WorldWideScience

Sample records for investigating solution-phase protein

  1. A direct comparison of protein structure in the gas and solution phase: the Trp-cage

    DEFF Research Database (Denmark)

    Patriksson, Alexandra; Adams, Christopher M; Kjeldsen, Frank

    2007-01-01

    Molecular dynamics simulations of zwitterions of the Trp-cage protein in the gas phase show that the most stable ion in vacuo has preserved the charge locations acquired in solution. A direct comparison of the gas and solution-phase structures reveals that, despite the similarity in charge location......, there is significant difference in the structures, with a substantial increase in hydrogen bonds and exposure of hydrophobic parts in the gas phase. The structure of the salt bridge in the gas phase is also much more stable than in the (experimental) solution structure....

  2. Determination of Rate Constants and Equilibrium Constants for Solution-Phase Drug–Protein Interactions by Ultrafast Affinity Extraction

    Science.gov (United States)

    2015-01-01

    A method was created on the basis of ultrafast affinity extraction to determine both the dissociation rate constants and equilibrium constants for drug–protein interactions in solution. Human serum albumin (HSA), an important binding agent for many drugs in blood, was used as both a model soluble protein and as an immobilized binding agent in affinity microcolumns for the analysis of free drug fractions. Several drugs were examined that are known to bind to HSA. Various conditions to optimize in the use of ultrafast affinity extraction for equilibrium and kinetic studies were considered, and several approaches for these measurements were examined. The dissociation rate constants obtained for soluble HSA with each drug gave good agreement with previous rate constants reported for the same drugs or other solutes with comparable affinities for HSA. The equilibrium constants that were determined also showed good agreement with the literature. The results demonstrated that ultrafast affinity extraction could be used as a rapid approach to provide information on both the kinetics and thermodynamics of a drug–protein interaction in solution. This approach could be extended to other systems and should be valuable for high-throughput drug screening or biointeraction studies. PMID:24911267

  3. Solution-Phase Processes of Macromolecular Crystallization

    Science.gov (United States)

    Pusey, Marc L.; Minamitani, Elizabeth Forsythe

    2004-01-01

    We have proposed, for the tetragonal form of chicken egg lysozyme, that solution phase assembly processes are needed to form the growth units for crystal nucleation and growth. The starting point for the self-association process is the monomeric protein, and the final crystallographic symmetry is defined by the initial dimerization interactions of the monomers and subsequent n-mers formed, which in turn are a function of the crystallization conditions. It has been suggested that multimeric proteins generally incorporate the underlying multimers symmetry into the final crystallographic symmetry. We posed the question of what happens to a protein that is known to grow as an n-mer when it is placed in solution conditions where it is monomeric. The trypsin-treated, or cut, form of the protein canavalin (CCAN) has been shown to nucleate and grow crystals as a trimer from neutral to slightly acidic solutions. Under these conditions the solution is composed almost wholly of trimers. The insoluble protein can be readily dissolved by weakly basic solution, which results in a solution that is monomeric. There are three possible outcomes to an attempt at crystallization of the protein under monomeric (high pH) conditions: 1) we will obtain the same crystals as under trimer conditions, but at different protein concentrations governed by the self association equilibria; 2) we will obtain crystals having a different symmetry, based upon a monomeric growth unit; 3) we will not obtain crystals. Obtaining the first result would be indicative that the solution-phase self-association process is critical to the crystal nucleation and growth process. The second result would be less clear, as it may also reflect a pH-dependent shift in the trimer-trimer molecular interactions. The third result, particularly for experiments in the transition pH's between trimeric and monomeric CCAN, would indicate that the monomer does not crystallize, and that solution phase self association is not part

  4. Spectroscopic investigation of protein corona

    Science.gov (United States)

    Choudhary, Poonam

    Nanotechnology has revolutionalized the landscape of modern science and technology, including materials, electronics, therapeutics, bioimaging, sensing, and the environment. Research in the past decade has examined the fate of nanomaterials in vitro and in vivo, as well as the interactions between nanoparticles and biological and ecosystems using primarily toxicological and ecotoxicological approaches. However, due to the versatility in the physical and physicochemical properties of nanoparticles, and due to the vast complexity of their hosting systems, the solubility, transformation, and biocompatibility of nanomaterials are still poorly understood. Nanotechnology has been undergoing tremendous development in recent decades, driven by realized perceived applications of nanomaterials in electronics, therapeutics, imaging, sensing, environmental remediation, and consumer products. Nanoparticles on entering the blood stream undergo an identity change, they become coated with proteins. There are different kind of proteins present in blood. Proteins compete for getting coated over the surface of nanoparticle and this whole entity of proteins coated over nanoparticle surface is called Protein Corona. Proteins tightly bound to the surface of nanoparticle form hard corona and the ones loosely bound on the outer surface form soft corona. This dissertation is aimed at spectroscopic investigation of Protein Corona. Chapter I of this dissertation offers a comprehensive review of the literature based on nanomaterials with the focus on carbon based nanomaterilas and introduction to Protein Corona. Chapter II is based different methods used for Graphene Synthesis,different types of defects and doping. In Chapter III influence of defects on Graphene Protein Corona was investigated. Chapter IV is based on the study of Apoptosis induced cell death by Gold and silver nanoparticles. In vitro study of effect of Protein Corona on toxicity of cells was done.

