectively. These LTPs execute functions that affect both the location and metabolism of the lipids they bind. Molecular details describing the mechanisms of regulation of LTPs continue to emerge and reveal a number of critical processes, including competing phosphorylation and dephosphorylation reactions and binding interactions with regulatory proteins and lipids that influence the transport, organelle distribution and metabolism of sphingolipids. PMID:25382749

  12. The cDNA sequence for the protein-tyrosine kinase substrate p36 (calpactin I heavy chain) reveals a multidomain protein with internal repeats

    DEFF Research Database (Denmark)

    Sarin, C T; Tack, B F; Kristensen, Torsten; Glenney Jr., J R; Hunter, T

    1986-01-01

    We have isolated and sequenced a full-length cDNA clone for the protein-tyrosine kinase substrate p36 (calpactin I heavy chain). This sequence predicts a 339 amino acid (Mr 38,493) protein containing an N-terminal region of 20 amino acids, known to interact with a 10 kd protein (light chain), and...... A2 inhibitor lipocortin I were found to be 50% identical in sequence over the C-terminal 300 residues. The function of p36 and its relation to other proteins are discussed....

  13. PPAR-β/δ activation promotes phospholipid transfer protein expression.

    Science.gov (United States)

    Chehaibi, Khouloud; Cedó, Lídia; Metso, Jari; Palomer, Xavier; Santos, David; Quesada, Helena; Naceur Slimane, Mohamed; Wahli, Walter; Julve, Josep; Vázquez-Carrera, Manuel; Jauhiainen, Matti; Blanco-Vaca, Francisco; Escolà-Gil, Joan Carles

    2015-03-15

    The peroxisome proliferator-activated receptor (PPAR)-β/δ has emerged as a promising therapeutic target for treating dyslipidemia, including beneficial effects on HDL cholesterol (HDL-C). In the current study, we determined the effects of the PPAR-β/δ agonist GW0742 on HDL composition and the expression of liver HDL-related genes in mice and cultured human cells. The experiments were carried out in C57BL/6 wild-type, LDL receptor (LDLR)-deficient mice and PPAR-β/δ-deficient mice treated with GW0742 (10mg/kg/day) or a vehicle solution for 14 days. GW0742 upregulated liver phospholipid transfer protein (Pltp) gene expression and increased serum PLTP activity in mice. When given to wild-type mice, GW0742 significantly increased serum HDL-C and HDL phospholipids; GW0742 also raised serum potential to generate preβ-HDL formation. The GW0742-mediated effects on liver Pltp expression and serum enzyme activity were completely abolished in PPAR-β/δ-deficient mice. GW0742 also stimulated PLTP mRNA expression in mouse J774 macrophages, differentiated human THP-1 macrophages and human hepatoma Huh7. Collectively, our findings demonstrate a common transcriptional upregulation by GW0742-activated PPAR-β/δ of Pltp expression in cultured cells and in mouse liver resulting in enhanced serum PLTP activity. Our results also indicate that PPAR-β/δ activation may modulate PLTP-mediated preβ-HDL formation and macrophage cholesterol efflux. PMID:25662586

  14. Fast electron transfer through a single molecule natively structured redox protein

    OpenAIRE

    Della Pia, Eduardo Antonio; Chi, Qijin; Macdonald, J. Emyr; Ulstrup, Jens; Jones, D Dafydd; Elliott, Martin

    2012-01-01

    The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposi...

  15. Computational design and biochemical characterization of maize nonspecific lipid transfer protein variants for biosensor applications

    OpenAIRE

    Choi, Eun Jung; Mao, Jessica; Mayo, Stephen L.

    2007-01-01

    Lipid transfer proteins (LTPs) are a family of proteins that bind and transfer lipids. Utilizing the maize LTP, we have successfully engineered fluorescent reagentless biosensors for the natural ligand of LTPs; this was achieved by using computational protein design to remove a disulfide bridge and attaching a thio-reactive fluorophore. Conformational change induced by ligand titration is thought to affect the fluorescence of the fluorophore, allowing detection of ligand binding. Fluorescence...

  16. Plasmonics: Electromagnetic energy transfer and switching in nanoparticle chain-arrays below the diffraction limit

    Science.gov (United States)

    Brongersma, Mark; Hartman, John; Atwater, Harry

    2000-03-01

    Integrated optics faces the fundamental limitation that, for the guiding, modulation, and amplification of light, structures are needed that have dimensions comparable to the wavelength of light. Recently, it was theoretically shown that this problem can be circumvented by transporting electromagnetic energy along linear chains of closely spaced metal nanoparticles. This transport relies on the near-field electrodynamic interaction between metal particles that sets up coupled plasmon modes. We have modeled the transport properties of corners, T's, and switches that consist of chains of metal nanoparticles. It is shown that propagation is coherent and the group velocities can exceed saturated velocities of electrons in semiconductors ( ~ 105 m/s). High efficiency transmission of energy around sharp corners (bending radius plasmon mode. Finally, the operation of a plasmon switch is modeled in which plasmon waves can be switched. Suggestions are given for the choice of metal particle and host material. These "plasmonic devices" potentially are among the smallest structures with optical functionality.

  17. An 'adding' algorithm for the Markov chain formalism for radiation transfer

    Science.gov (United States)

    Esposito, L. W.

    1979-01-01

    An adding algorithm is presented, that extends the Markov chain method and considers a preceding calculation as a single state of a new Markov chain. This method takes advantage of the description of the radiation transport as a stochastic process. Successive application of this procedure makes calculation possible for any optical depth without increasing the size of the linear system used. It is determined that the time required for the algorithm is comparable to that for a doubling calculation for homogeneous atmospheres. For an inhomogeneous atmosphere the new method is considerably faster than the standard adding routine. It is concluded that the algorithm is efficient, accurate, and suitable for smaller computers in calculating the diffuse intensity scattered by an inhomogeneous planetary atmosphere.

  18. Impairment of Electron Transfer Chain Induced by Acute Carnosine Administration in Skeletal Muscle of Young Rats

    OpenAIRE

    José Roberto Macarini; Soliany Grassi Maravai; José Henrique Cararo; Nádia Webber Dimer; Cinara Ludvig Gonçalves; Luiza Wilges Kist; Mauricio Reis Bogo; Patrícia Fernanda Schuck; Emilio Luiz Streck; Gustavo Costa Ferreira

    2014-01-01

    Serum carnosinase deficiency is an inherited disorder that leads to an accumulation of carnosine in the brain tissue, cerebrospinal fluid, skeletal muscle, and other tissues of affected patients. Considering that high levels of carnosine are associated with neurological dysfunction and that the pathophysiological mechanisms involved in serum carnosinase deficiency remain poorly understood, we investigated the in vivo effects of carnosine on bioenergetics parameters, namely, respiratory chain ...

  19. Das Phosphatidylinositol-Transfer-Protein PITPnm2 in humanen Thrombozyten

    OpenAIRE

    Kramer, Daniel

    2013-01-01

    Die Analyse des Phosphoproteoms in ruhenden und in aktivierten humanen Plättchen führte zur Identifikation des PITPnm2-Proteins. Dieses Protein wird bei einer Stimulation von Thrombozyten mit dem Prostazyklinanalogon Iloprost phosphoryliert. Diese Ergebnisse gaben Anlass zu weiteren Untersuchungen zum Vorkommen und zur Funktion dieses Proteins in Thrombozyten. In der Arbeit wurde gezeigt, dass das PITPnm2-Protein das einzige Protein der PITP-Familie ist, welches in humanen Thrombozyten exprim...

  20. Control of zinc transfer between thionein, metallothionein, and zinc proteins

    OpenAIRE

    Jacob, Claus; Maret, Wolfgang; Vallee, Bert L.

    1998-01-01

    Metallothionein (MT), despite its high metal binding constant (KZn = 3.2 × 1013 M−1 at pH 7.4), can transfer zinc to the apoforms of zinc enzymes that have inherently lower stability constants. To gain insight into this paradox, we have studied zinc transfer between zinc enzymes and MT. Zinc can be transferred in both directions—i.e., from the enzymes to thionein (the apoform of MT) and from MT to the apoenzymes. Agents that mediate or enhance zinc transfer have be...

  1. Probing intermolecular protein-protein interactions in the calcium-sensing receptor homodimer using bioluminescence resonance energy transfer (BRET)

    DEFF Research Database (Denmark)

    Jensen, Anders A.; Hansen, Jakob L; Sheikh, Søren P;

    2002-01-01

    -induced intermolecular movements in the CaR homodimer using the new bioluminescence resonance energy transfer technique, BRET2, which is based on the transference of energy from Renilla luciferase (Rluc) to the green fluorescent protein mutant GFP2. We tagged CaR with Rluc and GFP2 at different intracellular locations...

  2. Uranium transfer in the food chain from soil to plants, animals and man

    International Nuclear Information System (INIS)

    Our investigations aimed at following up the scientific basis of uranium transfer from the soils of different geological origins and from the immediate vicinity of uranium waste dumps in the vegetation, in waters (drinking water, mineral water and medicinal water), vegetable and animal foodstuffs and beverages; the regional human uranium intake, excretion, apparent absorption and balance in Germany and Mexico. Another aim of the investigations was to draw conclusions from the rules of transfer of this element from the rocks and soils to plants, animals and man. (authors)

  3. Transfer of radionuclides from high polluted bottom sediments to marine organisms through benthic food chain in post Fukushima period

    Science.gov (United States)

    Bezhenar, Roman; Jung, Kyung Tae; Maderich, Vladimir; Willemsen, Stefan; de With, Govert; Qiao, Fangli

    2015-04-01

    A catastrophic earthquake and tsunami occurred on March 11, 2011 and severely damaged the Fukushima Daiichi Nuclear Power Plant (FDNPP) that resulted in an uncontrolled release of radioactivity into air and ocean. Around 80% of the radioactivity released due to the FDNPP accident in March-April 2011 was either directly discharged into the ocean or deposited onto the ocean surface from the atmosphere. A large amount of long-lived radionuclides (mainly Cs-137) were released into the environment. The concentration of radionuclides in the ocean reached a maximum in mid-April of 2011, and then gradually decreased. From 2011 the concentration of Cs-137 in water essentially fell except the area around the FDNPP where leaks of contaminated water are continued. However, in the bottom sediment high concentrations of Cs-137 were found in the first months after the accident and slowly decreased with time. Therefore, it should be expected that a time delay is found of sediment-bound radionuclides in marine organisms. For the modeling of radionuclide transfer from highly polluted bottom sediments to marine organisms the dynamical food chain model BURN-POSEIDON (Heling et al, 2002; Maderich et al., 2014) was extended. In this model marine organisms are grouped into a limited number of classes based on their trophic level and type of species. These include: phytoplankton, zooplankton, fishes (two types: piscivorous and non-piscivorous), crustaceans, and molluscs for pelagic food chain and bottom sediment invertebrates, demersal fishes and bottom predators for benthic food chain and whole water column predators feeding by pelagial and benthic fishes. Bottom invertebrates consume organic parts of bottom sediments with adsorbed radionuclides which then migrate through the food chain. All organisms take radionuclides directly from water as well as via food. In fishes where radioactivity is not homogeneously distributed over all tissues of the organism, it is assumed that radionuclide

  4. Short-Chain Chromate Ion Transporter Proteins from Bacillus subtilis Confer Chromate Resistance in Escherichia coli▿

    Science.gov (United States)

    Díaz-Magaña, Amada; Aguilar-Barajas, Esther; Moreno-Sánchez, Rafael; Ramírez-Díaz, Martha I.; Riveros-Rosas, Héctor; Vargas, Eréndira; Cervantes, Carlos

    2009-01-01

    Tandem paired genes encoding putative short-chain monodomain protein members of the chromate ion transporter (CHR) superfamily (ywrB and ywrA) were cloned from genomic DNA of Bacillus subtilis strain 168. The transcription of the paired genes, renamed chr3N and chr3C, respectively, was shown to occur via a bicistronic mRNA generated from a promoter upstream of the chr3N gene. The chr3N and chr3C genes conferred chromate resistance when expressed in Escherichia coli strain W3110. The cloned chr3N gene alone did not confer chromate resistance on E. coli, suggesting that both chr3N and chr3C genes are required for function. E. coli cells expressing paired chr3N and chr3C genes demonstrated diminished uptake of chromate compared to that by a vector-only control strain. These results suggest that short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm. PMID:19581367

  5. Short-chain fluorescent tryptophan tags for on-line detection of functional recombinant proteins

    Directory of Open Access Journals (Sweden)

    Siepert Eva-Maria

    2012-09-01

    Full Text Available Abstract Background Conventional fluorescent proteins, such as GFP, its derivatives and flavin mononucleotide based fluorescent proteins (FbFPs are often used as fusion tags for detecting recombinant proteins during cultivation. These reporter tags are state-of-the-art; however, they have some drawbacks, which can make on-line monitoring challenging. It is discussed in the literature that the large molecular size of proteins of the GFP family may stress the host cell metabolism during production. In addition, fluorophore formation of GFP derivatives is oxygen-dependent resulting in a lag-time between expression and fluorescence detection and the maturation of the protein is suppressed under oxygen-limited conditions. On the contrary, FbFPs are also applicable in an oxygen-limited or even anaerobic environment but are still quite large (58% of the size of GFP. Results As an alternative to common fluorescent tags we developed five novel tags based on clustered tryptophan residues, called W-tags. They are only 5-11% of the size of GFP. Based on the property of tryptophan to fluoresce in absence of oxygen it is reasonable to assume that the functionality of our W-tags is also given under anaerobic conditions. We fused these W-tags to a recombinant protein model, the anti-CD30 receptor single-chain fragment variable antibody (scFv Ki-4(scFv and the anti-MucI single-chain fragment variable M12(scFv. During cultivation in Microtiter plates, the overall tryptophan fluorescence intensity of all cultures was measured on-line for monitoring product formation via the different W-tags. After correlation of the scattered light signal representing biomass concentration and tryptophan fluorescence for the uninduced cultures, the fluorescence originating from the biomass was subtracted from the overall tryptophan signal. The resulting signal, thus, represents the product fluorescence of the tagged and untagged antibody fragments. The product fluorescence signal

  6. Isolation of two glycolipid transfer proteins from bovine brain: reactivity toward gangliosides and neutral glycosphingolipids.

    Science.gov (United States)

    Gammon, C M; Vaswani, K K; Ledeen, R W

    1987-09-22

    Two glycolipid transfer proteins that catalyze the transfer of gangliosides and neutral glycosphingolipids from phosphatidylcholine vesicles to erythrocyte ghosts have been isolated from calf brain. Purification procedures included differential centrifugation, precipitation at pH 5.1, ammonium sulfate precipitation, and gel filtration on Sephadex G-50 and G-75. The final stage employed fast protein liquid chromatography (Mono S), producing two peaks of activity. Apparent purity of the major peak (TP I) was approximately 85-90%, as judged by sodium dodecyl sulfate/urea-polyacrylamide gel electrophoresis. That of the minor fraction (TP II) was less. The major band of both fractions had a molecular mass of approximately 20,000 daltons. Both proteins catalyzed the transfer of ganglioside GM1 as well as asialo-GM1, but transfer protein I was more effective with di- and trisialogangliosides. Transfer protein II appeared to be somewhat more specific for neutral glycolipids in that GA1 was transferred more rapidly than any of the gangliosides; however, lactosylceramide transfer was relatively slow. Neither protein catalyzed transfer of phosphatidylcholine. PMID:3689771

  7. Isolation of two glycolipid transfer proteins from bovine brain: reactivity toward gangliosides and neutral glycosphingolipids

    International Nuclear Information System (INIS)

    Two glycolipid transfer proteins that catalyze the transfer of gangliosides and neutral glycosphingolipids from phosphatidylcholine vesicles to erythrocyte ghosts have been isolated from calf brain. Purification procedures included differential centrifugation, precipitation at pH 5.1, ammonium sulfate precipitation, and gel filtration on Sephadex G-50 and G-75. The final stage employed fast protein liquid chromatography (Mono S), producing two peaks of activity. Apparent purity of the major peak (TP I) was approximately 85-90%, as judged by sodium dodecyl sulfate/urea-polyacrylamide gel electrophoresis. Radiolabeled glycolipids were used in the analysis. That of the minor fraction (TP II) was less. The major band of both fractions had a molecular mass of approximately 20,000 daltons. Both proteins catalyzed the transfer of ganglioside GM1 as well as asialo-GM1, but transfer protein I was more effective with di- and trisialogangliosides. Transfer protein II appeared to be somewhat more specific for neutral glycolipids in that GA1 was transferred more rapidly than any of the gangliosides; however, lactosylceramide transfer was relatively slow. Neither protein catalyzed transfer of phosphatidylcholine

  8. Studies of vitamin E binding and transfer by a rat liver cytosolic protein

    Energy Technology Data Exchange (ETDEWEB)

    Posch, K.C.; Mavis, R.D.

    1986-05-01

    In vitro vitamin E binding and transfer were examined using a semipurified (sephadex G-75 fraction) vitamin E binding and transfer protein (VE-TBP) from the rat liver cytosol. Binding and transfer studies thus far indicate that the protein is very specific for d-..cap alpha..-tocopherol. Among the other lipophilic ligands examined only d-..gamma..-tocopherol at high concentrations was competitive with d-..cap alpha..-tocopherol binding. Specificity studies also indicate the protein to be stereospecific in nature since dl-..cap alpha..-tocopherol was only partially competitive. Studies using PMSF and NEM also indicate that neither a hydroxyl nor a sulfhydryl functional group on the protein is required for vitamin E binding. Transfer studies show that the VE-TBP is capable of specifically transferring equal amounts of vitamin E from liposomes to both mitochondria and microsomes when comparable protein concentrations are used. This indicates that no preferential transfer to one membrane type occurs. Pretreatment of mitochondria and microsomes with heat, pronase or trypsin also does not affect transfer of vitamin E. Thus, transfer of vitamin E is not dependent on a membrane protein. Finally, the VE-TBP is capable of unidirectional transport of vitamin E from prelabelled microsomes to vitamin E free liposomes.

  9. Counting electrons transferred through a thin alumina film into Au chains

    OpenAIRE

    N. Nilius, N.; Ganduglia-Pirovano, M.; Brázdová, V.; Kulawik, M.; Sauer, J; Freund, H

    2008-01-01

    Low-temperature STM measurements combined with density functional theory calculations are employed to study the adsorption of gold on alumina/NiAl(110). The binding of Au monomers involves breaking of an oxide Al-O bond below the adatom and stabilizing the hence undercoordinated O ion by forming a new bond to an Al atom in the NiAl. The adsorption implies negative charging of the adatom. The linear arrangement of favorable binding sites induces the self-organization of Au atoms into chains. F...

  10. Turning the corner: efficient energy transfer in bent plasmonic nanoparticle chain waveguides.

    Science.gov (United States)

    Solis, David; Paul, Aniruddha; Olson, Jana; Slaughter, Liane S; Swanglap, Pattanawit; Chang, Wei-Shun; Link, Stephan

    2013-10-01

    For integrating and multiplexing of subwavelength plasmonic waveguides with other optical and electric components, complex architectures such as junctions with sharp turns are necessary. However, in addition to intrinsic losses, bending losses severely limit plasmon propagation. In the current work, we demonstrate that propagation of surface plasmon polaritons around 90° turns in silver nanoparticle chains occurs without bending losses. Using a far-field fluorescence method, bleach-imaged plasmon propagation (BlIPP), which creates a permanent map of the plasmonic near-field through bleaching of a fluorophore coated on top of a plasmonic waveguide, we measured propagation lengths at 633 nm for straight and bent silver nanoparticle chains of 8.0 ± 0.5 and 7.8 ± 0.4 μm, respectively. These propagation lengths were independent of the input polarization. We furthermore show that subradiant plasmon modes yield a longer propagation length compared to energy transport via excitation of super-radiant modes. PMID:24020385

  11. Electrochemical studies of a reconstituted photosynthetic electron-transfer chain or towards a biomimetic photoproduction of hydrogen; Etudes electrochimiques de chaines de transfert d'electrons photosynthetiques ou vers une photoproduction biomimetique d'hydrogene

    Energy Technology Data Exchange (ETDEWEB)

    Fourmond, V

    2007-04-15

    The aim of this work is to find an efficient process to convert solar energy into hydrogen. The electrons transfers in reconstituted photosynthetic chains have been particularly studied with the aims 1)in one hand, to better understand the interactions of the different molecules of the photosynthetic chain in order to optimize the changes of the entire organisms for hydrogen production 2)in another hand, to insert the hydrogenases in a photosynthetic chain and then to photo reduce them in order to obtain kinetic data to better understand how it works. (O.M.)

  12. Ethylene homo- and copolymerization chain-transfers: A perspective from supported (nBuCp)2ZrCl2 catalyst active centre distribution

    Indian Academy of Sciences (India)

    Muhammad Atiqullah; Mamdouh A Al-Harthi; Siripon Anantawaraskul; Abdul-hamid M Emwas

    2015-04-01

    Polymerization chain termination reactions and unsaturation of the polymer backbone end are related. Therefore, in this study, the parameters resulting from the modelling of the active centre distribution of the supported catalyst—silica/MAO/(nBuCp)2ZrCl2—were applied to evaluate the active-centredependent ethylene homo- and copolymerization rates, as well as the corresponding chain termination rates. This approach, from a microkinetic mechanistic viewpoint, elucidates better the 1-hexene-induced positive comonomer effect and chain transfer phenomenon. The kinetic expressions, developed on the basis of the proposed polymerization mechanisms, illustrate how the active site type-dependent chain transfer phenomenon is influenced by the different apparent termination rate constants and momoner concentrations. The active centrespecific molecular weight Mni (for the above homo- and copolymer), as a function of chain transfer probability, pCTi, varied as follows: log(pCTi) = log(mwru)−log(Mni) where mwru is the molecular weight of the repeat unit. The physical significance of this finding has been explained. The homo- and copolymer backbones showed all the three chain end unsaturations (vinyl, vinylidene, and trans-vinylene). The postulated polymerization mechanisms reveal the underlying polymer chemistry. The results of the present study will contribute to develop in future supported metallocene catalysts that will be useful to synthesize polyethylene precursors having varying chain end unsaturations, which can be eventually used to prepare functional polyethylenes.

  13. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

    Directory of Open Access Journals (Sweden)

    Todd J Treangen

    Full Text Available Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus, average-sized genomes (Bacillus, Enterobacteriaceae, and large genomes (Pseudomonas, Bradyrhizobiaceae to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes--xenologs--persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes--paralogs--are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

  14. Computational study of ligand binding in lipid transfer proteins: Structures, interfaces, and free energies of protein-lipid complexes

    OpenAIRE

    Fernandez Pacios, Luis; Gomez Casado, Cristina; Tordesillas Villuendas, Leticia; Palacín Gómez, Aranzazu; Sanchez-Monge Laguna De Rins, Maria Rosa; Díaz Perales, Araceli

    2012-01-01

    Plant nonspecific lipid transfer proteins (nsLTPs) bind a wide variety of lipids, which allows them to perform disparate functions. Recent reports on their multifunctionality in plant growth processes have posed new questions on the versatile binding abilities of these proteins. The lack of binding specificity has been customarily explained in qualitative terms on the basis of a supposed structural flexibility and nonspecificity of hydrophobic protein-ligand interactions. We present here a co...

  15. Uptake and transfer of14C-simetryne through the laboratory freshwater food chain

    Science.gov (United States)

    Xu, Ying; Lay, J. P.; Zhang, Yongyuan

    1989-03-01

    This paper deals with the bioconcentration of14C-simetryne from water by aquatic test organisms: green algae— Monoraphidium minutum, rotifers— Brachionus rubens, daphnids— Daphnia magna, and fish— Brachydanio rerio. The chemical was bioconcentrated rapidly in all test species during the first 48 hours of experiment. The BCF values (bioconcentration factor) from all uptake studies show that simetryne has higher accumulation in algae than in rotifers, daphnids and zebra fish. The logarithm of the n-octanol/water partition coefficient of simetryne measured as 2.06±0.05 was correlated with the BCFs in the organisms as based on the lipid contents. 14C-simetryne uptake via the food-chain amounted to only 22% to 42% of the bioconcentration from water. Clearance of14C-derived residues from fish was rapid with a half-life of 2.1 days.

  16. A dynamic compartmental food chain model of radiocaesium transfer to Apodemus sylvaticus in woodland ecosystems

    International Nuclear Information System (INIS)

    A study was undertaken to quantify the activity concentrations of 137Cs in Apodemus sylvaticus (the woodmouse) in two woodland sites, Lady Wood and Longrigg Wood, adjacent to British Nuclear Fuels Ltd. (BNFL) Sellafield, Cumbria, UK. A deterministic dynamic compartmental food chain model was also constructed to predict 137Cs activity concentration [Bq kg-1 dry weight (dw)] in A. sylvaticus on a seasonal basis given the activity concentrations in its diet. Within the coniferous woodland site (Lady Wood), significant differences were found between seasons (Px/2.3 Bq kg-1 dw) being attributed to mycophagy. Fungal concentrations ranged from 2-3213 Bq kg-1 dw. The modelled activity concentrations fell between the confidence intervals of the observed data in four of the six seasonal cohorts sampled. Disparities between predicted and observed activity concentrations are attributed to uncertainties surrounding the fundamental feeding ecology of small mammals

  17. Modified fabrication process of protein chips using a short-chain self-assembled monolayer.

    Science.gov (United States)

    Jang, Ling-Sheng; Keng, Hao-Kai

    2008-04-01

    In previous work a short chain SAM, 4,4-Dithiodibutyric Acid (DTBA) was found to be a thin monolayer in protein chips. However, obtaining uniform fluorescent intensity remains difficult because water-soluble carbodiimides (EDC) in an aqueous system cause the hydrolysis of N-hydroxysuccinimide ester (NHS esters). The hydrolysis of NHS esters reduces coupling yields and therefore reduces the fluorescent intensity of protein chips. The NHS can increase the stability of active intermediate resulting from the reaction of EDC and NHS, but the ratio of the concentration of EDC to that of NHS strongly affects this stability. The effects of the solvents used in the washing step are studied to solve this problem. The results reveal that PBST (PBS + 5% Tween20) is more effective in reducing the hydrolysis of NHS esters than deionized water. Additionally, the effects of 3:1 and 5:2 EDC/NHS ratios on the chips are examined. The 3:1 EDC/NHS ratio yields a higher fluorescent intensity than the 5:2 ratio. The effects on the chips of dissolving EDC in DI water, DI water + 0.1 M MES and alcohol are also investigated. The results show that alcohol provides higher fluorescent intensity than other solvents and the reaction time of 4 h yields a high fluorescent intensity with 3:1 EDC/NHS ratio. A modified fabrication process of protein chips using 4,4-DTBA is developed. In this work, 160 mM 4,4-DTBA is used as a self-assembled monolayer in the fabrication of protein chips. Experiments to characterize 4,4-DTBA are performed by contact angle goniometry and Fourier transform infrared spectroscopy (FTIR). Furthermore, the immobilized protein A-FITC (fluorescein isothiocyanate) is adopted in fluorescent assays. PMID:17849186

  18. Innovations in the supply chain and construction engineering of nuclear-based heat transfer components

    International Nuclear Information System (INIS)

    Equipos Nucleares S.A. (Ensa) and Tecnicas Reunidas S.A. (TR), both long-established Spanish companies, have brought together innovative approaches for the supply of heat transfer solution packages by combining their respective experiences in heat exchanger design (TR), manufacturing (Ensa), and nuclear materials procurement (Ensa and TR), thereby founding a new potent European component supplier for nuclear power plants with over 50 years of experience in the global nuclear market. The combined strategy of the Ensa-TR association which addresses the problems currently faced by nuclear component suppliers is described herein. (authors)

  19. Innovations in the supply chain and construction engineering of nuclear-based heat transfer components

    Energy Technology Data Exchange (ETDEWEB)

    Perales, A. [Equipos Nucleares, S.A. - Ensa, Jose Ortega y Gasset, 28006 Madrid (Spain); Woolf, G. [Tecnicas Reunidas - TR, Arapiles, 28014 Madrid (Spain)

    2010-07-01

    Equipos Nucleares S.A. (Ensa) and Tecnicas Reunidas S.A. (TR), both long-established Spanish companies, have brought together innovative approaches for the supply of heat transfer solution packages by combining their respective experiences in heat exchanger design (TR), manufacturing (Ensa), and nuclear materials procurement (Ensa and TR), thereby founding a new potent European component supplier for nuclear power plants with over 50 years of experience in the global nuclear market. The combined strategy of the Ensa-TR association which addresses the problems currently faced by nuclear component suppliers is described herein. (authors)

  20. Inosine Nucleobase Acts as Guanine in Interactions with Protein Side Chains.

    Science.gov (United States)

    Hajnic, Matea; Ruiter, Anita de; Polyansky, Anton A; Zagrovic, Bojan

    2016-05-01

    A central intermediate in purine catabolism, the inosine nucleobase hypoxanthine is also one of the most abundant modified nucleobases in RNA and plays key roles in the regulation of gene expression and determination of cell fate. It is known that hypoxanthine acts as guanine when interacting with other nucleobases and base pairs most favorably with cytosine. However, its preferences when it comes to interactions with amino acids remain unknown. Here we present for the first time the absolute binding free energies and the associated interaction modes between hypoxanthine and all standard, non-glycyl/non-prolyl amino acid side chain analogs as derived from molecular dynamics simulations and umbrella sampling in high- and low-dielectric environments. We illustrate the biological relevance of the derived affinities by providing a quantitative explanation for the specificity of hypoxanthine-guanine phosphoribosyltransferase, a key enzyme in the purine salvage pathway. Our results demonstrate that in its affinities for protein side chains, hypoxanthine closely matches guanine, much more so than its precursor adenine. PMID:27093234

  1. In vitro thermodynamic dissection of human copper transfer from chaperone to target protein.

    Directory of Open Access Journals (Sweden)

    Moritz S Niemiec

    Full Text Available Transient protein-protein and protein-ligand interactions are fundamental components of biological activity. To understand biological activity, not only the structures of the involved proteins are important but also the energetics of the individual steps of a reaction. Here we use in vitro biophysical methods to deduce thermodynamic parameters of copper (Cu transfer from the human copper chaperone Atox1 to the fourth metal-binding domain of the Wilson disease protein (WD4. Atox1 and WD4 have the same fold (ferredoxin-like fold and Cu-binding site (two surface exposed cysteine residues and thus it is not clear what drives metal transfer from one protein to the other. Cu transfer is a two-step reaction involving a metal-dependent ternary complex in which the metal is coordinated by cysteines from both proteins (i.e., Atox1-Cu-WD4. We employ size exclusion chromatography to estimate individual equilibrium constants for the two steps. This information together with calorimetric titration data are used to reveal enthalpic and entropic contributions of each step in the transfer process. Upon combining the equilibrium constants for both steps, a metal exchange factor (from Atox1 to WD4 of 10 is calculated, governed by a negative net enthalpy change of ∼10 kJ/mol. Thus, small variations in interaction energies, not always obvious upon comparing protein structures alone, may fuel vectorial metal transfer.

  2. A silica-immobilized pt2+catalyst for the selective, aerobic oxidation of methane via an electron-transfer chain

    Institute of Scientific and Technical Information of China (English)

    Zengjian An; Xiulian Pan; Xiumei Liu; Xiuwen Han; Xinhe Bao

    2008-01-01

    The combination of Pt2+, benzoquinone and NaNO2 forms an electron-transfer chain, which leads to the oxidation of methane by O2 in CF3COOH aqueous solution. The overall turnover number per hour (TOF) of methane at 120 ℃ is 0.5 h-1, however, only about one fourth (23%) of methane is converted to the desired product of methanol in the formation of CF3COOCH3. The over-oxidation of methane to CO2, over the catalyst with the Pt2+ species immobilized via 2,2'-bipyridyl as a ligand on the silica substrate, is depressed distinctly. Under the same conditions, the conversion to methanol dominates, and no CO2 is observed, on account of the over-oxidation of methane, as confirmed by the isotope experiment.

  3. Thermo-Responsive and Biocompatible Diblock Copolymers Prepared via Reversible Addition-Fragmentation Chain Transfer (RAFT Radical Polymerization

    Directory of Open Access Journals (Sweden)

    Kenichi Fukuda

    2014-03-01

    Full Text Available Poly(2-(methacryloyloxyethyl phosphorylcholine-b-poly(N,N-diethyl acrylamide (PMPCm-PDEAn was synthesized via reversible addition-fragmentation chain transfer (RAFT controlled radical polymerization. Below, the critical aggregation temperature (CAT the diblock copolymer dissolved in water as a unimer with a hydrodynamic radius (Rh of ca. 5 nm. Above the CAT the diblock copolymers formed polymer micelles composed of a PDEA core and biocompatible PMPC shells, due to hydrophobic self-aggregation of the thermo-responsive PDEA block. A fluorescence probe study showed that small hydrophobic small guest molecules could be incorporated into the core of the polymer micelle above the CAT. The incorporated guest molecules were released from the core into the bulk aqueous phase when the temperature decreased to values below the CAT because of micelle dissociation.

  4. Ultrafast Energy Transfer and Enhanced Two-Photon Absorption in a Novel Porphyrin Side-Chain Polymer

    Institute of Scientific and Technical Information of China (English)

    WANG Hui; HUANG Ya-Ping; DENG Li; ZHAO Fu-Li; LIN Wei-Zhu; WANG Jian; LIANG Zhao-Xi

    2004-01-01

    @@ Ultrafast relaxation processes and transient two-photon absorption are studied in a novel porphyrin side-chain polymer, 5-hydroxy-10, 15,20-triphenyl-porphyrin-poly(glycidyl methacrylate) (HTPP-PGMA), by using picosecond luminescence spectroscopy and femtosecond pump-probe techniques. HTPP-PGMA exhibits the ultrafast initial luminescence decay (~300ps), which is absent in the conventional porphyrin monomer such as TPP. Enhanced two-photon absorption was observed in HTPP-PGMA; the corresponding Im x(a) is about 2.8× 10-11 esu, which is almost one order of magnitude larger than that of the conventional porphyrin monomer (TPP) (~1.3 × 10-12 esu).The ultrafast energy transfer plays an important role in the excited-state relaxation dynamics observed in HTPPPGMA. The potential application of HTPP-PGMA in optical switching is discussed.

  5. DNAzyme-based biosensor for Cu(2+) ion by combining hybridization chain reaction with fluorescence resonance energy transfer technique.

    Science.gov (United States)

    Chen, Ying; Chen, Ling; Ou, Yidian; Wang, Zhenhua; Fu, Fengfu; Guo, Liangqia

    2016-08-01

    A novel signal amplification strategy based on Cu(2+)-dependent DNAzyme was developed for sensing Cu(2+) ion by combining hybridization chain reaction (HCR) with fluorescence resonance energy transfer (FRET) technique. In the presence of Cu(2+) ion, the substrate strands of Cu(2+)-dependent DNAzyme immobilized on magnetic beads were specifically cleaved and released. The released strands initiated the HCR process of hairpin H1 and H2 labeled with FAM as the donor and TAMRA as the acceptor, respectively. Long nicked dsDNA structures were self-assembled to bring the donor and the acceptor in close proximity, resulting in a FRET process. The relative ratio of fluorescent intensities of the acceptor and donor was used to quantitatively detect Cu(2+) ion with a limit of detection of 0.5nmolL(-1). This proposed biosensor was applied to detect Cu(2+) ion in tap water with satisfactory results. PMID:27216680

  6. Study on the performance of polycarboxylate-based superplasticizers synthesized by reversible addition-fragmentation chain transfer (RAFT) polymerization

    Science.gov (United States)

    Yu, Binbin; Zeng, Zhong; Ren, Qinyu; Chen, Yang; Liang, Mei; Zou, Huawei

    2016-09-01

    A series of block type polycarboxylate-based superplasticizers (PCs) with different molecular architectures were synthesized with macromonomer butenyl alkylene polyoxyethylene-polyoxypropylene ether (BAPP) and acrylic acid (AA) by reversible addition-fragmentation chain transfer (RAFT) polymerization. Fourier-Transformed Infrared (FTIR) Spectroscopy and dynamic light scattering (DLS) were applied to investigate the PCs' molecular structure. The dispersion capacity of the PCs in cement were also measured, and the results showed that the polycarboxylic dispersing agents prepared by this method were suitable for portlant cement. It was found that the PCs could affect the hydration process, which was performed through retarding the generation of ettringite in the hydrated product. Our studies with X-ray diffraction (XRD), scanning electron microscopy (SEM) and compressive strength measurement of hydrated production were all supporting this conclusion.

  7. Comparison of predictions from internationally recognized assessment models for the transfer of selected radionuclides through terrestrial food chains

    International Nuclear Information System (INIS)

    Six internationally recognized terrestrial food-chain models developed in Sweden, the United States, the United Kingdom, the Federal Republic of Germany, and the International Atomic Energy Agency are compared. This comparison includes the data bases and predictions for the transfer of Co-60, Sr-90, I-131, and Cs-137 into milk, and leafy and nonleafy vegetables from a hypothetical 30-yr continuous rate of atmospheric deposition onto agricultural systems. Model predictions are compared against United Nations summaries of empirical relationships between atmospheric deposition and concentrations in food of Sr-90 and Cs-137. The results of statistical analyses of the effect of parameter uncertainties on model predictions are also included for Sr-90, Cs-137, and I-131. Discrepancies among model predictions vary between factors of 6 and 30. These results reflect differences in model assumptions rather than uncertainties in model parameters

  8. FARMLAND. A dynamic model for the transfer of radionuclides through terrestrial food chains

    International Nuclear Information System (INIS)

    Models to simulate the transfer of radionuclides through terrestrial foods have been developed at NRPB and regularly used over the last 20 years. The foodchain model is named FARMLAND (Food Activity from Radionuclide Movement on LAND) and it contains a suite of submodels, each of which simulates radionuclide transfer through a different part of the foodchain. These models can be combined in various orders so that they can be used for different situations of radiological interest. The main foods considered are green vegetables, grain products, root vegetables, milk, meat and offal from cattle, and meat and offal from sheep. A large variety of elements can be considered, although the degree of complexity with which some are modelled is greater than that for others; isotopes of caesium, strontium and iodine are treated in greatest detail. This report gives an overview of the FARMLAND model with the aim of consolidating all the information on the model available in past NRPB publications. In addition, recent model developments are described. The use of FARMLAND for different applications is addressed. In particular, the generation of a set of parameter values and assumptions for use in general applications in countries in the European Union are discussed. Activity concentrations in foods are presented for a few important radionuclides for both routine and accidental release applications. The conclusions of verification and validation studies performed using FARMLAND are also outlined. (author)

  9. Thermostable Mismatch-Recognizing Protein MutS Suppresses Nonspecific Amplification during Polymerase Chain Reaction (PCR

    Directory of Open Access Journals (Sweden)

    Seiki Kuramitsu

    2013-03-01

    Full Text Available Polymerase chain reaction (PCR-related technologies are hampered mainly by two types of error: nonspecific amplification and DNA polymerase-generated mutations. Here, we report that both errors can be suppressed by the addition of a DNA mismatch-recognizing protein, MutS, from a thermophilic bacterium. Although it had been expected that MutS has a potential to suppress polymerase-generated mutations, we unexpectedly found that it also reduced nonspecific amplification. On the basis of this finding, we propose that MutS binds a mismatched primer-template complex, thereby preventing the approach of DNA polymerase to the 3' end of the primer. Our simple methodology improves the efficiency and accuracy of DNA amplification and should therefore benefit various PCR-based applications, ranging from basic biological research to applied medical science.

  10. Funktionelle Charakterisierung zweier Lipid Transfer Proteine in der Arabidopsis thaliana Pathogenantwort

    OpenAIRE

    Bieber, Michael

    2013-01-01

    Die Multigenfamilie der Lipid Transfer Proteine (LTP) stellt eine Gruppe von kleinen Proteinen dar, welche in allen höheren Landpflanzen vorkommen. In der Modellpflanze Arabidopsis thaliana werden 92 Proteine zur Klasse der LTPs gezählt. Die Benennung der Proteinfamilie basiert auf dem beobachteten in vitro Transfer von Lipiden zwischen zwei Membranen. Alle LTPs weisen ein konserviertes, 8 Cysteine beinhaltendes Motiv und eine hydrophobe Tasche auf, welche für die Bindung hydrophober Moleküle...

  11. Glycolipid Transfer Protein Interaction with Bilayer Vesicles: Modulation by Changing Lipid Composition

    OpenAIRE

    Rao, Chetan S; Chung, Taeowan; Pike, Helen M.; Brown, Rhoderick E.

    2005-01-01

    Glycosphingolipids (GSLs) are important constituents of lipid rafts and caveolae, are essential for the normal development of cells, and are adhesion sites for various infectious agents. One strategy for modulating GSL composition in lipid rafts is to selectively transfer GSL to or from these putative membrane microdomains. Glycolipid transfer protein (GLTP) catalyzes selective intermembrane transfer of GSLs. To enable effective use of GLTP as a tool to modify the glycolipid content of membra...

  12. Preferential transfer of certain plasma membrane proteins onto T and B cells by trogocytosis.

    Directory of Open Access Journals (Sweden)

    Sandrine Daubeuf

    Full Text Available T and B cells capture antigens via membrane fragments of antigen presenting cells (APC in a process termed trogocytosis. Whether (and how a preferential transfer of some APC components occurs during trogocytosis is still largely unknown. We analyzed the transfer onto murine T and B cells of a large panel of fluorescent proteins with different intra-cellular localizations in the APC or various types of anchors in the plasma membrane (PM. Only the latter were transferred by trogocytosis, albeit with different efficiencies. Unexpectedly, proteins anchored to the PM's cytoplasmic face, or recruited to it via interaction with phosphinositides, were more efficiently transferred than those facing the outside of the cell. For proteins spanning the PM's whole width, transfer efficiency was found to vary quite substantially, with tetraspanins, CD4 and FcRgamma found among the most efficiently transferred proteins. We exploited our findings to set immunodiagnostic assays based on the capture of preferentially transferred components onto T or B cells. The preferential transfer documented here should prove useful in deciphering the cellular structures involved in trogocytosis.

  13. RADFOOD--a dynamic model for radioactivity transfer through the human food chain

    International Nuclear Information System (INIS)

    Radioactive fallout presents a short-term risk due to its direct deposition on agricultural crops, as well as a long-term risk resulting from its deposition on soil and subsequent uptake by crops. A dynamic model, RADFOOD, was developed, based on different existing models. It simulates transport of fallout radionuclides through agricultural food chains to man and evaluates the radiation doses resulting from consumption of contaminated food. Transport was modeled through compartments representing various environmental elements of food products. Internal radiation doses (whole-body weighted doses) following ingestion of contaminated foodstuffs were then estimated. Specific types of crops, soils and diet of man and livestock were considered. A sample calculation was performed in which individual and collective radiation doses, as well as associated health effects, resulting from fallout contamination were evaluated. They were estimated for food consumption beginning at various times after the fallout deposition and for different consumption durations. A sensitivity analysis, performed for the main model parameters, showed that the radiation dose is sensitive, for the short-term period, to changes in initial deposition levels and in the parameters characterizing initial fallout interception and resuspension

  14. Early Career: Templating of Liquid Crystal Microstructures by Reversible Addition-Fragmentation Chain Transfer Polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Heinen, Jennifer M

    2014-12-31

    This research has shown that the microstructure of self-assembled copolymers can be decoupled from the polymer chemistry. The simplest polymer architecture, linear block copolymers, is valuable for a broad range of applications, including adhesives and coatings, medical devices, electronics and energy storage, because these block copolymers reproducibly self-assemble into microphase separated nanoscale domains. Unfortunately, the self-assembled microstructure is tuned by polymer composition, thus limiting the potential to simultaneously optimize chemical, mechanical, and transport properties for desired applications. To this end, much work was been put into manipulating block copolymer self-assembly independently of polymer composition. These efforts have included the use of additives or solvents to alter polymer chain conformation, the addition of a third monomer to produce ABC triblock terpolymers, architectures with mixed blocks, such as tapered/gradient polymers, and the synthesis of other nonlinear molecular architectures. This work has shown that the microstructures formed by linear ABC terpolymers can be altered by controlling the architecture of the polymer molecules at a constant monomer composition, so that the microstructure is tuned independently from the chemical properties.

  15. Direct 'in situ', low VOC, high yielding, CO2 expanded phase catalytic chain transfer polymerisation: towards scale-up.

    Science.gov (United States)

    Adlington, Kevin; Green, Anthony; Wang, Wenxin; Howdle, Steven M; Irvine, Derek J

    2013-01-01

    The successful application of catalytic chain transfer polymerisation (CCTP) by adopting an 'in situ' catalyst preparation methodology in several polymerisation media is described. More specifically, this study is focused on reporting the development of 'in situ' CCTP within a CO(2) expanded phase polymerisation process, which achieved high yields of polymer whilst minimising both VOC footprint and CO(2) compression costs. The 'in situ' method is shown to be effective in controlling polymerisations conducted in both conventional solvents and bulk under inert atmosphere, delivering molecular weight reductions and a Cs value of appropriate similar magnitude to those achieved by the benchmark, commercially sourced CoPhBF catalyst. The 'in situ' effect has been achieved with equal efficiency when both using catalysts with different axial ligands and where the complex is required to undergo a facile ligand dissociation in order to create the required catalyst necessary to achieve CCTP control. Furthermore, both catalysts are shown to effectively control polymerisations in a CO(2) expanded phase process, in which a small amount of compressed CO(2) is introduced to reduce the viscosity of the reaction mixture, allowing for easy heat transfer and good catalyst diffusion during reaction. In this way, yield limitations imposed to avoid the Trommsdorff effect required in bulk processing and the need for post precipitation have been successfully overcome. Both of these factors further improve the sustainability of such a polymerisation process. However, the 'in situ', high pressure expanded phase environment was observed to retard the ligand dissociation required for catalyst activation. PMID:23085824

  16. The transfer of titanium dioxide nanoparticles from the host plant to butterfly larvae through a food chain

    Science.gov (United States)

    Kubo-Irie, Miyoko; Yokoyama, Masaaki; Shinkai, Yusuke; Niki, Rikio; Takeda, Ken; Irie, Masaru

    2016-03-01

    This study aimed to examine the transfer of nanoparticles within a terrestrial food chain. Oviposited eggs of the swallowtail butterfly (Atrophaneura alcinous) were hatched on the leaves of the host plant (Aristolochia debilis), and the root stock and root hairs were submerged in a suspension of 10 μg/ml titanium dioxide nanoparticles (TiO2-NPs) in a 100 ml bottle. The presence of TiO2-NPs in the veins of the leaves was confirmed by X-ray analytical microscopy (X-ray AM). The hatched 1st instar larvae fed on the leaves to moult into 2nd instar larvae. Small agglomerates of TiO2-NPs less than 150 nm in diameter were identified in the vascular tissue of the exposed plant, the midgut and the excreta of the larvae by transmission electron microscopy. The image of Ti elemental mapping by X-ray AM was analysed with the quantitative spatial information mapping (QSIM) technique. The results demonstrated that TiO2-NPs were transferred from the plant to the larvae and they were disseminated throughout the environment via larval excreta.

  17. Heat transfer models for predicting Salmonella enteritidis in shell eggs through supply chain distribution.

    Science.gov (United States)

    Almonacid, S; Simpson, R; Teixeira, A

    2007-11-01

    Egg and egg preparations are important vehicles for Salmonella enteritidis infections. The influence of time-temperature becomes important when the presence of this organism is found in commercial shell eggs. A computer-aided mathematical model was validated to estimate surface and interior temperature of shell eggs under variable ambient and refrigerated storage temperature. A risk assessment of S. enteritidis based on the use of this model, coupled with S. enteritidis kinetics, has already been reported in a companion paper published earlier in JFS. The model considered the actual geometry and composition of shell eggs and was solved by numerical techniques (finite differences and finite elements). Parameters of interest such as local (h) and global (U) heat transfer coefficient, thermal conductivity, and apparent volumetric specific heat were estimated by an inverse procedure from experimental temperature measurement. In order to assess the error in predicting microbial population growth, theoretical and experimental temperatures were applied to a S. enteritidis growth model taken from the literature. Errors between values of microbial population growth calculated from model predicted compared with experimentally measured temperatures were satisfactorily low: 1.1% and 0.8% for the finite difference and finite element model, respectively. PMID:18034720

  18. The role of profilin and lipid transfer protein in strawberry allergy in the Mediterranean area

    NARCIS (Netherlands)

    L. Zuidmeer; E. Salentijn; M.F. Rivas; E.G. Mancebo; R. Asero; C.I. Matos; K.T.B. Pelgrom; L.J.W.J. Gilissen; R. van Ree

    2006-01-01

    Background In contrast to other Rosaceae fruit, only few cases of patients with adverse reactions to strawberry are listed in literature. Objective To identify allergenic proteins in strawberry and to express and characterize recombinant strawberry lipid transfer protein (LTP; rFra a 3). Methods Est

  19. Direct observation of resonance tryptophan-to-chromophore energy transfer in visible fluorescent proteins

    NARCIS (Netherlands)

    Visser, NV; Borst, JW; Hink, MA; van Hoek, A; Visser, AJWG

    2005-01-01

    Visible fluorescent proteins from Aequorea victoria contain next to the fluorophoric group a single tryptophan residue. Both molecules form a single donor-acceptor pair for resonance energy transfer (RET) within the protein. Time-resolved fluorescence experiments using tryptophan excitation have sho

  20. A new classification of free combined or connected tissue transfers: introduction to the concept of bridge, siamese, chimeric, mosaic, and chain-circle flaps.

    OpenAIRE

    Koshima, Isao

    2001-01-01

    Recently, combined tissues or flaps have been used for the repair of extensively massive or wide defects resulting from radical wide resection. To further advance the development of combined tissue transfers, they should be reclassified. Based on our cases with free tissue transfers, we have created a new classification of combined flaps composed of "bridge", "chimeric", "siamese", "mosaic", and "chain-circle" flaps. The bridge flap is fabricated out together of separate flaps with short vasc...

  1. The Role of Short-Chain Conjugated Poly-(R-3-Hydroxybutyrate (cPHB in Protein Folding

    Directory of Open Access Journals (Sweden)

    Rosetta N. Reusch

    2013-05-01

    Full Text Available Poly-(R-3-hydroxybutyrate (PHB, a linear polymer of R-3-hydroxybutyrate (R-3HB, is a fundamental constituent of biological cells. Certain prokaryotes accumulate PHB of very high molecular weight (10,000 to >1,000,000 residues, which is segregated within granular deposits in the cytoplasm; however, all prokaryotes and all eukaryotes synthesize PHB of medium-chain length (~100–200 residues which resides within lipid bilayers or lipid vesicles, and PHB of short-chain length (<12 residues which is conjugated to proteins (cPHB, primarily proteins in membranes and organelles. The physical properties of cPHB indicate it plays important roles in the targeting and folding of cPHB-proteins. Here we review the occurrence, physical properties and molecular characteristics of cPHB, and discuss its influence on the folding and structure of outer membrane protein A (OmpA of Escherichia coli.

  2. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    Science.gov (United States)

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-12-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave-accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MALDI-TOF and LC-ESI-MS to identify the peptide products. RNase A and B each contains four disulfide bonds, and the addition of a reducing reagent, such as dithiothreitol, was found to be required to achieve efficient acidic proteolysis. The linkage of the glycosidic group to the asparagine side chain in ribonuclease B was found not to be cleaved by brief microwave treatment in 12.5% acetic acid. The distribution of the heterogeneous carbohydrate side chain in the glycopeptide products of acid cleavage was compared to that of the glycopeptide products of tryptic digestion. Hydrolysis within the carbohydrate chain itself is minimal under the conditions used. The O-linked side chain on alpha crystalline A was found to be cleaved during acid cleavage of the protein.

  3. Extension of microwave-accelerated residue-specific acid cleavage to proteins with carbohydrate side chains and disulfide linkages

    OpenAIRE

    Li, Jinxi; Shefcheck, Kevin; Callahan, John; Fenselau, Catherine

    2008-01-01

    This laboratory has introduced a chemical method for residue-specific protein cleavage and has provided a preliminary assessment of the suitability of microwave accelerated acid cleavage as a proteomic tool. This report is a continuing assessment of the fate of common protein modifications in microwave-accelerated acid cleavage. We have examined the cleavage of ribonuclease A and the related N-linked glycoprotein ribonuclease B, and the O-linked glycoprotein alpha crystallin A chain, using MA...

  4. Differentiation of Neisseria gonorrhoeae strains by polymerase chain reaction and restriction fragment length polymorphism of outer membrane protein IB genes.

    OpenAIRE

    Lau, Q C; Chow, V T; Poh, C. L.

    1995-01-01

    OBJECTIVES--To employ polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) analysis for the rapid differentiation of Neisseria gonorrhoeae protein IB (PIB) isolates and to compare its usefulness with the widely accepted auxotype/serovar classification scheme. METHODS--The outer membrane protein IB genes of 47 gonococcal isolates belonging to 10 different serovars were amplified by PCR. The approximately 1 kb DNA products were then digested separately with restri...

  5. Surprisingly high stability of barley lipid transfer protein, LTP1, towards denaturant, heat and proteases

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Winther, J R

    2001-01-01

    Barley LTP1 belongs to a large family of plant proteins termed non-specific lipid transfer proteins. The in vivo function of these proteins is unknown, but it has been suggested that they are involved in responses towards stresses such as pathogens, drought, heat, cold and salt. Also, the proteins...... have been suggested as transporters of monomers for cutin synthesis. We have analysed the stability of LTP1 towards denaturant, heat and proteases and found it to be a highly stable protein, which apparently does not denature at temperatures up to 100 degrees C. This high stability may be important...

  6. LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates

    Directory of Open Access Journals (Sweden)

    Samudrala Ram

    2011-09-01

    Full Text Available Abstract Background Successful protein structure prediction requires accurate low-resolution scoring functions so that protein main chain conformations that are close to the native can be identified. Once that is accomplished, a more detailed and time-consuming treatment to produce all-atom models can be undertaken. The earliest low-resolution scoring used simple distance-based "contact potentials," but more recently, the relative orientations of interacting amino acids have been taken into account to improve performance. Results We developed a new knowledge-based scoring function, LoCo, that locates the interaction partners of each individual residue within a local coordinate system based only on the position of its main chain N, Cα and C atoms. LoCo was trained on a large set of experimentally determined structures and optimized using standard sets of modeled structures, or "decoys." No structure used to train or optimize the function was included among those used to test it. When tested against 29 other published main chain functions on a group of 77 commonly used decoy sets, our function outperformed all others in Cα RMSD rank of the best-scoring decoy, with statistically significant p-values Conclusions Our function demonstrates an unmatched combination of accuracy, speed, and simplicity and shows excellent promise for protein structure prediction. Broader applications may include protein-protein interactions and protein design.

  7. Saturation transfer difference NMR studies of protein-ligand interactions

    OpenAIRE

    Szczepina, Monica Gabriela

    2011-01-01

    The mycolyl–arabinogalactan–peptidoglycan complex coats the surface of Mycobacterium tuberculosis. It is a structure composed of galactofuranosyl (Galf) residues attached via alternating β-(1→6) and β-(1→5) linkages synthesized by bifunctional galactofuranosyltransferases, GlfT1 and GlfT2. We have used Saturation Transfer Difference (STD) NMR spectroscopy to examine the active site architecture of GlfT2 using trisaccharide acceptor substrates, β-D-Galf-(1→6)-β-D-Galf-(1→5)-β-D-Galf-O(CH2)7CH...

  8. Gold nanoparticle assisted assembly of a heme protein for enhancement of long-range interfacial electron transfer

    DEFF Research Database (Denmark)

    Jensen, Palle Skovhus; Chi, Qijin; Grumsen, Flemming Bjerg;

    2007-01-01

    -defined stoichiometry. The systems were investigated in homogeneous solution and at liquid/solid interface. Conjugation of cyt c results in a small but consistent broadening of the nanoparticle plasmon band. This phenomenon can be explained in terms of long-range electronic interactions between the gold nanoparticle...... with that of cyt c in the absence of AuNPs is observed. AuNPs appear to serve as excellent ET relays, most likely by facilitating the electronic coupling between the protein redox center and the electrode surface.......Interfacial electron transfer (ET) of biological macromolecules such as metalloproteins is the key process in bioelectrochemistry, enzymatic electrocatalysis, artificial ET chains, single-molecule electronic amplification and rectification, and other phenomena associated with the area...

  9. Asynchronous through-bond homonuclear isotropic mixing: application to carbon–carbon transfer in perdeuterated proteins under MAS

    Energy Technology Data Exchange (ETDEWEB)

    Kulminskaya, Natalia; Vasa, Suresh Kumar; Giller, Karin; Becker, Stefan; Linser, Rasmus, E-mail: rali@nmr.mpibpc.mpg.de [Max Planck Institute for Biophysical Chemistry, Department of NMR-based Structural Biology (Germany)

    2015-11-15

    Multiple-bond carbon–carbon homonuclear mixing is a hurdle in extensively deuterated proteins and under fast MAS due to the absence of an effective proton dipolar-coupling network. Such conditions are now commonly employed in solid-state NMR spectroscopy. Here, we introduce an isotropic homonuclear {sup 13}C–{sup 13}C through-bond mixing sequence, MOCCA, for the solid state. Even though applied under MAS, this scheme performs without rotor synchronization and thus does not pose the usual hurdles in terms of power dissipation for fast spinning. We compare its performance with existing homonuclear {sup 13}C–{sup 13}C mixing schemes using a perdeuterated and partially proton-backexchanged protein. Based on the analysis of side chain carbon–carbon correlations, we show that particularly MOCCA with standard 180-degree pulses and delays leading to non-rotor-synchronized spacing performs exceptionally well. This method provides high magnetization transfer efficiency for multiple-bond transfer in the aliphatic region compared with other tested mixing sequences. In addition, we show that this sequence can also be tailor-made for recoupling within a selected spectral region using band-selective pulses.

  10. Asynchronous through-bond homonuclear isotropic mixing: application to carbon–carbon transfer in perdeuterated proteins under MAS

    International Nuclear Information System (INIS)

    Multiple-bond carbon–carbon homonuclear mixing is a hurdle in extensively deuterated proteins and under fast MAS due to the absence of an effective proton dipolar-coupling network. Such conditions are now commonly employed in solid-state NMR spectroscopy. Here, we introduce an isotropic homonuclear 13C–13C through-bond mixing sequence, MOCCA, for the solid state. Even though applied under MAS, this scheme performs without rotor synchronization and thus does not pose the usual hurdles in terms of power dissipation for fast spinning. We compare its performance with existing homonuclear 13C–13C mixing schemes using a perdeuterated and partially proton-backexchanged protein. Based on the analysis of side chain carbon–carbon correlations, we show that particularly MOCCA with standard 180-degree pulses and delays leading to non-rotor-synchronized spacing performs exceptionally well. This method provides high magnetization transfer efficiency for multiple-bond transfer in the aliphatic region compared with other tested mixing sequences. In addition, we show that this sequence can also be tailor-made for recoupling within a selected spectral region using band-selective pulses

  11. Multi-label multi-kernel transfer learning for human protein subcellular localization.

    Directory of Open Access Journals (Sweden)

    Suyu Mei

    Full Text Available Recent years have witnessed much progress in computational modelling for protein subcellular localization. However, the existing sequence-based predictive models demonstrate moderate or unsatisfactory performance, and the gene ontology (GO based models may take the risk of performance overestimation for novel proteins. Furthermore, many human proteins have multiple subcellular locations, which renders the computational modelling more complicated. Up to the present, there are far few researches specialized for predicting the subcellular localization of human proteins that may reside in multiple cellular compartments. In this paper, we propose a multi-label multi-kernel transfer learning model for human protein subcellular localization (MLMK-TLM. MLMK-TLM proposes a multi-label confusion matrix, formally formulates three multi-labelling performance measures and adapts one-against-all multi-class probabilistic outputs to multi-label learning scenario, based on which to further extends our published work GO-TLM (gene ontology based transfer learning model for protein subcellular localization and MK-TLM (multi-kernel transfer learning based on Chou's PseAAC formulation for protein submitochondria localization for multiplex human protein subcellular localization. With the advantages of proper homolog knowledge transfer, comprehensive survey of model performance for novel protein and multi-labelling capability, MLMK-TLM will gain more practical applicability. The experiments on human protein benchmark dataset show that MLMK-TLM significantly outperforms the baseline model and demonstrates good multi-labelling ability for novel human proteins. Some findings (predictions are validated by the latest Swiss-Prot database. The software can be freely downloaded at http://soft.synu.edu.cn/upload/msy.rar.

  12. Structure–function–folding relationships and native energy landscape of dynein light chain protein: nuclear magnetic resonance insights

    Indian Academy of Sciences (India)

    P M Krishna Mohan; Ramakrishna V Hosur

    2009-09-01

    The detailed characterization of the structure, dynamics and folding process of a protein is crucial for understanding the biological functions it performs. Modern biophysical and nuclear magnetic resonance (NMR) techniques have provided a way to obtain accurate structural and thermodynamic information on various species populated on the energy landscape of a given protein. In this context, we review here the structure–function–folding relationship of an important protein, namely, dynein light chain protein (DLC8). DLC8, the smallest subunit of the dynein motor complex, acts as a cargo adaptor. The protein exists as a dimer under physiological conditions and dissociates into a pure monomer below pH 4. Cargo binding occurs at the dimer interface. Dimer stability and relay of perturbations through the dimer interface are anticipated to be playing crucial roles in the variety of functions the protein performs. NMR investigations have provided great insights into these aspects of DLC8 in recent years.

  13. Ethylene homo- and copolymerization chain-transfers: A perspective from supported (n BuCp) 2 ZrCl 2 catalyst active centre distribution

    KAUST Repository

    Atiqullah, Muhammad

    2015-04-01

    Polymerization chain termination reactions and unsaturation of the polymer backbone end are related. Therefore, in this study, the parameters resulting from the modelling of the active centre distribution of the supported catalyst - silica/MAO/(nBuCp)2ZrCl2 - were applied to evaluate the active-centre-dependent ethylene homo- and copolymerization rates, as well as the corresponding chain termination rates. This approach, from a microkinetic mechanistic viewpoint, elucidates better the 1-hexene-induced positive comonomer effect and chain transfer phenomenon. The kinetic expressions, developed on the basis of the proposed polymerization mechanisms, illustrate how the active site type-dependent chain transfer phenomenon is influenced by the different apparent termination rate constants and momoner concentrations. The active centre-specific molecular weight M ni (for the above homo- and copolymer), as a function of chain transfer probability, p CTi, varied as follows: log (p C Ti) = log (mwru) - log (Mn i), where mw ru is the molecular weight of the repeat unit. The physical significance of this finding has been explained. The homo- and copolymer backbones showed all the three chain end unsaturations (vinyl, vinylidene, and trans-vinylene). The postulated polymerization mechanisms reveal the underlying polymer chemistry. The results of the present study will contribute to develop in future supported metallocene catalysts that will be useful to synthesize polyethylene precursors having varying chain end unsaturations, which can be eventually used to prepare functional polyethylenes. [Figure not available: see fulltext.] © 2015 Indian Academy of Sciences.

  14. Branched-chain Amino Acid Biosensing Using Fluorescent Modified Engineered Leucine/Isoleucine/Valine Binding Protein

    Directory of Open Access Journals (Sweden)

    Koji Sode

    2007-06-01

    Full Text Available A novel fluorescence sensing system for branched-chain amino acids (BCAAswas developed based on engineered leucine/isoleucine/valine-binding proteins (LIVBPsconjugated with environmentally sensitive fluorescence probes. LIVBP was cloned fromEscherichia coli and Gln149Cys, Gly227Cys, and Gln254Cys mutants were generated bygenetic engineering. The mutant LIVBPs were then modified with environmentallysensitive fluorophores. Based on the fluorescence intensity change observed upon thebinding of the ligands, the MIANS-conjugated Gln149Cys mutant (Gln149Cys-M showedthe highest and most sensitive response. The BCAAs Leu, Ile, and Val can each bemonitored at the sub-micromolar level using Gln149Cys-M. Measurements were alsocarried out on a mixture of BCAFAs and revealed that Gln149Cys-M-based measurementis not significantly affected by the change in the molar ratio of Leu, Ile and Val in thesample. Its high sensitivity and group-specific molecular recognition ability make the newsensing system ideally suited for the measurement of BCAAs and the determination of theFischer ratio, an indicator of hepatic disease involving metabolic dysfunction.

  15. Gamma radiation induced synthesis of poly(N-isopropylacrylamide) mediated by Reversible Addition-Fragmentation Chain Transfer (RAFT) process

    Science.gov (United States)

    Kiraç, Feyza; Güven, Olgun

    2015-07-01

    Poly(N-isopropylacrylamide) (PNiPAAm) is synthesized by gamma radiation induced Reversible Addition-Fragmentation Chain Transfer (RAFT) polymerization. The monomer is polymerized in the presence of two different trithiocarbonate-based RAFT agents i.e., Cyanomethyldodecyltrithiocarbonate (CDTC) and 2-(Dodecylthiocarbonothioylthio)-2-methylpropionic acid (DMPA) in dimethylformamide (DMF) at room temperature under nitrogen atmosphere. Number-average molecular weights (Mn) and dispersities of the polymers were determined by Size Exclusion Chromatography (SEC). Dispersities (Ɖ) of the resulting polymers are narrow, i.e., Ɖ≤1.18, indicating the occurrence of well-controlled polymerization via radiation induced RAFT process. %Conversion is determined by gravimetric method and also confirmed by Proton Nuclear Magnetic Resonance (1H-NMR) Spectroscopy. By selecting proper [Monomer]/[RAFT] ratio and controlling conversion it is possible to synthesize PNiPAAm in the molecular weight range of 2400-72400 with extremely low molecular weight distributions with the anticipation of preparing corresponding size-controlled nanogels. The phase transition of PNiPAAm with low dispersity synthesized by RAFT is sharper than PNiPAAm synthesized by free radical polymerization.

  16. A hermetic self-sustained microbial solar cell based on Chlorella vulgaris and a versatile charge transfer chain

    Science.gov (United States)

    Pan, Keliang; Zhou, Peijiang

    2015-10-01

    A hermetic noble-metal-free membrane-less microbial solar cell (MSC) is established. The substances decomposition and regeneration in this MSC are carried out only by Chlorella vulgaris simultaneously. The conversion of metabolism types of C. vulgaris is controlled only by illumination. By using a pleiotropic redox mediator and a cupric hexacyanoferrate modified cathode, a two-phase three-stage charge transfer chain is formed. Through this pathway, the one microorganism self-sustained system gets a long-term power output up to 0.04773 mW/cm2 at 0.423 V without any material exchange with external, which is 50 times higher than that obtained from the original system. Benefiting from this electron buffer system, the battery will achieve an electricity generation in both light and dark conditions. There is almost no consumption of any substrates throughout the stabilized process, and no more additions are required. This maintenance-free and extremely inexpensive reactor with a simple structure and a long service life demonstrates the possibility of combining the microbial, chemical and photo cells.

  17. Scale-up of the Reversible Addition-Fragmentation Chain Transfer (RAFT Polymerization Using Continuous Flow Processing

    Directory of Open Access Journals (Sweden)

    Nenad Micic

    2014-01-01

    Full Text Available A controlled radical polymerization process using the Reversible Addition-Fragmentation Chain Transfer (RAFT approach was scaled up by a factor of 100 from a small laboratory scale of 5 mL to a preparative scale of 500 mL, using batch and continuous flow processing. The batch polymerizations were carried out in a series of different glass vessels, using either magnetic or overhead stirring, and different modes of heating: Microwave irradiation or conductive heating in an oil bath. The continuous process was conducted in a prototype tubular flow reactor, consisting of 6 mm ID stainless steel tubing, fitted with static mixers. Both reactor types were tested for polymerizations of the acid functional monomers acrylic acid and 2-acrylamido-2-methylpropane-1-sulfonic acid in water at 80 °C with reaction times of 30 to 40 min. By monitoring the temperature during the exothermic polymerization process, it was observed that the type and size of reactor had a significant influence on the temperature profile of the reaction.

  18. Structural geometry and kinematic processes at the intracontinental Daloushan mountain chain: Implications for tectonic transfer in the Yangtze Block interior

    Science.gov (United States)

    Deng, Bin; Li, Zhi-Wu; Liu, Shu-Gen; Wang, Guo-Zhi; Li, Shuang-Jian; Qin, Zuo-Pen; Li, Jing-Xi; Jansa, Luba

    2016-02-01

    The Daloushan mountain chain, located in the centre of the upper Yangtze continental block, is considered to represent the locus of the tectonic shortening resulting from the eastward growth of the Tibetan Plateau and NW-thrusting of the Xuefeng Orogen. Structural data and apatite fission-track ages have been used to decipher the geometry and the kinematic evolution of the Daloushan. The latter is subdivided into two domains: the eastern domain, governed by west- to NW-verging thrusting and deformation with dextral transpression, and a western domain, governed by south-verging thrusting and deformation. Both domains experienced four episodes of deformation, synchronous with the four stages of post-Cretaceous denudation, marked by rapid cooling propagating eastward from 20 to 5 Ma, at a rate of ∼0.1 mm/year. In particular, the last two episodes of denudation are closely related to the growth of the Tibetan Plateau. This indicates an intra-continental transfer of tectonic forcing from the Palaeo-Pacific to the Tethys-Himalayan Tectonic Domain across the Daloushan.

  19. Markov Chain Method for Radiative Transfer Modeling: A Case Study of Aerosol/Surface Retrieval using AirMSPI Measurements

    Science.gov (United States)

    Xu, F.; Diner, D. J.; Davis, A. B.; Latyshev, S.; Garay, M. J.; Kalashnikova, O.; Ge, C.; Wang, J.

    2013-12-01

    A vector Markov chain (MarCh) radiative transfer (RT) code developed at JPL that includes forward modeling of radiance and polarization fields and linearization (analytical estimation of Jacobians) was incorporated into an aerosol and surface retrieval package for a plane-parallel atmosphere/surface system. The RT computation by MarCh is based on matrix operations. To improve the code's computational efficiency, the forward model is currently undergoing acceleration through the exploration of different strategies for matrix operation and inversion, including numerical optimization, multi-threading/multi-processing techniques on a CPU. Implementation on a graphics processing unit (GPU) is also planned. Following a benchmarking study of the forward model, the performance of MarCh in aerosol and surface retrieval is being tested. With an optimized algorithm, we started from aerosol optical depth and surface retrieval using imagery acquired by Airborne Multiangle SpectroPolarimetric Imager (AirMSPI) over Fresno, CA. Aerosol properties including concentration and size distribution of different species provided by the Weather Research and Forecasting (WRF)-Chem model were used to constrain the retrieval and reduce the parameter space. The assumptions of spectral invariance in the angular shape of surface bidirectional reflectance factors (BRFs) and the magnitude of polarized surface BRFs were tested. The aerosol and surface properties are then relaxed in a stepwise way to refine the aerosol retrieval results and enable comparison with independent retrievals obtained from a collocated AErosol RObotic NETwork (AERONET) station.

  20. Food chain transfer of cadmium and lead to cattle in a lead-zinc smelter in Guizhou, China

    International Nuclear Information System (INIS)

    Cadmium (Cd) and Lead (Pb) are environmental pollutants. Environmental samples and bovine tissues were collected from the areas around a lead-zinc smelter in Guizhou, China for Cd, Pb, zinc (Zn) and copper (Cu) analysis. Cd in soil (10 mg/kg) and feed (6.6 mg/kg) from the polluted areas was 10 times higher than the Chinese Standards, resulting in higher Cd in bovine kidney (38 mg/kg) and liver (2.5 mg/kg). Pb in feed (132 mg/kg) from the polluted area was much higher than unpolluted areas, causing higher Pb levels in bovine tissues. Environmental Zn was elevated, but bovine tissue Zn was normal. Cu in bovine liver decreased with increased Cd and Pb. Metals in drinking water and in bovine muscle were within the Standard range. Thus, in the areas of this lead-zinc smelter, the environment has been contaminated with Cd and Pb, which has been transferred to cattle through the food chain. - Cd and Pb from lead-zinc smelters contaminate the environment and accumulate in bovine tissues.

  1. Lipid-regulated sterol transfer between closely apposed membranes by oxysterol-binding protein homologues

    OpenAIRE

    Schulz, Timothy A.; Choi, Mal-Gi; Raychaudhuri, Sumana; Mears, Jason A.; Ghirlando, Rodolfo; Hinshaw, Jenny E.; Prinz, William A.

    2009-01-01

    Sterols are transferred between cellular membranes by vesicular and poorly understood nonvesicular pathways. Oxysterol-binding protein–related proteins (ORPs) have been implicated in sterol sensing and nonvesicular transport. In this study, we show that yeast ORPs use a novel mechanism that allows regulated sterol transfer between closely apposed membranes, such as organelle contact sites. We find that the core lipid-binding domain found in all ORPs can simultaneously bind two membranes. Usin...

  2. Extended synaptotagmins are Ca2+-dependent lipid transfer proteins at membrane contact sites.

    Science.gov (United States)

    Yu, Haijia; Liu, Yinghui; Gulbranson, Daniel R; Paine, Alex; Rathore, Shailendra S; Shen, Jingshi

    2016-04-19

    Organelles are in constant communication with each other through exchange of proteins (mediated by trafficking vesicles) and lipids [mediated by both trafficking vesicles and lipid transfer proteins (LTPs)]. It has long been known that vesicle trafficking can be tightly regulated by the second messenger Ca(2+), allowing membrane protein transport to be adjusted according to physiological demands. However, it remains unclear whether LTP-mediated lipid transport can also be regulated by Ca(2+) In this work, we show that extended synaptotagmins (E-Syts), poorly understood membrane proteins at endoplasmic reticulum-plasma membrane contact sites, are Ca(2+)-dependent LTPs. Using both recombinant and endogenous mammalian proteins, we discovered that E-Syts transfer glycerophospholipids between membrane bilayers in the presence of Ca(2+) E-Syts use their lipid-accommodating synaptotagmin-like mitochondrial lipid binding protein (SMP) domains to transfer lipids. However, the SMP domains themselves cannot transport lipids unless the two membranes are tightly tethered by Ca(2+)-bound C2 domains. Strikingly, the Ca(2+)-regulated lipid transfer activity of E-Syts was fully recapitulated when the SMP domain was fused to the cytosolic domain of synaptotagmin-1, the Ca(2+)sensor in synaptic vesicle fusion, indicating that a common mechanism of membrane tethering governs the Ca(2+)regulation of lipid transfer and vesicle fusion. Finally, we showed that microsomal vesicles isolated from mammalian cells contained robust Ca(2+)-dependent lipid transfer activities, which were mediated by E-Syts. These findings established E-Syts as a novel class of LTPs and showed that LTP-mediated lipid trafficking, like vesicular transport, can be subject to tight Ca(2+)regulation. PMID:27044075

  3. Inhibition of cholesterol ester transfer protein CGS 25159 and changes in lipoproteins in hamsters.

    Science.gov (United States)

    Kothari, H V; Poirier, K J; Lee, W H; Satoh, Y

    1997-01-01

    As a result of screening, several isoflavans were identified to be antagonists of cholesterol ester transfer protein (CETP) activity. The present study evaluates CGS 25159, a synthetic isoflavan, as a putative inhibitor of CETP activity of human and hamster plasma. Determined by [3]CE transfer from HDL to VLDL + LDL fraction or by fluorescent-CE transfer assay, CGS 25159 inhibited CETP in both human plasma bottom fraction (d = 1.21 g/ml) and in plasma from Golden Syrian Hamsters with an IC50 contention that pharmacological down regulation of CETP activity could result in favorable changes in lipoprotein profile. PMID:9051198

  4. Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data.

    Science.gov (United States)

    Smith, Lorna J; Roby, Ysobel; Allison, Jane R; van Gunsteren, Wilfred F

    2013-07-30

    Experimental studies of barley and maize lipid transfer proteins (LTPs) show that the two proteins bind the ligand palmitate in opposite orientations in their internal cavities. Moreover, maize LTP is reported to bind the ligand caprate in the internal cavity in a mixture of two orientations with approximately equal occupancy. Six 30 ns molecular dynamics (MD) simulations of maize and barley LTP with ligands bound in two orientations (modes M and B) have been used to understand the different ligand binding preferences. The simulations show that both maize and barley LTP could bind palmitate in the orientation observed experimentally for maize LTP (mode M), with the predominant interaction being a salt bridge between the ligand carboxylate headgroup and a conserved arginine side chain. However, the simulation of barley LTP with palmitate in the mode B orientation shows the most favorable protein-ligand interaction energy. In contrast, the simulations of maize LTP with palmitate and with caprate in the mode B orientation show no persistent ligand binding, the ligands leaving the cavity during the simulations. Sequence differences between maize and barley LTP in the AB loop region, in residues at the base of the hydrophobic cavity, and in the helix A region are identified as contributing to the different behavior. The simulations reproduce well the experimentally observed binding preferences for palmitate and suggest that the experimental data for maize LTP with caprate reflect ligand mobility in binding mode M rather than the population of binding modes M and B. PMID:23834513

  5. Misfolding, degradation, and aggregation of variant proteins. The molecular pathogenesis of short chain acyl-CoA dehydrogenase (SCAD) deficiency

    DEFF Research Database (Denmark)

    Pedersen, Christina Bak; Bross, P.; Winter, V.S.; Corydon, Thomas Juhl; Bolund, Lars; Bartlett, K.; Vockley, J.; Gregersen, N.

    2003-01-01

    type, associate with mitochondrial hsp60 chaperonins; however, the variant SCAD proteins remained associated with hsp60 for prolonged periods of time. Biogenesis experiments at two temperatures revealed that some of the variant proteins (R22W, G68C, W153R, and R359C) caused severe misfolding, whereas......Short chain acyl-CoA dehydrogenase (SCAD) deficiency is an inborn error of the mitochondrial fatty acid metabolism caused by rare variations as well as common susceptibility variations in the SCAD gene. Earlier studies have shown that a common variant SCAD protein (R147W) was impaired in folding...... SCAD proteins either triggered proteolytic degradation by mitochondrial proteases or, especially at elevated temperature, aggregation of non-native conformers. The latter finding may indicate that accumulation of aggregated SCAD proteins may play a role in the pathogenesis of SCAD deficiency....

  6. Toxic response caused by a misfolding variant of the mitochondrial protein short-chain acyl-CoA dehydrogenase

    DEFF Research Database (Denmark)

    Schmidt, Stinne P; Corydon, Thomas J; Pedersen, Christina B;

    2011-01-01

    disease-associated misfolding variant of SCAD protein, p.Arg107Cys, disturbs mitochondrial function. METHODS: We have developed a cell model system, stably expressing either the SCAD wild-type protein or the misfolding SCAD variant protein, p.Arg107Cys (c.319 C > T). The model system was used for......BACKGROUND: Variations in the gene ACADS, encoding the mitochondrial protein short-chain acyl CoA-dehydrogenase (SCAD), have been observed in individuals with clinical symptoms. The phenotype of SCAD deficiency (SCADD) is very heterogeneous, ranging from asymptomatic to severe, without a clear...... increased demand for the mitochondrial antioxidant SOD2. In addition, we found markers of apoptotic activity in the p.Arg107Cys expressing cells, which points to a possible pathophysiological role of this variant protein....

  7. Fast electron transfer through a single molecule natively structured redox protein

    DEFF Research Database (Denmark)

    Della Pia, Eduardo Antonio; Chi, Qijin; Macdonald, J. Emyr;

    2012-01-01

    The electron transfer properties of proteins are normally measured as molecularly averaged ensembles. Through these and related measurements, proteins are widely regarded as macroscopically insulating materials. Using scanning tunnelling microscopy (STM), we present new measurements of the...... conductance through single-molecules of the electron transfer protein cytochrome b562 in its native conformation, under pseudo-physiological conditions. This is achieved by thiol (SH) linker pairs at opposite ends of the molecule through protein engineering, resulting in defined covalent contact between a...... gold surface and a platinum–iridium STM tip. Two different orientations of the linkers were examined: a long-axis configuration (SH-LA) and a short-axis configuration (SH-SA). In each case, the molecular conductance could be ‘gated’ through electrochemical control of the heme redox state. Reproducible...

  8. Human Immunodeficiency Virus Type 1 Employs the Cellular Dynein Light Chain 1 Protein for Reverse Transcription through Interaction with Its Integrase Protein

    OpenAIRE

    Jayappa, Kallesh Danappa; Ao, Zhujun; Wang, Xiaoxia; Mouland, Andrew J.; Shekhar, Sudhanshu; Yang, Xi; Yao, Xiaojian

    2015-01-01

    In this study, we examined the requirement for host dynein adapter proteins such as dynein light chain 1 (DYNLL1), dynein light chain Tctex-type 1 (DYNLT1), and p150Glued in early steps of human immunodeficiency virus type 1 (HIV-1) replication. We found that the knockdown (KD) of DYNLL1, but not DYNLT1 or p150Glued, resulted in significantly lower levels of HIV-1 reverse transcription in cells. Following an attempt to determine how DYNLL1 could impact HIV-1 reverse transcription, we detected...

  9. Molecularly Imprinted Electropolymer for a Hexameric Heme Protein with Direct Electron Transfer and Peroxide Electrocatalysis

    OpenAIRE

    Lei Peng; Aysu Yarman; Jetzschmann, Katharina J.; Jae-Hun Jeoung; Daniel Schad; Holger Dobbek; Ulla Wollenberger; Scheller, Frieder W.

    2016-01-01

    For the first time a molecularly imprinted polymer (MIP) with direct electron transfer (DET) and bioelectrocatalytic activity of the target protein is presented. Thin films of MIPs for the recognition of a hexameric tyrosine-coordinated heme protein (HTHP) have been prepared by electropolymerization of scopoletin after oriented assembly of HTHP on a self-assembled monolayer (SAM) of mercaptoundecanoic acid (MUA) on gold electrodes. Cavities which should resemble the shape and size of HTHP wer...

  10. Flavoproteins, iron proteins, and hemoproteins as electron-transfer components of the sulfate-reducing bacteria

    Energy Technology Data Exchange (ETDEWEB)

    LeGall, J. (Centre National de la Recherche Scientifique, Marseille, France); DerVartanian, D.V.; Peck, H.D. Jr.

    1979-01-01

    This review article with 105 references discusses the most recent publications that deal with the discovery of new redox proteins of the sulfate-reducing bacteria belonging to the genera Desulfotomaculum and Desulfovibrio and proposes explanations for their physical and biological functions. The redox proteins studied as part of the electron-transfer system of these bacteria include flavodoxins, ferredoxins, rubredoxins, cytochromes and several reductose-type enzymes. (KRM)

  11. The biochemistry and biology of extracellular plant lipid-transfer proteins (LTPs)

    OpenAIRE

    Trevor H Yeats; Rose, Jocelyn K.C.

    2008-01-01

    Plant lipid-transfer proteins (LTPs) are abundant, small, lipid binding proteins that are capable of exchanging lipids between membranes in vitro. Despite their name, a role in intracellular lipid transport is considered unlikely, based on their extracellular localization. A number of other biological roles, including antimicrobial defense, signaling, and cell wall loosening, have been proposed, but conclusive evidence is generally lacking, and these functions are not well correlated with in ...

  12. Measuring protein interactions using Förster resonance energy transfer and fluorescence lifetime imaging microscopy

    OpenAIRE

    Day, Richard N

    2013-01-01

    The method of fluorescence lifetime imaging microscopy (FLIM) is a quantitative approach that can be used to detect Förster Resonance Energy Transfer (FRET). The use of FLIM to measure the FRET that results from the interactions between proteins labeled with fluorescent proteins (FPs) inside living cells provides a non-invasive method for mapping interactomes. Here, the use of the phasor plot method to analyze frequency domain (FD) FLIM measurements is described, and measurements obtained fro...

  13. Drug discovery opportunities and challenges at G protein coupled receptors for long chain free fatty acids

    Directory of Open Access Journals (Sweden)

    Nicholas D Holliday

    2012-01-01

    Full Text Available Discovery of G protein coupled receptors for long chain free fatty acids (FFAs, FFA1 (GPR40 and GPR120, has expanded our understanding of these nutrients as signalling molecules. These receptors have emerged as important sensors for FFA levels in the circulation or the gut lumen, based on evidence from in vitro and rodent models, and an increasing number of human studies. Here we consider their promise as therapeutic targets for metabolic disease, including type 2 diabetes and obesity. FFA1 directly mediates acute FFA-induced glucose-stimulated insulin secretion in pancreatic beta-cells, while GPR120 and FFA1 trigger release of incretins from intestinal endocrine cells, and so indirectly enhance insulin secretion and promote satiety. GPR120 signalling in adipocytes and macrophages also results in insulin sensitizing and beneficial anti-inflammatory effects. Drug discovery has focussed on agonists to replicate acute benefits of FFA receptor signalling, with promising early results for FFA1 agonists in man. Controversy surrounding chronic effects of FFA1 on beta-cells illustrates that long term benefits of antagonists also need exploring. It has proved challenging to generate highly selective potent ligands for FFA1 or GPR120 subtypes, given that both receptors have hydrophobic orthosteric binding sites, which are not completely defined and have modest ligand affinity. Structure activity relationships are also reliant on functional read outs, in the absence of robust binding assays to provide direct affinity estimates. Nevertheless synthetic ligands have already helped dissect specific contributions of FFA1 and GPR120 signalling from the many possible cellular effects of FFAs. Approaches including use of fluorescent ligand binding assays, and targeting allosteric receptor sites, may improve further preclinical ligand development at these receptors, to exploit their unique potential to target multiple facets of diabetes.