  5. Aerosol spray pyrolysis & solution phase synthesis of nanostructures

    Science.gov (United States)

    Zhang, Hongwang

    This dissertation focuses on the synthesis of nanomaterials by both solution phase and gas phase methods. By the solution phase method, we demonstrate the synthesis of Au/CdS binary hybrid nanoparticles and the Au-induced growth of CdS nanorods. At higher reaction temperature, extremely uniform CdS nanorods were obtained. The size of the Au seed nanoparticles has an important influence on the length and diameter of the nanorods. In addition, preparation of peanut-like FePt-CdS hybrid nanoparticles by spontaneous epitaxial nucleation and growth of CdS onto FePt-seed nanoparticles in high-temperature organic solution is reported. The FePt-CdS hybrid nanoparticles reported here are an example of a bifunctional nanomaterial that combines size-dependent magnetic and optical properties. In the gas phase method, a spray pyrolysis aerosol synthesis method was used to produce tellurium dioxide nanoparticles and zinc sulfide nanoparticles. Tellurite glasses (amorphous TeO2 based materials) have two useful optical properties, high refractive index and high optical nonlinearity, that make them attractive for a range of applications. In the work presented here, TeO2 nanoparticles were prepared by spray pyrolysis of an aqueous solution of telluric acid, Te(OH)6. This laboratory-scale process is capable of producing up to 80 mg/hr of amorphous TeO2-nanoparticles with primary particle diameters from 10 to 40 nm, and allows their synthesis in significant quantities from an inexpensive and environmentally friendly precursor. Furthermore, both Er3+ doped and Er3+ and Yb3+ co-doped tellurium dioxide nanoparticles were synthesized by spray pyrolysis of an aqueous mixture of telluric acid with erbium/ytterbium salts, which exhibit the infrared to green visible upconversion phenomena. ZnS nanoparticles (NPs) were prepared by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor. The home-built scanning mobility particle spectrometer (SMPS) is a useful tool for

  6. Polymer solution phase separation: Microgravity simulation

    Science.gov (United States)

    Cerny, Lawrence C.; Sutter, James K.

    1989-01-01

    In many multicomponent systems, a transition from a single phase of uniform composition to a multiphase state with separated regions of different composition can be induced by changes in temperature and shear. The density difference between the phase and thermal and/or shear gradients within the system results in buoyancy driven convection. These differences affect kinetics of the phase separation if the system has a sufficiently low viscosity. This investigation presents more preliminary developments of a theoretical model in order to describe effects of the buoyancy driven convection in phase separation kinetics. Polymer solutions were employed as model systems because of the ease with which density differences can be systematically varied and because of the importance of phase separation in the processing and properties of polymeric materials. The results indicate that the kinetics of the phase separation can be performed viscometrically using laser light scattering as a principle means of following the process quantitatively. Isopycnic polymer solutions were used to determine the viscosity and density difference limits for polymer phase separation.

  7. Sucrose and KF quenching system for solution phase parallel synthesis.

    Science.gov (United States)

    Chavan, Sunil; Watpade, Rahul; Toche, Raghunath

    2016-01-01

    The KF, sucrose (table sugar) exploited as quenching system in solution phase parallel synthesis. Excess of electrophiles were covalently trapped with hydroxyl functionality of sucrose and due to polar nature of sucrose derivative was solubilize in water. Potassium fluoride used to convert various excess electrophilic reagents such as acid chlorides, sulfonyl chlorides, isocyanates to corresponding fluorides, which are less susceptible for hydrolysis and subsequently sucrose traps these fluorides and dissolves them in water thus removing them from reaction mixture. Various excess electrophilic reagents such as acid chlorides, sulfonyl chlorides, and isocyanates were quenched successfully to give pure products in excellent yields.

  8. A solution phase fabrication of magnetic nanoparticles encapsulated in carbon

    International Nuclear Information System (INIS)

    Wei Xianwen; Zhu Guoxing; Xia Chuanjun; Ye Yin

    2006-01-01

    To avoid high energy consumption, intensive use of hardware and high cost in the manufacture of nanoparticles encapsulated in carbon, a simple, efficient and economical solution-phase method for the fabrication of FeNi at C nanostructures has been explored. The reaction to the magnetic metal at C structures here is conducted at a relatively low temperature (160 deg. C) and this strategy can be transferred to prepare other transition metal at C core-shell nanostructures. The saturation magnetization of metal in metal at C nanostructures is similar to those of the corresponding buck metals. Magnetic metal at C nanostructures with magnetic metal nanoparticles inside and a functionalized carbon surface outside may not only provide the opportunity to tailor the magnetic properties for magnetic storage devices and therapeutics but also make possible the loading of other functional molecules (e.g. enzymes, antigens) for clinic diagnostics, molecular biology, bioengineering, and catalysis

  9. Theory of the thermodynamic influence of solution-phase additives in shape-controlled nanocrystal synthesis.

    Science.gov (United States)

    Qi, Xin; Fichthorn, Kristen A

    2017-10-19

    Though many experimental studies have documented that certain solution-phase additives can play a key role in the shape-selective synthesis of metal nanocrystals, the origins and mechanisms of this shape selectivity are still unclear. One possible role of such molecules is to thermodynamically induce the equilibrium shape of a nanocrystal by altering the interfacial free energies of the facets. Using a multi-scheme thermodynamic integration method that we recently developed [J. Chem. Phys., 2016, 145, 194108], we calculate the solid-liquid interfacial free energies γ sl and investigate the propensity to achieve equilibrium shapes in such syntheses. We first apply this method to Ag(100) and Ag(111) facets in ethylene glycol solution containing polyvinylpyrrolidone (PVP), to mimic the environment in polyol synthesis of Ag nanocrystals. We find that although PVP has a preferred binding to Ag(100), its selectivity is not sufficient to induce a thermodynamic preference for {100}-faceted nanocubes, as has been observed experimentally. This indicates that PVP promotes Ag nanocube formation kinetically rather than thermodynamically. We further quantify the thermodynamic influence of adsorbed solution-phase additives for generic molecules, by building a γ sl ratio/nanocrystal shape map as a function of zero-temperature binding energies. This map can be used to gauge the efficacy of candidate additive molecules for producing targeted thermodynamic nanocrystal shapes. The results indicate that only additives with a strong facet selectivity can impart significant thermodynamic-shape change. Therefore, many of the nanocrystals observed in experiments are likely kinetic products.