  14. Human liver alcohol dehydrogenase. 2. The primary structure of the gamma 1 protein chain.

    Science.gov (United States)

    Bühler, R; Hempel, J; Kaiser, R; de Zalenski, C; von Wartburg, J P; Jörnvall, H

    1984-12-17

    The primary structure of the gamma 1 subunit of human liver alcohol dehydrogenase isoenzyme gamma 1 gamma 1 was deduced by characterization of 36 tryptic and 2 CNBr peptides. The polypeptide chain is composed of 373 amino acid residues. gamma 1 differs from the beta 1 subunit of human liver alcohol dehydrogenase at 21 positions, and from the E subunit of horse liver alcohol dehydrogenase at 43 positions including a gap at position 128 as in the beta 1 subunit. All zinc-liganding residues from the E subunit of the horse protein and the beta 1 subunit of the human enzyme are conserved, but like beta 1, gamma 1 also has an additional cysteine residue at position 286 (in the positional numbering system of the horse enzyme) due to a Tyr----Cys exchange. Most amino acid exchanges preserve the properties of the residues affected and are largely located on the surface of the molecules, away from the active site and the coenzyme binding region. However, eight positions with charge differences in relation to the E subunit of the horse enzyme are noticed. These result in a net positive charge increase of one in gamma 1 versus E, explaining the electrophoretic mobilities on starch gels. Of functional significance is the conservation of Ser-48 in gamma 1 relative to E. The residue is close to the active site but different (Thr-48) in the beta 1 subunit of the human enzyme. Thus, the closer structural relationship between human gamma 1 and horse E enzyme subunit than between beta 1 and E is also reflected in functionally important residues, explaining a greater similarity between gamma 1 gamma 1 and EE than between beta 1 beta 1 and EE. PMID:6391921

  15. Postnatal development of cerebellar zones revealed by neurofilament heavy chain protein expression

    Directory of Open Access Journals (Sweden)

    Joshua J White

    2013-05-01

    Full Text Available The cerebellum is organized into parasagittal zones that control sensory-motor behavior. Although the architecture of adult zones is well understood, very little is known about how zones emerge during development. Understanding the process of zone formation is an essential step towards unraveling how circuits are constructed to support specific behaviors. Therefore, we focused this study on postnatal development to determine the spatial and temporal changes that establish zonal patterns during circuit formation. We used a combination of wholemount and tissue section immunohistochemistry in mice to show that the cytoskeletal protein neurofilament heavy chain (NFH is a robust marker for postnatal cerebellar zonal patterning. The patterned expression of NFH is initiated shortly after birth, and compared to the domains of several known zonal markers such as zebrin II, HSP25, neurogranin, and phospholipase Cβ4 (PLCβ4, NFH does not exhibit transient expression patterns that are typically remodeled between stages, and the adult zones do not emerge after a period of uniform expression in all lobules. Instead, we found that throughout postnatal development NFH gradually reveals distinct zones in each cerebellar lobule. The boundaries of individual NFH zones sharpen over time, as zones are refined during the second and third weeks after birth. Double labeling with neurogranin and PLCβ4 further revealed that although the postnatal expression of NFH is spatially and temporally unique, its pattern of zones respects a fundamental and well-known molecular topography in the cerebellum. The dynamics of NFH expression support the hypothesis that adult circuits are derived from an embryonic map that is refined into zones during the first three-weeks of life.

  16. Premalignant quiescent melanocytic nevi do not express the MHC class I chain-related protein A

    Directory of Open Access Journals (Sweden)

    Mercedes B. Fuertes

    2011-08-01

    Full Text Available The MHC class I chain-related protein A (MICA is an inducible molecule almost not expressed by normal cells but strongly up-regulated in tumor cells. MICA-expressing cells are recognized by natural killer (NK cells, CD8+ aßTCR and ?dTCR T lymphocytes through the NKG2D receptor. Engagement of NKG2D by MICA triggers IFN-? secretion and cytotoxicity against malignant cells. Although most solid tumors express MICA and this molecule is a target during immune surveillance against tumors, it has been observed that high grade tumors from different histotypes express low amounts of cell surface MICA due to a metalloprotease- induced shedding. Also, melanomas develop after a complex process of neotransformation of normal melanocytes. However, the expression of MICA in premalignant stages (primary human quiescent melanocytic nevi remains unknown. Here, we assessed expression of MICA by flow cytometry using cell suspensions from 15 primary nevi isolated from 11 patients. When collected material was abundant, cell lysates were prepared and MICA expression was also analyzed by Western blot. We observed that MICA was undetectable in the 15 primary nevi (intradermic, junction, mixed, lentigo and congenital samples as well as in normal skin, benign lesions (seborrheic keratosis, premalignant lesions (actinic keratosis and benign basocellular cancer. Conversely, a primary recently diagnosed melanoma showed intense cell surface MICA. We conclude that the onset of MICA expression is a tightly regulated process that occurs after melanocytes trespass the stage of malignant transformation. Thus, analysis of MICA expression in tissue sections of skin samples may constitute a useful marker to differentiate between benign and malignant nevi.

  17. Main-Chain and Side-Chain Sequence-Regulated Vinyl Copolymers by Iterative Atom Transfer Radical Additions and 1:1 or 2:1 Alternating Radical Copolymerization.

    Science.gov (United States)

    Soejima, Takamasa; Satoh, Kotaro; Kamigaito, Masami

    2016-01-27

    Main- and side-chain sequence-regulated vinyl copolymers were prepared by a combination of iterative atom transfer radical additions (ATRAs) of vinyl monomers for side-chain control and 1:1 or 2:1 alternating radical copolymerization of the obtained side-chain sequenced "oligomonomers" and vinyl comonomers for main-chain control. A complete set of sequence-regulated trimeric vinyl oligomers of styrene (S) and/or methyl acrylate (A) were first synthesized via iterative ATRAs of these monomers to a halide of monomeric S or A unit (X-S or X-A) under optimized conditions with appropriate ruthenium or copper catalysts, which were selected depending on the monomers and halides. The obtained halogen-capped oligomers were then converted into a series of maleimide (M)-ended oligomonomers with different monomer compositions and sequences (M-SSS, M-ASS, M-SAS, M-AAS, M-SSA, M-ASA, M-SAA, M-AAA) by a substitution reaction of the halide with furan-protected maleimide anion followed by deprotection of the furan units. These maleimide-ended oligomonomers were then radically copolymerized with styrene or limonene to enable the 1:1 or 2:1 monomer-sequence regulation in the main chain and finally result in the main- and side-chain sequence-regulated vinyl copolymers with high molecular weights in high yield. The properties of the sequence-regulated vinyl copolymers depended on not only the monomer compositions but also the monomer sequences. The solubility was highly affected by the outer monomer units in the side chains whereas the glass transition temperatures were primarily affected by the two successive monomer sequences. PMID:26761148

  18. Gamma radiation induced synthesis of poly(N-isopropylacrylamide) mediated by Reversible Addition–Fragmentation Chain Transfer (RAFT) process

    International Nuclear Information System (INIS)

    Poly(N-isopropylacrylamide) (PNiPAAm) is synthesized by gamma radiation induced Reversible Addition–Fragmentation Chain Transfer (RAFT) polymerization. The monomer is polymerized in the presence of two different trithiocarbonate-based RAFT agents i.e., Cyanomethyldodecyltrithiocarbonate (CDTC) and 2-(Dodecylthiocarbonothioylthio)-2-methylpropionic acid (DMPA) in dimethylformamide (DMF) at room temperature under nitrogen atmosphere. Number-average molecular weights (Mn) and dispersities of the polymers were determined by Size Exclusion Chromatography (SEC). Dispersities (Ɖ) of the resulting polymers are narrow, i.e., Ɖ≤1.18, indicating the occurrence of well-controlled polymerization via radiation induced RAFT process. %Conversion is determined by gravimetric method and also confirmed by Proton Nuclear Magnetic Resonance (1H-NMR) Spectroscopy. By selecting proper [Monomer]/[RAFT] ratio and controlling conversion it is possible to synthesize PNiPAAm in the molecular weight range of 2400–72400 with extremely low molecular weight distributions with the anticipation of preparing corresponding size-controlled nanogels. The phase transition of PNiPAAm with low dispersity synthesized by RAFT is sharper than PNiPAAm synthesized by free radical polymerization. - Highlights: • Poly(N-isopropylacrylamide) is synthesized by RAFT-mediated radiation induced polymerization. • Dispersities of polymers are narrow Ɖ≤1.18, proving the controlled fashion of polymerization. • By proper selection of [monomer]/[RAFT] ratio and conversion, MW range of 2400–72400 was achieved. • Phase transition of PNiPAAm synthesized by RAFT is sharper than PNiPAAm synthesized by free radical polymerization

  19. Long-range protein electron transfer observed at the single-molecule level

    DEFF Research Database (Denmark)

    Chi, Qijin; Farver, Ole; Ulstrup, Jens

    2005-01-01

    A biomimetic long-range electron transfer (ET) system consisting of the blue copper protein azurin, a tunneling barrier bridge, and a gold single-crystal electrode was designed on the basis of molecular wiring self-assembly principles. This system is sufficiently stable and sensitive in a quasi...

  20. Linker proteins enable ultrafast excitation energy transfer in the phycobilisome antenna system of Thermosynechococcus vulcanus.

    Science.gov (United States)

    Nganou, C; David, L; Adir, N; Mkandawire, M

    2016-01-01

    We applied a femtosecond flash method, using induced transient absorption changes, to obtain a time-resolved view of excitation energy transfer in intact phycobilisomes of Thermosynechococcus vulcanus at room temperature. Our measurement of an excitation energy transfer rate of 888 fs in phycobilisomes shows the existence of ultrafast kinetics along the phycocyanin rod subcomplex to the allophycocyanin core that is faster than expected for previous excitation energy transfer based on Förster theory in phycobilisomes. Allophycocyanin in the core further transfers energy to the terminal emitter(s) in 17 ps. In the phycobilisome, rod doublets composed of hexameric phycocyanin discs and internal linker proteins are arranged in a parallel fashion, facilitating direct rod-rod interactions. Excitonic splitting likely drives rod absorption at 635 nm as a result of strong coupling between β84 chromophores (20 ± 1 Å) in adjacent hexamers. In comparison to the absorbance of the phycobilisome antenna system of the cyanobacterium Acaryochloris marina, which possesses a single rod structure, the linkers in T. vulcanus rods induce a 17 nm red shift in the absorbance spectrum. Furthermore, the kinetics of 888 fs indicates that the presence of the linker protein induces ultrafast excitation energy transfer between phycocyanin and allophycocyanin inside the phycobilisome, which is faster than all previous excitation energy transfer in phycobilisome subunits or sub-complexes reported to date. PMID:26537632

  1. MHC class I chain-related protein A antibodies and shedding are associated with the progression of multiple myeloma

    OpenAIRE

    Jinushi, Masahisa; Vanneman, Matthew; Munshi, Nikhil C.; Tai, Yu-Tzu; Prabhala, Rao H.; Ritz, Jerome; Neuberg, Donna; Anderson, Kenneth C; Carrasco, Daniel Ruben; Dranoff, Glenn

    2008-01-01

    Monoclonal gammopathy of undetermined significance (MGUS) is a common disorder of aging and a precursor lesion to full-blown multiple myeloma (MM). The mechanisms underlying the progression from MGUS to MM are incompletely understood but include the suppression of innate and adaptive antitumor immunity. Here, we demonstrate that NKG2D, an activating receptor on natural killer (NK) cells, CD8+ T lymphocytes, and MHC class I chain-related protein A (MICA), an NKG2D ligand induced in malignant p...

  2. The effect of polyelectrolyte chain length on layer-by-layer protein/polyelectrolyte assembly - an experimental study

    Czech Academy of Sciences Publication Activity Database

    Houska, Milan; Brynda, Eduard; Bohatá, Karolína

    2004-01-01

    Roč. 273, č. 1 (2004), s. 140-147. ISSN 0021-9797 R&D Projects: GA AV ČR IAA4050006; GA ČR GA203/02/1326; GA ČR GA102/03/0633 Institutional research plan: CEZ:AV0Z4050913 Keywords : layer-by-layer adsorption * protein/ polyelectrolyte assemblies * effect of polyelectrolyte chain length Subject RIV: CD - Macromolecular Chemistry Impact factor: 1.784, year: 2004

  3. Microsomal Triglyceride Transfer Protein (MTP) Associates with Cytosolic Lipid Droplets in 3T3-L1 Adipocytes

    OpenAIRE

    Love, Joseph D.; Suzuki, Takashi; Robinson, Delia B.; Harris, Carla M.; Johnson, Joyce E.; Mohler, Peter J.; Jerome, W. Gray; Swift, Larry L.

    2015-01-01

    Lipid droplets are intracellular energy storage organelles composed of a hydrophobic core of neutral lipid, surrounded by a monolayer of phospholipid and a diverse array of proteins. The function of the vast majority of these proteins with regard to the formation and/or turnover of lipid droplets is unknown. Our laboratory was the first to report that microsomal triglyceride transfer protein (MTP), a lipid transfer protein essential for the assembly of triglyceride-rich lipoproteins, was expr...

  4. Role of pigment-protein coupling and pathways of excitation energy transfer in FMO complex

    CERN Document Server

    Singh, Davinder

    2016-01-01

    We theoretically investigate the effect of different pigment-protein couplings and the role of quantum interference among different energy transfer channels in excitation energy transfer (EET) in FMO complex. We employ the non-Markovian master equation that allows the use of different values of pigment-protein couplings and cut-off frequencies for different BChla sites, in the adiabatic limit of electron transfer in FMO complex. Several pathways of EET are identified and investigated using a realistic set of pigment-pigment couplings and the site energy of each BChla site. We analyze that it is the destructive interference between different channels of a particular pathway that is responsible for the time-scales of oscillations of excitation energy as observed in the recent experiments.

  5. Purification and antipathogenic activity of lipid transfer proteins (LTPs) from the leaves of Arabidopsis and spinach

    OpenAIRE

    Segura, Ana; Moreno, Manuel; García Olmedo, Francisco

    1993-01-01

    Two homogeneous proteins active in vitro against the bacterial pathogen Clavibacter michiganensis subsp. sepedonicus were obtained from a crude cell-wall preparation from the leaves of Columbia wild-type Arabidopsis. The N-terminal amino acid sequences of these proteins allowed their identification as lipid transfer proteins (LTP-a1, LTP-a2); the LTP1-a1 sequence was identical to that deduced from a previously described cDNA (EMBL M80566) and LTP-a2 was quite divergent (44% identical position...

  6. Identificazione e caratterizzazione dell'allergene Lipid Transfer Protein di pomodoro

    OpenAIRE

    Rasore, Claudia

    2013-01-01

    Le non specific lipid transfer proteins appartengono alla famiglia delle LTP1 e rappresentano le più importanti proteine allergeniche in grado di causare reazioni IgE-mediate nell'area Mediterranea. Sebbene i casi più noti di reazioni avverse alle nsLTPs siano allergie ai frutti di Rosaceae, fra le proteine allergeniche del pomodoro è stata identificata Lyc e 3 (LTP di pomodoro). Inoltre è stato osservato che Lyc e 3 è in grado di conservare la sua reattività immunologica anche a seguito di p...

  7. Molecular imprinted polymer with positively charged, assistant recognition polymer chains for adsorption/enrichment of low content target protein

    Institute of Scientific and Technical Information of China (English)

    LONG Yi; SUN Yang; WANG Ying; XING XiaoCui; ZHAO Zhuo; WANG ChunHong; FAN YunGe; MI HuaiFeng

    2008-01-01

    Here, we introduce a new type of molecular imprinted polymer (MIP) with immobilized assistant recog-nition polymer chains (ARPCs) to create effective recognition sites and with bacterial cloned protein as template for adsorbing the low content target protein from cell extract. In this work, cloned pig cyclo-philin 18 (pCyP18), a peptidyl-prolyl cis/trans-isomerase, was used as template. The template protein was selectively assembled with ARPCs from their library, which consists of numerous limited length polymer chains with randomly distributed recognition sites of positively charged amino groups and immobilizing sites. These assemblies were adsorbed by porous microsphers and immobilized on them.After removing the template, binding sites complementary to the target protein in size, shape and the position of recognition groups were exposed, and their confirmation was preserved by the cross-linked structure. The synthesized MIP was used to adsorb the cellular pCyP18, and its proportional content was enriched more than hundred times. The extended experiment on imprinting bovine serum albumin (BSA) with ARPCs shows that this method is also suitable for large protein.

  8. Insulinotropic and Muscle Protein Synthetic Effects of Branched-Chain Amino Acids: Potential Therapy for Type 2 Diabetes and Sarcopenia

    Directory of Open Access Journals (Sweden)

    Darren G. Candow

    2012-11-01

    Full Text Available The loss of muscle mass and strength with aging (i.e., sarcopenia has a negative effect on functional independence and overall quality of life. One main contributing factor to sarcopenia is the reduced ability to increase skeletal muscle protein synthesis in response to habitual feeding, possibly due to a reduction in postprandial insulin release and an increase in insulin resistance. Branched-chain amino acids (BCAA, primarily leucine, increases the activation of pathways involved in muscle protein synthesis through insulin-dependent and independent mechanisms, which may help counteract the “anabolic resistance” to feeding in older adults. Leucine exhibits strong insulinotropic characteristics, which may increase amino acid availability for muscle protein synthesis, reduce muscle protein breakdown, and enhance glucose disposal to help maintain blood glucose homeostasis.

  9. Handling of human short-chain acyl-CoA dehydrogenase (SCAD) variant proteins in transgenic mice

    DEFF Research Database (Denmark)

    Kragh, Peter M; Pedersen, Christina B; Schmidt, Stine P;

    2007-01-01

    results may indicate that the two hSCAD folding variants are degraded by the mouse mitochondrial protein quality control system. Indeed, pulse-chase studies with isolated mitochondria revealed that soluble variant hSCAD protein was rapidly eliminated. This is in agreement with the fact that no disease......Abstract To investigate the in vivo handling of human short-chain acyl-CoA dehydrogenase (SCAD) variant proteins, three transgenic mouse lines were produced by pronuclear injection of cDNA encoding the wild-type, hSCAD-wt, and two disease causing folding variants hSCAD-319C > T and hSCAD-625G > A...... phenotype developed for any of the lines transgenic for the hSCAD folding variants. The indicated remarkable efficiency of the mouse protein quality control system in the degradation of SCAD folding variants should be further substantiated and investigated, since it might indicate ways to prevent disease...

  10. Influence of insulin sensitivity and the TaqIB cholesteryl ester transfer protein gene polymorphism on plasma lecithin : Cholesterol acyltransferase and lipid transfer protein activities and their response to hyperinsulinaemia in nondiabetic men.

    NARCIS (Netherlands)

    Riemens, SC; Van Tol, A; Stulp, BK; Dullaart, RPF

    1999-01-01

    Lecithin:cholesteryl acyltransferase (LCAT), cholesteryl ester transfer protein (CETP), phospholipid transfer protein (PLTP), and lipoprotein lipases are involved in high density lipoprotein (HDL) metabolism. We evaluated the influence of insulin sensitivity and of the TaqIB CETP gem polymorphism (B

  11. Ameliorated stress related proteins are associated with improved cardiac function by sarcoplasmic reticulum calcium ATPase gene transfer in heart failure

    Institute of Scientific and Technical Information of China (English)

    Zhi-Qing Fu; Xiao-Ying Li; Xiao-Chun Lu; Ya-Fei Mi; Tao Liu; Wei-Hua Ye

    2012-01-01

    Background Previous studies showed that overexpression of sarco-endoplasmic reticulum calcium ATPase (SERCA2a) in a variety of heart failure (HF) models was associated with greatly enhanced cardiac performance. However, it still undefined the effect of SERCA2a overexpression on the systemic inflammatory response and neuro-hormonal factors. Methods A rapid right ventricular pacing model of experimental HF was used in beagles. Then the animals underwent recombinant adeno-associated virus 1 (rAAV1) mediated gene transfection by direct intra-myocardium injection. HF animals were randomized to receive the SERCA2a gene, enhanced green fluorescent protein (control) gene, or equivalent phosphate buffered saline. Thirty days after gene delivery, the cardiac function was evaluated by echocardiographic testing. The protein level of SERCA2a was measured by western blotting. The proteomic analysis of left ventricular (LV) sample was determined using two-dimensional (2-D) gel electrophoresis and MALDI-TOF-MS. The serum levels of the systemic inflammatory and neuro-hormonal factors were assayed using radioimmunoassay kits. Results The cardiac function improved after SERCA- 2a gene transfer due to the significantly increased SERCA2a protein level. Beagles treated with SERCA2a had significantly decreased serum levels of the inflammatory markers (interleukin-6 and tumor necrosis factor-α) and neuro-hormonal factors (brain natriuretic peptide, endothelin-1 and angiotensin Ⅱ) compared with HF animals. The myocardial proteomic analysis showed that haptoglobin heavy chain, heat shock protein (alpha-crystallin-related, B6) were down-regulated, and galectin-1 was up-regulated in SERCA2a group compared with HF group, companied by up-regulated contractile proteins and NADH dehydrogenase. Conclusions These findings demonstrate that regional intramyocardial injections of rAAV1-SERCA2a vectors may improve global LV function, correlating with reverse activation of the systemic inflammatory

  12. Reaction mechanisms in the radiolysis of peptides, polypeptides and proteins II reactions at side-chain loci in model systems

    International Nuclear Information System (INIS)

    The major emphasis in radiation biology at the molecular level has been on the nucleic acid component of the nucleic acid-protein complex because of its primary genetic importance. But there is increasing evidence that radiation damage to the protein component also has important biological implications. Damage to capsid protein now appears to be a major factor in the radiation inactivation of phage and other viruses. And, there is increasing evidence that radiation-chemical change in the protein component of chromation leads to changes in the stability of the repressor-operator complexes involved in gene expression. Knowledge of the radiation chemistry of protein is also of importance in other fields such as the application of radiation sterilization to foods and drugs. Recent findings that a class of compounds, the α,α'-diaminodicarboxylic acids, not normally present in food proteins, are formed in protein radiolysis is of particular significance since certain of their peptide derivatives have been showing to exhibit immunological activity. The purpose of this review is to bring together and to correlate our present knowledge of products and mechanisms in the radiolysis of peptides, polypeptides and proteins both aqueous and solid-state. In part 1 we presented a discussion of the radiation-induced reactions of the peptide main-chain in model peptide and polypeptide systems. Here in part 2 the emphasis is on the competing radiation chemistry at side-chain loci of peptide derivatives of aliphatic, aromatic-unsaturated and sulfur-containing amino acids in similar systems. Information obtained with the various experimental techniques of product analysis, competition kinetics, spin-trapping, pulse radiolysis, and ESR spectroscopy are included

  13. Progress and challenges in simulating and understanding electron transfer in proteins.

    Science.gov (United States)

    de la Lande, Aurélien; Gillet, Natacha; Chen, Shufeng; Salahub, Dennis R

    2015-09-15

    This Review presents an overview of the most common numerical simulation approaches for the investigation of electron transfer (ET) in proteins. We try to highlight the merits of the different approaches but also the current limitations and challenges. The article is organized into three sections. Section 2 deals with direct simulation algorithms of charge migration in proteins. Section 3 summarizes the methods for testing the applicability of the Marcus theory for ET in proteins and for evaluating key thermodynamic quantities entering the reaction rates (reorganization energies and driving force). Recent studies interrogating the validity of the theory due to the presence of non-ergodic effects or of non-linear responses are also described. Section 4 focuses on the tunneling aspects of electron transfer. How can the electronic coupling between charge transfer states be evaluated by quantum chemistry approaches and rationalized? What interesting physics regarding the impact of protein dynamics on tunneling can be addressed? We will illustrate the different sections with examples taken from the literature to show what types of system are currently manageable with current methodologies. We also take care to recall what has been learned on the biophysics of ET within proteins thanks to the advent of atomistic simulations. PMID:26116376

  14. Trophic transfer of lead through a model marine four-level food chain: Tetraselmis suecica, Artemia franciscana, Litopenaeus vannamei, and Haemulon scudderi.

    Science.gov (United States)

    Soto-Jiménez, M F; Arellano-Fiore, C; Rocha-Velarde, R; Jara-Marini, M E; Ruelas-Inzunza, J; Páez-Osuna, F

    2011-08-01

    The objective of this investigation was to assess the transfer of lead (Pb) along an experimental, four-level food chain: Tetraselmis suecica (phytoplankton) → Artemia franciscana (crustacean, brine shrimp) → Litopenaeus vannamei (crustacean, white shrimp) → Haemulon scudderi (fish, grunt). T. suecica was exposed to a sublethal dose of Pb in solution and then used as the base of a marine food chain. Significant differences in Pb concentrations were found between exposed organisms of the different trophic levels and the control. Particularly, Pb concentrations in fish of the simulated trophic chain were two-to three times higher in the exposed specimens than in the control. Levels of Pb in phytoplankton showed a substantial increase with respect to the solution (level I), with bioconcentration factors averaging from 930 to 3630. In contrast, a strong decrease in Pb concentration from phytoplankton to zooplankton (level II) and from zooplankton to shrimp tissues (level III) was evidenced by bioaccumulation factors metal transfer observed in these two predators, Pb concentration in the grunt fish (level IV) was higher than in the shrimp (level III) (bioaccumulation factor >1.0). Some of the added Pb is transferred from the phytoplankton along the food chain, thus producing a net accumulation of Pb mainly in fish and, to a lesser extent, in shrimp tissues. Because Pb is one of the most pervasive contaminants in coastal ecosystems, its transference by way of diet and potential net accumulation in higher predators is of ecologic importance for marine life. In addition, because shrimp and adult Haemulon scudderi are commercially important resources, this issue is of particular relevance to the safety of marine products. PMID:21082317

  15. Lipid transfer proteins do their thing anchored at membrane contact sites… but what is their thing?

    Science.gov (United States)

    Wong, Louise H; Levine, Tim P

    2016-04-15

    Membrane contact sites are structures where two organelles come close together to regulate flow of material and information between them. One type of inter-organelle communication is lipid exchange, which must occur for membrane maintenance and in response to environmental and cellular stimuli. Soluble lipid transfer proteins have been extensively studied, but additional families of transfer proteins have been identified that are anchored into membranes by transmembrane helices so that they cannot diffuse through the cytosol to deliver lipids. If such proteins target membrane contact sites they may be major players in lipid metabolism. The eukaryotic family of so-called Lipid transfer proteins Anchored at Membrane contact sites (LAMs) all contain both a sterol-specific lipid transfer domain in the StARkin superfamily (related to StART/Bet_v1), and one or more transmembrane helices anchoring them in the endoplasmic reticulum (ER), making them interesting subjects for study in relation to sterol metabolism. They target a variety of membrane contact sites, including newly described contacts between organelles that were already known to make contact by other means. Lam1-4p target punctate ER-plasma membrane contacts. Lam5p and Lam6p target multiple contacts including a new category: vacuolar non-NVJ cytoplasmic ER (VancE) contacts. These developments confirm previous observations on tubular lipid-binding proteins (TULIPs) that established the importance of membrane anchored proteins for lipid traffic. However, the question remaining to be solved is the most difficult of all: are LAMs transporters, or alternately are they regulators that affect traffic more indirectly? PMID:27068964

  16. Transfer of the uranium decay products, polonium-210 and lead-210, through the lichen-caribou-wolf food chain in northern Canada (manuscript report)

    International Nuclear Information System (INIS)

    The main purpose of this study is to investigate the accumulation and transfer of polonium-210 and lead-210 in the arctic food chain, lichen-caribou-wolf, in the Northwest Territories. Polonium-210 arises from lead-210 decay and is a widespread alpha-emitting radionuclide. It seeks soft tissue and has the potential to accumulate in the food chain. Caribou, wolves and other wildlife may become exposed to enhanced levels of these two uranium-series radionuclides if the proposed uranium mine near Baker Lake, Northwest Territories, proceeds. Baker Lake lies at the crossroads of the ranges of the Beverly, the Kaminuriak and the Wager Bay caribou herds. Therefore, it is important to establish baseline concentrations and natural food chain transfer of uranium series radionuclides, in this study. This information can be used for baseline data before any further mining development takes place. This study will also provide data regarding the statistical uncertainty attached to transfer coefficients. This can help ensure reliable and appropriate future monitoring of environmental change. With the participation of the hunters of Baker Lake, caribou and wolf samples were collected and analyzed for polonium. Results indicate that polonium-210 activity in caribou tissues were somewhat higher than previous data reported from Alaska. Transfer coefficients for polonium-210 from caribou to wolf were near unity for many tissues. However, polonium-210 does not appear to cross the placenta in caribou. Further study includes lichen collections and collection of further caribou samples from the beverly herd in order to determine transfer from lichens to caribou in both the Baker Lake and Snowdrift areas in the Northwest Territories. (author). 26 refs., 3 tabs

  17. Automatic polymerase chain reaction product detection system for food safety monitoring using zinc finger protein fused to luciferase

    Energy Technology Data Exchange (ETDEWEB)

    Yoshida, Wataru; Kezuka, Aki; Murakami, Yoshiyuki; Lee, Jinhee; Abe, Koichi [Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588 (Japan); Motoki, Hiroaki; Matsuo, Takafumi; Shimura, Nobuaki [System Instruments Co., Ltd., 776-2 Komiya-cho, Hachioji, Tokyo 192-0031 (Japan); Noda, Mamoru; Igimi, Shizunobu [Division of Biomedical Food Research, National Institute of Health Sciences, 1-18-1 Kamiyoga, Setagaya-ku, Tokyo 158-8501 (Japan); Ikebukuro, Kazunori, E-mail: ikebu@cc.tuat.ac.jp [Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588 (Japan)

    2013-11-01

    Graphical abstract: -- Highlights: •Zif268 fused to luciferase was used for E. coli O157, Salmonella and coliform detection. •Artificial zinc finger protein fused to luciferase was constructed for Norovirus detection. •An analyzer that automatically detects PCR products by zinc finger protein fused to luciferase was developed. •Target pathogens were specifically detected by the automatic analyzer with zinc finger protein fused to luciferase. -- Abstract: An automatic polymerase chain reaction (PCR) product detection system for food safety monitoring using zinc finger (ZF) protein fused to luciferase was developed. ZF protein fused to luciferase specifically binds to target double stranded DNA sequence and has luciferase enzymatic activity. Therefore, PCR products that comprise ZF protein recognition sequence can be detected by measuring the luciferase activity of the fusion protein. We previously reported that PCR products from Legionella pneumophila and Escherichia coli (E. coli) O157 genomic DNA were detected by Zif268, a natural ZF protein, fused to luciferase. In this study, Zif268–luciferase was applied to detect the presence of Salmonella and coliforms. Moreover, an artificial zinc finger protein (B2) fused to luciferase was constructed for a Norovirus detection system. In the luciferase activity detection assay, several bound/free separation process is required. Therefore, an analyzer that automatically performed the bound/free separation process was developed to detect PCR products using the ZF–luciferase fusion protein. By means of the automatic analyzer with ZF–luciferase fusion protein, target pathogenic genomes were specifically detected in the presence of other pathogenic genomes. Moreover, we succeeded in the detection of 10 copies of E. coli BL21 without extraction of genomic DNA by the automatic analyzer and E. coli was detected with a logarithmic dependency in the range of 1.0 × 10 to 1.0 × 10{sup 6} copies.

  18. Automatic polymerase chain reaction product detection system for food safety monitoring using zinc finger protein fused to luciferase

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Zif268 fused to luciferase was used for E. coli O157, Salmonella and coliform detection. •Artificial zinc finger protein fused to luciferase was constructed for Norovirus detection. •An analyzer that automatically detects PCR products by zinc finger protein fused to luciferase was developed. •Target pathogens were specifically detected by the automatic analyzer with zinc finger protein fused to luciferase. -- Abstract: An automatic polymerase chain reaction (PCR) product detection system for food safety monitoring using zinc finger (ZF) protein fused to luciferase was developed. ZF protein fused to luciferase specifically binds to target double stranded DNA sequence and has luciferase enzymatic activity. Therefore, PCR products that comprise ZF protein recognition sequence can be detected by measuring the luciferase activity of the fusion protein. We previously reported that PCR products from Legionella pneumophila and Escherichia coli (E. coli) O157 genomic DNA were detected by Zif268, a natural ZF protein, fused to luciferase. In this study, Zif268–luciferase was applied to detect the presence of Salmonella and coliforms. Moreover, an artificial zinc finger protein (B2) fused to luciferase was constructed for a Norovirus detection system. In the luciferase activity detection assay, several bound/free separation process is required. Therefore, an analyzer that automatically performed the bound/free separation process was developed to detect PCR products using the ZF–luciferase fusion protein. By means of the automatic analyzer with ZF–luciferase fusion protein, target pathogenic genomes were specifically detected in the presence of other pathogenic genomes. Moreover, we succeeded in the detection of 10 copies of E. coli BL21 without extraction of genomic DNA by the automatic analyzer and E. coli was detected with a logarithmic dependency in the range of 1.0 × 10 to 1.0 × 106 copies

  19. Impact of glucose polymer chain length on heat and physical stability of milk protein-carbohydrate nutritional beverages.

    Science.gov (United States)

    Chen, Biye; O'Mahony, James A

    2016-11-15

    This study investigated the impact of glucose polymer chain length on heat and physical stability of milk protein isolate (MPI)-carbohydrate nutritional beverages containing 8.5% w/w total protein and 5% w/w carbohydrate. The maltodextrin and corn syrup solids glucose polymers used had dextrose equivalent (DE) values of 17 or 38, respectively. Increasing DE value of the glucose polymers resulted in a greater increase in brown colour development, ionic calcium, protein particle size, apparent viscosity and pseudoplastic rheological behaviour, and greater reduction in pH, hydration and heat stability on sterilisation at 120°C. Incorporation of glucose polymers with MPI retarded sedimentation of protein during accelerated physical stability testing, with maltodextrin DE17 causing a greater reduction in sedimentation velocity and compressibility of sediment formed than corn syrup solids DE38. The results demonstrate that chain length of the glucose polymer used strongly impacts heat and physical stability of MPI-carbohydrate nutritional beverages. PMID:27283657

  20. Acoustic transfer of protein crystals from agarose pedestals to micromeshes for high-throughput screening

    Energy Technology Data Exchange (ETDEWEB)

    Cuttitta, Christina M. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); The City University of New York, 2800 Victory Boulevard, Staten Island, NY 10314 (United States); Ericson, Daniel L. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); University at Buffalo, SUNY, 12 Capen Hall, Buffalo, NY 14260 (United States); Scalia, Alexander [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Binghamton University, 4400 Vestal Parkway East, Binghamton, NY 11973-5000 (United States); Roessler, Christian G. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Teplitsky, Ella [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Stony Brook University, Stony Brook, NY 11794-5215 (United States); Joshi, Karan [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); PEC University of Technology, Chandigarh (India); Campos, Olven [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Florida Atlantic University, 777 Glades Road, Boca Raton, FL 33414 (United States); Agarwal, Rakhi; Allaire, Marc [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Orville, Allen M. [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Brookhaven National Laboratory, Upton, NY 11973-5000 (United States); Sweet, Robert M.; Soares, Alexei S., E-mail: soares@bnl.gov [Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)

    2015-01-01

    An acoustic high-throughput screening method is described for harvesting protein crystals and combining the protein crystals with chemicals such as a fragment library. Acoustic droplet ejection (ADE) is an emerging technology with broad applications in serial crystallography such as growing, improving and manipulating protein crystals. One application of this technology is to gently transfer crystals onto MiTeGen micromeshes with minimal solvent. Once mounted on a micromesh, each crystal can be combined with different chemicals such as crystal-improving additives or a fragment library. Acoustic crystal mounting is fast (2.33 transfers s{sup −1}) and all transfers occur in a sealed environment that is in vapor equilibrium with the mother liquor. Here, a system is presented to retain crystals near the ejection point and away from the inaccessible dead volume at the bottom of the well by placing the crystals on a concave agarose pedestal (CAP) with the same chemical composition as the crystal mother liquor. The bowl-shaped CAP is impenetrable to crystals. Consequently, gravity will gently move the crystals into the optimal location for acoustic ejection. It is demonstrated that an agarose pedestal of this type is compatible with most commercially available crystallization conditions and that protein crystals are readily transferred from the agarose pedestal onto micromeshes with no loss in diffraction quality. It is also shown that crystals can be grown directly on CAPs, which avoids the need to transfer the crystals from the hanging drop to a CAP. This technology has been used to combine thermolysin and lysozyme crystals with an assortment of anomalously scattering heavy atoms. The results point towards a fast nanolitre method for crystal mounting and high-throughput screening.

  1. First isolation and antinociceptive activity of a lipid transfer protein from noni (Morinda citrifolia) seeds.

    Science.gov (United States)

    Campos, Dyély C O; Costa, Andrea S; Lima, Amanda D R; Silva, Fredy D A; Lobo, Marina D P; Monteiro-Moreira, Ana Cristina O; Moreira, Renato A; Leal, Luzia K A M; Miron, Diogo; Vasconcelos, Ilka M; Oliveira, Hermógenes D

    2016-05-01

    In this study a novel heat-stable lipid transfer protein, designated McLTP1, was purified from noni (Morinda citrifolia L.) seeds, using four purification steps which resulted in a high-purified protein yield (72mg McLTP1 from 100g of noni seeds). McLTP1 exhibited molecular masses of 9.450 and 9.466kDa, determined by electrospray ionisation mass spectrometry. The N-terminal sequence of McLTP1 (AVPCGQVSSALSPCMSYLTGGGDDPEARCCAGV), as analysed by NCBI-BLAST database, revealed a high degree of identity with other reported plant lipid transfer proteins. In addition, this protein proved to be resistant to pepsin, trypsin and chymotrypsin digestion. McLTP1 given intraperitoneally (1, 2, 4 and 8mg/kg) and orally (8mg/kg) caused an inhibition of the writhing response induced by acetic acid in mice. This protein displayed thermostability, retaining 100% of its antinociceptive activity after 30min incubation at 80°C. Pretreatment of mice with McLTP1 (8mg/kg, i.p. and p.o.) also decreased neurogenic and inflammatory phases of nociception in the formalin test. Naloxone (2mg/kg, i.p.) antagonised the antinociceptive effect of McLTP1 suggesting that the opioid mechanisms mediate the analgesic properties of this protein. PMID:26783638

  2. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes.

    Science.gov (United States)

    Lermyte, Frederik; Sobott, Frank

    2015-08-01

    Top-down sequencing approaches are becoming ever more popular for protein characterization, due to the ability to distinguish and characterize different protein isoforms. Under non-denaturing conditions, electron transfer dissociation (ETD) can furthermore provide important information on the exposed surface of proteins or complexes, thereby contributing to the characterization of their higher-order structure. Here, we investigate this approach using top-down ETD of tetrameric hemoglobin, concanavalin A, and alcohol dehydrogenase combined with ion mobility (IM) on a commercially available quadrupole/ion mobility/time-of-flight instrument (Waters Synapt G2). By applying supplemental activation in the transfer cell (post-IM), we release ETD fragments and attain good sequence coverage in the exposed terminal regions of the protein. We investigate the correlation between observed sites of fragmentation with regions of solvent accessibility, as derived from the crystal structure. Ion acceleration prior to ETD is also used to cause collision-induced unfolding (CIU) of the complexes without monomer ejection, as evidenced by the IM profiles. These partially unfolded tetramers show efficient fragmentation in some regions which are not sequenced under more gentle MS conditions. We show that by increasing CIU in small increments and monitoring the changes in the fragmentation pattern, it is possible to follow the initial steps of gas-phase protein unfolding. Fragments from partially unfolded protein complexes are released immediately after electron transfer, prior to IM (they do not share the drift time of their precursor), and observed without the need for supplemental activation. This is further evidence that the higher-order structure in these protein regions has been disrupted. PMID:26081219

  3. A bioinformatics approach to investigate the function of non specific lipid transfer proteins in Arabidopsis thaliana

    OpenAIRE

    Jayachandra Pandiyan, Muneeswaran

    2010-01-01

    Plant non specific lipid transfer proteins (nsLTPs) enhance in vitro transfer of phospholipids between membranes. Our analysis exploited the large amount of Arabidopsis transcriptome data in public databases to learn more about the function of nsLTPs. The analysis revealed that some nsLTPs are expressed only in roots, some are seed specific, and others are specific for tissues above ground whereas certain nsLTPs show a more general expression pattern. Only few nsLTPs showed a strong up or dow...

  4. Lipid binding in rice nonspecific lipid transfer protein-1 complexes from Oryza sativa

    OpenAIRE

    Cheng, Hui-Chun; Cheng, Pei-Tsung; Peng, Peiyu; Lyu, Ping-Chiang; Sun, Yuh-Ju

    2004-01-01

    Nonspecific lipid transfer proteins (nsLTPs) facilitate the transfer of phospholipids, glycolipids, fatty acids and steroids between membranes, with wide-ranging binding affinities. Three crystal structures of rice nsLTP1 from Oryza sativa, complexed with myristic (MYR), palmitic (PAL) or stearic acid (STE) were determined. The overall structures of the rice nsLTP1 complexes belong to the four-helix bundle folding with a long C-terminal loop. The nsLTP1–MYR and the nsLTP1–STE complexes bind a...