  10. A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis

    Energy Technology Data Exchange (ETDEWEB)

    Chowdhury, Saiful M. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Shi, Liang [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Yoon, Hyunjin [Dartmouth College, Hanover, NH (United States); Ansong, Charles [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Rommereim, Leah M. [Dartmouth College, Hanover, NH (United States); Norbeck, Angela D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Auberry, Kenneth J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Moore, R. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Adkins, Joshua N. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Heffron, Fred [Oregon Health and Science Univ., Portland, OR (United States); Smith, Richard D. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2009-02-10

    We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins- HimD, PduB and PhoP- with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .

  11. Bio-templated CdSe quantum dots green synthesis in the functional protein, lysozyme, and biological activity investigation

    International Nuclear Information System (INIS)

    Wang, Qisui; Li, Song; Liu, Peng; Min, Xinmin

    2012-01-01

    Bifunctional fluorescence (CdSe Quantum Dots) – protein (Lysozyme) nanocomposites were synthesized at room temperature by a protein-directed, solution-phase, green-synthetic method. Fluorescence (FL) and absorption spectra showed that CdSe QDs were prepared successfully with Lyz. The average particle size and crystalline structure of QDs were investigated by high-resolution transmission electron microscopy (HRTEM) and X-ray diffraction (XRD), respectively. With attenuated total reflection-fourier transform infrared (ATR-FTIR) spectra and thermogravimetric (TG) analysis, it was confirmed that there is interaction between QDs and amide I, amide II groups in Lyz. FL polarization was measured and FL imaging was done to monitor whether QDs could be responsible for possible changes in the conformation and activity of Lyz. Interestingly, the results showed Lyz still retain the biological activity after formation of QDs, but the secondary structure of the Lyz was changed. And the advantage of this synthesis method is producing excellent fluorescent QDs with specifically biological function. -- Highlights: ► Lysozyme-directed green synthesis of CdSe quantum dots. ► Lysozyme still retain the biological activity after formation of CdSe. ► The method is the production of fluorescent QDs with highly specific and functions.

  12. Fundamental aspects of nucleation and growth in the solution-phase synthesis of germanium nanocrystals

    KAUST Repository

    Codoluto, Stephen C.

    2010-01-01

    Colloidal Ge nanocrystals (NCs) were synthesized via the solution phase reduction of germanium(ii) iodide. We report a systematic investigation of the nanocrystal nucleation and growth as a function of synthesis conditions including the nature of coordinating solvents, surface bound ligands, synthesis duration and temperature. NC synthesis in reaction environments with weakly bound phosphine surface ligand led to the coalescence of nascent particles leading to ensembles with broad lognormal particle diameter distributions. Synthesis in the presence of amine or alkene ligands mitigated particle coalescence. High-resolution transmission electron micrographs revealed that NCs grown in the presence of weak ligands had a high crystal defect density whereas NCs grown in amine solutions were predominantly defect-free. We applied infrared spectroscopy to study the NC surface chemistry and showed that alkene ligands project the NCs from surface oxidation. Photoluminescence spectroscopy measurements showed that alkene ligands passivate surface traps, as indicated by infrared fluorescence, conversely oxidized phosphine and amine passivated NCs did not fluoresce. © 2010 The Royal Society of Chemistry.

  13. Electrochemical processing of nitrate waste solutions. Phase 2, Final report

    Energy Technology Data Exchange (ETDEWEB)

    Genders, D.; Weinberg, N.; Hartsough, D. [Electrosynthesis Co., Inc., Cheektowaga, NY (US)

    1992-10-07

    The second phase of research performed at The Electrosynthesis Co., Inc. has demonstrated the successful removal of nitrite and nitrate from a synthetic effluent stream via a direct electrochemical reduction at a cathode. It was shown that direct reduction occurs at good current efficiencies in 1,000 hour studies. The membrane separation process is not readily achievable for the removal of nitrites and nitrates due to poor current efficiencies and membrane stability problems. A direct reduction process was studied at various cathode materials in a flow cell using the complete synthetic mix. Lead was found to be the cathode material of choice, displaying good current efficiencies and stability in short and long term tests under conditions of high temperature and high current density. Several anode materials were studied in both undivided and divided cell configurations. A divided cell configuration was preferable because it would prevent re-oxidation of nitrite by the anode. The technical objective of eliminating electrode fouling and solids formation was achieved although anode materials which had demonstrated good stability in short term divided cell tests corroded in 1,000 hour experiments. The cause for corrosion is thought to be F{sup {minus}} ions from the synthetic mix migrating across the cation exchange membrane and forming HF in the acid anolyte. Other possibilities for anode materials were explored. A membrane separation process was investigated which employs an anion and cation exchange membrane to remove nitrite and nitrate, recovering caustic and nitric acid. Present research has shown poor current efficiencies for nitrite and nitrate transport across the anion exchange membrane due to co-migration of hydroxide anions. Precipitates form within the anion exchange membranes which would eventually result in the failure of the membranes. Electrochemical processing offers a highly promising and viable method for the treatment of nitrate waste solutions.