  5. Immune response in mice to ingested soya protein: antibody production, oral tolerance and maternal transfer.

    Science.gov (United States)

    Christensen, Hanne R; Brix, Susanne; Frøkiaer, Hanne

    2004-05-01

    While allergic reactions to soya are increasingly investigated, the normal immune response to ingested soya is scarcely described. In the present study, we wanted to characterise the soya-specific immune response in healthy mice ingesting soya protein. Mice fed a soya-containing diet (F0) and mice of the first (F1) and second (F2) offspring generation bred on a soya protein-free diet were used either directly or were transferred between the soya-containing and soya protein-free diet during pregnancy or neonatal life. The mice were compared as to levels of naturally occurring specific antibodies analysed by ELISA, and to the presence of oral tolerance detected as a suppressed antibody and cell-proliferation response upon immunisation with soya protein. F0 mice generated soya-specific antibodies, while oral tolerance to the same soya proteins was also clearly induced. When F0 dams were transferred to soya protein-free feed before mating, the F1 and F2 offspring generations showed no significantly different response, indicating that soya-specific immune components were not maternally transmitted. However, the ingestion of dietary soya protein by F1 mice during late pregnancy and lactation caused a lasting antibody response in the offspring, but in this case in the absence of oral tolerance. This indicates that, under certain conditions, factors involved in spontaneous antibody production can be transmitted from mother to offspring. Understanding the immune response to soya protein ingested under healthy conditions is important in the assessment of adverse effects of soya protein and in the use of animal allergy models. The present results add to this understanding. PMID:15137924

  6. Molecular Mechanics of Chitin-Protein Interface: Terminus and Side Chain

    CERN Document Server

    Yu, Zechuan

    2016-01-01

    Chitin and protein are two main building blocks for many natural biomaterials. The interaction between chitin and protein critically determines the properties of the composite biological materials. As living organisms usually encounter complex ambient conditions like water, pH and ions are critical factors towards the structural integrity of biomaterials. It is therefore essential to study the chitin-protein interface under different environmental conditions. Here, an atomistic model consisting of a chitin substrate and a protein filament is constructed, which is regarded as a representative of the chitin-protein interface existing in many chitin-based biomaterials. Based on this model, the mechanical properties of chitin-protein interface under different moisture and pH values are investigated through molecular dynamics simulations. The results reveal a weakening effect of water towards the chitin-protein interface, as well as acidity, i.e. the protonated protein forms a stronger adhesion to chitin than that...

  7. The interplay between transient a-helix formation and side chain rotamer distributions in disordered proteins probed by methyl chemical shifts

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Iesmantavicius, Vytautas; Poulsen, Flemming M

    2011-01-01

    shifts can in principle report the conformations of aliphatic side chains in disordered proteins and in order to examine this two model systems were chosen: the acid denatured state of acyl-CoA binding protein (ACBP) and the intrinsically disordered activation domain of the activator for thyroid hormone...... allow a quantitative analysis of the ensemble of ¿(2)-angles of especially leucine residues in disordered proteins. The changes in the rotamer distributions upon denaturation correlate to the changes upon helix induction by the co-solvent trifluoroethanol, suggesting that the side chain conformers are......The peptide backbones of disordered proteins are routinely characterized by NMR with respect to transient structure and dynamics. Little experimental information is, however, available about the side chain conformations and how structure in the backbone affects the side chains. Methyl chemical...

  8. Genetically encoded protein photocrosslinker with a transferable mass spectrometry-identifiable label

    Science.gov (United States)

    Yang, Yi; Song, Haiping; He, Dan; Zhang, Shuai; Dai, Shizhong; Lin, Shixian; Meng, Rong; Wang, Chu; Chen, Peng R.

    2016-01-01

    Coupling photocrosslinking reagents with mass spectrometry has become a powerful tool for studying protein–protein interactions in living systems, but it still suffers from high rates of false-positive identifications as well as the lack of information on interaction interface due to the challenges in deciphering crosslinking peptides. Here we develop a genetically encoded photo-affinity unnatural amino acid that introduces a mass spectrometry-identifiable label (MS-label) to the captured prey proteins after photocrosslinking and prey–bait separation. This strategy, termed IMAPP (In-situ cleavage and MS-label transfer After Protein Photocrosslinking), enables direct identification of photo-captured substrate peptides that are difficult to uncover by conventional genetically encoded photocrosslinkers. Taking advantage of the MS-label, the IMAPP strategy significantly enhances the confidence for identifying protein–protein interactions and enables simultaneous mapping of the binding interface under living conditions. PMID:27460181

  9. Probability weighted ensemble transfer learning for predicting interactions between HIV-1 and human proteins.

    Directory of Open Access Journals (Sweden)

    Suyu Mei

    Full Text Available Reconstruction of host-pathogen protein interaction networks is of great significance to reveal the underlying microbic pathogenesis. However, the current experimentally-derived networks are generally small and should be augmented by computational methods for less-biased biological inference. From the point of view of computational modelling, data scarcity, data unavailability and negative data sampling are the three major problems for host-pathogen protein interaction networks reconstruction. In this work, we are motivated to address the three concerns and propose a probability weighted ensemble transfer learning model for HIV-human protein interaction prediction (PWEN-TLM, where support vector machine (SVM is adopted as the individual classifier of the ensemble model. In the model, data scarcity and data unavailability are tackled by homolog knowledge transfer. The importance of homolog knowledge is measured by the ROC-AUC metric of the individual classifiers, whose outputs are probability weighted to yield the final decision. In addition, we further validate the assumption that only the homolog knowledge is sufficient to train a satisfactory model for host-pathogen protein interaction prediction. Thus the model is more robust against data unavailability with less demanding data constraint. As regards with negative data construction, experiments show that exclusiveness of subcellular co-localized proteins is unbiased and more reliable than random sampling. Last, we conduct analysis of overlapped predictions between our model and the existing models, and apply the model to novel host-pathogen PPIs recognition for further biological research.

  10. Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water

    Energy Technology Data Exchange (ETDEWEB)

    Dalvit, Claudio; Pevarello, Paolo; Tato, Marco; Veronesi, Marina; Vulpetti, Anna; Sundstroem, Michael [Pharmacia (Italy)

    2000-09-15

    A powerful screening by NMR methodology (WaterLOGSY), based on transfer of magnetization from bulk water, for the identification of compounds that interact with target biomolecules (proteins, RNA and DNA fragments) is described. The method exploits efficiently the large reservoir of H{sub 2}O magnetization. The high sensitivity of the technique reduces the amount of biomolecule and ligands needed for the screening, which constitutes an important requirement for high throughput screening by NMR of large libraries of compounds. Application of the method to a compound mixture against the cyclin-dependent kinase 2 (cdk2) protein is presented.

  11. Regulation of non-specific lipid transfer proteins in abiotically stressed Physcomitrella patens

    OpenAIRE

    Jansson, Sandra

    2011-01-01

    Non-specific lipid transfer proteins is a large and diverse protein family found in plants, with roles in biological systems ranging from long distance signaling to plant pathogen defense. Little is known about the roles of nsLTPs, but recent studies have cast some light on the issue, among other things proposing that they may be involved in the cutice formation on land-living liverworts, mosses and non-seedbearing plants. Increased cuticle formation is thought to be a part of a plants defens...

  12. Structural and Functional Characterization of Recombinant Isoforms of the Lentil Lipid Transfer Protein

    OpenAIRE

    Bogdanov, I. V.; Finkina, E. I.; Balandin, S. V.; Melnikova, D. N.; Stukacheva, E. A.; Ovchinnikova, T. V.

    2015-01-01

    The recombinant isoforms Lc-LTP1 and Lc-LTP3 of the lentil lipid transfer protein were overexpressed in E. coli cells. It was confirmed that both proteins are stabilized by four disulfide bonds and characterized by a high proportion of the α-helical structure. It was found that Lc-LTP1 and Lc-LTP3 possess antimicrobial activity and can bind fatty acids. Both isoforms have the ability to bind specific IgE from sera of patients with food allergies, which recognize similar epitopes of the major ...

  13. STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF RECOMBINANT ISOFORMS OF THE LENTIL LIPID TRANSFER PROTEIN

    OpenAIRE

    Bogdanov, I. V.; Finkina, E. I.; Balandin, S. V.; Melnikova, D. N.; Stukacheva, E. A.; Ovchinnikova, T. V.

    2015-01-01

    The recombinant isoforms Lc-LTP1 and Lc-LTP3 of the lentil lipid transfer protein were overexpressed in E. coli cells. It was confirmed that both proteins are stabilized by four disulfide bonds and characterized by a high proportion of the α-helical structure. It was found that Lc-LTP1 and Lc-LTP3 possess antimicrobial activity and can bind fatty acids. Both isoforms have the ability to bind specific IgE from sera of patients with food allergies, which recognize similar epitopes of the major ...

  14. Microsomal Triglyceride Transfer Protein Enhances Cellular Cholesteryl Esterification by Relieving Product Inhibition*

    OpenAIRE

    Iqbal, Jahangir; Rudel, Lawrence L.; Hussain, M. Mahmood

    2008-01-01

    Cholesteryl ester synthesis by the acyl-CoA:cholesterol acyltransferase enzymes ACAT1 and ACAT2 is, in part, a cellular homeostatic mechanism to avoid toxicity associated with high free cholesterol levels. In hepatocytes and enterocytes, cholesteryl esters are secreted as part of apoB lipoproteins, the assembly of which is critically dependent on microsomal triglyceride transfer protein (MTP). Conditional genetic ablation of MTP reduces cholesteryl esters and enhances ...

  15. No association between microsomal triglyceride transfer protein (MTP) haplotype and longevity in humans

    OpenAIRE

    Nebel, Almut; Croucher, Peter J. P.; Stiegeler, Rieke; Nikolaus, Susanna; Krawczak, Michael; Schreiber, Stefan

    2005-01-01

    Human longevity is a multifactorial condition with a significant genetic contribution. A recent association study in two independent samples of long-lived U.S. Caucasians [long-lived individuals (LLI)] identified a SNP haplotype of the microsomal triglyceride transfer protein (MTP, 4q25) that was underrepresented among LLI when compared with younger controls. This suggested that variation in the MTP gene might modify human longevity. Because of its function in lipid metabolism, the MTP gene p...

  16. Activation of transfer RNA-guanine ribosyltransferase by protein kinase C.

    OpenAIRE

    Morris, R C; Brooks, B. J.; Eriotou, P; Kelly, D F; Sagar, S.; Hart, K L; Elliott, M.S.

    1995-01-01

    Transfer RNA-guanine ribosyltransferase (TGRase) irreversibly incorporates queuine into the first position in the anticodon of four tRNA isoacceptors. Rat brain protein kinase C (PKC) was shown to stimulate rat liver TGRase activity. TGRase preparations derived from rat liver have been observed to decrease in activity over time in storage at -20 or -70 degrees C. Contamination of the samples by phosphatases was indicated by a p-nitrophenylphosphate conversion test. The addition of micromolar ...

  17. The α-Tocopherol Transfer Protein Is Essential for Vertebrate Embryogenesis

    OpenAIRE

    Galen W Miller; Lynn Ulatowski; Labut, Edwin M.; Lebold, Katie M.; Danny Manor; Jeffrey Atkinson; Barton, Carrie L.; Tanguay, Robert L.; Traber, Maret G.

    2012-01-01

    The hepatic α-tocopherol transfer protein (TTP) is required for optimal α-tocopherol bioavailability in humans; mutations in the human TTPA gene result in the heritable disorder ataxia with vitamin E deficiency (AVED, OMIM #277460). TTP is also expressed in mammalian uterine and placental cells and in the human embryonic yolk-sac, underscoring TTP's significance during fetal development. TTP and vitamin E are essential for productive pregnancy in rodents, but their precise physiological role ...

  18. The hepatic alpha tocopherol transfer protein (TTP): ligand-induced protection from proteasomal degradation†

    OpenAIRE

    Thakur, Varsha; Morley, Samantha; Manor, Danny

    2010-01-01

    There are eight naturally occurring forms of the dietary antioxidant vitamin E. Of these, only α-tocopherol is retained at high levels in vertebrate plasma and tissues. This selectivity is achieved in part by the action of the hepatic alpha tocopherol transfer protein (TTP), which facilitates the selective incorporation of dietary α-tocopherol into circulating lipoproteins. We examined the effects of vitamin E on TTP expression in cultured hepatocytes. Treatment with vitamin E brought about a...

  19. Expression pattern of GPI-anchored non-specific lipid transfer proteins in Physcomitrella patens

    OpenAIRE

    Höglund, Andrey

    2011-01-01

    During the water-to-land transition, that occurred approximately 450 MYA, novel habitats wererevealed to the emerging plants. This terrestrial habitat was a harsh environment compared to theaquatic, with shifting substrate content, irregular supply of water, damaging UV-radiation andrapid fluctuating temperatures. Non-specific lipid transfer proteins (nsLTP) are today only foundin the land living plants and not in the green algae. This suggests that these genes might haveevolved to help the p...

  20. An extracellular lipid transfer protein is relocalized intracellularly during seed germination.

    Science.gov (United States)

    Pagnussat, Luciana; Burbach, Christian; Baluska, Frantisek; de la Canal, Laura

    2012-11-01

    Plant lipid transfer proteins (LTPs) constitute a family of small proteins recognized as being extracellular. In agreement with this notion, several lines of evidence have shown the apoplastic localization of HaAP10, a LTP from Helianthus annuus dry seeds. However, HaAP10 was recently detected intracellularly in imbibing seeds. To clarify its distribution, immunolocalization experiments were performed during the course of germination and confirmed its intracellular localization upon early seed imbibition. Further assays using a hydrophobic dye, FM4-64, inhibitors of vesicular traffic, and immunolocalization of the pectin rhamnogalacturonan-II, allowed the conclusion that endocytosis is activated as soon as seed imbibition starts. Furthermore, this study demonstrated that HaAP10 is endocytosed throughout imbibition. Biochemical and cellular approaches indicate that the intracellular fraction of this LTP appears associated with oil bodies and some evidence also suggest its presence in glyoxysomes. So, HaAP10 is apoplastic in dry seeds and upon imbibition is rapidly internalized and relocalized to organelles involved in lipid metabolism. The results suggest that HaAP10 may be acting as a fatty acid shuttle between the oil body and the glyoxysome during seed germination. This concept is consistent with the initial proposition that LTPs participate in the intracellular transfer of lipids which was further denied based on their apparent extracellular localization. This report reveals for the first time the relocalization of a lipid transfer protein and opens new perspectives on its role. PMID:23162115

  1. The surface protein Shr of Streptococcus pyogenes binds heme and transfers it to the streptococcal heme-binding protein Shp

    OpenAIRE

    Lei Benfang; Liu Mengyao; Zhu Hui

    2008-01-01

    Abstract Background The heme acquisition machinery in Streptococcus pyogenes is believed to consist of the surface proteins, Shr and Shp, and heme-specific ATP-binding cassette transporter HtsABC. Shp has been shown to rapidly transfer its heme to the lipoprotein component, HtsA, of HtsABC. The function of Shr and the heme source of Shp have not been established. Results The objective of this study was to determine whether Shr binds heme and is a heme source of Shp. To achieve the objective, ...

  2. Chain reconfiguration in active noise

    Science.gov (United States)

    Samanta, Nairhita; Chakrabarti, Rajarshi

    2016-05-01

    In a typical single molecule experiment, the dynamics of an unfolded protein is studied by determining the reconfiguration time using long-range Förster resonance energy transfer, where the reconfiguration time is the characteristic decay time of the position correlation between two residues of the protein. In this paper we theoretically calculate the reconfiguration time for a single flexible polymer in the presence of active noise. The study suggests that though the mean square displacement grows faster, the chain reconfiguration is always slower in the presence of long-lived active noise with exponential temporal correlation. Similar behavior is observed for a worm-like semi-flexible chain and a Zimm chain. However it is primarily the characteristic correlation time of the active noise and not the strength that controls the increase in the reconfiguration time. In brief, such active noise makes the polymer move faster but the correlation loss between the monomers becomes slow.

  3. Chain reconfiguration in active noise

    International Nuclear Information System (INIS)

    In a typical single molecule experiment, the dynamics of an unfolded protein is studied by determining the reconfiguration time using long-range Förster resonance energy transfer, where the reconfiguration time is the characteristic decay time of the position correlation between two residues of the protein. In this paper we theoretically calculate the reconfiguration time for a single flexible polymer in the presence of active noise. The study suggests that though the mean square displacement grows faster, the chain reconfiguration is always slower in the presence of long-lived active noise with exponential temporal correlation. Similar behavior is observed for a worm-like semi-flexible chain and a Zimm chain. However it is primarily the characteristic correlation time of the active noise and not the strength that controls the increase in the reconfiguration time. In brief, such active noise makes the polymer move faster but the correlation loss between the monomers becomes slow. (paper)

  4. Measuring protein interactions using Förster resonance energy transfer and fluorescence lifetime imaging microscopy.

    Science.gov (United States)

    Day, Richard N

    2014-03-15

    The method of fluorescence lifetime imaging microscopy (FLIM) is a quantitative approach that can be used to detect Förster resonance energy transfer (FRET). The use of FLIM to measure the FRET that results from the interactions between proteins labeled with fluorescent proteins (FPs) inside living cells provides a non-invasive method for mapping interactomes. Here, the use of the phasor plot method to analyze frequency domain (FD) FLIM measurements is described, and measurements obtained from cells producing the 'FRET standard' fusion proteins are used to validate the FLIM system for FRET measurements. The FLIM FRET approach is then used to measure both homologous and heterologous protein-protein interactions (PPI) involving the CCAAT/enhancer-binding protein alpha (C/EBPα). C/EBPα is a transcription factor that controls cell differentiation, and localizes to heterochromatin where it interacts with the heterochromatin protein 1 alpha (HP1α). The FLIM-FRET method is used to quantify the homologous interactions between the FP-labeled basic leucine zipper (BZip) domain of C/EBPα. Then the heterologous interactions between the C/EBPa BZip domain and HP1a are quantified using the FRET-FLIM method. The results demonstrate that the basic region and leucine zipper (BZip) domain of C/EBPα is sufficient for the interaction with HP1α in regions of heterochromatin. PMID:23806643

  5. Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure

    Directory of Open Access Journals (Sweden)

    Serrano Luis

    2008-10-01

    Full Text Available Abstract Background Efficient communication between distant sites within a protein is essential for cooperative biological response. Although often associated with large allosteric movements, more subtle changes in protein dynamics can also induce long-range correlations. However, an appropriate formalism that directly relates protein structural dynamics to information exchange between functional sites is still lacking. Results Here we introduce a method to analyze protein dynamics within the framework of information theory and show that signal transduction within proteins can be considered as a particular instance of communication over a noisy channel. In particular, we analyze the conformational correlations between protein residues and apply the concept of mutual information to quantify information exchange. Mapping out changes of mutual information on the protein structure then allows visualizing how distal communication is achieved. We illustrate the approach by analyzing information transfer by the SH2 domain of Fyn tyrosine kinase, obtained from Monte Carlo dynamics simulations. Our analysis reveals that the Fyn SH2 domain forms a noisy communication channel that couples residues located in the phosphopeptide and specificity binding sites and a number of residues at the other side of the domain near the linkers that connect the SH2 domain to the SH3 and kinase domains. We find that for this particular domain, communication is affected by a series of contiguous residues that connect distal sites by crossing the core of the SH2 domain. Conclusion As a result, our method provides a means to directly map the exchange of biological information on the structure of protein domains, making it clear how binding triggers conformational changes in the protein structure. As such it provides a structural road, next to the existing attempts at sequence level, to predict long-range interactions within protein structures.

  6. Development of single chain variable fragment (scFv) antibodies against surface proteins of 'Ca. Liberibacter asiaticus'.

    Science.gov (United States)

    Yuan, Qing; Jordan, Ramon; Brlansky, Ronald H; Minenkova, Olga; Hartung, John

    2016-03-01

    'Candidatus Liberibacter asiaticus' is the causal agent of citrus huanglongbing, the most serious disease of citrus worldwide. We have developed and applied immunization and affinity screening methods to develop a primary library of recombinant single chain variable fragment (scFv) antibodies in an M13 vector, pKM19. The antibody population is enriched for antibodies that bind antigens of 'Ca. Liberibacter asiaticus'. The primary library has more than 10(7) unique antibodies and the genes that encode them. We have screened this library for antibodies that bind to specifically-chosen proteins that are present on the surface of 'Ca. Liberibacter asiaticus'. These proteins were used as targets for affinity-based selection of scFvs that bind to the major outer membrane protein, OmpA; the polysaccharide capsule protein KpsF; a protein component of the type IV pilus (CapF); and, two flagellar proteins FlhA and FlgI. These scFvs have been used in ELISA and dot blot assays against purified protein antigens and 'Ca. Liberibacter asiaticus' infected plant extracts. We have also recloned many of these scFvs into a plasmid expression vector designed for the production of scFvs. Screening of these scFvs was more efficient when phage-bound, rather than soluble scFvs, were used. We have demonstrated a technology to produce antibodies at will and against any protein target encoded by 'Ca. Liberibacter asiaticus'. Applications could include advanced diagnostic methods for huanglongbing and the development of immune labeling reagents for in planta applications. PMID:26744234

  7. Plasma phospholipid transfer protein activity is related to insulin resistance : impaired acute lowering by insulin in obese Type II diabetic patients

    NARCIS (Netherlands)

    Riemens, SC; van Tol, A; Sluiter, WJ; Dullaart, RPF

    1998-01-01

    Cholesteryl ester transfer protein (CETP) and phospholipid transfer protein (PLTP) have important functions in high density lipoprotein (HDL) metabolism. We determined the association of plasma CETP and PLTP activities (measured with exogenous' substrate assays) with insulin resistance, plasma trigl

  8. Purification and partial characterization of single-chain ribosome-inactivating proteins from the seeds of Phytolacca dioica L.

    Science.gov (United States)

    Parente, A; De Luca, P; Bolognesi, A; Barbieri, L; Battelli, M G; Abbondanza, A; Sande, M J; Gigliano, G S; Tazzari, P L; Stirpe, F

    1993-10-19

    Three ribosome-inactivating proteins (RIPs) similar to those already known (Stirpe et al. (1992) Bio/Technology 10, 405-412) were purified from the seeds of Phytolacca dioica. These proteins, called Phytolacca dioica RIPs (PD-S1, PD-S2 and PD-S3 RIPs), are glycoproteins, with M(r) approx. 30,000, inhibit protein synthesis by a rabbit reticulocyte lysate and phenylalanine polymerization by isolated ribosomes, and depurinate rat liver rRNA in an apparently identical manner as the A-chain of ricin and other RIPs (Endo et al. (1987) J. Biol. Chem. 262, 5908-5912). Part of the purified rat liver ribosomes appeared resistant to the action of PD-S RIPs. The most abundant protein, PD-S2 RIP, gave a weak or nil cross-reaction with sera against various other RIPs, including a pokeweed antiviral protein from the roots of Phytolacca americana. PD-S2 RIP was linked to a monoclonal antibody (Ber-H2) against the CD30 human lymphocyte antigen and the resulting immunotoxin was selectively toxic to the CD30 + Hodgkin's lymphoma-derived L540 cell line. PMID:8218414

  9. Energy patterns in coupled α-helix protein chains with diagonal and off-diagonal couplings

    Science.gov (United States)

    Tabi, C. B.; Ondoua, R. Y.; Ekobena Fouda, H. P.; Kofané, T. C.

    2016-07-01

    We introduce off-diagonal effects in the three-stranded model of α-helix chains, which bring about additional nonlinear terms to enhance the way energy spreads among the coupled spines. This is analyzed through the modulational instability theory. The linear stability analysis of plane wave solutions is performed and the competitive effects of diagonal and off-diagonal interactions are studied, followed by direct numerical simulations. Some features of the obtained solitonic structures are discussed.

  10. Factors affecting the concentration in seven-spotted ladybirds (Coccinella septempunctata L.) of Cd and Zn transferred through the food chain

    Energy Technology Data Exchange (ETDEWEB)

    Green, I.D., E-mail: igreen@bournemouth.ac.u [Centre for Conservation Ecology and Environmental Change, School of Conservation Sciences, Bournemouth University, Talbot Campus, Poole, Dorset BH12 5BB (United Kingdom); Diaz, A., E-mail: adiaz@bournemouth.ac.u [Centre for Conservation Ecology and Environmental Change, School of Conservation Sciences, Bournemouth University, Talbot Campus, Poole, Dorset BH12 5BB (United Kingdom); Tibbett, M., E-mail: mark.tibbett@uwa.edu.a [Centre for Land Rehabilitation, School of Earth and Environment, Faculty of Natural and Agricultural Sciences, University of Western Australia, 35 Stirling Highway, Crawley WA 6009 (Australia)

    2010-01-15

    The transfer of Cd and Zn from soils amended with sewage sludge was followed through a food chain consisting of wheat, aphids and the predator Coccinella septempunctata. Multiple regression models were generated to predict the concentrations of Cd and Zn in C. septempunctata. No significant model could be generated for Cd, indicting that the concentration of this metal was maintained within relatively narrow limits. A model predicting 64% of the variability in the Zn concentration of C. septempunctata was generated from of the concentration of Zn in the diet, time and rate of Zn consumption. The results suggest that decreasing the rate of food consumption is an effective mechanism to prevent the accumulation of Zn and that the availability of Zn in the aphid prey increased with the concentration in the aphids. The results emphasise the importance of using ecologically relevant food chains and exposure pathways during ecotoxicological studies. - Arthropod predators can regulate trace metal body burden through physiological and behavioural mechanisms.

  11. Discovery of Novel Splice Variants and Regulatory Mechanisms for Microsomal Triglyceride Transfer Protein in Human Tissues.

    Science.gov (United States)

    Suzuki, Takashi; Swift, Larry L

    2016-01-01

    Microsomal triglyceride transfer protein (MTP) is a unique lipid transfer protein essential for the assembly of triglyceride-rich lipoproteins by the liver and intestine. Previous studies in mice identified a splice variant of MTP with an alternate first exon. Splice variants of human MTP have not been reported. Using PCR approaches we have identified two splice variants in human tissues, which we have named MTP-B and MTP-C. MTP-B has a unique first exon (Ex1B) located 10.5 kb upstream of the first exon (Ex1A) for canonical MTP (MTP-A); MTP-C contains both first exons for MTP-A and MTP-B. MTP-B was found in a number of tissues, whereas MTP-C was prominent in brain and testis. MTP-B does not encode a protein; MTP-C encodes the same protein encoded by MTP-A, although MTP-C translation is strongly inhibited by regulatory elements within its 5'-UTR. Using luciferase assays, we demonstrate that the promoter region upstream of exon 1B is quite adequate to drive expression of MTP. We conclude that alternate splicing plays a key role in regulating cellular MTP levels by introducing distinct promoter regions and unique 5'-UTRs, which contain elements that alter translation efficiency, enabling the cell to optimize MTP activity. PMID:27256115

  12. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

    Science.gov (United States)

    O'Brien, Evan S; Wand, A Joshua; Sharp, Kim A

    2016-06-01

    Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O(2) values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R(2) of 0.8. PMID:26990788

  13. KONSTRUKSI MUTAN PROTEIN FOSFATASE ptc2D Saccharomyces cerevisiae DENGAN METODE PENGGANTIAN GEN TARGET DENGAN POLYMERASE CHAIN REACTION (PCR

    Directory of Open Access Journals (Sweden)

    Hermansyah

    2011-05-01

    Full Text Available Yeast Saccharomyces cerevisiae is an excellent model to studi genes function of eukarotic cells such as study of gene encoding protein phosphatase PTC2. Novel phenotypic caused by mutated gene is an important step to study function of gene. In this study constructed mutant of PTC2 gene encoding protein phosphatase. Method that used in this construction was replacement of target gene (PTC2 with auxotroph marker Candida albicans HIS3 by Polymer Chain Reaction (PCR or called by PCR-mediated disruption. Mutant colonies which grew in selective medium SC without histidine were confirmed by PCR amplification. By using 1% Agarose gel electrophoresis the result showed that size of ptc2D::CgHIS3 transformant was 3.52 kb while wild type strain was 2.9 kb, indicated that ptc2D::CgHIS3 has integrated on chromosome V replacing PTC2 wild type.

  14. Anti-Human Endoglin (hCD105 Immunotoxin—Containing Recombinant Single Chain Ribosome-Inactivating Protein Musarmin 1

    Directory of Open Access Journals (Sweden)

    Begoña Barriuso

    2016-06-01

    Full Text Available Endoglin (CD105 is an accessory component of the TGF-β receptor complex, which is expressed in a number of tissues and over-expressed in the endothelial cells of tumor neovasculature. Targeting endoglin with immunotoxins containing type 2 ribosome-inactivating proteins has proved an effective tool to reduce blood supply to B16 mice tumor xenografts. We prepared anti-endoglin immunotoxin (IT—containing recombinant musarmin 1 (single chain ribosome-inactivating proteins linked to the mouse anti-human CD105 44G4 mouse monoclonal antibody via N-succinimidyl 3-(2-pyridyldithio propionate (SPDP. The immunotoxin specifically killed L929 fibroblast mouse cells transfected with the short form of human endoglin with IC50 values in the range of 5 × 10−10 to 10−9 M.

  15. Two- and three-dimensional sup 1 H NMR studies of a wheat phospholipid transfer protein: Sequential resonance assignments and secondary structure

    Energy Technology Data Exchange (ETDEWEB)

    Simorre, J.P.; Caille, A. (Centre National de la Recherche Scientifique, Orleans (France)); Marion, D. (Laboratoire de Resonance Magnetique en Biologie et Medecine, Grenoble (France)); Marion, D. (INRA, Nantes (France)); Ptak, M. (Centre National de la Recherche Scientifique, Orleans (France) Univ. d' Orleans (France))

    1991-12-10

    Two- and three-dimensional {sup 1}H NMR experiments have been used to sequentially assign nearly all proton resonances of the 90 residues of wheat phospholipid transfer protein. Only a few side-chain protons were not identified because of degeneracy or overlapping. The identification of spin systems and the sequential assignment were made at the same time by combining the data of the two- and three-dimensional experiments. The classical two-dimensional COSY, HOHAHA, and NOESY experiments benefit from both good resolution and high sensitivity, allowing the detection of long-range dipolar connectivities. The three-dimensional HOHAHA-NOESY experiment offers the advantage of a faster and unambiguous assignment. As a matter of fact, homonuclear three-dimensional NMR spectroscopy prove to be a very efficient method for resonance assignments of protein {sup 1}H NMR spectra which cannot be unraveled by 2D methods. An assignment strategy which overcomes most of the ambiguities has been proposed, in which each individual assignment toward the C-terminal end is supported by another in the opposite direction originating from a completely different part of the spectrum. Location of secondary structures of the phospholipid transfer protein was determined by using the method of analysis introduced here and was confirmed by {sup 3}J{sub {alpha}NH} coupling and NH exchange rates. Except for the C-terminal part, the polypeptide chain appears to be organized mainly as helical fragments connected by disulfide bridges. Further modeling will display the overall folding of the protein and should provide a better understanding of its interactions with lipids.

  16. Purification and structural characterisation of lipid transfer protein from red wine and grapes.

    Science.gov (United States)

    Jaeckels, Nadine; Tenzer, Stefan; Rosfa, Susanne; Schild, Hansjoerg; Decker, Heinz; Wigand, Petra

    2013-05-01

    Lipid transfer proteins (LTP) play a major role in plant defence and are of particular interest due to their known ability to cause allergic reactions. These proteins are expressed in grapes and also remain detectable after vinification, especially in red wine. However, it remains unknown whether the protein undergoes any changes during the vinification process. Here, we present a purification method for LTPs from Dornfelder grapes and wine. By liquid-chromatography-mass spectroscopy (LC-MS/MS) we identified LTPs from two different species (Vitis vinifera and Vitis aestivalis). Additionally, the purified LTPs were characterised using spectrometric methods, confirming their high purity and structural stability during vinification. We conclude that LTPs are resistant to the alcohol content (13.5 vol%), acidic milieu of wine and other ingredients present during the vinification process, indicating that the allergenic potential of grape LTP is not diminished by the vinification process. PMID:23265486

  17. Slow and fast singlet energy transfers in BODIPY-gallium(III)corrole dyads linked by flexible chains.

    Science.gov (United States)

    Brizet, Bertrand; Desbois, Nicolas; Bonnot, Antoine; Langlois, Adam; Dubois, Adrien; Barbe, Jean-Michel; Gros, Claude P; Goze, Christine; Denat, Franck; Harvey, Pierre D

    2014-04-01

    Red (no styryl), green (monostyryl), and blue (distyryl) BODIPY-gallium(III) (BODIPY = boron-dipyrromethene) corrole dyads have been prepared in high yields using click chemistry, and their photophysical properties are reported. An original and efficient control of the direction of the singlet energy transfers is reported, going either from BODIPY to the gallium-corrole units or from gallium-corroles to BODIPY, depending upon the nature of the substitution on BODIPY. In one case (green), both directions are possible. The mechanism for the energy transfers is interpreted by means of through-space Förster resonance energy transfer (FRET). PMID:24661249

  18. Transfer of radiocaesium from contaminated bottom sediments to marine organisms through benthic food chains in post-Fukushima and post-Chernobyl periods

    Science.gov (United States)

    Bezhenar, Roman; Jung, Kyung Tae; Maderich, Vladimir; Willemsen, Stefan; de With, Govert; Qiao, Fangli

    2016-05-01

    After the earthquake and tsunami on 11 March 2011 damaged the Fukushima Dai-ichi Nuclear Power Plant (FDNPP), an accidental release of a large amount of radioactive isotopes into both the air and the ocean occurred. Measurements provided by the Japanese agencies over the past 5 years show that elevated concentrations of 137Cs still remain in sediments, benthic organisms, and demersal fishes in the coastal zone around the FDNPP. These observations indicate that there are 137Cs transfer pathways from bottom sediments to the marine organisms. To describe the transfer quantitatively, the dynamic food chain biological uptake model of radionuclides (BURN) has been extended to include benthic marine organisms. The extended model takes into account both pelagic and benthic marine organisms grouped into several classes based on their trophic level and type of species: phytoplankton, zooplankton, and fishes (two types: piscivorous and non-piscivorous) for the pelagic food chain; deposit-feeding invertebrates, demersal fishes fed by benthic invertebrates, and bottom omnivorous predators for the benthic food chain; crustaceans, mollusks, and coastal predators feeding on both pelagic and benthic organisms. Bottom invertebrates ingest organic parts of bottom sediments with adsorbed radionuclides which then migrate up through the food chain. All organisms take radionuclides directly from water as well as food. The model was implemented into the compartment model POSEIDON-R and applied to the north-western Pacific for the period of 1945-2010, and then for the period of 2011-2020 to assess the radiological consequences of 137Cs released due to the FDNPP accident. The model simulations for activity concentrations of 137Cs in both pelagic and benthic organisms in the coastal area around the FDNPP agree well with measurements for the period of 2011-2015. The decrease constant in the fitted exponential function of simulated concentration for the deposit-feeding invertebrates (0.45 yr-1

  19. Magnetization transfer magnetic resonance of human atherosclerotic plaques ex vivo detects areas of high protein density

    Directory of Open Access Journals (Sweden)

    Qiao Ye

    2011-11-01

    Full Text Available Abstract Background Proteins are major plaque components, and their degradation is related to the plaque instability. We sought to assess the feasibility of magnetization transfer (MT magnetic resonance (MR for identifying fibrin and collagen in carotid atherosclerotic plaques ex vivo. Methods Human carotid artery specimens (n = 34 were obtained after resection from patients undergoing endarterectomy. MR was completed within 12 hr after surgery on an 11.7T MR microscope prior to fixation. Two sets of T1W spoiled gradient echo images were acquired with and without the application of a saturation pulse set to 10 kHz off resonance. The magnetization transfer ratio (MTR was calculated, and the degree of MT contrast was correlated with histology. Results MT with appropriate calibration clearly detected regions with high protein density, which showed a higher MTR (thick fibers (collagen type I (54 ± 8% compared to regions with a low amount of protein including lipid (46 ± 8% (p = 0.05, thin fibers (collagen type III (11 ± 6% (p = 0.03, and calcification (6.8 ± 4% (p = 0.02. Intraplaque hemorrhage (IPH with different protein density demonstrated different MT effects. Old (rich in protein debris and recent IPH (rich in fibrin had a much higher MTR 69 ± 6% and 55 ± 9%, respectively, compared to fresh IPH (rich in intact red blood cells(9 ± 3%. Conclusions MT MR enhances plaque tissue contrast and identifies the protein-rich regions of carotid artery specimens. The additional information from MTR of IPH may provide important insight into the role of IPH on plaque stability, evolution, and the risk for future ischemic events.

  20. Construction and structural modeling of a single-chain Fv-asparaginase fusion protein resistant to proteolysis.

    Science.gov (United States)

    Guo, L; Wang, J; Qian, S; Yan, X; Chen, R; Meng, G

    2000-11-20

    In this study, we construct a fusion protein composed of L-asparaginase (ASNase; from Escherichia coli AS 1.357) and a protective single-chain Fv (scFv), which was selected from a phage-display scFv library from our previous studies. The antibody moiety of the fusion protein was fused to the N-terminus of the enzyme moiety via a linker peptide, (Gly(4)Ser)(6). Recombinant plasmid pET-SLA was constructed to express scFv-ASNase fusion to high levels in E. coli and the expressed product was found to form inclusion bodies. We obtained a soluble fusion protein by refolding and purification. The soluble fusion protein exhibited about 82% of the enzymatic activity of the native ASNase at the same molar concentration, and had a K(m) value similar to that of the native enzyme for the substrate L-asparagine. Importantly, the fusion protein was more stable than native ASNase. In addition: (1) following treatment with trypsin, alpha-chymotrypsin, and rennet, at 37 degrees C for 30 min, scFv-ASNase fusion retained 94.0%, 88.8%, and 84.5% of its original activity, respectively, whereas native ASNase became inactive; and (2) ScFv-ASNase fusion had a much longer in vitro half-life (9 h) in serum than the native enzyme (2 h). The three-dimensional structure of the fusion protein was obtained by modeling with the Homology and Discover modules of the INSIGHT II software package. On the basis of the structural evidence and biochemical properties, we propose that the scFv moiety of the fusion protein may confer ASNase moiety resistance to proteolysis as a result of both steric hindrance and a change in the electrostatic surface of the enzyme. PMID:11005928

  1. Transfers

    OpenAIRE

    Xavier Sala-i-Martin

    1992-01-01

    In this paper I develop a positive theory of intergenerational transfers. I argue that transfers are a means to induce retirement. that is, to buy the elderly out of the labor force. The reason why societies choose to do such a thing is that aggregate output is higher if the elderly do not work. I model this idea through positive externalities in the average stock of human capital: because skills depreciate with age. one implication of these externalities is that the elderly have a negative e...

  2. Derivation of a Markov state model of the dynamics of a protein-like chain immersed in an implicit solvent

    Energy Technology Data Exchange (ETDEWEB)

    Schofield, Jeremy, E-mail: jmschofi@chem.utoronto.ca; Bayat, Hanif, E-mail: hbayat@chem.utoronto.ca [Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6 (Canada)

    2014-09-07

    A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local structure and bonding in a coarse-grained sense. The model is based on the assumption that the implicit solvent interacts on a fast time scale with the monomers of the chain compared to the time scale for structural rearrangements of the chain and provides sufficient friction so that the motion of monomers is governed by the Smoluchowski equation. A microscopic theory for the dynamics of the system is developed that reduces to a Markovian model of the kinetics under well-defined conditions. Microscopic expressions for the rate constants that appear in the Markov state model are analyzed and expressed in terms of a temperature-dependent linear combination of escape rates that themselves are independent of temperature. Excellent agreement is demonstrated between the theoretical predictions of the escape rates and those obtained through simulation of a stochastic model of the dynamics of bond formation. Finally, the Markov model is studied by analyzing the eigenvalues and eigenvectors of the matrix of transition rates, and the equilibration process for a simple helix-forming system from an ensemble of initially extended configurations to mainly folded configurations is investigated as a function of temperature for a number of different chain lengths. For short chains, the relaxation is primarily single-exponential and becomes independent of temperature in the low-temperature regime. The profile is more complicated for longer chains, where multi-exponential relaxation behavior is seen at intermediate temperatures followed by a low temperature regime in which the folding becomes rapid and single exponential. It is demonstrated that the behavior of the equilibration profile as the temperature is lowered can be understood in terms of the

  3. Derivation of a Markov state model of the dynamics of a protein-like chain immersed in an implicit solvent

    International Nuclear Information System (INIS)

    A Markov state model of the dynamics of a protein-like chain immersed in an implicit hard sphere solvent is derived from first principles for a system of monomers that interact via discontinuous potentials designed to account for local structure and bonding in a coarse-grained sense. The model is based on the assumption that the implicit solvent interacts on a fast time scale with the monomers of the chain compared to the time scale for structural rearrangements of the chain and provides sufficient friction so that the motion of monomers is governed by the Smoluchowski equation. A microscopic theory for the dynamics of the system is developed that reduces to a Markovian model of the kinetics under well-defined conditions. Microscopic expressions for the rate constants that appear in the Markov state model are analyzed and expressed in terms of a temperature-dependent linear combination of escape rates that themselves are independent of temperature. Excellent agreement is demonstrated between the theoretical predictions of the escape rates and those obtained through simulation of a stochastic model of the dynamics of bond formation. Finally, the Markov model is studied by analyzing the eigenvalues and eigenvectors of the matrix of transition rates, and the equilibration process for a simple helix-forming system from an ensemble of initially extended configurations to mainly folded configurations is investigated as a function of temperature for a number of different chain lengths. For short chains, the relaxation is primarily single-exponential and becomes independent of temperature in the low-temperature regime. The profile is more complicated for longer chains, where multi-exponential relaxation behavior is seen at intermediate temperatures followed by a low temperature regime in which the folding becomes rapid and single exponential. It is demonstrated that the behavior of the equilibration profile as the temperature is lowered can be understood in terms of the

  4. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil

    International Nuclear Information System (INIS)

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region. (paper)

  5. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil.

    Science.gov (United States)

    Burban, David J; Haglund, Ellinor; Capraro, Dominique T; Jennings, Patricia A

    2015-09-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region. PMID:26291198

  6. Heterogeneous side chain conformation highlights a network of interactions implicated in hysteresis of the knotted protein, minimal tied trefoil

    Science.gov (United States)

    Burban, David J.; Haglund, Ellinor; Capraro, Dominique T.; Jennings, Patricia A.

    2015-09-01

    Hysteresis is a signature for a bistability in the native landscape of a protein with significant transition state barriers for the interconversion of stable species. Large global stability, as in GFP, contributes to the observation of this rare hysteretic phenomenon in folding. The signature for such behavior is non-coincidence in the unfolding and refolding transitions, despite waiting significantly longer than the time necessary for complete denaturation. Our work indicates that hysteresis in the knotted protein, the minimal tied trefoil from Thermotoga maritma (MTTTm), is mediated by a network of side chain interactions within a tightly packed core. These initially identified interactions include proline 62 from a tight β-like turn, phenylalanine 65 at the beginning of the knotting loop, and histidine 114 that initiates the threading element. It is this tightly packed region and the knotting element that we propose is disrupted with prolonged incubation in the denatured state, and is involved in the observed hysteresis. Interestingly, the disruption is not linked to backbone interactions, but rather to the packing of side chains in this critical region.

  7. Transcriptional modulation of hepatic lipoprotein assembly and secretion : coordinate regulation of the liver-fatty acid binding protein and microsomal triglyceride transfer protein genes

    OpenAIRE

    Spann, Nathanael J.

    2006-01-01

    Hepatic production of apolipoprotein (apo) B-containing lipoproteins provides a means to transport essential lipids and fat-soluble nutrients to peripheral tissues for utilization and storage. Liver-fatty acid binding protein (L-FABP) and microsomal triglyceride transfer protein (MTP) bind fatty acids and glycerolipids, respectively and facilitate their transfer into the VLDL assembly and secretion pathway. Sequence analysis reveals that the proximal promoter regions of L-FABP and MTP contain...

  8. Interactions of the C-terminus of lung surfactant protein B with lipid bilayers are modulated by acyl chain saturation.

    Science.gov (United States)

    Antharam, Vijay C; Farver, R Suzanne; Kuznetsova, Anna; Sippel, Katherine H; Mills, Frank D; Elliott, Douglas W; Sternin, Edward; Long, Joanna R

    2008-11-01

    Lung surfactant protein B (SP-B) is critical to minimizing surface tension in the alveoli. The C-terminus of SP-B, residues 59-80, has much of the surface activity of the full protein and serves as a template for the development of synthetic surfactant replacements. The molecular mechanisms responsible for its ability to restore lung compliance were investigated with circular dichroism, differential scanning calorimetry, and (31)P and (2)H solid-state NMR spectroscopy. SP-B(59-80) forms an amphipathic helix which alters lipid organization and acyl chain dynamics in fluid lamellar phase 4:1 DPPC:POPG and 3:1 POPC:POPG MLVs. At higher levels of SP-B(59-80) in the POPC:POPG lipid system a transition to a nonlamellar phase is observed while DPPC:POPG mixtures remain in a lamellar phase. Deuterium NMR shows an increase in acyl chain order in DPPC:POPG MLVs on addition of SP-B(59-80); in POPC:POPG MLVs, acyl chain order parameters decrease. Our results indicate SP-B(59-80) penetrates deeply into DPPC:POPG bilayers and binds more peripherally to POPC:POPG bilayers. Similar behavior has been observed for KL(4), a peptide mimetic of SP-B which was originally designed using SP-B(59-80) as a template and has been clinically demonstrated to be successful in treating respiratory distress syndrome. The ability of these helical peptides to differentially partition into lipid lamellae based on their degree of monounsaturation and subsequent changes in lipid dynamics suggest a mechanism for lipid organization and trafficking within the dynamic lung environment. PMID:18694722

  9. Transfer of natural radionuclides from the thorium radioactive family in the food chain in an area with elevated Th concentrations in the soil

    International Nuclear Information System (INIS)

    The study was intended to derive from radioecological findings predictive information on the nuclide ratios of ingested radionuclides from the thorium radioactive familiy which are of significance in faecal excretion analyses. Over a period from 1989 until 1997, several studies examined the transfer of Th-232, Th-228 and Ra-228, to some extent also Ra-226 and Th-230, by experimental analyses of food chains. As to forest ecosystems, the ingestion pathway particularly examined was that of transfer from plants to deer. Based on the findings, a conservative assessment is derived of annual intake of radioactivity due to the nuclides Th-232, Th-228 and Ra-228, both for adults or infants. (orig./CB)

  10. The transfer of 137Cs through the soil-plant-sheep food chain in different pasture ecosystems

    International Nuclear Information System (INIS)

    A grazing experiment with sheep was carried out in 1990-1993 on natural, semi-natural and cultivated pasture on clay soil. The pastures were located in Southern Finland and were moderately contaminated with 137 Cs by Chernobyl fallout. Natural pasture refers to forest pasture and semi-natural pasture to set-aside field pasture, the latter having been under cultivation about 15 years ago. The transfer of 137 Cs to sheep was clearly higher from forest pasture than from the other two pastures and it was lowest from cultivated pasture. The transfer was higher to muscle and kidney than to liver and heart. The transfer of 137 Cs to plants and to meat varied with years. Seasonal variation in the plant 137 Cs was followed-up on forest and set-aside field pasturerespect to 137 Cs transfer to plants, the mean soil-plant transfer factors of 137 Cs for forest, set-aside field and cultivated pastures were 1.78, 0.36 and 0.09, and soil-meat aggregated transfer factors 11.0, 0.28 and 0.03, respectively

  11. Transfer of protein antigens into milk after intravenous injection into lactating mice

    International Nuclear Information System (INIS)

    We investigated the transfer of bovine serum 125I-albumin (125I-BSA), bovine 125I-gamma-globulin (125I-BGG), 125I-ovalbumin (125I-OVA), and 125I-beta-lactoglobulin (125I-BLG) from the blood into the milk of lactating mice. Equal amounts (by weight) of the radiolabeled proteins were injected intravenously into mice 1 wk postpartum. Total radioactivity, trichloroacetic acid-precipitable radioactivity, and specifically immunoprecipitable radioactivity were measured in serum, mammary gland homogenate, and milk. Clearance of immunoreactive OVA (iOVA) and iBLG from the circulation was more rapid than iBSA and iBGG. The radioactivity in mammary tissue associated with BSA and BGG was greater than 70% immunoprecipitable throughout the 4-h test interval; 125I-OVA and 125I-BLG were less than 12% precipitable 1 and 4 h after injection. In milk obtained at 4 h, there was an approximately 10-fold greater accumulation of iBSA or iBGG than of iOVA or iBLG. These experiments demonstrate that protein antigens differ in their ability to transfer from maternal circulation into milk. The transfer into milk appeared to be in proportion to persistence of the antigens in the maternal circulation

  12. Expression and secretion of rabbit plasma cholesteryl ester transfer protein by Pichia pastoris.

    Science.gov (United States)

    Kotake, H; Li, Q; Ohnishi, T; Ko, K W; Agellon, L B; Yokoyama, S

    1996-03-01

    The rabbit cholesteryl ester transfer protein (CETP) was expressed in the methylotrophic yeast Pichia pastoris by introducing the CETP cDNA under the control of the methanol-inducible alcohol oxidase promoter. The cDNA was cloned from in vitro amplified cDNA of rabbit liver mRNA. The nucleotide sequence of the cloned cDNA differed slightly from the previously published sequence that changed the amino acid sequence in six residues. Interestingly, five of these replacements are identical to the corresponding residues in human CEPT. In addition, the encoded mature N-terminal sequence was changed from Cys- to Arg-Glu-Phe- to link the CETP sequence to the yeast acid phosphatase signal peptide. The culture medium of the transformed cells induced with 1% methanol contained both cholesteryl ester and triglyceride transfer activity comparable to that of rabbit plasma. Like rabbit plasma, the lipid transfer activity in the medium could be inhibited by monoclonal antibodies that block CE/TG transfer or TG transfer alone. Immunoblot analysis of M(r) = 80 K and minor species of M(r) = 60-100 K. In spite of these differences, the specific transfer activity of the recombinant CETP was indistinguishable from that of rabbit plasma CETP of M(r) = 74 K. N-Glycosidase F treatment converted both the recombinant and plasma CETP to a single species of M(r) = 55 K. Both the plasma and recombinant CETP lost their activity after removal of N-linked carbohydrate and sialic acid. A single 55 K component was found in the cell-lysates. The intracellular form of the recombinant CETP was not modified by N-glycosidase F treatment. In conclusion, the recombinant CETP is synthesized as an inactive polypeptide that is processed and secreted as a functional glycoprotein. In addition, the N-terminal Cys residue of the plasma CETP is not required for its activity. PMID:8728322

  13. Retroviral-mediated transfer of genomic globin genes leads to regulated production of RNA and protein

    International Nuclear Information System (INIS)

    A high-titer amphotropic retroviral vector containing the neomycin resistance gene and a hybrid γ-β genomic human globin gene has been constructed. Mouse erythroleukemia cells infected with this virus were found to contain the full transcriptional unit of the transferred human globin gene by Southern blot analysis. These cells contain normally initiated, spliced, and terminated human globin mRNA. The human globin mRNA level increased 5- to 10-fold upon induction of the mouse erythroleukemia cells. Human globin chains were produced but only in a fraction of the cells as detected by immunofluorescent staining. A similar retrovirus containing a human β-globin gene was used to transduce mouse erythroleukemia cells resulting in much higher levels of human globin synthesis than detected in mouse erythroleukemia cells transduced with the γ-β globin virus

  14. Fasciola hepatica calcium-binding protein FhCaBP2: structure of the dynein light chain-like domain.

    Science.gov (United States)

    Nguyen, Thanh H; Thomas, Charlotte M; Timson, David J; van Raaij, Mark J

    2016-07-01

    The common liver fluke Fasciola hepatica causes an increasing burden on human and animal health, partly because of the spread of drug-resistant isolates. As a consequence, there is considerable interest in developing new drugs to combat liver fluke infections. A group of potential targets is a family of calcium-binding proteins which combine an N-terminal domain with two EF-hand motifs and a C-terminal domain with predicted similarity to dynein light chains (DLC-like domain). The function of these proteins is unknown, although in several species, they have been localised to the tegument, an important structure at the host-parasite interface. Here, we report the X-ray crystal structure of the DLC-like domain of F. hepatica calcium-binding protein 2 (FhCaBP2), solved using single-wavelength anomalous diffraction and refined at 2.3 Å resolution in two different crystal forms. The FhCaBP2 DLC-like domain has a structure similar to other DLC domains, with an anti-parallel β-sheet packed against an α-helical hairpin. Like other DLC domains, it dimerises through its β2-strand, which extends in an arch and forms the fifth strand in an extended β-sheet of the other monomer. The structure provides molecular details of the dimerisation of FhCaBP2, the first example from this family of parasite proteins. PMID:27083189

  15. Cholesteryl ester transfer protein, low density lipoprotein particle size and intima media thickness in patients with coronary heart disease

    OpenAIRE

    Tosheska, Katerina; Labudovic, Danica; Jovanova, Silvana; Jaglikovski, Branko; Alabakovska, Sonja

    2011-01-01

    Cholesteryl ester transfer protein (CETP) plays a key role in reverse cholesterol transport and high density lipoprotein (HDL) metabolism. Predominance of small, dense LDL particles is associated with an increased risk of atherosclerosis and coronary heart disease (CHD).

  16. An inhibitor of the microsomal triglyceride transfer protein inhibits apoB secretion from HepG2 cells.

    OpenAIRE

    Jamil, H.; Gordon, D A; Eustice, D C; Brooks, C M; Dickson, J K; Chen, Y; Ricci, B.; C. H. Chu; Harrity, T W; Ciosek, C P; Biller, S A; Gregg, R E; Wetterau, J. R.

    1996-01-01

    The microsomal triglyceride (TG) transfer protein (MTP) is a heterodimeric lipid transfer protein that catalyzes the transport of triglyceride, cholesteryl ester, and phosphatidylcholine between membranes. Previous studies showing that the proximal cause of abetalipoproteinemia is an absence of MTP indicate that MTP function is required for the assembly of the apolipoprotein B (apoB) containing plasma lipoproteins, i.e., very low density lipoproteins and chylomicrons. However, the precise rol...

  17. Genome-Wide Survey and Expression Analysis of the Putative Non-Specific Lipid Transfer Proteins in Brassica rapa L

    OpenAIRE

    Li, Jun; Gao, Guizhen; Xu, Kun; Chen, Biyun; Yan, Guixin; Li, Feng; Qiao, Jiangwei; Zhang, Tianyao; Wu, Xiaoming

    2014-01-01

    Background Plant non-specific lipid transfer proteins (nsLtps) are small, basic proteins encoded by multigene families and have reported functions in many physiological processes such as mediating phospholipid transfer, defense reactions against phytopathogens, the adaptation of plants to various environmental conditions, and sexual reproduction. To date, no genome-wide overview of the Brassica rapa nsLtp (BrnsLtp) gene family has been performed. Therefore, as the first step and as a helpful ...

  18. Molecularly Imprinted Electropolymer for a Hexameric Heme Protein with Direct Electron Transfer and Peroxide Electrocatalysis.

    Science.gov (United States)

    Peng, Lei; Yarman, Aysu; Jetzschmann, Katharina J; Jeoung, Jae-Hun; Schad, Daniel; Dobbek, Holger; Wollenberger, Ulla; Scheller, Frieder W

    2016-01-01

    For the first time a molecularly imprinted polymer (MIP) with direct electron transfer (DET) and bioelectrocatalytic activity of the target protein is presented. Thin films of MIPs for the recognition of a hexameric tyrosine-coordinated heme protein (HTHP) have been prepared by electropolymerization of scopoletin after oriented assembly of HTHP on a self-assembled monolayer (SAM) of mercaptoundecanoic acid (MUA) on gold electrodes. Cavities which should resemble the shape and size of HTHP were formed by template removal. Rebinding of the target protein sums up the recognition by non-covalent interactions between the protein and the MIP with the electrostatic attraction of the protein by the SAM. HTHP bound to the MIP exhibits quasi-reversible DET which is reflected by a pair of well pronounced redox peaks in the cyclic voltammograms (CVs) with a formal potential of -184.4 ± 13.7 mV vs. Ag/AgCl (1 M KCl) at pH 8.0 and it was able to catalyze the cathodic reduction of peroxide. At saturation the MIP films show a 12-fold higher electroactive surface concentration of HTHP than the non-imprinted polymer (NIP). PMID:26907299

  19. Molecularly Imprinted Electropolymer for a Hexameric Heme Protein with Direct Electron Transfer and Peroxide Electrocatalysis

    Directory of Open Access Journals (Sweden)

    Lei Peng

    2016-02-01

    Full Text Available For the first time a molecularly imprinted polymer (MIP with direct electron transfer (DET and bioelectrocatalytic activity of the target protein is presented. Thin films of MIPs for the recognition of a hexameric tyrosine-coordinated heme protein (HTHP have been prepared by electropolymerization of scopoletin after oriented assembly of HTHP on a self-assembled monolayer (SAM of mercaptoundecanoic acid (MUA on gold electrodes. Cavities which should resemble the shape and size of HTHP were formed by template removal. Rebinding of the target protein sums up the recognition by non-covalent interactions between the protein and the MIP with the electrostatic attraction of the protein by the SAM. HTHP bound to the MIP exhibits quasi-reversible DET which is reflected by a pair of well pronounced redox peaks in the cyclic voltammograms (CVs with a formal potential of −184.4 ± 13.7 mV vs. Ag/AgCl (1 M KCl at pH 8.0 and it was able to catalyze the cathodic reduction of peroxide. At saturation the MIP films show a 12-fold higher electroactive surface concentration of HTHP than the non-imprinted polymer (NIP.

  20. Fluorescence Resonance Energy Transfer in Quantum Dot-Protein Kinase Assemblies

    Directory of Open Access Journals (Sweden)

    Françisco M. Raymo

    2008-03-01

    Full Text Available In search of viable strategies to identify selective inhibitors of protein kinases, we have designed a binding assay to probe the interactions of human phosphoinositide-dependent protein kinase-1 (PDK1 with potential ligands. Our protocol is based on fluorescence resonance energy transfer (FRET between semiconductor quantum dots (QDs and organic dyes. Specifically, we have expressed and purified the catalytic kinase domain of PDK1 with an N-terminal histidine tag [His6-PDK1(ΔPH]. We have conjugated this construct to CdSe-ZnS core-shell QDs coated with dihydrolipoic acid (DHLA and tested the response of the resulting assembly to a molecular dyad incorporating an ATP ligand and a BODIPY chromophore. The supramolecular association of the BODIPY-ATP dyad with the His6-PDK1(ΔPH-QD assembly encourages the transfer of energy from the QDs to the BODIPY dyes upon excitation. The addition of ATP results in the displacement of BODIPY-ATP from the binding domain of the His6-PDK1(ΔPH conjugated to the nanoparticles. The competitive binding, however, does not prevent the energy transfer process. A control experiment with QDs, lacking the His6-PDK1(ΔPH, indicates that the BODIPY-ATP dyad adsorbs nonspecifically on the surface of the nanoparticles, promoting the transfer of energy from the CdSe core to the adsorbed BODIPY dyes. Thus, the implementation of FRET-based assays to probe the binding domain of PDK1 with luminescent QDs requires the identification of energy acceptors unable to interact nonspecifically with the surface of the nanoparticles.

  1. Toxicity and transfer of polyvinylpyrrolidone-coated silver nanowires in an aquatic food chain consisting of algae, water fleas, and zebrafish.

    Science.gov (United States)

    Chae, Yooeun; An, Youn-Joo

    2016-04-01

    Nanomaterials of various shapes and dimensions are widely used in the medical, chemical, and electronic industries. Multiple studies have reported the ecotoxicological effects of nanaoparticles when released in aquatic and terrestrial ecosystems; however, information on the toxicity of silver nanowires (AgNWs) to freshwater organisms and their transfer through the food webs is limited. In the present study, we aimed to evaluate the toxicity of 10- and 20-μm-long AgNWs to the alga Chlamydomonas reinhardtii, the water flea Daphnia magna, and the zebrafish and study their movement through this three-species food chain using a variety of qualitative and quantitative methods as well as optical techniques. We found that AgNWs directly inhibited the growth of algae and destroyed the digestive organs of water fleas. The results showed that longer AgNWs (20μm) were more toxic than shorter ones (10μm) to both algae and water fleas, but shorter AgNWs were accumulated more than longer ones in the body of the fish. Overall, this study suggests that AgNWs are transferred through food chains, and that they affect organisms at higher trophic levels, potentially including humans. Therefore, further studies that take into account environmental factors, food web complexity, and differences between nanomaterials are required to gain better understanding of the impact of nanomaterials on natural communities and human health. PMID:26854872

  2. Spatial frequency response of a volume hologram recorded in a ZrO2 nanoparticle-dispersed acrylate photopolymer film containing chain transfer agents

    Science.gov (United States)

    Guo, Jinxin; Fujii, Ryuta; Tomita, Yasuo

    2014-05-01

    Photopolymerizable nanoparticle-polymer composites (NPCs) have thus far shown their excellent performance in various applications, such as holographic data storage, nonlinear optics and neutron optics. Specifically, for such applications, a high spatial frequency material response is necessary, as it is the response to high spatial frequencies that determines their spatial resolution and diffraction properties. However, it is known that the spatial frequency response of a recorded hologram in multi-component photopolymers including NPCs and holographic polymer-dispersed liquid crystals exhibits a reduction in refractive index modulation at high spatial frequencies. In order to overcome this drawback, an addition of chain transfer agents (CTAs) may be useful as done for all-organic photopolymers to modify their nonlocal response and phase separation characteristics. In our work, we investigate the effect of CTAs on the spatial frequency response in NPCs. Here we employ various chain-transfer agents with three different thiol groups in a photopolymerizable ZrO2 NPC film. A range of CTA concentration is carried out, in order to explore the most effective material combination used in the examination of spatial frequency response. The significant improvement in spatial frequency response of NPCs through the addition of a CTA with the most appropriate concentration is presented.

  3. Barley lipid transfer protein, LTP1, contains a new type of lipid-like post-translational modification

    DEFF Research Database (Denmark)

    Lindorff-Larsen, Kresten; Lerche, Mathilde H.; Poulsen, Flemming Martin;

    2001-01-01

    In plants a group of proteins termed nonspecific lipid transfer proteins are found. These proteins bind and catalyze transfer of lipids in vitro, but their in vivo function is unknown. They have been suggested to be involved in different aspects of plant physiology and cell biology, including the...... formation of cutin and involvement in stress and pathogen responses, but there is yet no direct demonstration of an in vivo function. We have found and characterized a novel post-translational modification of the barley nonspecific lipid transfer protein, LTP1. The protein-modification bond is of a new type...... found to be lipid-like in nature. The modification does not resemble any standard lipid post-translational modification but is similar to a compound with known antimicrobial activity....

  4. Protein microarrays based on polymer brushes prepared via surface-initiated atom transfer radical polymerization.

    Science.gov (United States)

    Barbey, Raphael; Kauffmann, Ekkehard; Ehrat, Markus; Klok, Harm-Anton

    2010-12-13

    Polymer brushes represent an interesting platform for the development of high-capacity protein binding surfaces. Whereas the protein binding properties of polymer brushes have been investigated before, this manuscript evaluates the feasibility of poly(glycidyl methacrylate) (PGMA) and PGMA-co-poly(2-(diethylamino)ethyl methacrylate) (PGMA-co-PDEAEMA) (co)polymer brushes grown via surface-initiated atom transfer radical polymerization (SI-ATRP) as protein reactive substrates in a commercially available microarray system using tantalum-pentoxide-coated optical waveguide-based chips. The performance of the polymer-brush-based protein microarray chips is assessed using commercially available dodecylphosphate (DDP)-modified chips as the benchmark. In contrast to the 2D planar, DDP-coated chips, the polymer-brush-covered chips represent a 3D sampling volume. This was reflected in the results of protein immobilization studies, which indicated that the polymer-brush-based coatings had a higher protein binding capacity as compared to the reference substrates. The protein binding capacity of the polymer-brush-based coatings was found to increase with increasing brush thickness and could also be enhanced by copolymerization of 2-(diethylamino)ethyl methacrylate (DEAEMA), which catalyzes epoxide ring-opening of the glycidyl methacrylate (GMA) units. The performance of the polymer-brush-based microarray chips was evaluated in two proof-of-concept microarray experiments, which involved the detection of biotin-streptavidin binding as well as a model TNFα reverse assay. These experiments revealed that the use of polymer-brush-modified microarray chips resulted not only in the highest absolute fluorescence readouts, reflecting the 3D nature and enhanced sampling volume provided by the brush coating, but also in significantly enhanced signal-to-noise ratios. These characteristics make the proposed polymer brushes an attractive alternative to commercially available, 2D microarray

  5. REACH coarse-grained biomolecular simulation: transferability between different protein structural classes.

    Science.gov (United States)

    Moritsugu, Kei; Smith, Jeremy C

    2008-08-01

    Coarse graining of protein interactions provides a means of simulating large biological systems. The REACH (Realistic Extension Algorithm via Covariance Hessian) coarse-graining method, in which the force constants of a residue-scale elastic network model are calculated from the variance-covariance matrix obtained from atomistic molecular dynamics (MD) simulation, involves direct mapping between scales without the need for iterative optimization. Here, the transferability of the REACH force field is examined between protein molecules of different structural classes. As test cases, myoglobin (all alpha), plastocyanin (all beta), and dihydrofolate reductase (alpha/beta) are taken. The force constants derived are found to be closely similar in all three proteins. An MD version of REACH is presented, and low-temperature coarse-grained (CG) REACH MD simulations of the three proteins are compared with atomistic MD results. The mean-square fluctuations of the atomistic MD are well reproduced by the CGMD. Model functions for the CG interactions, derived by averaging over the three proteins, are also shown to produce fluctuations in good agreement with the atomistic MD. The results indicate that, similarly to the use of atomistic force fields, it is now possible to use a single, generic REACH force field for all protein studies, without having first to derive parameters from atomistic MD simulation for each individual system studied. The REACH method is thus likely to be a reliable way of determining spatiotemporal motion of a variety of proteins without the need for expensive computation of long atomistic MD simulations. PMID:18469078

  6. Identification of a Novel Transcript and Regulatory Mechanism for Microsomal Triglyceride Transfer Protein

    OpenAIRE

    Suzuki, Takashi; Brown, Judy J.; Swift, Larry L.

    2016-01-01

    Microsomal triglyceride transfer protein (MTP) is essential for the assembly of triglyceride-rich apolipoprotein B-containing lipoproteins. Previous studies in our laboratory identified a novel splice variant of MTP in mice that we named MTP-B. MTP-B has a unique first exon (1B) located 2.7 kB upstream of the first exon (1A) for canonical MTP (MTP-A). The two mature isoforms, though nearly identical in sequence and function, have different tissue expression patterns. In this study we report t...

  7. Microsomal triglyceride transfer protein regulates endogenous and exogenous antigen presentation by group 1 CD1 molecules

    OpenAIRE

    Kaser, Arthur; Hava, David L.; Dougan, Stephanie K.; Chen, Zhangguo; Zeissig, Sebastian; Brenner, Michael B.; Blumberg, Richard S.

    2008-01-01

    Lipid antigens are presented to T cells by the non-polymorphic MHC class I-related CD1 molecules. Microsomal triglyceride transfer protein (MTP) is an endoplasmic reticulum (ER)-resident chaperone that has been shown to lipidate the group 2 CD1 molecule CD1d and thus to regulate its function. We now report that MTP also regulates the function of group 1 CD1 molecules CD1a, CD1b, and CD1c. Pharmacological inhibition of MTP in monocyte-derived dendritic cells and lymphoblastoid B cell lines tra...

  8. Editing of CD1d-Bound Lipid Antigens by Endosomal Lipid Transfer Proteins

    OpenAIRE

    Zhou, Dapeng; Cantu, Carlos; Sagiv, Yuval; Schrantz, Nicolas; Kulkarni, Ashok B.; Qi, Xiaoyang; Mahuran, Don J.; Carlos R Morales; Grabowski, Gregory A.; Benlagha, Kamel; Savage, Paul; Bendelac, Albert; Teyton, Luc

    2003-01-01

    It is now established that CD1 molecules present lipid antigens to T cells, although it is not clear how the exchange of lipids between membrane compartments and the CD1 binding groove is assisted. We report that mice deficient in prosaposin, the precursor to a family of endosomal lipid transfer proteins (LTP), exhibit specific defects in CD1d-mediated antigen presentation and lack Vα14 NKT cells. In vitro, saposins extracted monomeric lipids from membranes and from CD1, thereby promoting the...

  9. Detection of nanosecond time scale side-chain jumps in a protein dissolved in water/glycerol solvent

    Energy Technology Data Exchange (ETDEWEB)

    Xu Jun; Xue, Yi; Skrynnikov, Nikolai R. [Purdue University, Department of Chemistry (United States)], E-mail: nikolai@purdue.edu

    2009-09-15

    In solution, the correlation time of the overall protein tumbling, {tau}{sub R}, plays a role of a natural dynamics cutoff-internal motions with correlation times on the order of {tau}{sub R} or longer cannot be reliably identified on the basis of spin relaxation data. It has been proposed some time ago that the 'observation window' of solution experiments can be expanded by changing the viscosity of solvent to raise the value of {tau}{sub R}. To further explore this concept, we prepared a series of samples of {alpha}-spectrin SH3 domain in solvent with increasing concentration of glycerol. In addition to the conventional {sup 15}N labeling, the protein was labeled in the Val, Leu methyl positions ({sup 13}CHD{sub 2} on a deuterated background). The collected relaxation data were used in asymmetric fashion: backbone {sup 15}N relaxation rates were used to determine {tau}{sub R} across the series of samples, while methyl {sup 13}C data were used to probe local dynamics (side-chain motions). In interpreting the results, it has been initially suggested that addition of glycerol leads only to increases in {tau}{sub R}, whereas local motional parameters remain unchanged. Thus the data from multiple samples can be analyzed jointly, with {tau}{sub R} playing the role of experimentally controlled variable. Based on this concept, the extended model-free model was constructed with the intent to capture the effect of ns time-scale rotameric jumps in valine and leucine side chains. Using this model, we made a positive identification of nanosecond dynamics in Val-23 where ns motions were already observed earlier. In several other cases, however, only tentative identification was possible. The lack of definitive results was due to the approximate character of the model-contrary to what has been assumed, addition of glycerol led to a gradual 'stiffening' of the protein. This and other observations also shed light on the interaction of the protein with glycerol

  10. IR-FEL-induced green fluorescence protein (GFP) gene transfer into plant cell

    International Nuclear Information System (INIS)

    A Free Electron Laser (FEL) holds potential for various biotechnological applications due to its characteristics such as flexible wavelength tunability, short pulse and high peak power. We could successfully introduce the Green Fluorescent Protein (GFP) gene into tobacco BY2 cells by IR-FEL laser irradiation. The irradiated area of the solution containing BY2 cells and plasmid was about 0.1 mm2. FEL irradiation at a wavelength of 5.75 and 6.1 μm, targeting absorption by the ester bond of the lipid and the amide I bond of the protein, respectively, was shown to cause the introduction of the fluorescent dye into the cell. On the other hand, transient expression of the GFP fluorescence was only observed after irradiation at 5.75 μm. The maximum transfer efficiency was about 0.5%

  11. IR-FEL-induced green fluorescence protein (GFP) gene transfer into plant cell

    CERN Document Server

    Awazu, K; Tamiya, E

    2002-01-01

    A Free Electron Laser (FEL) holds potential for various biotechnological applications due to its characteristics such as flexible wavelength tunability, short pulse and high peak power. We could successfully introduce the Green Fluorescent Protein (GFP) gene into tobacco BY2 cells by IR-FEL laser irradiation. The irradiated area of the solution containing BY2 cells and plasmid was about 0.1 mm sup 2. FEL irradiation at a wavelength of 5.75 and 6.1 mu m, targeting absorption by the ester bond of the lipid and the amide I bond of the protein, respectively, was shown to cause the introduction of the fluorescent dye into the cell. On the other hand, transient expression of the GFP fluorescence was only observed after irradiation at 5.75 mu m. The maximum transfer efficiency was about 0.5%.

  12. IR-FEL-induced green fluorescence protein (GFP) gene transfer into plant cell

    Science.gov (United States)

    Awazu, Kunio; Kinpara, Takeshi; Tamiya, Eiichi

    2002-05-01

    A Free Electron Laser (FEL) holds potential for various biotechnological applications due to its characteristics such as flexible wavelength tunability, short pulse and high peak power. We could successfully introduce the Green Fluorescent Protein (GFP) gene into tobacco BY2 cells by IR-FEL laser irradiation. The irradiated area of the solution containing BY2 cells and plasmid was about 0.1 mm 2. FEL irradiation at a wavelength of 5.75 and 6.1 μm, targeting absorption by the ester bond of the lipid and the amide I bond of the protein, respectively, was shown to cause the introduction of the fluorescent dye into the cell. On the other hand, transient expression of the GFP fluorescence was only observed after irradiation at 5.75 μm. The maximum transfer efficiency was about 0.5%.

  13. Structural and Functional Characterization of Recombinant Isoforms of the Lentil Lipid Transfer Protein.

    Science.gov (United States)

    Bogdanov, I V; Finkina, E I; Balandin, S V; Melnikova, D N; Stukacheva, E A; Ovchinnikova, T V

    2015-01-01

    The recombinant isoforms Lc-LTP1 and Lc-LTP3 of the lentil lipid transfer protein were overexpressed in E. coli cells. It was confirmed that both proteins are stabilized by four disulfide bonds and characterized by a high proportion of the α-helical structure. It was found that Lc-LTP1 and Lc-LTP3 possess antimicrobial activity and can bind fatty acids. Both isoforms have the ability to bind specific IgE from sera of patients with food allergies, which recognize similar epitopes of the major peach allergen Pru p 3. Both isoforms were shown to have immunological properties similar to those of other plant allergenic LTPs, but Lc-LTP3 displayed a less pronounced immunoreactivity. PMID:26483961

  14. Surface residues dynamically organize water bridges to enhance electron transfer between proteins

    CERN Document Server

    de la Lande, Aurélien; Řezáč, Jan; Sanders, Barry C; Salahub, Dennis R; 10.1073/pnas.0914457107

    2010-01-01

    Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins methylamine dehydrogenase and amicyanin from Paracoccus denitrificans. We used molecular dynamics simulations to generate configurations over a duration of 40ns (sampled at 100fs intervals) in conjunction with an ET pathway analysis to estimate the ET coupling strength of each configuration. In the wild type complex, we find that the most frequently occurring molecular configurations afford superior electronic coupling due to the consistent presence of a water molecule hydrogen-bonded between the donor and acceptor sites. We attribute the persistence of this water bridge to a "molecular breakwater" composed of several hydrophobic residues surrounding the acceptor site. The breakwater supports the function of nearby solvent-organizing residues by limiting the exchange of water molecul...

  15. Biodistribution and tumor imaging of an anti-CEA single-chain antibody-albumin fusion protein

    Energy Technology Data Exchange (ETDEWEB)

    Yazaki, Paul J. [Division of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States)], E-mail: pyazaki@coh.org; Kassa, Thewodros; Cheung, Chia-wei; Crow, Desiree M. [Division of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Sherman, Mark A. [Division of Information Sciences, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States); Bading, James R.; Anderson, Anne-Line J.; Colcher, David; Raubitschek, Andrew [Division of Cancer Immunotherapeutics and Tumor Immunology, Beckman Research Institute, City of Hope, Duarte, CA 91010 (United States)

    2008-02-15

    Albumin fusion proteins have demonstrated the ability to prolong the in vivo half-life of small therapeutic proteins/peptides in the circulation and thereby potentially increase their therapeutic efficacy. To evaluate if this format can be employed for antibody-based imaging, an anticarcinoembryonic antigen (CEA) single-chain antibody(scFv)-albumin fusion protein was designed, expressed and radiolabeled for biodistribution and imaging studies in athymic mice bearing human colorectal carcinoma LS-174T xenografts. The [{sup 125}I]-T84.66 fusion protein demonstrated rapid tumor uptake of 12.3% injected dose per gram (ID/g) at 4 h that reached a plateau of 22.7% ID/g by 18 h. This was a dramatic increase in tumor uptake compared to 4.9% ID/g for the scFv alone. The radiometal [{sup 111}In]-labeled version resulted in higher tumor uptake, 37.2% ID/g at 18 h, which persisted at the tumor site with tumor: blood ratios reaching 18:1 and with normal tissues showing limited uptake. Based on these favorable imaging properties, a pilot [{sup 64}Cu]-positron emission tomography imaging study was performed with promising results. The anti-CEA T84.66 scFv-albumin fusion protein demonstrates highly specific tumor uptake that is comparable to cognate recombinant antibody fragments. The radiometal-labeled version, which shows lower normal tissue accumulation than these recombinant antibodies, provides a promising and novel platform for antibody-based imaging agents.

  16. A tentative assessment of cesium 137 direct and indirect transfer rates in a simplified fresh water food chain

    International Nuclear Information System (INIS)

    A comparison was made of the direct transfer of cesium from water to carps and the indirect transfer via the food. In a first experiment on chronic contamination of carps by water, the kinetics and distribution of cesium in the organs of the carps were studied. Equilibrium was not reached on the 56th day, 4% of the initial water activity had been retained by the carps and the concentration factor was below 10. The highest specific activities were found in the transit organs. In a second experiment, the water activity varied by alternating contamination and decontamination. A fluctuating equilibrium was reached on the 22nd day. The concentration factor was of the same order of magnitude than in the previous experiment. Indirect contamination of fish by ingestion of contaminated daphnids was studied in a third experiment. Cesium levels in carps increased with the cumulated activities in meals, and the uptake rate in fish was 4%. Both decorporation and biological half-lives (30-40 days) were independent of the contamination routes. The respective significance of the transfer pathways is discussed taking into account the biomass pyramids to be found in the nature. It is estimated that in a cesium environment, 70% of the carp activity should come from the diet and 30% from the water. The concentration factor would then be 75 instead of 22 when only direct transfer of cesium from water to fish is considered

  17. A new classification of free combined or connected tissue transfers: introduction to the concept of bridge, siamese, chimeric, mosaic, and chain-circle flaps.

    Directory of Open Access Journals (Sweden)

    Koshima I

    2001-12-01

    Full Text Available Recently, combined tissues or flaps have been used for the repair of extensively massive or wide defects resulting from radical wide resection. To further advance the development of combined tissue transfers, they should be reclassified. Based on our cases with free tissue transfers, we have created a new classification of combined flaps composed of "bridge", "chimeric", "siamese", "mosaic", and "chain-circle" flaps. The bridge flap is fabricated out together of separate flaps with short vascular pedicles. These form a compound flap supplied with a solitary vascular source. The chimeric flap is compounded from multiple different flaps but consists of only a single different tissue form. Each of the flaps is usually supplied by different branches from the same source vessel. It differs from the bridge flap in that the pedicle of each flap or tissue has some length for its movement for transfer. The siamese connected flap has 2 adjacent flaps that are simultaneously elevated, and a disparate vascular pedicle for each flap must be reestablished. This connected flap has double isolated pedicles. Themosaic connected flap consists of 2 adjacent flaps that are simultaneously elevated, and the pedicle of the distal flap is anastomosed to the pedicle branch of the proximal flap in the "bridge" fashion. The vascular pedicle of the proximal flap is anastomosed to a single vascular source. The chain-circle flap has 2 or more flaps like the bridge and chimeric flaps, and the distal end of the vascular source is anastomosed to the branch of the recipient vessel. Based on results with our patients, the lateral circumflex femoral system seems to be the most suitable candidate for the axial pedicle of these combined flaps, because the system has several branches of large and small caliber, and several tissue components, such as the vascularized ilium, rectus femoris muscle, gracilis muscle, lateral femoral cutaneous nerve, and fascia lata, are located nearby.

  18. Improved side-chain torsion potentials for the Amber ff99SB protein force field

    OpenAIRE

    Lindorff-Larsen, Kresten; Piana, Stefano; Palmo, Kim; Maragakis, Paul; Klepeis, John L.; Dror, Ron O.; Shaw, David E.

    2010-01-01

    Recent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving t...

  19. In situ characterization of protein aggregates in human tissues affected by light chain amyloidosis: a FTIR microspectroscopy study

    Science.gov (United States)

    Ami, Diletta; Lavatelli, Francesca; Rognoni, Paola; Palladini, Giovanni; Raimondi, Sara; Giorgetti, Sofia; Monti, Luca; Doglia, Silvia Maria; Natalello, Antonino; Merlini, Giampaolo

    2016-01-01

    Light chain (AL) amyloidosis, caused by deposition of amyloidogenic immunoglobulin light chains (LCs), is the most common systemic form in industrialized countries. Still open questions, and premises for developing targeted therapies, concern the mechanisms of amyloid formation in vivo and the bases of organ targeting and dysfunction. Investigating amyloid material in its natural environment is crucial to obtain new insights on the molecular features of fibrillar deposits at individual level. To this aim, we used Fourier transform infrared (FTIR) microspectroscopy for studying in situ unfixed tissues (heart and subcutaneous abdominal fat) from patients affected by AL amyloidosis. We compared the infrared response of affected tissues with that of ex vivo and in vitro fibrils obtained from the pathogenic LC derived from one patient, as well as with that of non amyloid-affected tissues. We demonstrated that the IR marker band of intermolecular β-sheets, typical of protein aggregates, can be detected in situ in LC amyloid-affected tissues, and that FTIR microspectroscopy allows exploring the inter- and intra-sample heterogeneity. We extended the infrared analysis to the characterization of other biomolecules embedded within the amyloid deposits, finding an IR pattern that discloses a possible role of lipids, collagen and glycosaminoglycans in amyloid deposition in vivo. PMID:27373200

  20. Formation of long-lived radicals on proteins by radical transfer from heme enzymes--a common process?

    DEFF Research Database (Denmark)

    Ostdal, H; Andersen, H J; Davies, Michael Jonathan

    1999-01-01

    albumin via the heme edge of the peroxidase. In contrast, albumin radical formation by the HRP/H2O2/free tyrosine system was only marginally affected by proteolysis, consistent with free tyrosine phenoxyl radicals being the mediators of radical transfer, without significant protein-protein interaction...

  1. Forster Resonance Energy Transfer and Conformational Stability of Proteins: An Advanced Biophysical Module for Physical Chemistry Students

    Science.gov (United States)

    Sanchez, Katheryn M.; Schlamadinger, Diana E.; Gable, Jonathan E.; Kim, Judy E.

    2008-01-01

    Protein folding is an exploding area of research in biophysics and physical chemistry. Here, we describe the integration of several techniques, including absorption spectroscopy, fluorescence spectroscopy, and Forster resonance energy transfer (FRET) measurements, to probe important topics in protein folding. Cytochrome c is used as a model…

  2. The orchestra of lipid-transfer proteins at the crossroads between metabolism and signaling.

    Science.gov (United States)

    Chiapparino, Antonella; Maeda, Kenji; Turei, Denes; Saez-Rodriguez, Julio; Gavin, Anne-Claude

    2016-01-01

    Within the eukaryotic cell, more than 1000 species of lipids define a series of membranes essential for cell function. Tightly controlled systems of lipid transport underlie the proper spatiotemporal distribution of membrane lipids, the coordination of spatially separated lipid metabolic pathways, and lipid signaling mediated by soluble proteins that may be localized some distance away from membranes. Alongside the well-established vesicular transport of lipids, non-vesicular transport mediated by a group of proteins referred to as lipid-transfer proteins (LTPs) is emerging as a key mechanism of lipid transport in a broad range of biological processes. More than a hundred LTPs exist in humans and these can be divided into at least ten protein families. LTPs are widely distributed in tissues, organelles and membrane contact sites (MCSs), as well as in the extracellular space. They all possess a soluble and globular domain that encapsulates a lipid monomer and they specifically bind and transport a wide range of lipids. Here, we present the most recent discoveries in the functions and physiological roles of LTPs, which have expanded the playground of lipids into the aqueous spaces of cells. PMID:26658141

  3. Enhanced Dissociation of Intact Proteins with High Capacity Electron Transfer Dissociation

    Science.gov (United States)

    Riley, Nicholas M.; Mullen, Christopher; Weisbrod, Chad R.; Sharma, Seema; Senko, Michael W.; Zabrouskov, Vlad; Westphall, Michael S.; Syka, John E. P.; Coon, Joshua J.

    2016-03-01

    Electron transfer dissociation (ETD) is a valuable tool for protein sequence analysis, especially for the fragmentation of intact proteins. However, low product ion signal-to-noise often requires some degree of signal averaging to achieve high quality MS/MS spectra of intact proteins. Here we describe a new implementation of ETD on the newest generation of quadrupole-Orbitrap-linear ion trap Tribrid, the Orbitrap Fusion Lumos, for improved product ion signal-to-noise via ETD reactions on larger precursor populations. In this new high precursor capacity ETD implementation, precursor cations are accumulated in the center section of the high pressure cell in the dual pressure linear ion trap prior to charge-sign independent trapping, rather than precursor ion sequestration in only the back section as is done for standard ETD. This new scheme increases the charge capacity of the precursor accumulation event, enabling storage of approximately 3-fold more precursor charges. High capacity ETD boosts the number of matching fragments identified in a single MS/MS event, reducing the need for spectral averaging. These improvements in intra-scan dynamic range via reaction of larger precursor populations, which have been previously demonstrated through custom modified hardware, are now available on a commercial platform, offering considerable benefits for intact protein analysis and top down proteomics. In this work, we characterize the advantages of high precursor capacity ETD through studies with myoglobin and carbonic anhydrase.