  14. Spectral analysis and quantum chemical studies of chair and twist-boat conformers of cycloheximide in gas and solution phases

    Science.gov (United States)

    Tokatli, A.; Ucun, F.; Sütçü, K.; Osmanoğlu, Y. E.; Osmanoğlu, Ş.

    2018-02-01

    In this study the conformational behavior of cycloheximide in the gas and solution (CHCl3) phases has theoretically been investigated by spectroscopic and quantum chemical properties using density functional theory (wB97X-D) method with 6-31++G(d,p) basis set, for the first time. The calculated IR results reveal that in the ground state the molecule exits as a mixture of the chair and twist-boat conformers in the gas phase, while the calculated NMR results reveal that it only exits as the chair conformer in the solution phase. In order to obtain the contributions coming from intramolecular interactions to the stability of the conformers in the gas and solution phases, the quantum theory of atoms in molecules (QTAIM), noncovalent interactions (NCI) method, and natural bond orbital analysis (NBO) have been employed. The QTAIM and NCI methods indicated that by intramolecular interactions with bond critical point (BCP) the twist-boat conformer is more stabilized than the chair conformer, while by steric interactions it is more destabilized. Considering that these interactions balance each other, the stabilities of the conformers are understood to be dictated by the van der Waals interactions. The NBO analyses show that the hyperconjugative and steric effects play an important role in the stabilization in the gas and solution phases. Furthermore, to get a better understanding of the chemical behavior of this important antibiotic drug we have evaluated and, commented the global and local reactivity descriptors of the both conformers. Finally, the EPR analysis of γ-irradiated cycloheximide has been done. The comparison of the experimental and calculated data have showed the inducement of a radical structure of (CH2)2ĊCH2 in the molecule. The experimental EPR spectrum has also confirmed that the molecule simultaneously exists in the chair and twist-boat conformers in the solid phase.

  15. Investigation on the turnover of plant proteins. 2

    International Nuclear Information System (INIS)

    Becker, R.; Winkler, E.; Jung, K.; Huebner, G.

    1981-01-01

    Based on kinetic analyses of amino acid and protein turnover by means of compartment models the synthesis and degradation of the soluble proteins in etiolated epicotyl segments of Pisum sativum L. as well as their dependence on the herbicide 2'-methyl-4'-chlorophenoxyacetic acid (MCPA) were determined quantitatively. The segments were incubated for 10 h in a medium containing 14 C-leucine and subsequently placed in an inactive medium. The radioactivity in the soluble proteins and in the amino acid fraction was followed up for a total of 24 h. A 3-pool model in which the total measurable amino acid pool was divided into a direct precursor pool for protein synthesis and into a degradation pool was best suited to interpret the data. The turnover rate for the soluble proteins of untreated epicotyl segments was determined to be 0.058 h -1 ; at an MCPA concentration of 10 -4 M this value was nearly doubled. An increased proteolytic activity in the epicotyl segments ran parallel to the change of the turnover rate in dependence on MCPA concentration. The heterogeneity of the soluble protein with respect to the turnover rate was investigated by means of 3 H/ 14 C double labelling for individual protein fractions separated by gel electrophoresis. The results obtained in this way were comparable with those of the total pool turnover. (author)

  16. Methods of reconstitution to investigate membrane protein function.

    Science.gov (United States)

    Skrzypek, Ruth; Iqbal, Shagufta; Callaghan, Richard

    2018-02-16

    Membrane proteins are notoriously difficult to investigate in isolation. The focus of this chapter is the key step following extraction and purification of membrane proteins; namely reconstitution. The process of reconstitution re-inserts proteins into a lipid bilayer that partly resembles their native environment. This native environment is vital to the stability of membrane proteins, ensuring that they undergo vital conformational transitions and maintain optimal interaction with their substrates. Reconstitution may take many forms and these have been classified into two broad categories. Symmetric systems enable unfettered access to both sides of a bilayer. Compartment containing systems contain a lumen and are ideally suited to measurement of transport processes. The investigator is encouraged to ascertain what aspects of protein function will be undertaken and to apply the most advantageous reconstitution system or systems. It is important to note that the process of reconstitution is not subject to defined protocols and requires empirical optimisation to specific targets. Copyright © 2018 Elsevier Inc. All rights reserved.

  17. Biochemical investigation of protein export in Escherichia coli.

    Science.gov (United States)

    Hardy, S J; Randall, L L

    1989-01-01

    Export of proteins from the bacterial cytoplasm to a final destination in the periplasm and outer membrane is one example of the fundamental process occurring in all cells whereby polypeptides are transferred across biological membranes. Investigations on a variety of different systems have indicated similarities in the mechanism of this process. In the cases of bacterial protein export and the transfer of polypeptides across the endoplasmic reticulum in eukaryotic cells the processes are so similar that understanding gleaned from studies of the one is usually directly applicable to the other. The study of protein export in E. coli has two advantages over that of eukaryotic secretion. Not only is there the possibility of doing sophisticated genetic experiments, but also one can carry out biochemical investigations in vivo, a facility not so readily available with eukaryotic organisms. Such studies have, for example, shown that membrane translocation can occur both cotranslationally and post-translationally, that export requires protonmotive force, that some component of the export apparatus prevents the exported protein from assuming its native structure in the cytosol, and that there are probably at least two functions for the leader sequence, one in targeting the protein to the export pathway and one in translocation across the membrane.

  18. Laser induced temperature jump investigations of fast protein folding dynamics

    Science.gov (United States)

    Qiu, Linlin

    Protein folding has a large parameter space, diverse mechanism, and multipath kinetics. However, there are some common features many proteins share in their folding processes: all seem to fold at the rates much faster than the random conformation search, and all fold into the structures which have the highly regular motifs like alpha-helices, beta-sheets and turns. Understanding how fast proteins can fold is one of the central issues in solving the protein folding problem. Ultrafast folding kinetics had not been accessible until a few sub-millisecond probes were invented and applied lately. We constructed a laser induced temperature jump spectrometer which is a great utility in identifying the local structure and tertiary contact formation of proteins on the time scale from 10 -8 to 10-3 s with time resolution of 10 -9 s. With this spectrometer we studied the fast folding mini-protein, TrpCage and a few short stable beta-hairpins, the TrpZip series. Studying TrpCage was a major breakthrough it was a pioneer protein model which brought experiment and simulation very close: its structures measured by NMR and predicted by the molecular dynamics were amazingly alike. Our kinetic results showed that it folds in 4 mus at room temperature which turned out to be the fastest ever known for protein-like molecules. Also this folding time constant is consistent with what was later on simulated by distributed computation. TrpZips are among the smallest and stablest polypeptide chains which form secondary structures. They are slightly different from each other based on structural stability and by forming various types of beta-hairpins which are the minimum units of beta tertiary structure. The beta-hairpins form in the time range of 1--10 mus that confirms the theory that loop formation is controlled by the diffusion process (˜mus). We also investigated the kinetics of the protein chain collapse, a very controversial problem. By comparing the collapse of the foldable 104

  19. Real-time protein NMR spectroscopy and investigation of assisted protein folding.

    Science.gov (United States)

    Kumar, Amit; Balbach, Jochen

    2015-10-01

    During protein-folding reactions toward the native structure, short-lived intermediate states can be populated. Such intermediates expose hydrophobic patches and can self-associate leading to non-productive protein misfolding. A major focus of current research is the characterization of short-lived intermediates and how molecular chaperones enable productive folding. Real-time NMR spectroscopy, together with the development of advanced methods, is reviewed here and the potential these methods have to characterize intermediate states as well as interactions with molecular chaperone proteins at single-residue resolution is highlighted. Various chaperone interactions can guide the protein-folding reaction and thus are important for protein structure formation, stability, and activity of their substrates. Chaperone-assisted protein folding, characterization of intermediates, and their molecular interactions using real-time NMR spectroscopy will be discussed. Additionally, recent advances in NMR methods employed for characterization of high-energy intermediates will be discussed. Real-time NMR combines high resolution with kinetic information of protein reactions, which can be employed not only for protein-folding studies and the characterization of folding intermediates but also to investigate the molecular mechanisms of assisted protein folding. Real-time NMR spectroscopy remains an effective tool to reveal structural details about the interaction between chaperones and transient intermediates. Methodologically, it provides in-depth understanding of how kinetic intermediates and their thermodynamics contribute to the protein-folding reaction. This review summarizes the most recent advances in this field. This article is part of a Special Issue titled Proline-directed Foldases: Cell Signaling Catalysts and Drug Targets. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Protein corona and nanoparticles: how can we investigate on?

    Science.gov (United States)

    Pederzoli, Francesca; Tosi, Giovanni; Vandelli, Maria Angela; Belletti, Daniela; Forni, Flavio; Ruozi, Barbara

    2017-11-01

    Nanoparticles (NPs) represent one of the most promising tools for drug-targeting and drug-delivery. However, a deeper understanding of the complex dynamics that happen after their in vivo administration is required. Particularly, plasma proteins tend to associate to NPs, forming a new surface named the 'protein corona' (PC). This surface is the most exposed as the 'visible side' of NPs and therefore, can have a strong impact on NP biodistribution, targeting efficacy and also toxicity. The PC consists of two poorly delimited layers, known as 'hard corona' (HC) and 'soft corona' (SC), that are affected by the complexity of the environment and the formed protein-surface equilibrium during in vivo blood circulation. The HC corona is formed by proteins strongly associated to the NPs, while the SC is an outer layer consisting of loosely bound proteins. Several studies attempted to investigate the HC, which is easier to be isolated, but yielded poor reproducibility, due to varying experimental conditions. As a consequence, full mapping of the HC for different NPs is still lacking. Moreover, the current knowledge on the SC, which may play a major role in the 'first' interaction of NPs once in vivo, is very limited, mainly due to the difficulties in preserving it after purification. Therefore, multi-disciplinary approaches leading to the obtainment of a major number of information about the PC and its properties is strongly needed to fully understand its impact and to better support a more safety and conscious application of nanotechnology in medicine. WIREs Nanomed Nanobiotechnol 2017, 9:e1467. doi: 10.1002/wnan.1467 For further resources related to this article, please visit the WIREs website. © 2017 Wiley Periodicals, Inc.

  1. Experimental investigation of interactions between proteins and carbon nanomaterials

    Science.gov (United States)

    Sengupta, Bishwambhar

    The global market for nanomaterials based products is forecasted to reach $1 trillion per annum per annum for 2015. Engineered nanomaterials (ENMs) exhibit unique physicochemical properties with potential to impact diverse aspects of society through applications in electronics, renewable energy, and medicine. While the research and proposed applications of ENMs continue to grow rapidly, the health and safety of ENMs still remains a major concern to the public as well as to policy makers and funding agencies. It is now widely accepted that focused efforts are needed for identifying the list of physicochemical descriptors of ENM before they can be evaluated for nanotoxicity and biological response. This task is surprisingly challenging, as many physicochemical properties of ENMs are closely inter related and cannot be varied independently (e.g. increasing the size of an ENM can introduce additional defects). For example, varying toxic response may ensue due to different methods of nanomaterial preparation, dissimilar impurities and defects. Furthermore, the inadvertent coating of proteins on ENM surface in any biological milieu results in the formation of the so-called "protein/bio-corona" which can in turn alter the fate of ENMs and their biological response. Carbon nanomaterials (CNMs) such as carbon nanotubes, graphene, and graphene oxide are widely used ENMs. It is now known that defects in CNMs play an important role not only in materials properties but also in the determination of how materials interact at the nano-bio interface. In this regard, this work investigates the influence of defect-induced hydrophilicity on the bio-corona formation using micro Raman, photoluminescence, infrared spectroscopy, electrochemistry, and molecular dynamics simulations. Our results show that the interaction of proteins (albumin and fibrinogen) with CNMs is strongly influenced by charge transfer between them, inducing protein unfolding which enhances conformational entropy and