  4. Ultrafast quenching of tryptophan fluorescence in proteins: Interresidue and intrahelical electron transfer

    International Nuclear Information System (INIS)

    Quenching of tryptophan fluorescence in proteins has been critical to the understanding of protein dynamics and enzyme reactions using tryptophan as a molecular optical probe. We report here our systematic examinations of potential quenching residues with more than 40 proteins. With site-directed mutation, we placed tryptophan to desired positions or altered its neighboring residues to screen quenching groups among 20 amino acid residues and of peptide backbones. With femtosecond resolution, we observed the ultrafast quenching dynamics within 100 ps and identified two ultrafast quenching groups, the carbonyl- and sulfur-containing residues. The former is glutamine and glutamate residues and the later is disulfide bond and cysteine residue. The quenching by the peptide-bond carbonyl group as well as other potential residues mostly occurs in longer than 100 ps. These ultrafast quenching dynamics occur at van der Waals distances through intraprotein electron transfer with high directionality. Following optimal molecular orbital overlap, electron jumps from the benzene ring of the indole moiety in a vertical orientation to the LUMO of acceptor quenching residues. Molecular dynamics simulations were invoked to elucidate various correlations of quenching dynamics with separation distances, relative orientations, local fluctuations and reaction heterogeneity. These unique ultrafast quenching pairs, as recently found to extensively occur in high-resolution protein structures, may have significant biological implications

  5. Cardiolipin molecular species with shorter acyl chains accumulate in Saccharomyces cerevisiae mutants lacking the acyl coenzyme A-binding protein Acb1p: new insights into acyl chain remodeling of cardiolipin.

    Science.gov (United States)

    Rijken, Pieter J; Houtkooper, Riekelt H; Akbari, Hana; Brouwers, Jos F; Koorengevel, Martijn C; de Kruijff, Ben; Frentzen, Margrit; Vaz, Frédéric M; de Kroon, Anton I P M

    2009-10-01

    The function of the mitochondrial phospholipid cardiolipin (CL) is thought to depend on its acyl chain composition. The present study aims at a better understanding of the way the CL species profile is established in Saccharomyces cerevisiae by using depletion of the acyl-CoA-binding protein Acb1p as a tool to modulate the cellular acyl chain content. Despite the presence of an intact CL remodeling system, acyl chains shorter than 16 carbon atoms (C16) were found to accumulate in CL in cells lacking Acb1p. Further experiments revealed that Taz1p, a key CL remodeling enzyme, was not responsible for the shortening of CL in the absence of Acb1p. This left de novo CL synthesis as the only possible source of acyl chains shorter than C16 in CL. Experiments in which the substrate specificity of the yeast cardiolipin synthase Crd1p and the acyl chain composition of individual short CL species were investigated, indicated that both CL precursors (i.e. phosphatidylglycerol and CDP-diacylglycerol) contribute to comparable extents to the shorter acyl chains in CL in acb1 mutants. Based on the findings, we conclude that the fatty acid composition of mature CL in yeast is governed by the substrate specificity of the CL-specific lipase Cld1p and the fatty acid composition of the Taz1p substrates. PMID:19656950

  6. Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography.

    Science.gov (United States)

    Eibauer, Matthias; Hoffmann, Christian; Plitzko, Jürgen M; Baumeister, Wolfgang; Nickell, Stephan; Engelhardt, Harald

    2012-12-01

    Cryo-electron tomography in combination with subtomogram averaging allows to investigate the structure of protein assemblies in their natural environment in a close to live state. To make full use of the structural information contained in tomograms it is necessary to analyze the contrast transfer function (CTF) of projections and to restore the phases of higher spatial frequencies. CTF correction is however hampered by the difficulty of determining the actual defocus values from tilt series data, which is due to the low signal-to-noise ratio of electron micrographs. In this study, an extended acquisition scheme is introduced that enables an independent CTF determination. Two high-dose images are recorded along the tilt axis on both sides of each projection, which allow an accurate determination of the defocus values of these images. These values are used to calculate the CTF for each image of the tilt series. We applied this scheme to the mycobacterial outer membrane protein MspA reconstituted in lipid vesicles and tested several variants of CTF estimation in combination with subtomogram averaging and correction of the modulation transfer function (MTF). The 3D electron density map of MspA was compared with a structure previously determined by X-ray crystallography. We were able to demonstrate that structural information up to a resolution of 16.8Å can be recovered using our CTF correction approach, whereas the uncorrected 3D map had a resolution of only 26.2Å. PMID:23000705

  7. Paper-based fluorescence resonance energy transfer assay for directly detecting nucleic acids and proteins.

    Science.gov (United States)

    Li, Hua; Fang, Xueen; Cao, Hongmei; Kong, Jilie

    2016-06-15

    Paper-based fluorescence resonance energy transfer assay (FRET) is gaining great interest in detecting macro-biological molecule. It is difficult to achieve conveniently and fast detection for macro-biological molecule. Herein, a graphene oxide (GO)-based paper chip (glass fiber) integrated with fluorescence labeled single-stranded DNA (ssDNA) for fast, inexpensive and direct detection of biological macromolecules (proteins and nucleic acids) has been developed. In this paper, we employed the Cy3/FAM-labeled ssDNA as the reporter and the GO as quencher and the original glass fiber paper as data acquisition substrates. The chip which was designed and fabricated by a cutting machine is a miniature biosensor that monitors fluorescence recovery from resonance energy transfer. The hybridization assays and fluorescence detection were all simplified, and the surface of the chip did not require immobilization or washing. A Nikon Eclipse was employed as excited resource and a commercial digital camera was employed for capturing digital images. This paper-based microfluidics chip has been applied in the detection of proteins and nucleic acids. The biosensing capability meets many potential requirements for disease diagnosis and biological analysis. PMID:26807518

  8. Green fluorescent protein (GFP) transgenic pig produced by somatic cell nuclear transfer

    Institute of Scientific and Technical Information of China (English)

    LIU ZhongHua; SUN Shuang; LI YuTian; WANG HongBin; R S PRATHER; SONG Jun; WANG ZhenKun; TIAN JiangTian; KONG QingRan; ZHENG Zhong; YIN Zhi; GAO Li; MA HaiKun

    2008-01-01

    Transgenic somatic cell nuclear transfer is a very promising route for producing transgenic farm ani-mals. Research on GFP transgenic pigs can provide useful information for breeding transgenic pigs, human disease models and human organ xenotransplantation. In this study, a liposomal transfection system was screened and transgenic embryos were reconstructed by nuclear transfer of GFP positive cells into enucleated in vitro matured oocytes. The development of reconstructed embryos both in vitro and in vivo was observed, and GFP expression was determined. The results showed that porcine fe-tal-derived fibroblast cells cultured with 4.0 plJmL liposome and 1.6 pg/mL plasmid DNA for 6 h re-sulted in the highest transfection rate (3.6%). The percentage of GFP reconstructed embryos that de-veloped in vitro to the blastocyst stage was 10%. Of those the GFP positive percentage was 48%. Re-constructed transgenic embryos were transferred to 10 recipients. 5 of them were pregnant, and 3 de-livered 6 cloned piglets in which 4 piglets were transgenic for the GFP as verified by both GFP protein expression and GFP DNA sequence analysis. The percentage of reconstructed embryos that resulted in cloned piglets was 1.0%; while the percentage of piglets that were transgenic was 0.7%. This is the first group of transgenic cloned pigs born in China, marking a great progress in Chinese transgenic cloned pig research.

  9. In situ generated half-lanthanidocene based catalysts for the controlled oligomerisation of styrene: Selectivity, block copolymerisation and chain transfer

    OpenAIRE

    Zinck, Philippe; Valente, Andreia; Mortreux, André; Visseaux, Marc

    2007-01-01

    The Cp*Nd(BH4)2(THF)2/n-butylethylmagnesium combination affords a controlled and syndioselective oligomerisation of styrene. Living oligostyrenes can be used as macromonomers for block copolymerisation, leading to the unprecedented synthesis of a (polystyrene)-block- (1,4-trans polyisoprene) copolymer. Reversible transmetallation between the neodymium and the magnesium atom is further established with a transfer efficiency close to 100%.

  10. Structural determinants of stability to proteolysis, processing and impact on allergenic potential of non-specific lipid transfer proteins

    OpenAIRE

    Abdullah, Syed Umer

    2012-01-01

    Lipid transfer proteins (LTPs) are a class of low molecular weight hydrophobic conserved proteins comprising four intramolecular disulphide bonds making the structure very resistant to proteolysis and harsh food processing conditions. These proteins are identified as strong allergens sensitizing through the gut and share epitopes with LTPs from closely related species. Peach LTP, Pru p 3 is the primary sensitizer in the Mediterranean area being the most frequent food allergen. Wheat LTP, Tri ...

  11. Measurements of 129I in human and bovine thyroids in Europe--transfer of 129I into the food chain

    International Nuclear Information System (INIS)

    Bovine thyroid glands from different countries in Europe and human thyroid glands from Lower Saxony (Federal Republic of Germany) show isotopic 129I/127I ratios of 2.1 X 10(-9) to 8.2 X 10(-8) for cattle and 2.1 X 10(-9) to 8 X 10(-8) in humans. These values give information about the concentration of fallout 129I in Europe since most of these glands were collected in areas without nuclear facilities. Some of the human thyroids were collected after the Chernobyl accident between May 1986 and February 1988. Results obtained from human thyroids taken in some locations of Lower Saxony show no significant increase of the 129I during this time. Higher concentrations of 129I were only found in cattle grazing in the vicinity of a reprocessing plant in Mol, Belgium. Samples of soil, vegetation, milk, and water from this area contained higher than normal concentrations of 129I. The long-term transfer of radioiodine from the soil to the plant and the translocation within the soil were studied using a soil monolith with a 129I-contaminated surface. During the 4 y of the experiment, the transfer factor plant/soil decreased from 0.3 to 2.2 X 10(-3). Soil samples taken in 5-cm steps to a depth of 30 cm then at 40 and 50 cm depths showed that the transport of radioiodine to lower layers proceeds very slowly. In an in-vivo study with a dairy cow, the transfer of radioiodine from feed to milk to cow meat and to pig thyroid gland was followed for 53 d using 129I-labeled pasture grass contaminated via roots. A part of the milk obtained from the cow was fed to a pig as a substitute for humans. The mean value of the transfer factor milk/feed was 2.4 X 10(-3) d kg-1. The values of the transfer factor cow meat/feed obtained for different muscle cuts and organs (excluding thyroid) ranged between 3.0 X 10(-4) (kidney) and 5.4 X 10(-2) d kg-1 f.w

  12. Object-adapted trapping and shape-tracking to probe a bacterial protein chain motor

    Science.gov (United States)

    Roth, Julian; Koch, Matthias; Rohrbach, Alexander

    2015-03-01

    The helical bacterium Spiroplasma is a motile plant and anthropod pathogen which swims by propagating pairs of kinks along its cell body. As a well suited model system for bacterial locomotion, understanding the cell's molecular motor is of vital interest also regarding the combat of bacterial diseases. The extensive deformations related to these kinks are caused by a contractile cytoskeletal protein ribbon representing a linear motor in contrast to common rotary motors as, e.g., flagella. We present new insights into the working of this motor through experiments with object-adapted optical traps and shape-tracking techniques. We use the given laser irradiation from the optical trap to hinder bacterial energy (ATP) production through the production of O2 radicals. The results are compared with experiments performed under the influence of an O2-Scavenger and ATP inhibitors, respectively. Our results show clear dependences of the kinking properties on the ATP concentration inside the bacterium. The experiments are supported by a theoretical model which we developed to describe the switching of the ribbon's protein subunits.

  13. A 100-kilodalton protein is associated with the murine interleukin 2 receptor: Biochemical evidence that p100 is distinct from the α and β chains

    International Nuclear Information System (INIS)

    Two proteins that specifically bind the T-cell growth factor interleukin 2 (IL-2) have been identified previously on the surface of T cells; these proteins have been designated IL-2Rα and IL-2Rβ for the α and β chains of the IL-2 receptor (IL-2R). The association of these independent binding proteins with each other on the surface of activated T cells correlates with the generation of high-affinity binding sites. These high-affinity sites transduce the major mitogenic signal of IL-2, yet the mechanisms of association of the α and β chains with each other as well as signal transduction in response to IL-2 are unknown. Cotransfection experiments of cDNAs encoding the α and β chains in T cells and fibroblasts have suggested functional requirements for other T cell-specific factor(s). The authors now provide biochemical evidence for a distinct 100-kDa protein that interacts with the α or β chains, or both, on the surface of the IL-2-dependent cell line CTLL-2 as well as activated murine splenocytes. This same 100-kDa protein is capable of being chemically cross-linked to 125I-labeled IL-2

  14. Anomalous charge and negative-charge-transfer insulating state in cuprate chain-compound KCuO_2

    OpenAIRE

    Choudhury, D.; Rivero, P.; Meyers, D.; Liu, X.; Cao, Y; Middey, S.; Whitaker, M. J.; Barraza-Lopez, S.; Freeland, J. W.; Greenblatt, M.; Chakhalian, J.

    2015-01-01

    Using a combination of X-ray absorption spectroscopy experiments with first principle calculations, we demonstrate that insulating KCuO_2 contains Cu in an unusually-high formal-3+ valence state, the ligand-to-metal (O to Cu) charge transfer energy is intriguingly negative (Delta~ -1.5 eV) and has a dominant (~60%) ligand-hole character in the ground state akin to the high Tc cuprate Zhang-Rice state. Unlike most other formal Cu^{3+} compounds, the Cu 2p XAS spectra of KCuO_2 exhibits pronoun...

  15. A quantitative real time polymerase chain reaction approach for estimating processed animal proteins in feed: preliminary data

    Directory of Open Access Journals (Sweden)

    Maria Cesarina Abete

    2013-04-01

    Full Text Available Lifting of the ban on the use of processed animal proteins (PAPs from non-ruminants in non-ruminant feed is in the wind, avoiding intraspecies recycling. Discrimination of species will be performed through polymerase chain reaction (PCR, which is at a moment a merely qualitative method. Nevertheless, quantification of PAPs in feed is needed. The aim of this study was to approach the quantitative determination of PAPs in feed through Real Time (RT-PCR technique; three different protocols picked up from the literature were tested. Three different kind of matrices were examined: pure animal meals (bovine, chicken and pork; one feed sample certified by the European reference laboratory on animal proteins (EURL AP in feed spiked with 0.1% bovine meal; and genomic DNAs from bovine, chicken and pork muscles. The limit of detection (LOD of the three protocols was set up. All the results obtained from the three protocols considered failed in the quantification process, most likely due to the uncertain copy numbers of the analytical targets chosen. This preliminary study will allow us to address further investigations, with the purpose of developing a RT-PCR quantitative method.

  16. Giardia duodenalis Surface Cysteine Proteases Induce Cleavage of the Intestinal Epithelial Cytoskeletal Protein Villin via Myosin Light Chain Kinase.

    Directory of Open Access Journals (Sweden)

    Amol Bhargava

    Full Text Available Giardia duodenalis infections are among the most common causes of waterborne diarrhoeal disease worldwide. At the height of infection, G. duodenalis trophozoites induce multiple pathophysiological processes within intestinal epithelial cells that contribute to the development of diarrhoeal disease. To date, our understanding of pathophysiological processes in giardiasis remains incompletely understood. The present study reveals a previously unappreciated role for G. duodenalis cathepsin cysteine proteases in intestinal epithelial pathophysiological processes that occur during giardiasis. Experiments first established that Giardia trophozoites indeed produce cathepsin B and L in strain-dependent fashion. Co-incubation of G. duodenalis with human enterocytes enhanced cathepsin production by Assemblage A (NF and S2 isolates trophozoites, but not when epithelial cells were exposed to Assemblage B (GSM isolate trophozoites. Direct contact between G. duodenalis parasites and human intestinal epithelial monolayers resulted in the degradation and redistribution of the intestinal epithelial cytoskeletal protein villin; these effects were abolished when parasite cathepsin cysteine proteases were inhibited. Interestingly, inhibition of parasite proteases did not prevent degradation of the intestinal tight junction-associated protein zonula occludens 1 (ZO-1, suggesting that G. duodenalis induces multiple pathophysiological processes within intestinal epithelial cells. Finally, this study demonstrates that G. duodenalis-mediated disruption of villin is, at least, in part dependent on activation of myosin light chain kinase (MLCK. Taken together, this study indicates a novel role for parasite cathepsin cysteine proteases in the pathophysiology of G. duodenalis infections.

  17. Molecular Detection of Methicillin-Resistant Staphylococcus aureus by Non-Protein Coding RNA-Mediated Monoplex Polymerase Chain Reaction

    Science.gov (United States)

    Soo Yean, Cheryl Yeap; Selva Raju, Kishanraj; Xavier, Rathinam; Subramaniam, Sreeramanan; Gopinath, Subash C. B.; Chinni, Suresh V.

    2016-01-01

    Non-protein coding RNA (npcRNA) is a functional RNA molecule that is not translated into a protein. Bacterial npcRNAs are structurally diversified molecules, typically 50–200 nucleotides in length. They play a crucial physiological role in cellular networking, including stress responses, replication and bacterial virulence. In this study, by using an identified npcRNA gene (Sau-02) in Methicillin-resistant Staphylococcus aureus (MRSA), we identified the Gram-positive bacteria S. aureus. A Sau-02-mediated monoplex Polymerase Chain Reaction (PCR) assay was designed that displayed high sensitivity and specificity. Fourteen different bacteria and 18 S. aureus strains were tested, and the results showed that the Sau-02 gene is specific to S. aureus. The detection limit was tested against genomic DNA from MRSA and was found to be ~10 genome copies. Further, the detection was extended to whole-cell MRSA detection, and we reached the detection limit with two bacteria. The monoplex PCR assay demonstrated in this study is a novel detection method that can replicate other npcRNA-mediated detection assays. PMID:27367909

  18. A chimera of green fluorescent protein with single chain variable fragment antibody against ginsenosides for fluorescence-linked immunosorbent assay.

    Science.gov (United States)

    Sakamoto, Seiichi; Tanizaki, Yusuke; Pongkitwitoon, Benyakan; Tanaka, Hiroyuki; Morimoto, Satoshi

    2011-05-01

    A chimera of green fluorescent protein extracted from Aequorea coerulescens (AcGFP), a mutant that has been codon optimized for mammalian expression, with single-chain variable fragment (scFv) antibody against ginsenoside Re (GRe-scFv), named fluobody, has been successfully expressed in Escherichia coli (E. coli) to develop simple, speedy, and sensitive fluorescence-linked immunosorbent assay (FLISA). Two chimera proteins were constructed to contain GRe-scFv at the C-terminus of AcGFP (C-fluobody) and at the N-terminus of AcGFP (N-fluobody). These fluobodies were then purified by ion metal affinity chromatography and refolded by stepwise dialysis. The characterization of both fluobodies revealed that C-fluobody was found to be appropriate probe for FLISA as compare with N-fluobody. Furthermore, improvement of limit of detection (LOD) was observed in FLISA using C-fluobody (10 ng/mL) due to its strong fluorescence intensity of AcGFP compared with conventional enzyme-linked immunosorbent assay (ELISA) using parental monoclonal antibody against ginsenoside Re (G-Re), MAb-4G10 (100 ng/mL). Since some steps required in ELISA can be avoided in this present FLISA, speedy and sensitive immunoassay also could be performed using fluobody instead of monoclonal antibody and scFv. PMID:21277981

  19. Isolation and full characterisation of a potentially allergenic lipid transfer protein (LTP) in almond.

    Science.gov (United States)

    Buhler, Sofie; Tedeschi, Tullia; Faccini, Andrea; Garino, Cristiano; Arlorio, Marco; Dossena, Arnaldo; Sforza, Stefano

    2015-01-01

    Non-specific lipid transfer proteins (nsLTP) were shown to be among the most significant allergens, in particular in several fruits belonging to the Rosaceae family. The molecular features of LTPs, such as the presence of eight cysteine residues forming four disulfide bridges, confer a compact structure, decreasing the probability of degradation due to cooking or digestion, thereby increasing the chance of systemic absorption and severe allergic reactions. Few studies on LTP-induced allergies regarding almond (Prunus dulcis L) are available in the literature. In the present work, we describe for the first time the extraction and purification of an almond LTP, achieving its full characterisation by using liquid chromatography and exact mass spectrometry; the full sequence was identified by means of LC-ESI-Orbitrap-MS applying a bottom-up approach. The characterised protein consists of 92 amino acids and has a calculated exact MW of 9579.0. The presence of four disulfide bridges was confirmed after reduction, as shown by a mass increment of 8 Da. Finally, its potential allergenicity was confirmed via an in silico approach. The results presented here demonstrate the enormous potential of advanced MS techniques for obtaining high-quality structural and functional data of allergenic proteins in a short time. PMID:25658292

  20. Association of -971 G/A Cholesteryl-Ester Transfer Protein Gene Polymorphism with Lipid Profile in Primary Hyperlipidemia

    Directory of Open Access Journals (Sweden)

    A Barkhordari

    2012-10-01

    Full Text Available Background: Coronary heart disease (CHD is a leading cause of death worldwide and hypertriglyceridemia and hypercholesterolemia are major risk factors for the disease. Considering the role of hyperlipidemia as the underlying cause of cardiovascular mortalities and morbidities, and the limited and conflicting results of studies on CETP gene polymorphisms in Iran, we aimed to study -971 G/A polymorphism of cholesterol ester transfer protein gene in patients with primary hyperlipidemia.Methods: In this case-control study performed in Hamadan University of Medical Sciences (from May 2010 to April 2011, we recruited 200 patients with primary hyperlipidemia (total cholesterol >250 mg/dl and/or triglyceride >200 mg/dl as the cases and 200 healthy individuals with normal cholesterol and triglyceride as the control group. Gene segments were replicated by polymerase chain reaction (PCR and -971 G/A polymorphism genotypes were identified by RFLP technique. Subsequently, plasma CETP activity was measured enzymeatically by a kit in a fluorescence spectrometer.Results: The allele and genotype frequencies were not significantly different (P>0.05 between the two groups (in the control group: AA 24%, GA 47% and GG 28.5% and in the case group: AA 18%, GA 51% and GG 31%. In the case group, homozygous individuals with A alleles (AA genotype had greater cholesterol and HDL-c concentrations than those with other alleles (GG and GA. In both cases and controls, individuals with AA genotype had lower CETP concentrations.Conclusion: We conclude that -971 G/A polymorphism in CETP gene promoter can affect lipid profile and alter CETP activity.

  1. The Relationship Between Genetic Variations of the Cholesteryl Ester Transfer Protein Gene and Coronary Artery Disease in Turkish Subjects

    Science.gov (United States)

    Gundogdu, Fuat; Gurlertop, Yekta; Pirim, Ibrahim; Sevimli, Serdar; Dogan, Hasan; Arslan, Sakir; Aksoy, Hulya; Karakelloglu, Sule; Senocak, Huseyin

    2009-01-01

    Objective Although the relationship between cholesteryl ester transfer protein (CETP) and cholesterol metabolism has been characterized in recent years, the effect of CETP genetic variants associated with coronary artery disease (CAD) is still unclear. Therefore, we investigated the association between CETP gene polymorphism and levels of lipid in patients with CAD. Materials and Methods We conducted a case-control study that included 194 unrelated subjects who underwent coronary angiography for suspected ischemic heart disease. This group was divided into 96 patients with angiographically documented CAD and 98 subjects (individuals matched for age and gender) without angiographically documented CAD (CAD-free subjects), all of whom were studied to examine the genotypic distribution of the CETP gene polymorphism in CAD. Genotyping was performed via polymerase chain reaction. Results Of the 96 patients with CAD, 38 (40%) were B1B1, 42 (44%) B1B2 and 16 (16%) B2B2, compared with the control subjects, of which 35 (36%) were B1B1, 44 (45%) B1B2 and 19 (19%) B2B2. There were no significant differences between patients with CAD and control subjects in the distribution of the CETP gene polymorphism. Patients with the B1B1 genotype had lower high-density lipoprotein-cholesterol (HDL-C) and higher triglyceride (TG) levels than patients with the B2B2 genotype (p<0.05). In addition, among control subjects HDL-C levels were significantly higher in subjects with the B2B2 genotype than in subjects with the B1B1 genotype (p<0.01). Conclusion Our results suggest that genetic variations of the CTEP gene may be responsible for low HDL-C levels but may not be considered as a risk factor for CAD in the Turkish population. PMID:25610061

  2. Resonance Energy Transfer between protein and rhamnolipid capped ZnS quantum dots: Application in in-gel staining of proteins

    Science.gov (United States)

    Janakiraman, Narayanan; Mohan, Abhilash; Kannan, Ashwin; Pennathur, Gautam

    The interaction of proteins with quantum dots is an interesting field of research. These interactions occur at the nanoscale. We have probed the interaction of Bovine Serum Albumin (BSA) and Candida rugosa lipase (CRL) with rhamnolipid capped ZnS (RhlZnSQDs) using absorption and fluorescence spectroscopy. Optical studies on mixtures of RhlZnSQDs and proteins resulted in Förster's Resonance Energy Transfer (FRET) from proteins to QDs. This phenomenon has been exploited to detect proteins in agarose gel electrophoresis. The activity of the CRL was unaffected on the addition of QDs as revealed by zymography.

  3. Polyunsaturated Branched-Chain Fatty Acid Geranylgeranoic Acid Induces Unfolded Protein Response in Human Hepatoma Cells.

    Directory of Open Access Journals (Sweden)

    Chieko Iwao

    Full Text Available The acyclic diterpenoid acid geranylgeranoic acid (GGA has been reported to induce autophagic cell death in several human hepatoma-derived cell lines; however, the molecular mechanism for this remains unknown. In the present study, several diterpenoids were examined for ability to induce XBP1 splicing and/or lipotoxicity for human hepatoma cell lines. Here we show that three groups of diterpenoids emerged: 1 GGA, 2,3-dihydro GGA and 9-cis retinoic acid induce cell death and XBP1 splicing; 2 all-trans retinoic acid induces XBP1 splicing but little cell death; and 3 phytanic acid, phytenic acid and geranylgeraniol induce neither cell death nor XBP1 splicing. GGA-induced ER stress/ unfolded protein response (UPR and its lipotoxicity were both blocked by co-treatment with oleic acid. The blocking activity of oleic acid for GGA-induced XBP1 splicing was not attenuated by methylation of oleic acid. These findings strongly suggest that GGA at micromolar concentrations induces the so-called lipid-induced ER stress response/UPR, which is oleate-suppressive, and shows its lipotoxicity in human hepatoma cells.

  4. Concentrations of long-chain acyl-acyl carrier proteins during fatty acid synthesis by chloroplasts isolated from pea (Pisum sativum), safflower (Carthamus tinctoris), and amaranthus (Amaranthus lividus) leaves

    International Nuclear Information System (INIS)

    Fatty acid synthesis from [1-14C]acetate by chloroplasts isolated from peas and amaranthus was linear for at least 15 min, whereas incorporation of the tracer into long-chain acyl-acyl carrier protein (ACP) did not increase after 2-3 min. When reactions were transferred to the dark after 3-5 min, long-chain acyl-ACPs lost about 90% of their radioactivity and total fatty acids retained all of theirs. Half-lives of the long-chain acyl-ACPs were estimated to be 10-15 s. Concentrations of palmitoyl-, stearoyl-, and oleoyl-ACP as indicated by equilibrium labeling during steady-state fatty acid synthesis, ranged from 0.6-1.1, 0.2-0.7, and 0.4-1.6 microM, respectively, for peas and from 1.6-1.9, 1.3-2.6, and 0.6-1.4 microM, respectively, for amaranthus. These values are based on a chloroplast volume of 47 microliters/mg chlorophyll and varied according to the mode of the incubation. A slow increase in activity of the fatty acid synthetase in safflower chloroplasts resulted in long-chain acyl-ACPs continuing to incorporate labeled acetate for 10 min. Upon re-illumination following a dark break, however, both fatty acid synthetase activity and acyl-ACP concentrations increased very rapidly. Palmitoyl-ACP was present at concentrations up to 2.5 microM in safflower chloroplasts, whereas those of stearoyl- and oleoyl-ACPs were in the lower ranges measured for peas. Acyl-ACPs were routinely separated from extracts of chloroplasts that had been synthesising long-chain fatty acids from labeled acetate by a minor modification of the method of Mancha et al. The results compared favorably with those obtained using alternative analytical methods such as adsorption to filter paper and partition chromatography on silicic acid columns

  5. Cannabinoid receptor 2 expression modulates Gβ(1)γ(2) protein interaction with the activator of G protein signalling 2/dynein light chain protein Tctex-1.

    Science.gov (United States)

    Nagler, Marina; Palkowitsch, Lysann; Rading, Sebastian; Moepps, Barbara; Karsak, Meliha

    2016-01-01

    The activator of G protein signalling AGS2 (Tctex-1) forms protein complexes with Gβγ, and controls cell proliferation by regulating cell cycle progression. A direct interaction of Tctex-1 with various G protein-coupled receptors has been reported. Since the carboxyl terminal portion of CB2 carries a putative Tctex-1 binding motif, we investigated the potential interplay of CB2 and Tctex-1 in the absence and presence of Gβγ. The supposed interaction of cannabinoid receptor CB2 with Tctex-1 and the influence of CB2 on the formation of Tctex-1-Gβγ-complexes were studied by co- and/or immunoprecipitation experiments in transiently transfected HEK293 cells. The analysis on Tctex-1 protein was performed in the absence and presence of the ligands JWH 133, 2-AG, and AM 630, the protein biosynthesis inhibitor cycloheximide or the protein degradation blockers MG132, NH4Cl/leupeptin or bafilomycin. Our results show that CB2 neither directly nor indirectly via Gβγ interacts with Tctex-1, but competes with Tctex-1 in binding to Gβγ. The Tctex-1-Gβγ protein interaction was disrupted by CB2 receptor expression resulting in a release of Tctex-1 from the complex, and its degradation by the proteasome and partly by lysosomes. The decrease in Tctex-1 protein levels is induced by CB2 expression "dose-dependently" and is independent of stimulation by agonist or blocking by an inverse agonist treatment. The results suggest that CB2 receptor expression independent of its activation by agonists is sufficient to competitively disrupt Gβγ-Tctex-1 complexes, and to initiate Tctex-1 degradation. These findings implicate that CB2 receptor expression modifies the stability of intracellular protein complexes by a non-canonical pathway. PMID:26410677

  6. Inhibition of Breast Cancer Metastasis and Angiogenesis by Antiosteopontin Single-Chain Fv-Fc Fusion Protein

    Directory of Open Access Journals (Sweden)

    Ling Peng

    2009-05-01

    Full Text Available Osteopontin (OPN is associated with many diseases, and its role in tumor growth and metastasis has been studied in breast cancers. Previous studies have described anti-OPN antibodies that could inhibit tumor cell adhesion and invasion in vitro, but until now, there are no systematic studies on antitumor effects of anti-OPN antibodies in vivo. In the present study, we have raised several anti-OPN single-chain variable fragments from phage antibody library and expressed them as single-chain variable fragment-constant region fragment fusion proteins in Chinese hamster ovary cells. Of them, two antibodies (1A12 and 2H8 were able to inhibit MDA-MB-435s breast cancer cell attachment, invasion, migration, and colony formation in soft agar. Furthermore, 1A12 and 2H8 inhibited the anti-apoptotic and prosurvival functions of OPN in human umbilical vein endothelial cell. In human umbilical vein endothelial cell capillary tube formation, chicken chorioallantoic membrane assay, and rabbit corneal micropocket assay, the two antibodies showed markedly inhibitory effects toward angiogenesis. We investigated antitumor effects of anti-OPN antibodies in nude mice by assessing xenograft tumor growth and lung metastasis potential. The results showed that the two antibodies were capable of delaying primary tumor growth and reducing spontaneous lung metastasis. Epitope mappings of these two anti-OPN antibodies were performed, and a new binding site of 1A12 was revealed. In summary, the present study has demonstrated the roles of anti-OPN antibodies in blocking the function of OPN, suggesting that they may have the potential to be developed for future clinical use.

  7. Identification of Bach2 as a B-cell-specific partner for small maf proteins that negatively regulate the immunoglobulin heavy chain gene 3' enhancer.

    OpenAIRE

    Muto, A; Hoshino, H.; Madisen, L; Yanai, N; Obinata, M; Karasuyama, H.; Hayashi, N.; Nakauchi, H; M. Yamamoto; Groudine, M; K. Igarashi

    1998-01-01

    Maf family transcription factors are important regulators in various differentiation systems. Putative Maf recognition elements (MAREs) are found in the 3' enhancer region of the immunoglobulin heavy chain (IgH) gene. These elements are bound in B-cell extracts by a heterodimeric protein complex containing both Bach2 and a small Maf protein. Analysis of normal hematopoietic cells revealed that Bach2 is specifically expressed in B cells. Bach2 is abundantly expressed in the early stages of B-c...

  8. Double heterozygosity for mutations in the β-myosin heavy chain and in the cardiac myosin binding protein C genes in a family with hypertrophic cardiomyopathy

    OpenAIRE

    Richard, P.; Isnard, R.; Carrier, L.; Dubourg, O.; Donatien, Y.; Mathieu, B.; Bonne, G.; Gary, F; Charron, P; HAGEGE, A.; Komajda, M; Schwartz, K.; Hainque, B

    1999-01-01

    Familial hypertrophic cardiomyopathy is a genetically heterogeneous autosomal dominant disease, caused by mutations in several sarcomeric protein genes. So far, seven genes have been shown to be associated with the disease with the β-myosin heavy chain (MYH7) and the cardiac myosin binding protein C (MYBPC3) genes being the most frequently involved.
We performed electrocardiography (ECG) and echocardiography in 15 subjects with hypertrophic cardiomyopathy from a French Caribbean family. Genet...

  9. Multivalent interactions of the SUMO-interaction motifs in RING finger protein 4 determine the specificity for chains of the SUMO.

    Science.gov (United States)

    Keusekotten, Kirstin; Bade, Veronika N; Meyer-Teschendorf, Katrin; Sriramachandran, Annie Miriam; Fischer-Schrader, Katrin; Krause, Anke; Horst, Christiane; Schwarz, Günter; Hofmann, Kay; Dohmen, R Jürgen; Praefcke, Gerrit J K

    2014-01-01

    RNF4 (RING finger protein 4) is a STUbL [SUMO (small ubiquitin-related modifier)-targeted ubiquitin ligase] controlling PML (promyelocytic leukaemia) nuclear bodies, DNA double strand break repair and other nuclear functions. In the present paper, we describe that the sequence and spacing of the SIMs (SUMO-interaction motifs) in RNF4 regulate the avidity-driven recognition of substrate proteins carrying SUMO chains of variable length. PMID:24151981

  10. Using nonfluorescent Förster resonance energy transfer acceptors in protein binding studies.

    Science.gov (United States)

    Ruan, Qiaoqiao; Skinner, Joseph P; Tetin, Sergey Y

    2009-10-15

    The purpose of this article is to highlight the versatility of nonfluorescent Förster resonance energy transfer (FRET) acceptors in determination of protein equilibrium dissociation constants and kinetic rates. Using a nonfluorescent acceptor eliminates the necessity to spectrally isolate the donor fluorescence when performing binding titrations covering a broad range of reagent concentrations. Moreover, random distribution of the donor and acceptor chromophores on the surface of proteins increases the probability of FRET occurring on their interaction. Three high-affinity antibodies are presented in this study as characteristic protein systems. Monoclonal antibody (mAb) 106.3 binds brain natriuretic peptide (BNP)5-13(C10A) and full-length BNP1-32 with the dissociation constants 0.26+/-0.01 and 0.05+/-0.02 nM, respectively, which was confirmed by kinetic measurements. For anti-hCG (human chorionic gonadotropin) mAb 8F11, studied at two incorporation ratios (IRs=1.9 and 3.8) of the nonfluorescent FRET acceptor, K(D) values of 0.04+/-0.02 and 0.059(-0.004)(+0.006) nM, respectively, were obtained. Likewise, the binding of goat anti-hamster immunoglobulin G (IgG) antibody was not affected by conjugation and yielded K(D) values of 1.26+/-0.04, 1.25+/-0.05, and 1.14+/-0.04 nM at IRs of 1.7, 4.7, and 8.1, respectively. We conclude that this FRET-based method offers high sensitivity, practical simplicity, and versatility in protein binding studies. PMID:19563765

  11. Electron transfer patterns of the di-heme protein cytochrome c(4) from Pseudomonas stutzeri

    DEFF Research Database (Denmark)

    Raffalt, Anders Christer; Schmidt, L.; Christensen, Hans Erik Mølager;

    2009-01-01

    We report kinetic data for the two-step electron transfer (ET) oxidation and reduction of the two-domain di-heme redox protein Pseudomonas stutzeri cytochrome (cyt) c(4) by [Co(bipy)(3)](2- 3-) (bipy = 2,2'-bipyridine). Following earlier reports, the data accord with both bi- and tri......-exponential kinetics. A complete kinetic scheme includes both "cooperative" intermolecular ET between each heme group and the external reaction partner, and intramolecular ET between the two heme groups. A now data analysis scheme shows unequivocally that two-ET oxidation and reduction of P. stutzeri cyt c(4) is...... entirely dominated by intermolecular ET between the heme groups and the external reaction partner in the ms time range, with virtually no contribution from intramolecular interheme ET in this time range. This is in striking contrast to two-ET electrochemical oxidation or reduction of P. stutzeri cyt c(4...

  12. Light-induced conformational changes and energy transfer in red fluorescent protein

    International Nuclear Information System (INIS)

    Reversible conformational changes have been photo-induced in the red fluorescent protein DsRed at low temperature by wavelength-selective laser irradiation. We have found two new fluorescent forms: a shifted-red (SR-) and a new green (G'-) form that absorb and emit, respectively, ∼14 nm to the red and ∼80 nm to the blue of the 'mature' red (R-) form present in an un-illuminated sample of DsRed. Further, we have identified the 0-0 transitions of the various forms by spectral hole burning and estimated their ground-state energy differences and barrier heights by means of temperature-dependent excitation and fluorescence spectroscopy between 1.6 and 295 K. We have also proven that 'downhill' energy transfer takes place between these forms within the tetrameric structure of DsRed

  13. How anacetrapib inhibits the activity of the cholesteryl ester transfer protein? Perspective through atomistic simulations.

    Directory of Open Access Journals (Sweden)

    Tarja Äijänen

    2014-11-01

    Full Text Available Cholesteryl ester transfer protein (CETP mediates the reciprocal transfer of neutral lipids (cholesteryl esters, triglycerides and phospholipids between different lipoprotein fractions in human blood plasma. A novel molecular agent known as anacetrapib has been shown to inhibit CETP activity and thereby raise high density lipoprotein (HDL-cholesterol and decrease low density lipoprotein (LDL-cholesterol, thus rendering CETP inhibition an attractive target to prevent and treat the development of various cardiovascular diseases. Our objective in this work is to use atomistic molecular dynamics simulations to shed light on the inhibitory mechanism of anacetrapib and unlock the interactions between the drug and CETP. The results show an evident affinity of anacetrapib towards the concave surface of CETP, and especially towards the region of the N-terminal tunnel opening. The primary binding site of anacetrapib turns out to reside in the tunnel inside CETP, near the residues surrounding the N-terminal opening. Free energy calculations show that when anacetrapib resides in this area, it hinders the ability of cholesteryl ester to diffuse out from CETP. The simulations further bring out the ability of anacetrapib to regulate the structure-function relationships of phospholipids and helix X, the latter representing the structural region of CETP important to the process of neutral lipid exchange with lipoproteins. Altogether, the simulations propose CETP inhibition to be realized when anacetrapib is transferred into the lipid binding pocket. The novel insight gained in this study has potential use in the development of new molecular agents capable of preventing the progression of cardiovascular diseases.

  14. Surface-tuned electron transfer and electrocatalysis of hexameric tyrosine-coordinated heme protein.

    Science.gov (United States)

    Peng, Lei; Utesch, Tillmann; Yarman, Aysu; Jeoung, Jae-Hun; Steinborn, Silke; Dobbek, Holger; Mroginski, Maria Andrea; Tanne, Johannes; Wollenberger, Ulla; Scheller, Frieder W

    2015-05-11

    Molecular modeling, electrochemical methods, and quartz crystal microbalance were used to characterize immobilized hexameric tyrosine-coordinated heme protein (HTHP) on bare carbon or on gold electrodes modified with positively and negatively charged self-assembled monolayers (SAMs), respectively. HTHP binds to the positively charged surface but no direct electron transfer (DET) is found due to the long distance of the active sites from the electrode surfaces. At carboxyl-terminated surfaces, the neutrally charged bottom of HTHP can bind to the SAM. For this "disc" orientation all six hemes are close to the electrode and their direct electron transfer should be efficient. HTHP on all negatively charged SAMs showed a quasi-reversible redox behavior with rate constant ks values between 0.93 and 2.86 s(-1) and apparent formal potentials ${E{{0{^{\\prime }}\\hfill \\atop {\\rm app}\\hfill}}}$ between -131.1 and -249.1 mV. On the MUA/MU-modified electrode, the maximum surface concentration corresponds to a complete monolayer of the hexameric HTHP in the disc orientation. HTHP electrostatically immobilized on negatively charged SAMs shows electrocatalysis of peroxide reduction and enzymatic oxidation of NADH. PMID:25825040

  15. Transfer of Immunity from Mother to Offspring Is Mediated via Egg-Yolk Protein Vitellogenin.

    Science.gov (United States)

    Salmela, Heli; Amdam, Gro V; Freitak, Dalial

    2015-07-01

    Insect immune systems can recognize specific pathogens and prime offspring immunity. High specificity of immune priming can be achieved when insect females transfer immune elicitors into developing oocytes. The molecular mechanism behind this transfer has been a mystery. Here, we establish that the egg-yolk protein vitellogenin is the carrier of immune elicitors. Using the honey bee, Apis mellifera, model system, we demonstrate with microscopy and western blotting that vitellogenin binds to bacteria, both Paenibacillus larvae--the gram-positive bacterium causing American foulbrood disease--and to Escherichia coli that represents gram-negative bacteria. Next, we verify that vitellogenin binds to pathogen-associated molecular patterns; lipopolysaccharide, peptidoglycan and zymosan, using surface plasmon resonance. We document that vitellogenin is required for transport of cell-wall pieces of E. coli into eggs by imaging tissue sections. These experiments identify vitellogenin, which is distributed widely in oviparous species, as the carrier of immune-priming signals. This work reveals a molecular explanation for trans-generational immunity in insects and a previously undescribed role for vitellogenin. PMID:26230630

  16. Epidural ropivacaine hydrochloride during labour: protein binding, placental transfer and neonatal outcome.

    LENUS (Irish Health Repository)

    Porter, J M

    2012-02-03

    This study was undertaken: (i) to quantify the effects of labour and epidural analgesia on plasma alpha1-acid glycoprotein concentration, (ii) to examine the effects of changes in plasma alpha1-acid glycoprotein concentration on plasma protein binding and placental transfer of ropivacaine, and (iii) to examine the association between umbilical venous ropivacaine concentration and neurobehavioural function in the neonate. Multiparous patients undergoing induction of labour received a continuous epidural infusion of 0.1% ropivacaine following an epidural bolus. A significant association was demonstrated between maternal plasma alpha1-acid glycoprotein concentration and 1\\/free fraction of ropivacaine 60 min after starting ropivacaine administration (r(2) = 0.77) but not at delivery. No significant correlation was demonstrable between maternal unbound ropivacaine concentration and either neonatal (cord) ropivacaine concentration or UV\\/MV (a measure of placental transfer). Thirty minutes after delivery, 9\\/10 neonates had neurological and adaptive capacity scores < 35, whereas only three infants had scores < 35 at 2 h. All scores exceeded 35 16 h after delivery. No association between mean (SD) umbilical venous ropivacaine concentration [0.09 (0.08) mg x l(-1)] and neurological and adaptive capacity scores was demonstrated.