  2. Investigation of the pH-dependence of dye-doped protein-protein interactions.

    Science.gov (United States)

    Nudelman, Roman; Gloukhikh, Ekaterina; Rekun, Antonina; Richter, Shachar

    2016-11-01

    Proteins can dramatically change their conformation under environmental conditions such as temperature and pH. In this context, Glycoprotein's conformational determination is challenging. This is due to the variety of domains which contain rich chemical characters existing within this complex. Here we demonstrate a new, straightforward and efficient technique that uses the pH-dependent properties of dyes-doped Pig Gastric Mucin (PGM) for predicting and controlling protein-protein interaction and conformation. We utilize the PGM as natural host matrix which is capable of dynamically changing its conformational shape and adsorbing hydrophobic and hydrophilic dyes under different pH conditions and investigate and control the fluorescent properties of these composites in solution. It is shown at various pH conditions, a large variety of light emission from these complexes such as red, green and white is obtained. This phenomenon is explained by pH-dependent protein folding and protein-protein interactions that induce different emission spectra which are mediated and controlled by means of dye-dye interactions and surrounding environment. This process is used to form the technologically challenging white light-emitting liquid or solid coating for LED devices. © 2016 The Protein Society.

  3. Formation of soft magnetic high entropy amorphous alloys composites containing in situ solid solution phase

    Science.gov (United States)

    Wei, Ran; Sun, Huan; Chen, Chen; Tao, Juan; Li, Fushan

    2018-03-01

    Fe-Co-Ni-Si-B high entropy amorphous alloys composites (HEAACs), which containing high entropy solid solution phase in amorphous matrix, show good soft magnetic properties and bending ductility even in optimal annealed state, were successfully developed by melt spinning method. The crystallization phase of the HEAACs is solid solution phase with body centered cubic (BCC) structure instead of brittle intermetallic phase. In addition, the BCC phase can transformed into face centered cubic (FCC) phase with temperature rise. Accordingly, Fe-Co-Ni-Si-B high entropy alloys (HEAs) with FCC structure and a small amount of BCC phase was prepared by copper mold casting method. The HEAs exhibit high yield strength (about 1200 MPa) and good plastic strain (about 18%). Meanwhile, soft magnetic characteristics of the HEAs are largely reserved from HEAACs. This work provides a new strategy to overcome the annealing induced brittleness of amorphous alloys and design new advanced materials with excellent comprehensive properties.

  4. First-principles study of ternary fcc solution phases from special quasirandom structures

    International Nuclear Information System (INIS)

    Shin Dongwon; Wang Yi; Liu Zikui; Walle, Axel van de

    2007-01-01

    In the present work, ternary special quasirandom structures (SQSs) for a fcc solid solution phase are generated at different compositions, x A =x B =x C =(1/3) and x A =(1/2), x B =x C =(1/4), whose correlation functions are satisfactorily close to those of a random fcc solution. The generated SQSs are used to calculate the mixing enthalpy of the fcc phase in the Ca-Sr-Yb system. It is observed that first-principles calculations of all the binary and ternary SQSs in the Ca-Sr-Yb system exhibit very small local relaxation. It is concluded that the fcc ternary SQSs can provide valuable information about the mixing behavior of the fcc ternary solid solution phase. The SQSs presented in this work can be widely used to study the behavior of ternary fcc solid solutions

  5. Silica-supported aluminum chloride-assisted solution phase synthesis of pyridazinone-based antiplatelet agents.

    Science.gov (United States)

    El Maatougui, Abdelaziz; Azuaje, Jhonny; Sotelo, Eddy; Caamaño, Olga; Coelho, Alberto

    2011-01-10

    A solution phase protocol that enabled the synthesis of three diverse libraries of pyridazin-3-ones incorporating α,β-unsaturated moieties at position 5 of the heterocyclic core has been developed using silica-supported aluminum trichloride as a heterogeneous and reusable catalyst. This robust procedure has facilitated the hit to lead process for these series of compounds and allowed the identification of new potent derivatives that elicit antiplatelet activity in the low micromolar range.

  6. Parallel Solution-Phase Synthesis and General Biological Activity of a Uridine Antibiotic Analog Library

    OpenAIRE

    Moukha-chafiq, Omar; Reynolds, Robert C.

    2014-01-01

    A small library of ninety four uridine antibiotic analogs was synthesized, under the Pilot Scale Library (PSL) Program of the NIH Roadmap initiative, from amine 2 and carboxylic acids 33 and 77 in solution-phase fashion. Diverse aldehyde, sulfonyl chloride, and carboxylic acid reactant sets were condensed to 2, leading after acid-mediated hydrolysis, to the targeted compounds 3?32 in good yields and high purity. Similarly, treatment of 33 with diverse amines and sulfonamides gave 34?75. The c...