  17. Characterization of a new antifungal non-specific lipid transfer protein (nsLTP) from sugar beet leaves

    DEFF Research Database (Denmark)

    Kristensen, A K; Brunstedt, J; Madsen, M T;

    2000-01-01

    cysteines at conserved positions, the protein can be classified as a member of the plant family of non-specific lipid transfer proteins (nsLTPs). The protein is 47% identical to IWF1, an antifungal nsLTP previously isolated from leaves of sugar beet. A potential site for N-linked glycosylation present in...... sequence of 26 amino acid residues. The protein shows a strong in vitro antifungal activity against Cercospora beticola (causal agent of leaf spot disease in sugar beet) and inhibits fungal growth at concentrations below 10 µg ml(-1)....

  18. Effect of protein restriction on (15)N transfer from dietary [(15)N]alanine and [(15)N]Spirulina platensis into urea.

    Science.gov (United States)

    Hamadeh, M J; Hoffer, L J

    2001-08-01

    Six normal men consumed a mixed test meal while adapted to high (1.5 g. kg(-1) x day(-1)) and low (0.3 g. kg(-1) x day(-1)) protein intakes. They completed this protocol twice: when the test meals included 3 mg/kg of [(15)N]alanine ([(15)N]Ala) and when they included 30 mg/kg of intrinsically labeled [(15)N]Spirulina platensis ([(15)N]SPI). Six subjects with insulin-dependent diabetes mellitus (IDDM) receiving conventional insulin therapy consumed the test meal with added [(15)N]Ala while adapted to their customary high-protein diet. Protein restriction increased serum alanine, glycine, glutamine, and methionine concentrations and reduced those of leucine. Whether the previous diet was high or low in protein, there was a similar increase in serum alanine, methionine, and branched-chain amino acid concentrations after the test meal and a similar pattern of (15)N enrichment in serum amino acids for a given tracer. When [(15)N]Ala was included in the test meal, (15)N appeared rapidly in serum alanine and glutamine, to a minor degree in leucine and isoleucine, and not at all in other circulating amino acids. With [(15)N]SPI, there was a slow appearance of the label in all serum amino acids analyzed. Despite the different serum amino acid labeling, protein restriction reduced the postmeal transfer of dietary (15)N in [(15)N]Ala or [(15)N]SPI into [(15)N]urea by similar amounts (38 and 43%, respectively, not significant). The response of the subjects with IDDM was similar to that of the normal subjects. Information about adaptive reductions in dietary amino acid catabolism obtained by adding [(15)N]Ala to a test meal appears to be equivalent to that obtained using an intrinsically labeled protein tracer. PMID:11440912

  19. Expression of VEGF protein of lung and liver in GM-CSF gene transferred mice after neutron acute injury

    International Nuclear Information System (INIS)

    Objective: To study lung and liver vascular endothelial growth factor (VEGF) protein expression changes in granulocyte-macrophage colony-stimulating factor(GM-CSF) transgene mice after neutron exposure. Methods: Male BALB/C mice were irradiated with neutron, in dose of 0.6Gy, the mice were divided into the non-transfer group and the gene transfer group. In the gene transfer group, hGM-CSF gene was transfered by electroporation in vivo 24 h prior to exposure. Animals in the two groups were sacrificed at the 1st, 14th, 28th day, using pathologic test, immunohistochemica test and Western blot to study VEGF protein expression in lung and liver. Results: From 14 d to 28 d after exposure, the levels of VEGF protein expression in the mice in the genetransfer group was significantly higher than that in the non-transfer group. Conclusion: GM-CSF in vivo gene transfer in mice significantly promote angiogenesis and restoration in the climax and recovery phase acute injury caused by neutron. (authors)

  20. Design of a bifunctional fusion protein for ovarian cancer drug delivery: single-chain anti-CA125 core-streptavidin fusion protein.

    Science.gov (United States)

    Wang, Welson Wen-Shang; Das, Dipankar; McQuarrie, Stephen A; Suresh, Mavanur R

    2007-03-01

    We have developed a universal ovarian cancer cell targeting vehicle that can deliver biotinylated therapeutic drugs. A single-chain antibody variable domain (scFv) that recognizes the CA125 antigen of ovarian cancer cells was fused with a core-streptavidin domain (core-streptavidin-VL-VH and VL-VH-core-streptavidin orientations) using recombinant DNA technology and then expressed in Escherichia coli using the T7 expression system. The bifunctional fusion protein (bfFp) was expressed in a shaker flask culture, extracted from the periplasmic soluble protein, and affinity purified using an IMAC column. The two distinct activities (biotin binding and anti-CA125) of the bfFp were demonstrated using ELISA, Western blot and confocal laser-scanning microscopy (CLSM). The ELISA method utilized human NIH OVCAR-3 cells along with biotinylated bovine serum albumin (B-BSA) or biotinylated liposomes, whereas, the Western blot involved probing with B-BSA. The CLSM study has shown specificity in binding to the OVCAR-3 cell-line. ELISA and Western blot studies have confirmed the bifunctional activity and specificity. In the presence of bfFp, there was enhanced binding of biotinylated antigen and liposome to OVCAR-3 cells. In contrast, the control EMT6 cells, which do not express the CA125 antigen, showed minimal binding of the bfFp. Consequently, bfFp based targeting of biotinylated therapeutic drugs, proteins, liposomes, or nanoparticles could be an alternative, convenient method to deliver effective therapy to ovarian cancer patients. Peritoneal infusion of the bfFp-therapeutic complex could also be effective in locally targeting the most common site of metastatic spread. PMID:17257818

  1. THE INTEGRITY OF THE α-HELICAL DOMAIN OF INTESTINAL FATTY ACID BINDING PROTEIN IS ESSENTIAL FOR THE COLLISION-MEDIATED TRANSFER OF FATTY ACIDS TO PHOSPHOLIPID MEMBRANES

    OpenAIRE

    Franchini, G. R.; Storch, J.; Corsico, B.

    2008-01-01

    Intestinal FABP (IFABP) and liver FABP (LFABP), homologous proteins expressed at high levels in intestinal absorptive cells, employ markedly different mechanisms of fatty acid transfer to acceptor model membranes. Transfer from IFABP occurs during protein-membrane-collisional interactions, while for LFABP transfer occurs by diffusion through the aqueous phase. In addition, transfer from IFABP is markedly faster than from LFABP. The overall goal of this study was to further explore the structu...

  2. Characterization of G-protein coupled receptor kinase interaction with the neurokinin-1 receptor using bioluminescence resonance energy transfer

    DEFF Research Database (Denmark)

    Jorgensen, Rasmus; Holliday, Nicholas D; Hansen, Jakob L;

    2007-01-01

    To analyze the interaction between the neurokinin-1 (NK-1) receptor and G-protein coupled receptor kinases (GRKs), we performed bioluminescence resonance energy transfer(2) (BRET(2)) measurements between the family A NK-1 receptor and GRK2 and GRK5 as well as their respective kinase-inactive muta......To analyze the interaction between the neurokinin-1 (NK-1) receptor and G-protein coupled receptor kinases (GRKs), we performed bioluminescence resonance energy transfer(2) (BRET(2)) measurements between the family A NK-1 receptor and GRK2 and GRK5 as well as their respective kinase...

  3. Measuring ligand-dependent and ligand-independent interactions between nuclear receptors and associated proteins using Bioluminescence Resonance Energy Transfer (BRET2)

    OpenAIRE

    Koterba, Kristen L.; Rowan, Brian G.

    2006-01-01

    Bioluminescent resonance energy transfer (BRET2) is a recently developed technology for the measurement of protein-protein interactions in a live, cell-based system. BRET2 is characterized by the efficient transfer of excited energy between a bioluminescent donor molecule (Renilla luciferase) and a fluorescent acceptor molecule (a mutant of Green Fluorescent Protein (GFP2)). The BRET2 assay offers advantages over fluorescence resonance energy transfer (FRET) because it does not require an ext...

  4. Sec14-like phosphatidylinositol transfer proteins and the biological landscape of phosphoinositide signaling in plants.

    Science.gov (United States)

    Huang, Jin; Ghosh, Ratna; Bankaitis, Vytas A

    2016-09-01

    Phosphoinositides and soluble inositol phosphates are essential components of a complex intracellular chemical code that regulates major aspects of lipid signaling in eukaryotes. These involvements span a broad array of biological outcomes and activities, and cells are faced with the problem of how to compartmentalize and organize these various signaling events into a coherent scheme. It is in the arena of how phosphoinositide signaling circuits are integrated and, and how phosphoinositide pools are functionally defined and channeled to privileged effectors, that phosphatidylinositol (PtdIns) transfer proteins (PITPs) are emerging as critical players. As plant systems offer some unique advantages and opportunities for study of these proteins, we discuss herein our perspectives regarding the progress made in plant systems regarding PITP function. We also suggest interesting prospects that plant systems hold for interrogating how PITPs work, particularly in multi-domain contexts, to diversify the biological outcomes for phosphoinositide signaling. This article is part of a Special Issue entitled: Plant Lipid Biology edited by Kent D. Chapman and Ivo Feussner. PMID:27038688

  5. Vitamin E and Phosphoinositides Regulate the Intracellular Localization of the Hepatic α-Tocopherol Transfer Protein.

    Science.gov (United States)

    Chung, Stacey; Ghelfi, Mikel; Atkinson, Jeffrey; Parker, Robert; Qian, Jinghui; Carlin, Cathleen; Manor, Danny

    2016-08-12

    α-Tocopherol (vitamin E) is an essential nutrient for all vertebrates. From the eight naturally occurring members of the vitamin E family, α-tocopherol is the most biologically active species and is selectively retained in tissues. The hepatic α-tocopherol transfer protein (TTP) preferentially selects dietary α-tocopherol and facilitates its transport through the hepatocyte and its secretion to the circulation. In doing so, TTP regulates body-wide levels of α-tocopherol. The mechanisms by which TTP facilitates α-tocopherol trafficking in hepatocytes are poorly understood. We found that the intracellular localization of TTP in hepatocytes is dynamic and responds to the presence of α-tocopherol. In the absence of the vitamin, TTP is localized to perinuclear vesicles that harbor CD71, transferrin, and Rab8, markers of the recycling endosomes. Upon treatment with α-tocopherol, TTP- and α-tocopherol-containing vesicles translocate to the plasma membrane, prior to secretion of the vitamin to the exterior of the cells. The change in TTP localization is specific to α-tocopherol and is time- and dose-dependent. The aberrant intracellular localization patterns of lipid binding-defective TTP mutants highlight the importance of protein-lipid interaction in the transport of α-tocopherol. These findings provide the basis for a proposed mechanistic model that describes TTP-facilitated trafficking of α-tocopherol through hepatocytes. PMID:27307040

  6. VirB8-like protein TraH is crucial for DNA transfer in Enterococcus faecalis.

    Science.gov (United States)

    Fercher, Christian; Probst, Ines; Kohler, Verena; Goessweiner-Mohr, Nikolaus; Arends, Karsten; Grohmann, Elisabeth; Zangger, Klaus; Meyer, N Helge; Keller, Walter

    2016-01-01

    Untreatable bacterial infections caused by a perpetual increase of antibiotic resistant strains represent a serious threat to human healthcare in the 21(st) century. Conjugative DNA transfer is the most important mechanism for antibiotic resistance and virulence gene dissemination among bacteria and is mediated by a protein complex, known as type IV secretion system (T4SS). The core of the T4SS is a multiprotein complex that spans the bacterial envelope as a channel for macromolecular secretion. We report the NMR structure and functional characterization of the transfer protein TraH encoded by the conjugative Gram-positive broad-host range plasmid pIP501. The structure exhibits a striking similarity to VirB8 proteins of Gram-negative secretion systems where they play an essential role in the scaffold of the secretion machinery. Considering TraM as the first VirB8-like protein discovered in pIP501, TraH represents the second protein affiliated with this family in the respective transfer operon. A markerless traH deletion in pIP501 resulted in a total loss of transfer in Enterococcus faecalis as compared with the pIP501 wild type (wt) plasmid, demonstrating that TraH is essential for pIP501 mediated conjugation. Moreover, oligomerization state and topology of TraH in the native membrane were determined providing insights in molecular organization of a Gram-positive T4SS. PMID:27103580

  7. Intrinsic Tryptophan Fluorescence in the Detection and Analysis of Proteins: A Focus on Förster Resonance Energy Transfer Techniques

    Directory of Open Access Journals (Sweden)

    Amar B. T. Ghisaidoobe

    2014-12-01

    Full Text Available F resonance energy transfer (FRET occurs when the distance between a donor fluorophore and an acceptor is within 10 nm, and its application often necessitates fluorescent labeling of biological targets. However, covalent modification of biomolecules can inadvertently give rise to conformational and/or functional changes. This review describes the application of intrinsic protein fluorescence, predominantly derived from tryptophan (\\(\\uplambda_{\\textsc{ex}}\\sim\\ nm, \\(\\uplambda_{\\textsc{em}}\\sim\\ 350 nm, in protein-related research and mainly focuses on label-free FRET techniques. In terms of wavelength and intensity, tryptophan fluorescence is strongly influenced by its (or the proteinlocal environment, which, in addition to fluorescence quenching, has been applied to study protein conformational changes. Intrinsic F resonance energy transfer (iFRET, a recently developed technique, utilizes the intrinsic fluorescence of tryptophan in conjunction with target-specific fluorescent probes as FRET donors and acceptors, respectively, for real time detection of native proteins.

  8. Association between myosin heavy chain protein isoforms and intramuscular anabolic signaling following resistance exercise in trained men.

    Science.gov (United States)

    Gonzalez, Adam M; Hoffman, Jay R; Townsend, Jeremy R; Jajtner, Adam R; Wells, Adam J; Beyer, Kyle S; Willoughby, Darryn S; Oliveira, Leonardo P; Fukuda, David H; Fragala, Maren S; Stout, Jeffrey R

    2015-01-01

    Resistance exercise stimulates an increase in muscle protein synthesis regulated by intracellular anabolic signaling molecules in a mammalian/mechanistic target of rapamycin (mTOR)-dependent pathway. The purpose of this study was to investigate acute anabolic signaling responses in experienced, resistance-trained men, and to examine the association between myosin heavy chain (MHC) isoform composition and the magnitude of anabolic signaling. Eight resistance-trained men (24.9 ± 4.3 years; 91.2 ± 12.4 kg; 176.7 ± 8.0 cm; 13.3 ± 3.9 body fat %) performed a whole body, high-volume resistance exercise protocol (REX) and a control protocol (CTL) in a balanced, randomized order. Participants were provided a standardized breakfast, recovery drink, and meal during each protocol. Fine needle muscle biopsies were completed at baseline (BL), 2 h (2H) and 6 h post-exercise (6H). BL biopsies were analyzed for MHC isoform composition. Phosphorylation of proteins specific to the Akt/mTOR signaling pathway and MHC mRNA expression was quantified. Phosphorylation of p70S6k was significantly greater in REX compared to CTL at 2H (P = 0.04). MHC mRNA expression and other targets in the Akt/mTOR pathway were not significantly influenced by REX. The percentage of type IIX isoform was inversely correlated (P REX in experienced, resistance-trained men. Further, results also suggest that highly trained, stronger individuals have an attenuated acute anabolic response. PMID:25626869

  9. Exosomes: vehicles for the transfer of toxic proteins associated with neurodegenerative diseases?

    Directory of Open Access Journals (Sweden)

    Shayne Anthony Bellingham

    2012-05-01

    Full Text Available Exosomes are small membranous vesicles secreted by a number of cell types including neurons and can be isolated from conditioned cell media or bodily fluids such as urine and plasma. Exosome biogenesis involves the inward budding of endosomes to form multivesicular bodies (MVB. When fused with the plasma membrane, the MVB releases the vesicles into the extracellular environment as exosomes. Proposed functions of these vesicles include roles in cell-cell signaling, removal of unwanted proteins, and the transfer of pathogens between cells. One such pathogen which exploits this pathway is the prion, the infectious particle responsible for the transmissible neurodegenerative diseases such as Creutzfeldt-Jakob disease (CJD of humans or bovine spongiform encephalopathy (BSE of cattle. Similarly, exosomes are also involved in the processing of the amyloid precursor protein (APP which is associated with Alzheimer's disease (AD. Exosomes have been shown to contain full-length APP and several distinct proteolytically cleaved products of APP, including Aβ. In addition, these fragments can be modulated using inhibitors of the proteases involved in APP cleavage. These observations provide further evidence for a novel pathway in which PrP and APP fragments are released from cells. Other proteins such as superoxide dismutase I (SOD-1 and alpha-synuclein (involved in Amyotrophic Lateral Sclerosis (ALS and Parkinson’s disease respectively are also found associated with exosomes. This review will focus on the role of exosomes in neurodegenerative disorders and discuss the potential of these vesicles for the spread of neurotoxicity, therapeutics and diagnostics for these diseases.

  10. NMR of proteins (4Fe-4S): structural properties and intramolecular electron transfer

    International Nuclear Information System (INIS)

    NMR started to be applied to Fe-S proteins in the seventies. Its use has recently been enlarged as the problems arising from the paramagnetic polymetallic clusters ware overcome. Applications to [4Fe-4S] are presented herein. The information derived thereof deepens the understanding of the redox properties of these proteins which play a central role in the metabolism of bacterial cells. The secondary structure elements and the overall folding of Chromatium vinosum ferredoxin (Cv Fd) in solution have been established by NMR. The unique features of this sequence have been shown to fold as an α helix at the C-terminus and as a loop between two cysteines ligand of one cluster: these two parts localize in close proximity from one another. The interaction between nuclear and electronic spins is a source of additional structural information for (4Fe-AS] proteins. The conformation of the cysteine-ligands, as revealed by the Fe-(Sγ-Cβ-Hβ)Cys dihedral angles, is related to the chemical shifts of the signals associated with the protons of these residues. The longitudinal relaxation times of the protons depend on their distance to the cluster. A quantitative relationship has been established and used to show that the solution structure of the high-potential ferredoxin from Cv differs significantly from the crystal structure around Phe-48. Both parameters (chemical shifts and longitudinal relaxation times) give also insight into the electronic and magnetic properties of the [4Fe-4S] clusters. The rate of intramolecular electron transfer between the two [4FE-4S] clusters of ferredoxins has been measured by NMR. It is far slower in the case of Cv Fd than for shorter ferredoxins. The difference may be associated with changes in the magnetic and/or electronic properties of one cluster. The strong paramagnetism of the [4Fe-4S] clusters, which originally limited the applicability of NMR to proteins containing these cofactors, has been proven instrumental in affording new

  11. Horizontal gene transfer of zinc and non-zinc forms of bacterial ribosomal protein S4

    Directory of Open Access Journals (Sweden)

    Luthey-Schulten Zaida

    2009-07-01

    Full Text Available Abstract Background The universal ribosomal protein S4 is essential for the initiation of small subunit ribosomal assembly and translational accuracy. Being part of the information processing machinery of the cell, the gene for S4 is generally thought of as being inherited vertically and has been used in concatenated gene phylogenies. Here we report the evolution of ribosomal protein S4 in relation to a broad sharing of zinc/non-zinc forms of the gene and study the scope of horizontal gene transfer (HGT of S4 during bacterial evolution. Results In this study we present the complex evolutionary history of ribosomal protein S4 using 660 bacterial genomes from 16 major bacterial phyla. According to conserved characteristics in the sequences, S4 can be classified into C+ (zinc-binding and C- (zinc-free variants, with 26 genomes (mainly from the class Clostridia containing genes for both. A maximum likelihood phylogenetic tree of the S4 sequences was incongruent with the standard bacterial phylogeny, indicating a departure from strict vertical inheritance. Further analysis using the genome content near the S4 genes, which are usually located in a conserved gene cluster, showed not only that HGT of the C- gene had occurred at various stages of bacterial evolution, but also that both the C- and C+ genes were present before the individual phyla diverged. To explain the latter, we theorize that a gene pool existed early in bacterial evolution from which bacteria could sample S4 gene variants, according to environmental conditions. The distribution of the C+/- variants for seven other zinc-binding ribosomal proteins in these 660 bacterial genomes is consistent with that seen for S4 and may shed light on the evolutionary pressures involved. Conclusion The complex history presented for "core" protein S4 suggests the existence of a gene pool before the emergence of bacterial lineages and reflects the pervasive nature of HGT in subsequent bacterial evolution

  12. Protein kinase C activation and myosin light chain phosphorylation in 32P-labeled arterial smooth muscle

    International Nuclear Information System (INIS)

    Experiments using 32P-labeled strips of swine carotid artery medial smooth muscle were performed to define the relative contribution of myosin light chain (MLC) phosphorylation as an activation mechanism mediating contractile responses stimulated by phorbol dibutyrate (PDB). Tryptic phosphopeptide mapping of phosphorylated MLC indicated that near-maximal force responses were associated with increases in functional MLC phosphorylation of less than 10% of the total MLC content following tonic (45 min) stimulation by PDB. Significant phosphorylation of MLC residues, consistent with the specificity of protein kinase C, occurred in response to high concentrations of PDB (greater than 0.1 microM). Histamine (10 microM)-induced MLC phosphorylation after 2 min (72.5% of total MLC) or 45 min (61.7%) was restricted to serine residues on peptides thought to contain serine19. Although agonist (histamine)-induced responses were eliminated under conditions of Ca2+ depletion, near-maximal force in response to 10 microM PDB (89.4% of a standard KCl response) was associated with monophosphorylation of less than 9% of the total MLC on peptides interpreted as containing serine19. A substantial fraction of this was localized to threonine residues. The quantitative analysis of the relation between PDB-stimulated force and the residues in MLC phosphorylated supports the concept that PDB stimulation results in activation of arterial smooth muscle cross bridges by MLC-phosphorylation-independent mechanisms

  13. Protein kinase C activation and myosin light chain phosphorylation in sup 32 P-labeled arterial smooth muscle

    Energy Technology Data Exchange (ETDEWEB)

    Singer, H.A. (Geisinger Clinic, Danville, PA (USA))

    1990-10-01

    Experiments using 32P-labeled strips of swine carotid artery medial smooth muscle were performed to define the relative contribution of myosin light chain (MLC) phosphorylation as an activation mechanism mediating contractile responses stimulated by phorbol dibutyrate (PDB). Tryptic phosphopeptide mapping of phosphorylated MLC indicated that near-maximal force responses were associated with increases in functional MLC phosphorylation of less than 10% of the total MLC content following tonic (45 min) stimulation by PDB. Significant phosphorylation of MLC residues, consistent with the specificity of protein kinase C, occurred in response to high concentrations of PDB (greater than 0.1 microM). Histamine (10 microM)-induced MLC phosphorylation after 2 min (72.5% of total MLC) or 45 min (61.7%) was restricted to serine residues on peptides thought to contain serine19. Although agonist (histamine)-induced responses were eliminated under conditions of Ca2+ depletion, near-maximal force in response to 10 microM PDB (89.4% of a standard KCl response) was associated with monophosphorylation of less than 9% of the total MLC on peptides interpreted as containing serine19. A substantial fraction of this was localized to threonine residues. The quantitative analysis of the relation between PDB-stimulated force and the residues in MLC phosphorylated supports the concept that PDB stimulation results in activation of arterial smooth muscle cross bridges by MLC-phosphorylation-independent mechanisms.

  14. Protein loops, solitons and side-chain visualization with applications to the left-handed helix region

    CERN Document Server

    Lundgren, Martin; Sha, Fan

    2012-01-01

    Folded proteins have a modular assembly. They are constructed from regular secondary structures like alpha-helices and beta-strands that are joined together by loops. Here we develop a visualization technique that is adapted to describe this modular structure. In complement to the widely employed Ramachandran plot that is based on toroidal geometry, our approach utilizes the geometry of a two-sphere. Unlike the more conventional approaches that only describea given peptide unit, ours is capable of describing the entire backbone environment including the neighboring peptide units. It maps the positions of each atom to the surface of the two-sphere exactly how these atoms are seen by an observer who is located at the position of the central C-alpha atom. At each level of side-chain atoms we observe a strong correlation between the positioning of the atom and the underlying local secondary structure with very little if any variation between the different amino acids. As a concrete example we analyze the left-han...

  15. Concentrated Solutions of Single-Chain Nanoparticles: A Simple Model for Intrinsically Disordered Proteins under Crowding Conditions.

    Science.gov (United States)

    Moreno, Angel J; Lo Verso, Federica; Arbe, Arantxa; Pomposo, José A; Colmenero, Juan

    2016-03-01

    By means of large-scale computer simulations and small-angle neutron scattering (SANS), we investigate solutions of single-chain nanoparticles (SCNPs), covering the whole concentration range from infinite dilution to melt density. The analysis of the conformational properties of the SCNPs reveals that these synthetic nano-objects share basic ingredients with intrinsically disordered proteins (IDPs), as topological polydispersity, generally sparse conformations, and locally compact domains. We investigate the role of the architecture of the SCNPs in their collapse behavior under macromolecular crowding. Unlike in the case of linear macromolecules, which experience the usual transition from self-avoiding to Gaussian random-walk conformations, crowding leads to collapsed conformations of SCNPs resembling those of crumpled globules. This behavior is already found at volume fractions (about 30%) that are characteristic of crowding in cellular environments. The simulation results are confirmed by the SANS experiments. Our results for SCNPs-a model system free of specific interactions-propose a general scenario for the effect of steric crowding on IDPs: collapse from sparse conformations at high dilution to crumpled globular conformations in cell environments. PMID:26894933

  16. Specific adduction of plant lipid transfer protein by an allene oxide generated by 9-lipoxygenase and allene oxide synthase

    OpenAIRE

    Bakan, Benedicte; Hamberg, Mats; Perrocheau, Ludivine; Maume, Daniel; Rogniaux, Helene; Tranquet, Olivier; Rondeau, Corinne; Blein, J Pierre; Ponchet, Michel; Marion, Didier

    2006-01-01

    Lipid transfer proteins (LTPs) are ubiquitous plant lipid-binding proteins that have been associated with multiple developmental and stress responses. Although LTPs typically bind fatty acids and fatty acid derivatives in a non-covalent way, studies on the LTPs of barley seeds have identified an abundantly occurring covalently modified form, LTP1b, the lipid ligand of which has resisted clarification. In the present study, this adduct was identified as the {alpha}-ketol 9-hydroxy-10-oxo-12(Z)...

  17. Effect of a bovine lung surfactant protein isolate (SP-B/C) on egg phosphatidylglycerol acyl chain order in a lipid mixture with dipalmitoylphosphatidylcholine and palmitic acid.

    Science.gov (United States)

    Krill, S L; Gupta, S L

    1994-04-01

    Dynamic surface tension measurements of films of a d62 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine:L-alpha-phosphatidyl-DL - glycerol:d31 palmitic acid (d62-DPPC:EggPG:d31-PA) lipid matrix in the presence of a bovine pulmonary surfactant protein isolate (SP-B/C) demonstrate the improved surface activity over that of the lipids alone. Thus, significant interaction of the proteins with the lipid matrix is demonstrated. The effect of SP-B/C on the acyl chain order of the negatively charged EggPG within a d62-DPPC:EggPG:d31-PA lipid matrix in D2O saline was investigated in thermal perturbation Fourier transform IR spectroscopic studies. The EggPG thermotropic phase behavior was determined independently of the other lipid components with perdeuterated lipids and D2O. The data demonstrate the high degree of EggPG acyl chain disorder in the absence of the protein isolate. A broad transition occurs between 30 and 40 degrees C. The addition of the protein isolate did not alter the acyl chain order at 0.281 and 1.46 mg/mL of protein. However, alterations in the lipid carbonyl vibrational mode were observed. PMID:8046609

  18. Inhibition of the neutrophil oxidative burst by sphingoid long-chain bases: role of protein kinase C in the activation of the burst

    International Nuclear Information System (INIS)

    The neutrophil oxidative burst is triggered by a variety of both particulate (opsonized zymosan) and soluble agonists [formylmethionylleucylphenylalanine (FMLP), arachidonate, short-chained diacylglycerols (DAG) and phorbol myristate acetate (PMA)]. The authors show that the long-chain lipid bases sphinganine and sphingosine block activation of the burst in human neutrophils. Inhibition is reversible, does not alter cell viability, and does not affect phagocytosis. The inhibition affects the activation mechanism rather than the NADPH-oxidase enzyme. The structural requirements for inhibition include a hydrophobic carbon chain and an amino-containing headgroup, and the naturally occurring erythro sphinganine was more potent than the threo isomer. Activation of the oxidative burst by a variety of agonists was blocked by the same concentration of sphinganine indicating a common inhibited step. The authors suggest that the common step is protein kinase C, as evidenced by the following: 1) long-chain bases inhibit PKC in a micelle reconstituted system, 2) PMA-induced phophorylation is inhibited by sphinganine, and 3) sphinganine competes with (3H)-phorbol dibutyrate for its cytosolic receptor (i.e. protein kinase C). The authors suggest that sphingoid long-chain bases play a role in the cellular regulations

  19. Cardiolipin Molecular Species with Shorter Acyl Chains Accumulate in Saccharomyces cerevisiae Mutants Lacking the Acyl Coenzyme A-binding Protein Acb1p

    Science.gov (United States)

    Rijken, Pieter J.; Houtkooper, Riekelt H.; Akbari, Hana; Brouwers, Jos F.; Koorengevel, Martijn C.; de Kruijff, Ben; Frentzen, Margrit; Vaz, Frédéric M.; de Kroon, Anton I. P. M.

    2009-01-01

    The function of the mitochondrial phospholipid cardiolipin (CL) is thought to depend on its acyl chain composition. The present study aims at a better understanding of the way the CL species profile is established in Saccharomyces cerevisiae by using depletion of the acyl-CoA-binding protein Acb1p as a tool to modulate the cellular acyl chain content. Despite the presence of an intact CL remodeling system, acyl chains shorter than 16 carbon atoms (C16) were found to accumulate in CL in cells lacking Acb1p. Further experiments revealed that Taz1p, a key CL remodeling enzyme, was not responsible for the shortening of CL in the absence of Acb1p. This left de novo CL synthesis as the only possible source of acyl chains shorter than C16 in CL. Experiments in which the substrate specificity of the yeast cardiolipin synthase Crd1p and the acyl chain composition of individual short CL species were investigated, indicated that both CL precursors (i.e. phosphatidylglycerol and CDP-diacylglycerol) contribute to comparable extents to the shorter acyl chains in CL in acb1 mutants. Based on the findings, we conclude that the fatty acid composition of mature CL in yeast is governed by the substrate specificity of the CL-specific lipase Cld1p and the fatty acid composition of the Taz1p substrates. PMID:19656950

  20. Mechanism of phosphoryl transfer and protein-protein interaction in the PTS system-an NMR study

    International Nuclear Information System (INIS)

    HPr and Enzyme IIAGlc are two of the components of the bacterial PTS (phosphoenolpyruvate: sugar phosphotranferase system) and are involved in the phosphorylation and concomitant translocation of sugars across the membrane. These PTS protein complexes also regulate sugar transport. HPr, phosphorylated at a histidine N1 site by Enzyme I and phosphoenol pyruvate, transfers the phosphoryl group to a histidine N3 position in Enzyme IIAGlc. HPrs from Gram-positive bacteria undergo regulatory phosphorylation at Ser46, whereby phosphorylation of the histidine residue is inhibited. Conversely, histidine phosphorylation inhibits phosphorylation at Ser46. HPrs from Gram-negative bacteria possess a serine residue at position 46, but do not undergo regulatory phosphorylation. HPr forms an open-faced sandwich structure with a four-strand S-sheet and 2 to 3 helices lying on top of the sheet. The active-site histidine and Ser46 occur in conformationally flexible regions. P-His-HPr from the Gram-positive bacterium Bacillus subtilus has been investigated by both homonuclear and heteronuclear two-dimensional and three-dimensional NMR experiments using an in-situ enzymatic regeneration system to maintain a constant level of P-His-HPr. The results show that localized conformational changes occur in the vicinity of the active-site histidine and also near Ser46. HPr-Enzyme IIAGlc complexes from both Bacillus subtilis and Gram-negative Escherichia coli were also studied by a variety of 15N-edited two-dimensional NMR experiments, which were performed on uniformly 15N-labeled HPr complexed to unlabeled Enzyme IIAGlc. The complex is in fast exchange with a molecular weight of about 27 kDa. The focus of our work is to assess the changes undergone by HPr (the smaller of the two components), and so all the experiments were performed with excess Enzyme IIA present in the system

  1. Screening of α-Tocopherol Transfer Protein Sensitive Genes in Human Hepatoma Cells (HepG2).

    Science.gov (United States)

    Qu, Yang-Hua; Fu, Jun-Cai; Liu, Kun; Zuo, Zhao-Yun; Jia, Hui-Na; Ma, Yong; Luo, Hai-Ling

    2016-01-01

    α-Tocopherol transfer protein (α-TTP) is a ~32 kDa protein expressed mainly in hepatocytes. The major function of the protein is to bind specifically to α-tocopherol and, together, the complex transfers from late lysosomes to the cell membrane. A previous study indicated that some factors might be required in the transferring process. However, there is little information available about the potential transferring factors. In addition, there remains much to learn about other physiological processes which α-TTP might participate in. Thus, in this study a human α-TTP eukaryotic expression vector was successfully constructed and expressed in human hepatoma cells (HepG2). The sensitive genes related to α-TTP were then screened by microarray technology. Results showed that expression of the vector in HepG2 cells led to the identification of 323 genes showing differential expression. The differentially expressed transcripts were divided into four main categories, including (1) cell inflammation; (2) cell cycle and cell apoptosis; (3) cell signaling and gene regulation; and (4) cellular movement. A few cellular movement related transcripts were selected and verified by quantitative real-time PCR. Expressions of some were significantly increased in α-TTP-expressed group, which indicated that these factors were likely to play a role in the transferring process. PMID:27355945

  2. Cardiac expression of microsomal triglyceride transfer protein is increased in obesity and serves to attenuate cardiac triglyceride accumulation

    DEFF Research Database (Denmark)

    Bartels, Emil D; Nielsen, Jan M; Hellgren, Lars I;

    2009-01-01

    secretion of apolipoproteinB-containing (apoB) lipoproteins. Lipoprotein formation depends on expression of microsomal triglyceride transfer protein (MTP); the mouse expresses two isoforms of MTP, A and B. Since many aspects of the link between obesity-induced cardiac disease and cardiac lipid metabolism...

  3. CD1d-mediated presentation of endogenous lipid antigens by adipocytes requires microsomal triglyceride transfer protein (MTP)

    DEFF Research Database (Denmark)

    Rakhshandehroo, Maryam; Gijzel, Sanne M W; Siersbæk, Rasmus;

    2014-01-01

    microsomal triglyceride transfer protein (MTP), which we show is also under the transcriptional regulation of C/EBPβ and -δ, as a novel player in the presentation of endogenous lipid antigens by adipocytes. Overall, our findings indicate that adipocytes can function as non-professional lipid antigen...

  4. Transcript Profiles of Two Wheat Lipid Transfer Protein-encoding Genes are Altered During Attach by Hessian Fly Larvae

    Science.gov (United States)

    ‘GeneCalling’, an mRNA profiling technology, was used to identify a candidate lipid transfer protein (LTP) sequence that showed decreased mRNA abundance in wheat (Triticum aestivum L. em Thell) plants following attack by virulent Hessian fly (Mayetiola destructor Say) larvae (compatible interaction)...

  5. The alpha-helical domain of liver fatty acid binding protein is responsible for the diffusion-mediated transfer of fatty acids to phospholipid membranes.

    Science.gov (United States)

    Córsico, Betina; Liou, Heng Ling; Storch, Judith

    2004-03-30

    Intestinal fatty acid binding protein (IFABP) and liver FABP (LFABP), homologous proteins expressed at high levels in intestinal absorptive cells, employ markedly different mechanisms for the transfer of fatty acids (FAs) to acceptor membranes. Transfer from IFABP occurs during protein-membrane collisional interactions, while for LFABP, transfer occurs by diffusion through the aqueous phase. Earlier, we had shown that the helical domain of IFABP is critical in determining its collisional FA transfer mechanism. In the study presented here, we have engineered a pair of chimeric proteins, one with the "body" (ligand binding domain) of IFABP and the alpha-helical region of LFABP (alphaLbetaIFABP) and the other with the ligand binding pocket of LFABP and the helical domain of IFABP (alphaIbetaLFABP). The objective of this work was to determine whether the change in the alpha-helical domain of each FABP would alter the rate and mechanism of transfer of FA from the chimeric proteins in comparison with those of the wild-type proteins. The fatty acid transfer properties of the FABP chimeras were examined using a fluorescence resonance transfer assay. The results showed a significant modification of the absolute rate of FA transfer from the chimeric proteins compared to that of the wild type, indicating that the slower rate of FA transfer observed for wild-type LFABP relative to that of wild-type IFABP is, in part, determined by the helical domain of the proteins. In addition to these quantitative changes, it was of great interest to observe that the apparent mechanism of FA transfer also changed when the alpha-helical domain was exchanged, with transfer from alphaLbetaIFABP occurring by aqueous diffusion and transfer from alphaIbetaLFABP occurring via protein-membrane collisional interactions. These results demonstrate that the alpha-helical region of LFABP is responsible for its diffusional mechanism of fatty acid transfer to membranes. PMID:15035630

  6. Negative effects of a disulfide bond mismatch in anti-rabies G protein single-chain antibody variable fragment FV57.

    Science.gov (United States)

    Duan, Ye; Gu, Tiejun; Zhang, Xizhen; Jiang, Chunlai; Yuan, Ruosen; Li, Zhuang; Wang, Dandan; Chen, Xiaoxu; Wu, Chunlai; Chen, Yan; Wu, Yongge; Kong, Wei

    2014-06-01

    Rabies virus (RV) causes a fatal infectious disease requiring efficient post-exposure prophylaxis (PEP), which includes a rabies vaccine and rabies immunoglobulin (RIG). The single-chain antibody variable fragment (scFv), a small engineered antibody fragment derived from an antibody variable heavy chain and light chain, has the potential to replace the current application of RIG. In previous studies, we constructed and evaluated an anti-rabies virus G protein scFv (FV57) based on the monoclonal antibody CR57. Of the five cysteines in FV57, four are linked in intra-chain disulfide bonds (Cys-VH28/Cys-VH98 and Cys-VL16/Cys-VL84), and one is free (Cys-VL85). However, the thiol in Cys-VL85 neighboring Cys-VL84 in the CDR3 of the light chain is likely to mismatch with the thiol in Cys-VL16 during the renaturing process. In order to study effects of the mismatched disulfide bond, Cys-VL85 and Cys-VL84 of FV57 were mutated to serine to construct mutants FV57(VL85S) and FV57(VL84S). Furthermore, the disulfide bonds in the light chain of FV57, FV57(VL85S) and FV57(VL84S) were deleted by mutating Cys-VL16 to serine. All mutants were prepared and evaluated along with the original FV57. The results indicated that the mismatched disulfide bond of FV57 linking the light chain FR1 and CDR3 would confer deleterious negative effects on its activity against RV, likely due to spatial hindrance in the light chain CDR3. Moreover, avoidance of the disulfide bond mismatch provided an additional 30% protective efficacy against RV infection in the mouse RV challenge model. Thus, modifications of FV57 to eliminate the disulfide bond mismatch may provide a candidate therapeutic agent for effective PEP against rabies. PMID:24598312

  7. Structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, at 2.4 Å resolution: a putative member of the StAR-related lipid-transfer (START) domain superfamily

    International Nuclear Information System (INIS)

    The crystal structure of a conserved hypothetical protein, TTHA0849 from T. thermophilus HB8, has been determined at 2.4 Å resolution. The compact α+β structure shows the typical folding of the steroidogenic acute regulatory-related lipid-transfer (START) domain. The crystal structure of a conserved hypothetical protein, TTHA0849 from Thermus thermophilus HB8, has been determined at 2.4 Å resolution as a part of a structural and functional genomics project on T. thermophilus HB8. The main-chain folding shows a compact α+β motif, forming a hydrophobic cavity in the molecule. A structural similarity search reveals that it resembles those steroidogenic acute regulatory proteins that contain the lipid-transfer (START) domain, even though TTHA0849 shows comparatively weak sequence identity to polyketide cyclases. However, the size of the ligand-binding cavity is distinctly smaller than other START domain-containing proteins, suggesting that it catalyses the transfer of smaller ligand molecules

  8. Identification and characterization of human polyserase-3, a novel protein with tandem serine-protease domains in the same polypeptide chain

    Directory of Open Access Journals (Sweden)

    Garabaya Cecilia

    2006-03-01

    Full Text Available Abstract Background We have previously described the identification and characterization of polyserase-1 and polyserase-2, two human serine proteases containing three different catalytic domains within the same polypeptide chain. Polyserase-1 shows a complex organization and it is synthesized as a membrane-bound protein which can generate three independent serine protease domains as a consequence of post-translational processing events. The two first domains are enzymatically active. By contrast, polyserase-2 is an extracellular glycosylated protein whose three protease domains remain embedded in the same chain, and only the first domain possesses catalytic activity. Results Following our interest in the study of the human degradome, we have cloned a human liver cDNA encoding polyserase-3, a new protease with tandem serine protease domains in the same polypeptide chain. Comparative analysis of polyserase-3 with the two human polyserases described to date, revealed that this novel polyprotein is more closely related to polyserase-2 than to polyserase-1. Thus, polyserase-3 is a secreted protein such as polyserase-2, but lacks additional domains like the type II transmembrane motif and the low-density lipoprotein receptor module present in the membrane-anchored polyserase-1. Moreover, analysis of post-translational mechanisms operating in polyserase-3 maturation showed that its two protease domains remain as integral parts of the same polypeptide chain. This situation is similar to that observed in polyserase-2, but distinct from polyserase-1 whose protease domains are proteolytically released from the original chain to generate independent units. Immunolocalization studies indicated that polyserase-3 is secreted as a non-glycosylated protein, thus being also distinct from polyserase-2, which is a heavily glycosylated protein. Enzymatic assays indicated that recombinant polyserase-3 degrades the α-chain of fibrinogen as well as pro

  9. Changes in the content of protein p53, L-chains, of immunoglobulins, and Iron complexes in Mice of the leukosis line AKR irradiated at low doses

    International Nuclear Information System (INIS)

    Changes in the content of protein p53 (regulator of the cell cycle) L-chains of immunoglobulins, and iron complexes (Fe2+) during the development of spontaneous leukosis in mice and upon irradiation of animals at the dose of 1.2 cGy were studied by ESR spectroscopy, electrophoresis and immunoblotting. It was found that irradiation leads to an increase in the incidence of leukoses in males by 7% and a decrease in life span of females. A decrease in the content of protein p53 and L-chains in immunoglobulins in males and females was observed; however, in females, the decreases was less pronounced because the content of these proteins in females is naturally decreased. In mice irradiated at low doses at the age of three - to months, a decrease in the amount of iron complexes at a later age (seven - to eight months) was registered. These data suggest that there is a relationship between the induction of protein p53 and the content of immunoglobulin L-chains in the blood serum of animals

  10. The Effect of Allylic Sulfide-Mediated IrreversibleAddition-Fragment Chain Transfer on the EmulsionPolymerization Kinetics of Styrene

    Directory of Open Access Journals (Sweden)

    Li An

    2015-09-01

    Full Text Available The effect of the irreversible addition-fragment chain transfer agent, butyl(2-phenylallylsulfane (BPAS, on the course of the emulsion polymerization of styrene and on the product molecular weight was investigated. The emulsion polymerizations were performed using various amounts of sodium dodecyl sulfate (SDS as the surfactant and potassium peroxodisulfate (KPS as the initiator. The relationships between the rates of polymerization (\\(R_{p} \\ and the number of particles per volume (\\(N_{c} \\ with respect to the concentrations of KPS, SDS, and BPAS were found to be \\(R_{p} \\propto \\left\\lbrack KPS \\right\\rbrack^{0.29} \\, \\(N_{c} \\propto \\left\\lbrack KPS \\right\\rbrack^{0.26} \\,\\(R_{p} \\propto \\left\\lbrack SDS \\right\\rbrack^{0.68} \\, \\(N_{c} \\propto \\left\\lbrack SDS \\right\\rbrack^{0.72} \\, and \\(R_{p} \\propto \\left\\lbrack BPAS \\right\\rbrack^{- 0.73} \\ . The obtained relationships can be attributed to the exit of the leaving group radicals on BPAS from the polymer particles. The experimental values of the average number of radicals per particle (\\(\\overset{\\_}{n} \\ were strongly dependent on the BPAS concentration and were in good agreement with the theoretical values (\\({\\overset{\\_}{n}}_{theo} \\ from model calculations. The number-average molecular weight (\\(\\overset{\\_}{M_{n}} \\ can be controlled by BPAS over nearly the entire conversion range, which is also in agreement with the mathematical model. In addition, the transfer rate coefficient (\\(k_{tr} \\ of BPAS can be estimated as 326 L/mol/s at 70 \\(^\\circ\\C. Moreover, similar good results were found for the tested redox reactions at 30 \\(^\\circ\\C.