  7. All-Inorganic Colloidal Quantum Dot Photovoltaics Employing Solution-Phase Halide Passivation

    KAUST Repository

    Ning, Zhijun

    2012-09-12

    A new solution-phase halide passivation strategy to improve the electronic properties of colloidal quantum dot films is reported. We prove experimentally that the approach leads to an order-of-magnitude increase in mobility and a notable reduction in trap state density. We build solar cells having the highest efficiency (6.6%) reported using all-inorganic colloidal quantum dots. The improved photocurrent results from increased efficiency of collection of infrared-generated photocarriers. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. All-inorganic colloidal quantum dot photovoltaics employing solution-phase halide passivation

    Energy Technology Data Exchange (ETDEWEB)

    Ning, Zhijun; Ren, Yuan; Hoogland, Sjoerd; Voznyy, Oleksandr; Levina, Larissa; Stadler, Philipp; Lan, Xinzheng; Zhitomirsky, David; Sargent, Edward H. [Department of Electrical and Computer Engineering, University of Toronto, 10 King' s College Road, Toronto, Ontario, M5S 3G4 (Canada)

    2012-12-11

    A new solution-phase halide passivation strategy to improve the electronic properties of colloidal quantum dot films is reported. We prove experimentally that the approach leads to an order-of-magnitude increase in mobility and a notable reduction in trap state density. We build solar cells having the highest efficiency (6.6%) reported using all-inorganic colloidal quantum dots. The improved photocurrent results from increased efficiency of collection of infrared-generated photocarriers. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases

    Science.gov (United States)

    Glowacki, David R.; Orr-Ewing, Andrew J.; Harvey, Jeremy N.

    2011-06-01

    In this work, we report the first theoretical studies of post-transition state dynamics for reaction of CN with polyatomic organic species. Using electronic structure theory, a newly developed analytic reactive PES, a recently implemented rare-event acceleration algorithm, and a normal mode projection scheme, we carried out and analyzed quasi-classical and classical non-equilibrium molecular dynamics simulations of the reactions CN + propane (R1) and CN + cyclohexane (R2). For (R2), we carried out simulations in both the gas phase and in a CH2Cl2 solvent. Analysis of the results suggests that the solvent perturbations to the (R2) reactive free energy surface are small, leading to product energy partitioning in the solvent that is similar to the gas phase. The distribution of molecular geometries at the respective gas and solution phase variational association transition states is very similar, leading to nascent HCN which is vibrationally excited in both its CH stretching and HCN bending coordinates. This study highlights the fact that significant non-equilibrium energy distributions may follow in the wake of solution phase bimolecular reactions, and may persist for hundreds of picoseconds despite frictional damping. Consideration of non-thermal distributions is often neglected in descriptions of condensed-phase reactivity; the extent to which the present intriguing observations are widespread remains an interesting question.

  10. Investigation of the Josephin Domain protein-protein interaction by molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Marco A Deriu

    Full Text Available Spinocerebellar ataxia (SCA 3, the most common form of SCA, is a neurodegenerative rare disease characterized by polyglutamine tract expansion and self-assembly of Ataxin3 (At3 misfolded proteins into highly organized fibrillar aggregates. The At3 N-terminal Josephin Domain (JD has been suggested as being responsible for mediating the initial phase of the At3 double-step fibrillogenesis. Several issues concerning the residues involved in the JD's aggregation and, more generally, the JD clumping mechanism have not been clarified yet. In this paper we present an investigation focusing on the JD protein-protein interaction by means of molecular modeling. Our results suggest possible aminoacids involved in JD contact together with local and non-local effects following JD dimerization. Surprisingly, JD conformational changes following the binding may involve ubiquitin binding sites and hairpin region even though they do not pertain to the JD interaction surfaces. Moreover, the JD binding event has been found to alter the hairpin open-like conformation toward a closed-like arrangement over the simulated timescale. Finally, our results suggest that the JD aggregation might be a multi-step process, with an initial fast JD-JD binding mainly driven by Arg101, followed by slower structural global rearrangements involving the exposure to the solvent of Leu84-Trp87, which might play a role in a second step of JD aggregation.

  11. Isofocusing and immunological investigations on cephalopod lens proteins

    NARCIS (Netherlands)

    Brahma, S.K.; Lancieri, M.

    1979-01-01

    Soluble lens proteins from Octopus vulgaris, Sepia officinalis, and Loligo vulgaris were analyzed by thin-layer isoelectric focusing and compared by various immunochemical methods using antibodies directed against total soluble lens protein antigens from the said three species. The results show

  12. AESOP: A Python Library for Investigating Electrostatics in Protein Interactions.

    Science.gov (United States)

    Harrison, Reed E S; Mohan, Rohith R; Gorham, Ronald D; Kieslich, Chris A; Morikis, Dimitrios

    2017-05-09

    Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  13. Vectors for multi-color bimolecular fluorescence complementation to investigate protein-protein interactions in living plant cells

    Directory of Open Access Journals (Sweden)