  11. Identification of a Novel Transcript and Regulatory Mechanism for Microsomal Triglyceride Transfer Protein.

    Directory of Open Access Journals (Sweden)

    Takashi Suzuki

    Full Text Available Microsomal triglyceride transfer protein (MTP is essential for the assembly of triglyceride-rich apolipoprotein B-containing lipoproteins. Previous studies in our laboratory identified a novel splice variant of MTP in mice that we named MTP-B. MTP-B has a unique first exon (1B located 2.7 kB upstream of the first exon (1A for canonical MTP (MTP-A. The two mature isoforms, though nearly identical in sequence and function, have different tissue expression patterns. In this study we report the identification of a second MTP splice variant (MTP-C, which contains both exons 1B and 1A. MTP-C is expressed in all the tissues we tested. In cells transfected with MTP-C, protein expression was less than 15% of that found when the cells were transfected with MTP-A or MTP-B. In silico analysis of the 5'-UTR of MTP-C revealed seven ATGs upstream of the start site for MTP-A, which is the only viable start site in frame with the main coding sequence. One of those ATGs was located in the 5'-UTR for MTP-A. We generated reporter constructs in which the 5'-UTRs of MTP-A or MTP-C were inserted between an SV40 promoter and the coding sequence of the luciferase gene and transfected these constructs into HEK 293 cells. Luciferase activity was significantly reduced by the MTP-C 5'-UTR, but not by the MTP-A 5'-UTR. We conclude that alternative splicing plays a key role in regulating MTP expression by introducing unique 5'-UTRs, which contain elements that alter translation efficiency, enabling the cell to optimize MTP levels and activity.

  12. Immunogenicity and Protective Efficacy of Brugia malayi Heavy Chain Myosin as Homologous DNA, Protein and Heterologous DNA/Protein Prime Boost Vaccine in Rodent Model.

    Directory of Open Access Journals (Sweden)

    Jyoti Gupta

    Full Text Available We earlier demonstrated the immunoprophylactic efficacy of recombinant heavy chain myosin (Bm-Myo of Brugia malayi (B. malayi in rodent models. In the current study, further attempts have been made to improve this efficacy by employing alternate approaches such as homologous DNA (pcD-Myo and heterologous DNA/protein prime boost (pcD-Myo+Bm-Myo in BALB/c mouse model. The gene bm-myo was cloned in a mammalian expression vector pcDNA 3.1(+ and protein expression was confirmed in mammalian Vero cell line. A significant degree of protection (79.2%±2.32 against L3 challenge in pcD-Myo+Bm-Myo immunized group was observed which was much higher than that exerted by Bm-Myo (66.6%±2.23 and pcD-Myo (41.6%±2.45. In the heterologous immunized group, the percentage of peritoneal leukocytes such as macrophages, neutrophils, B cells and T cells marginally increased and their population augmented further significantly following L3 challenge. pcD-Myo+Bm-Myo immunization elicited robust cellular and humoral immune responses as compared to pcD-Myo and Bm-Myo groups as evidenced by an increased accumulation of CD4+, CD8+ T cells and CD19+ B cells in the mouse spleen and activation of peritoneal macrophages. Though immunized animals produced antigen-specific IgG antibodies and isotypes, sera of mice receiving pcD-Myo+Bm-Myo or Bm-Myo developed much higher antibody levels than other groups and there was profound antibody-dependent cellular adhesion and cytotoxicity (ADCC to B. malayi infective larvae (L3. pcD-Myo+Bm-Myo as well as Bm-Myo mice generated a mixed T helper cell phenotype as evidenced by the production of both pro-inflammatory (IL-2, IFN-γ and anti-inflammatory (IL-4, IL-10 cytokines. Mice receiving pcD-Myo on contrary displayed a polarized pro-inflammatory immune response. The findings suggest that the priming of animals with DNA followed by protein booster generates heightened and mixed pro- and anti-inflammatory immune responses that are capable of

  13. Cleavage of lambda repressor and synthesis of RecA protein induced by transferred UV-damaged F sex factor

    International Nuclear Information System (INIS)

    Transfer of a UV-damaged F sex factor to a recipient lambda lysogen induces prophage lambda development. Under these conditions RecA protein synthesis was induced and lambda repressor cleaved, as observed upon direct induction, that ist, wehen the recipient lambda lysogen was directly exposed to UV-light. The efficiency of induction of RecA protein synthesis in recipient bacteria which had received an irradiated F-lac factor was about 80% of that measured upon direct induction. We observed the simultaneous disappearance of lambda repressor and a slight production of cleavage fragments; quantitation by densitometric scanning of the autoradiogram after correction for the efficiency of transfer indicated that 55% of lambda repressor was cleaved. Transfer of UV-damaged Hfr DNA failed to induce RecA protein synthesis. A lambda phage vector carrying oriF, the cloned origin of F plasmid replication, after exposure to UV-light and infection of a recipient lysogen, induced RecA protein synthesis and a moderate but significant cleavage of lambda repressor. Indirect induction by UV-damaged F sex factor or phage lambdaoriF resulted in biochemical cellular reactions similar to those observed upon direct induction. LexA repressor that negatively controls RecA protein synthesis appeared more susceptible to cleavage than did lambda repressor. (orig.)

  14. The assembly of triacylglycerol-rich lipoproteins: an essential role for the microsomal triacylglycerol transfer protein.

    Science.gov (United States)

    White, D A; Bennett, A J; Billett, M A; Salter, A M

    1998-09-01

    Raised plasma triacylglycerol is an independent risk factor for cardiovascular disease, and an understanding of factors which regulate the synthesis and degradation of lipoproteins which carry triacylglycerol in the blood may lead to novel approaches to the treatment of hypertriacylglycerolaemia. An active microsomal triacylglycerol transfer protein (MTP) is essential for the assembly of particles which transport triacylglycerol through the circulation. After absorption in the intestine, dietary fat and fat-soluble vitamins are incorporated into chylomicrons in the intestinal epithelial cells, and these lipoproteins reach the bloodstream via the lymphatic system. Patients with the rare genetic disorder, abetalipoproteinaemia, in which MTP activity is absent, present clinically with fat-soluble vitamin and essential fatty acid deficiency, indicating a key role for MTP in the movement of fat into the body. The triacylglycerol-rich lipoprotein found in fasting blood, VLDL, is assembled in the liver by an MTP-dependent process similar to chylomicron assembly, and transports triacylglycerol to extra-hepatic tissues such as adipose tissue and heart. In the absence of MTP activity, VLDL are not synthesized and only extremely low levels of triacylglycerol are present in the blood. Dietary components, including fat, cholesterol and ethanol, can modify the expression of the MTP gene and, hence, MTP activity. The present review summarizes current knowledge of the role of MTP in the assembly and secretion of triacylglycerol-rich lipoproteins, and the regulation of its activity in both animal and cell systems. PMID:9875061

  15. The α-tocopherol transfer protein is essential for vertebrate embryogenesis.

    Directory of Open Access Journals (Sweden)

    Galen W Miller

    Full Text Available The hepatic α-tocopherol transfer protein (TTP is required for optimal α-tocopherol bioavailability in humans; mutations in the human TTPA gene result in the heritable disorder ataxia with vitamin E deficiency (AVED, OMIM #277460. TTP is also expressed in mammalian uterine and placental cells and in the human embryonic yolk-sac, underscoring TTP's significance during fetal development. TTP and vitamin E are essential for productive pregnancy in rodents, but their precise physiological role in embryogenesis is unknown. We hypothesize that TTP is required to regulate delivery of α-tocopherol to critical target sites in the developing embryo. We tested to find if TTP is essential for proper vertebrate development, utilizing the zebrafish as a non-placental model. We verify that TTP is expressed in the adult zebrafish and its amino acid sequence is homologous to the human ortholog. We show that embryonic transcription of TTP mRNA increases >7-fold during the first 24 hours following fertilization. In situ hybridization demonstrates that Ttpa transcripts are localized in the developing brain, eyes and tail bud at 1-day post fertilization. Inhibiting TTP expression using oligonucleotide morpholinos results in severe malformations of the head and eyes in nearly all morpholino-injected embryos (88% compared with 5.6% in those injected with control morpholinos or 1.7% in non-injected embryos. We conclude that TTP is essential for early development of the vertebrate central nervous system.

  16. 植物脂质转移蛋白%Lipid Transfer Proteins in Plants

    Institute of Scientific and Technical Information of China (English)

    田爱梅; 曹家树

    2008-01-01

    脂质转移蛋白(lipid transfer proteins,LTPs)是植物生命活动中一类重要的活性蛋白质,在体外能够可逆地结合和转运多种脂质分子.目前已从多种植物中分离到LTPs基因.随着研究的深入,其不同水平的转录本在不同植物的不同发育阶段和生理条件下的不同组织中被发现,但LTPs体内确切的生理、生化功能和作用机制尚不明确.现介绍目前这一领域细胞与分子生物学方面的研究进展,并结合本课题组的研究结果进行了相关探讨,为进一步研究LTPs在植物生殖发育、抗性和防御反应及信号转导中的作用机制提供了新的线索.

  17. Quality Control System for Beer Developed with Monoclonal Antibodies Specific to Barley Lipid Transfer Protein

    Directory of Open Access Journals (Sweden)

    Yukie Murakami-Yamaguchi

    2012-10-01

    Full Text Available Non-specific lipid transfer protein (LTP in barley grain reacted with the IgE in sera drawn from food allergy patients. A sandwich-type of enzyme-linked immunosorbent assay (ELISA was developed with mouse monoclonal antibodies raised against LTP purified with barley flour. This ELISA showed a practical working range of 0.3–3 ng/mL and no cross-reactivity with wheat, adlay and rye. Using this ELISA, LTP was determined in several types of barley-foods, including fermented foods such as malt vinegar, barley-malt miso and beer. LTP content in beer of the same kind was approximately constant, even if manufacturing factory and production days were different. Not only as a factor of foam formation and stability but also as an allergen, controlling and monitoring of LTP in beer should be considered. Taken together, our LTP-detecting ELISA can be proposed as an appropriate system for the quality control of beer.

  18. Expression of Heat Shock Proteins in Human Fibroblast Cells under Magnetic Resonant Coupling Wireless Power Transfer

    Directory of Open Access Journals (Sweden)

    Kohei Mizuno

    2015-10-01

    Full Text Available Since 2007, resonant coupling wireless power transfer (WPT technology has been attracting attention and has been widely researched for practical use. Moreover, dosimetric evaluation has also been discussed to evaluate the potential health risks of the electromagnetic field from this WPT technology based on the International Commission on Non-Ionizing Radiation Protection (ICNIRP guidelines. However, there has not been much experimental evaluation of the potential health risks of this WPT technology. In this study, to evaluate whether magnetic resonant coupling WPT induces cellular stress, we focused on heat shock proteins (Hsps and determined the expression level of Hsps 27, 70 and 90 in WI38VA13 subcloned 2RA human fibroblast cells using a western blotting method. The expression level of Hsps under conditions of magnetic resonant coupling WPT for 24 h was not significantly different compared with control cells, although the expression level of Hsps for cells exposed to heat stress conditions was significantly increased. These results suggested that exposure to magnetic resonant coupling WPT did not cause detectable cell stress.

  19. Alpha-tocopherol transfer protein disruption confers resistance to malarial infection in mice

    Directory of Open Access Journals (Sweden)

    Takeya Motohiro

    2010-04-01

    Full Text Available Abstract Background Various factors impact the severity of malaria, including the nutritional status of the host. Vitamin E, an intra and extracellular anti-oxidant, is one such nutrient whose absence was shown previously to negatively affect Plasmodium development. However, mechanisms of this Plasmodium inhibition, in addition to means by which to exploit this finding as a therapeutic strategy, remain unclear. Methods α-TTP knockout mice were infected with Plasmodium berghei NK65 or Plasmodium yoelii XL-17, parasitaemia, survival rate were monitored. In one part of the experiments mice were fed with a supplemented diet of vitamin E and then infected. In addition, parasite DNA damage was monitored by means of comet assay and 8-OHdG test. Moreover, infected mice were treated with chloroquine and parasitaemia and survival rate were monitored. Results Inhibition of α-tocopherol transfer protein (α-TTP, a determinant of vitamin E concentration in circulation, confers resistance to malarial infection as a result of oxidative damage to the parasites. Furthermore, in combination with the anti-malarial drug chloroquine results were even more dramatic. Conclusion Considering that these knockout mice lack observable negative impacts typical of vitamin E deficiency, these results suggest that inhibition of α-TTP activity in the liver may be a useful strategy in the prevention and treatment of malaria infection. Moreover, a combined strategy of α-TTP inhibition and chloroquine treatment might be effective against drug resistant parasites.

  20. Communication: Microsecond dynamics of the protein and water affect electron transfer in a bacterial bc{sub 1} complex

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Daniel R.; Matyushov, Dmitry V., E-mail: dmitrym@asu.edu [Department of Physics and Department of Chemistry and Biochemistry, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287 (United States)

    2015-04-28

    Cross-membrane electron transport between cofactors localized in proteins of mitochondrial respiration and bacterial photosynthesis is the source of all biological energy. The statistics and dynamics of nuclear fluctuations in these protein/membrane/water heterogeneous systems are critical for their energetic efficiency. The results of 13 μs of atomistic molecular dynamics simulations of the membrane-bound bc{sub 1} bacterial complex are analyzed here. The reaction is affected by a broad spectrum of nuclear modes, with the slowest dynamics in the range of time-scales ∼0.1-1.6 μs contributing half of the reaction reorganization energy. Two reorganization energies are required to describe protein electron transfer due to dynamical arrest of protein conformations on the observation window. This mechanistic distinction allows significant lowering of activation barriers for reactions in proteins.

  1. The α and β chains of human platelet glycoprotein Ib are both transmembrane proteins containing a leucine-rich amino acid sequence

    International Nuclear Information System (INIS)

    The primary structure of the β chain of human glycoprotein Ib (GPIb), the platelet receptor for von Willebrand factor, has been established by a combination of cDNA cloning and amino acid sequence analysis. A λ phage cDNA expression library prepared from human erythroleukemia cells (HEL cells) was screened with a radiolabeled affinity-purified rabbit polyclonal antibody to the β chain of GPIb. Eighteen positive clones were isolated and plaque-purified and the nucleotide sequences of three were determined. The composite sequence spanned 968 nucleotides and included a 5' untranslated region of 22 nucleotides, an open reading frame of 618 nucleotides encoding a signal peptide of 28 amino acids and a mature protein of 181 amino acids, a stop codon, and a 3' noncoding region of 307 nucleotides. The 3' noncoding sequence also contained a polyadenylylation signal (AATAAA) 14 nucleotides upstream from the poly(A) tail of 18 nucleotides. Edman degradation of the intact β chain and of peptides produced by chemical cleavage yielded amino acid sequences spanning 76 residues that were identical to those predicted from the cDNA. The amino-terminal region of the β chain contains a leucine-rich sequence of 24 amino acids that is similar to a sequence that occurs as seven tandem repeats in the α chain of GPIb and nine tandem repeats in leucine-rich α2-glycoprotein. The amino-terminal region of the β chain of GPIb is followed by a transmembrane segment of 25 amino acids and an intracellular segment of 34 amino acids at the carboxyl terminus of the protein

  2. Thermally conductive, electrically insulating and melt-processable polystyrene/boron nitride nanocomposites prepared by in situ reversible addition fragmentation chain transfer polymerization.

    Science.gov (United States)

    Huang, Xingyi; Wang, Shen; Zhu, Ming; Yang, Ke; Jiang, Pingkai; Bando, Yoshio; Golberg, Dmitri; Zhi, Chunyi

    2015-01-01

    Thermally conductive and electrically insulating polymer/boron nitride (BN) nanocomposites are highly attractive for various applications in many thermal management fields. However, so far most of the preparation methods for polymer/BN nanocomposites have usually caused difficulties in the material post processing. Here, an in situ grafting approach is designed to fabricate thermally conductive, electrically insulating and post-melt processable polystyrene (PS)/BN nanosphere (BNNS) nanocomposites by initiating styrene (St) on the surface functionalized BNNSs via reversible addition fragmentation chain transfer polymerization. The nanocomposites exhibit significantly enhanced thermal conductivity. For example, at a St/BN feeding ratio of 5:1, an enhancement ratio of 1375% is achieved in comparison with pure PS. Moreover, the dielectric properties of the nanocomposites show a desirable weak dependence on frequency, and the dielectric loss tangent of the nanocomposites remains at a very low level. More importantly, the nanocomposites can be subjected to multiple melt processing to form different shapes. Our method can become a universal approach to prepare thermally conductive, electrically insulating and melt-processable polymer nanocomposites with diverse monomers and nanofillers. PMID:25493655

  3. Amphiphilic ruthenium bipyridine complex containing long-chain azopyridine group and the mechanism of electron transfer in Langmuir-Blodgett films

    International Nuclear Information System (INIS)

    We synthesized the amphiphilic bis(bipyridine) ruthenium complex [Ru(bipy)2Cl(L)]+ (bipy= 2,2′-bipyridine, L = 4-(4-dodecyloxyphenylazo) pyridine). The long-chain ligand contributed to the self-assembly of the complex at the liquid-air interface, enabling its deposition by the Langmuir-Blodgett technique. The UV-vis, Raman, and specular reflectance FTIR spectroscopies revealed the molecular organization in the LB films: in the free ligand LB film the alkoxyphenylazopyridine species were oriented in parallel to each other and parallel to the normal plane of the substrate, whilst in the ruthenium complex film the alkoxyphenylazopyridine species were oriented in parallel to each other and perpendicular to the normal plane of the substrate. We then prepared multilayer films consisting of layers of ligand L supporting a monolayer of the ruthenium complex and characterized them by electrochemistry. This hybrid film structure led to optimal orientation of the ruthenium centers for electrochemical response. The results indicated that the phenylazo low-lying π-orbital participated in the hopping mechanism that mediated the electron transfer in the LB films with few molecular layers

  4. Thermally conductive, electrically insulating and melt-processable polystyrene/boron nitride nanocomposites prepared by in situ reversible addition fragmentation chain transfer polymerization

    Science.gov (United States)

    Huang, Xingyi; Wang, Shen; Zhu, Ming; Yang, Ke; Jiang, Pingkai; Bando, Yoshio; Golberg, Dmitri; Zhi, Chunyi

    2015-01-01

    Thermally conductive and electrically insulating polymer/boron nitride (BN) nanocomposites are highly attractive for various applications in many thermal management fields. However, so far most of the preparation methods for polymer/BN nanocomposites have usually caused difficulties in the material post processing. Here, an in situ grafting approach is designed to fabricate thermally conductive, electrically insulating and post-melt processable polystyrene (PS)/BN nanosphere (BNNS) nanocomposites by initiating styrene (St) on the surface functionalized BNNSs via reversible addition fragmentation chain transfer polymerization. The nanocomposites exhibit significantly enhanced thermal conductivity. For example, at a St/BN feeding ratio of 5:1, an enhancement ratio of 1375% is achieved in comparison with pure PS. Moreover, the dielectric properties of the nanocomposites show a desirable weak dependence on frequency, and the dielectric loss tangent of the nanocomposites remains at a very low level. More importantly, the nanocomposites can be subjected to multiple melt processing to form different shapes. Our method can become a universal approach to prepare thermally conductive, electrically insulating and melt-processable polymer nanocomposites with diverse monomers and nanofillers.

  5. Food-chain transfer of zinc from contaminated Urtica dioica and Acer pseudoplatanus L. to the aphids Microlophium carnosum and Drepanosiphum platanoidis Schrank

    International Nuclear Information System (INIS)

    This study examines the food-chain transfer of Zn from two plant species, Urtica dioica (stinging nettle) and Acer pseudoplatanus (sycamore maple), into their corresponding aphid species, Microlophium carnosum and Drepanosiphum platanoidis. The plants were grown in a hydroponic system using solutions with increasing concentrations of Zn from 0.02 to 41.9 mg Zn/l. Above-ground tissue concentrations in U. dioica and M. carnosum increased with increasing Zn exposure (p < 0.001). Zn concentrations in A. pseudoplatanus also increased with solution concentration from the control to the 9.8 mg Zn/l solution, above which concentrations remained constant. Zn concentrations in both D. platanoidis and the phloem tissue of A. pseudoplatanus were not affected by the Zn concentration in the watering solution. It appears that A. pseudoplatanus was able to limit Zn transport in the phloem, resulting in constant Zn exposure to the aphids. Zn concentrations in D. platanoidis were around three times those in M. carnosum. - Concentrations of Zn in two aphid species are dependant on species and exposure.

  6. Food-chain transfer of zinc from contaminated Urtica dioica and Acer pseudoplatanus L. to the aphids Microlophium carnosum and Drepanosiphum platanoidis Schrank

    Energy Technology Data Exchange (ETDEWEB)

    Sinnett, Danielle, E-mail: danielle.sinnett@forestry.gsi.gov.u [Centre for Forestry and Climate Change, Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH (United Kingdom); Department of Soil Science, School of Human and Environmental Sciences, University of Reading, Whiteknights, Reading RG6 6DW (United Kingdom); Hutchings, Tony R., E-mail: tony.hutchings@forestry.gsi.gov.u [Centre for Forestry and Climate Change, Forest Research, Alice Holt Lodge, Farnham, Surrey GU10 4LH (United Kingdom); Hodson, Mark E., E-mail: m.e.hodson@reading.ac.u [Department of Soil Science, School of Human and Environmental Sciences, University of Reading, Whiteknights, Reading RG6 6DW (United Kingdom)

    2010-01-15

    This study examines the food-chain transfer of Zn from two plant species, Urtica dioica (stinging nettle) and Acer pseudoplatanus (sycamore maple), into their corresponding aphid species, Microlophium carnosum and Drepanosiphum platanoidis. The plants were grown in a hydroponic system using solutions with increasing concentrations of Zn from 0.02 to 41.9 mg Zn/l. Above-ground tissue concentrations in U. dioica and M. carnosum increased with increasing Zn exposure (p < 0.001). Zn concentrations in A. pseudoplatanus also increased with solution concentration from the control to the 9.8 mg Zn/l solution, above which concentrations remained constant. Zn concentrations in both D. platanoidis and the phloem tissue of A. pseudoplatanus were not affected by the Zn concentration in the watering solution. It appears that A. pseudoplatanus was able to limit Zn transport in the phloem, resulting in constant Zn exposure to the aphids. Zn concentrations in D. platanoidis were around three times those in M. carnosum. - Concentrations of Zn in two aphid species are dependant on species and exposure.

  7. Thermally conductive, electrically insulating and melt-processable polystyrene/boron nitride nanocomposites prepared by in situ reversible addition fragmentation chain transfer polymerization

    International Nuclear Information System (INIS)

    Thermally conductive and electrically insulating polymer/boron nitride (BN) nanocomposites are highly attractive for various applications in many thermal management fields. However, so far most of the preparation methods for polymer/BN nanocomposites have usually caused difficulties in the material post processing. Here, an in situ grafting approach is designed to fabricate thermally conductive, electrically insulating and post-melt processable polystyrene (PS)/BN nanosphere (BNNS) nanocomposites by initiating styrene (St) on the surface functionalized BNNSs via reversible addition fragmentation chain transfer polymerization. The nanocomposites exhibit significantly enhanced thermal conductivity. For example, at a St/BN feeding ratio of 5:1, an enhancement ratio of 1375% is achieved in comparison with pure PS. Moreover, the dielectric properties of the nanocomposites show a desirable weak dependence on frequency, and the dielectric loss tangent of the nanocomposites remains at a very low level. More importantly, the nanocomposites can be subjected to multiple melt processing to form different shapes. Our method can become a universal approach to prepare thermally conductive, electrically insulating and melt-processable polymer nanocomposites with diverse monomers and nanofillers. (paper)

  8. Fatty acid profile and composition of milk protein fraction in dairy cows fed long-chain unsaturated fatty acids during the transition period

    Directory of Open Access Journals (Sweden)

    Francisco Palma Rennó

    2013-11-01

    Full Text Available The objective of this study was to evaluate the utilization of different sources of unsaturated long-chain fatty acids in diets for dairy cows during the transition period and early lactation on the milk fatty acid profile and composition of the protein fraction. Thirty-six Holstein cows were divided into three groups, fed the following diets: control (C; soybean oil (SO; and calcium salts of long-chain unsaturated fatty acids (CS. The milk samples utilized for analysis were obtained weekly from parturition to twelve weeks of lactation; each one of the samples originated from two daily milkings. Milk composition and total nitrogen, non-protein nitrogen and non-casein nitrogen levels were analyzed. The cows receiving the diet with calcium salts had lower concentrations of non-protein nitrogen (%CP in milk compared with the animals fed the diet with soybean oil. There was a decrease in concentration of medium-chain fatty acids C12-C16, and a concomitant increase in concentrations of long-chain fatty acids >C18 in milk fat for the animals fed the diets CS and SO when compared with diet C. Soybean oil and CS diets increased milk-fat concentrations of the acids C18: 1 trans-11, C18: 2 cis-9, trans-11 and C18: 2 trans-10 cis-12 in relation to diet C. The utilization of sources of long-chain fatty acids in the diet of dairy cows increases the biological value of milk in early lactation due to higher concentrations of specific fatty acids such as CLA C18: 2cis-9, trans-11.

  9. Mechanism of phosphoryl transfer and protein-protein interaction in the PTS system-an NMR study

    Energy Technology Data Exchange (ETDEWEB)

    Rajagopal, P.; Klevit, R.E. [Univ. of Washington, Seattle, WA (United States)

    1994-12-01

    HPr and Enzyme IIA{sup Glc} are two of the components of the bacterial PTS (phosphoenolpyruvate: sugar phosphotranferase system) and are involved in the phosphorylation and concomitant translocation of sugars across the membrane. These PTS protein complexes also regulate sugar transport. HPr, phosphorylated at a histidine N1 site by Enzyme I and phosphoenol pyruvate, transfers the phosphoryl group to a histidine N3 position in Enzyme IIA{sup Glc}. HPrs from Gram-positive bacteria undergo regulatory phosphorylation at Ser{sup 46}, whereby phosphorylation of the histidine residue is inhibited. Conversely, histidine phosphorylation inhibits phosphorylation at Ser{sup 46}. HPrs from Gram-negative bacteria possess a serine residue at position 46, but do not undergo regulatory phosphorylation. HPr forms an open-faced sandwich structure with a four-strand S-sheet and 2 to 3 helices lying on top of the sheet. The active-site histidine and Ser{sup 46} occur in conformationally flexible regions. P-His-HPr from the Gram-positive bacterium Bacillus subtilus has been investigated by both homonuclear and heteronuclear two-dimensional and three-dimensional NMR experiments using an in-situ enzymatic regeneration system to maintain a constant level of P-His-HPr. The results show that localized conformational changes occur in the vicinity of the active-site histidine and also near Ser{sup 46}. HPr-Enzyme IIA{sup Glc} complexes from both Bacillus subtilis and Gram-negative Escherichia coli were also studied by a variety of {sup 15}N-edited two-dimensional NMR experiments, which were performed on uniformly {sup 15}N-labeled HPr complexed to unlabeled Enzyme IIA{sup Glc}. The complex is in fast exchange with a molecular weight of about 27 kDa. The focus of our work is to assess the changes undergone by HPr (the smaller of the two components), and so all the experiments were performed with excess Enzyme IIA present in the system.

  10. 100-N Area Strontium-90 Treatability Demonstration Project: Food Chain Transfer Studies for Phytoremediation Along the 100-N Columbia River Riparian Zone

    Energy Technology Data Exchange (ETDEWEB)

    Fellows, Robert J.; Fruchter, Jonathan S.; Driver, Crystal J.

    2009-04-01

    Strontium-90 (90Sr) exceeds the U.S. Environmental Protection Agency’s drinking water standards for groundwater (8 picocuries/L) by as much as a factor of 1000 at several locations within the Hanford 100-N Area and along the 100-N Area Columbia River shoreline). Phytoextraction, a managed remediation technology in which plants or integrated plant/rhizosphere systems are employed to phytoextract and/or sequester 90Sr, is being considered as a potential remediation system along the riparian zone of the Columbia River as part of a treatment train that includes an apatite barrier to immobilize groundwater transport of 90Sr. Phytoextraction would employ coyote willow (Salix exigua) to extract 90Sr from the vadose zone soil and aquifer sediments (phytoextraction) and filter 90Sr (rhizofiltration) from the shallow groundwater along the riparian zone of the Columbia River. The stem and foliage of coyote willows accumulating 90Sr may present not only a mechanism to remove the contaminant but also can be viewed as a source of nutrition for natural herbivores, therefore becoming a potential pathway for the isotope to enter the riparian food chain. Engineered barriers such as large and small animal fencing constructed around the field plot will control the intrusion of deer, rodents, birds, and humans. These efforts, however, will have limited effect on mobile phytophagous insects. Therefore, this study was undertaken to determine the potential for food chain transfer by insects prior to placement of the remediation technology at 100-N. Insect types include direct consumers of the sap or liquid content of the plants vascular system (xylem and phloem) by aphids as well as those that would directly consume the plant foliage such as the larvae (caterpillars) of Lepidoptera species. Heavy infestations of aphids feeding on the stems and leaves of willows growing in 90Sr-contaminated soil can accumulate a small amount (~0.15 ± 0.06%) of the total label removed from the soil by

  11. Effect of growth hormone replacement therapy on plasma lecithin : cholesterol acyltransferase and lipid transfer protein activities in growth hormone-deficient adults

    NARCIS (Netherlands)

    Beentjes, JAM; van Tol, A; Sluiter, WJ; Dullaart, RPF

    2000-01-01

    The effects of growth hormone (GH) replacement on plasma lecithin:cholesterol acyltransferase (LCAT), cholesteryl ester transfer protein (CETP), and phospholipid transfer protein (PLTP), factors involved in high density lipoprotein (HDL) metabolism, We unknown. We carried out a 6 mouths study in 24

  12. Gestation-related gene expression and protein localization in endometrial tissue of Suffolk and Cheviot ewes at gestation Day 19, after transfer of Suffolk or Cheviot embryos.

    Science.gov (United States)

    Sequeira, M; Pain, S J; de Brun, V; Meikle, A; Kenyon, P R; Blair, H T

    2016-10-01

    The objective of this study was to investigate the gene expression of progesterone and estrogen receptor α (PR, ERα), insulin-like growth factor (IGF) 1, IGF-2, their receptor (IGFR1), IGF-binding proteins (BP) 1 to 6, insulin receptor, adiponectin receptors (AdipoR1/2), cyclooxygenase 2 (PTGS2), mucin 1 and to localize PR, ERα, IGF-1, IGFR1, PTGS2, and proliferating cellular nuclear antigen (PCNA) in the endometrium of pregnant (Day 19) Suffolk and Cheviot ewes carrying Suffolk and Cheviot embryos transferred within and reciprocally between breeds. Gene expression was determined by real-time quantitative polymerase chain reaction (RT-qPCR), and antigen determination was measured by immunohistochemistry in the luminal epithelium (LE), superficial and deep glands (SG, DG, respectively) and superficial and deep stroma. Gene expression of PR, IGF-1, IGFBP2, and IGFBP5 was higher in Suffolk than that in Cheviot ewes (P interaction between ewe and embryo breed affected PTGS2 staining (P protein expression in the endometrium of Suffolk and Cheviot ewes is affected by both ewe and embryo breed at Day 19 of pregnancy. PMID:27325575

  13. SUMO chains: polymeric signals.

    Science.gov (United States)

    Vertegaal, Alfred C O

    2010-02-01

    Ubiquitin and ubiquitin-like proteins are conjugated to a wide variety of target proteins that play roles in all biological processes. Target proteins are conjugated to ubiquitin monomers or to ubiquitin polymers that form via all seven internal lysine residues of ubiquitin. The fate of these target proteins is controlled in a chain architecture-dependent manner. SUMO (small ubiquitin-related modifier) shares the ability of ubiquitin to form chains via internal SUMOylation sites. Interestingly, a SUMO-binding site in Ubc9 is important for SUMO chain synthesis. Similar to ubiquitin-polymer cleavage by USPs (ubiquitin-specific proteases), SUMO chain formation is reversible. SUMO polymers are cleaved by the SUMO proteases SENP6 [SUMO/sentrin/SMT3 (suppressor of mif two 3)-specific peptidase 6], SENP7 and Ulp2 (ubiquitin-like protease 2). SUMO chain-binding proteins including ZIP1, SLX5/8 (synthetic lethal of unknown function 5/8), RNF4 (RING finger protein 4) and CENP-E (centromere-associated protein E) have been identified that interact non-covalently with SUMO chains, thereby regulating target proteins that are conjugated to SUMO multimers. SUMO chains play roles in replication, in the turnover of SUMO targets by the proteasome and during mitosis and meiosis. Thus signalling via polymers is an exciting feature of the SUMO family. PMID:20074033

  14. Principles and application of intrinsic Förster resonance energy transfer (iFRET) for label-free detection of native proteins

    Science.gov (United States)

    Kang, Hyo Jin; Kim, Ju Hwan; Ghisaidoobe, Amar B. T.; Chung, Sang J.

    2015-07-01

    Tryptophan residues in proteins of interest were evaluated as FRET donors to facilitate the development of a label-free protein detection system, coined "intrinsic Förster (or fluorescence) resonance energy transfer (iFRET)". iFRET fluorescence probes, composed of an efficient and tryptophan-specific FRET acceptor in addition to a target protein-specific ligand, selectively bind to the target proteins thereby enabling Förster resonance energy transfer between the protein tryptophan residues and the iFRET probe. We have developed efficient iFRET acceptor fluorophores and a deep UV microscope, which were successfully applied to detect native target proteins in live cells.

  15. Design, Synthesis and Properties of Branch-chained Maltoside Detergents for Stabilization and Crystallization of Integral Membrane Proteins: Human Connexin 26

    OpenAIRE

    Hong, Wen-Xu; Baker, Kent A.; Ma, Xingquan; Stevens, Raymond C.; Yeager, Mark; Zhang, Qinghai

    2010-01-01

    A challenging requirement for structural studies of integral membrane proteins (IMPs) is the use of amphiphiles that replicate the hydrophobic environment of membranes. Progress has been impeded by the limited number of useful detergents and the need for a deeper understanding of their structure-activity relationships. To this end, we designed a family of detergents containing short, branched alkyl chains at the interface between the polar head and apolar tail. This design mimics the second a...

  16. Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41

    OpenAIRE

    Samuel, Buck S.; Shaito, Abdullah; Motoike, Toshiyuki; Rey, Federico E.; Backhed, Fredrik; Manchester, Jill K.; Hammer, Robert E.; Williams, S. Clay; Crowley, Jan; Yanagisawa, Masashi; Jeffrey I Gordon

    2008-01-01

    The distal human intestine harbors trillions of microbes that allow us to extract calories from otherwise indigestible dietary polysaccharides. The products of polysaccharide fermentation include short-chain fatty acids that are ligands for Gpr41, a G protein-coupled receptor expressed by a subset of enteroendocrine cells in the gut epithelium. To examine the contribution of Gpr41 to energy balance, we compared Gpr41−/− and Gpr41+/+ mice that were either conventionally-raised with a complete ...

  17. PROTEIN THERAPEUTICS FOR JUNCTIONAL EPIDERMOLYSIS BULLOSA: INCORPORATION OF RECOMBINANT β3 CHAIN INTO LAMININ 332 IN β3-/- KERATINOCYTES IN VITRO

    OpenAIRE

    Igoucheva, Olga; Kelly, Aislinn; Uitto, Jouni; Alexeev, Vitali

    2007-01-01

    Junctional epidermolysis bullosa (JEB) is an inherited mechanobullous disease characterized by reduced adherence of the epidermal keratinocytes to the underlying dermis and often caused by the absence of functional laminin 332 due to the lack or dysfunction of its β3 chain. As there are no specific therapies for the JEB, we tested whether protein replacement strategy could be applicable for the restoration of the laminin 332 assembly and reversion of the JEB phenotype in human keratinocytes t...

  18. Fluorescent n-3 and n-6 Very Long Chain Polyunsaturated Fatty Acids: THREE-PHOTON IMAGING IN LIVING CELLS EXPRESSING LIVER FATTY ACID-BINDING PROTEIN*

    OpenAIRE

    McIntosh, Avery L.; Huang, Huan; Atshaves, Barbara P.; Wellberg, Elizabeth; Kuklev, Dmitry V.; Smith, William L.; Kier, Ann B.; Schroeder, Friedhelm

    2010-01-01

    Despite the considerable beneficial effects of n-3 and n-6 very long chain polyunsaturated fatty acids (VLC-PUFAs), very little is known about the factors that regulate their uptake and intracellular distribution in living cells. This issue was addressed in cells expressing liver-type fatty acid-binding protein (L-FABP) by real time multiphoton laser scanning microscopy of novel fluorescent VLC-PUFAs containing a conjugated tetraene fluorophore near the carboxyl group and natural methylene-in...

  19. Apolipoprotein B-containing lipoprotein assembly in microsomal triglyceride transfer protein-deficient McA-RH7777 cells

    OpenAIRE

    Liu, Yanwen; Manchekar, Medha; Sun, Zhihuan; Richardson, Paul E.; Dashti, Nassrin

    2010-01-01

    Microsomal triglyceride transfer protein (MTP) is required for the assembly and secretion of apolipoprotein (apo) B-containing lipoproteins. Previously, we demonstrated that the N-terminal 1,000 residues of apoB (apoB:1000) are necessary for the initiation of apoB-containing lipoprotein assembly in rat hepatoma McA-RH7777 cells and that these particles are phospholipid (PL) rich. To determine if the PL transfer activity of MTP is sufficient for the assembly and secretion of primordial apoB:10...

  20. Gene gun transferring-bone morphogenetic protein 2 (BMP-2) gene enhanced bone fracture healing in rabbits

    OpenAIRE

    Li, Wenju; Wei, Haifeng; Xia, Chunmei; Zhu, Xiaomeng; Hou, Guozhu; Xu, Feng; Xinghua SONG; Zhan, Yulin

    2015-01-01

    Purpose: Transferring the bone morphogenetic protein 2 (BMP-2) genes into the tissues or cells can improve the bone healing of the fracture has been widely accepted. We evaluated the efficiency of using gene gun to transfer the BMP-2 gene thereby affected the healing of a fractured bone. Methods: The vector coding for BMP-2 was constructed by a non-replicating encephalo-myocarditis virus (ECMV)-based vector. The segmental bone defect (1.5 cm) model was created by a wire-saw at the middle part...