    Kuang Lin-Yun

    2008-10-01

    Full Text Available Abstract Background The investigation of protein-protein interactions is important for characterizing protein function. Bimolecular fluorescence complementation (BiFC has recently gained interest as a relatively easy and inexpensive method to visualize protein-protein interactions in living cells. BiFC uses "split YFP" tags on proteins to detect interactions: If the tagged proteins interact, they may bring the two split fluorophore components together such that they can fold and reconstitute fluorescence. The sites of interaction can be monitored using epifluorescence or confocal microscopy. However, "conventional" BiFC can investigate interactions only between two proteins at a time. There are instances when one may wish to offer a particular "bait" protein to several "prey" proteins simultaneously. Preferential interaction of the bait protein with one of the prey proteins, or different sites of interaction between the bait protein and multiple prey proteins, may thus be observed. Results We have constructed a series of gene expression vectors, based upon the pSAT series of vectors, to facilitate the practice of multi-color BiFC. The bait protein is tagged with the C-terminal portion of CFP (cCFP, and prey proteins are tagged with the N-terminal portions of either Venus (nVenus or Cerulean (nCerulean. Interaction of cCFP-tagged proteins with nVenus-tagged proteins generates yellow fluorescence, whereas interaction of cCFP-tagged proteins with nCerulean-tagged proteins generates blue fluorescence. Additional expression of mCherry indicates transfected cells and sub-cellular structures. Using this system, we have determined in both tobacco BY-2 protoplasts and in onion epidermal cells that Agrobacterium VirE2 protein interacts with the Arabidopsis nuclear transport adapter protein importin α-1 in the cytoplasm, whereas interaction of VirE2 with a different importin α isoform, importin α-4, occurs predominantly in the nucleus. Conclusion Multi

  14. An ordered metallic glass solid solution phase that grows from the melt like a crystal

    International Nuclear Information System (INIS)

    Chapman, Karena W.; Chupas, Peter J.; Long, Gabrielle G.; Bendersky, Leonid A.; Levine, Lyle E.; Mompiou, Frédéric; Stalick, Judith K.; Cahn, John W.

    2014-01-01

    We report structural studies of an Al–Fe–Si glassy solid that is a solid solution phase in the classical thermodynamic sense. We demonstrate that it is neither a frozen melt nor nanocrystalline. The glass has a well-defined solubility limit and rejects Al during formation from the melt. The pair distribution function of the glass reveals chemical ordering out to at least 12 Å that resembles the ordering within a stable crystalline intermetallic phase of neighboring composition. Under isothermal annealing at 305 °C the glass first rejects Al, then persists for approximately 1 h with no detectable change in structure, and finally is transformed by a first-order phase transition to a crystalline phase with a structure that is different from that within the glass. It is possible that this remarkable glass phase has a fully ordered atomic structure that nevertheless possesses no long-range translational symmetry and is isotropic

  15. The first preparative solution phase synthesis of melanotan II

    Directory of Open Access Journals (Sweden)

    2008-10-01

    Full Text Available Melanotan II is a synthetic cyclic heptapeptide used to prevent a sunlight-induced skin cancer by stimulating the skin tanning process. In this paper we report the first solution phase synthesis of the title compound. The hexapeptide sequence has been assembled by [(2+2+1+1] scheme. After removing the orthogonal protection, a carbodiimide mediated lactamization, involving the ε-amino group of lysine and γ-carboxy group of aspartic acid, led to a cyclic intermediate. Appending N-acetylnorleucine concluded the assembly of melanotan II molecule. Protection of the lateral groups in arginine and tryptophan was omitted for atom and step economy reasons. The total synthesis of melanotan II was accomplished in 12 steps with 2.6% overall yield, affording >90% pure peptide without using preparative chromatography.

  16. Solution-phase synthesis of chromium-functionalized single-walled carbon nanotubes

    KAUST Repository

    Kalinina, Irina V.

    2015-03-01

    The solution phase reactions of single-walled carbon nanotubes (SWNTs) with Cr(CO)6 and benzene-Cr(CO)3 can lead to the formation of small chromium clusters. The cluster size can be varied from less than 1 nm to about 4 nm by increasing the reaction time. TEM images suggest that the clusters are deposited predominantly on the exterior walls of the nanotubes. TGA analysis was used to obtain the Cr content and carbon to chromium ratio in the Cr-complexed SWNTs. It is suggested that the carbon nanotube benzenoid structure templates the condensation of chromium atoms and facilitates the loss of carbon monoxide leading to well defined metal clusters.

  17. Solution-Phase Synthesis of SnSe Nanocrystals for Use in Solar Cells

    KAUST Repository

    Franzman, Matthew A.

    2010-03-31

    Nanocrystals of phase-pure tin(II) selenide (SnSe) were synthesized via a solution-phase route employing stoichiometric amounts of di-tert-butyl dlselenlde as a novel and facile selenium source. The direct band gap of the resulting nanocrystals (E8 = 1.71 eV) is significantly blue-shifted relative to the bulk value (E8 = 1.30 eV), a likely consequence of quantum confinement resulting from the relatively small average diameter of the nanocrystals (μD < 20 nm). Preliminary solar cell devices incorporating SnSe nanocrystals into a poly[2-methoxy5-(3\\',7\\'-d1methyloctyloxy)-1,4- phenylenev1nylene] matrix demonstrate a significant enhancement In quantum efficiency and short-circuit current density, suggesting that this earth-abundant material could be a valuable component In future photovoltaic devices. Copyright © 2010 American Chemical Society.

  18. Amorphous and nanocrystalline titanium nitride and carbonitride materials obtained by solution phase ammonolysis of Ti(NMe2)4

    International Nuclear Information System (INIS)

    Jackson, Andrew W.; Shebanova, Olga; Hector, Andrew L.; McMillan, Paul F.

    2006-01-01

    Solution phase reactions between tetrakisdimethylamidotitanium (Ti(NMe 2 ) 4 ) and ammonia yield precipitates with composition TiC 0.5 N 1.1 H 2.3 . Thermogravimetric analysis (TGA) indicates that decomposition of these precursor materials proceeds in two steps to yield rocksalt-structured TiN or Ti(C,N), depending upon the gas atmosphere. Heating to above 700 deg. C in NH 3 yields nearly stoichiometric TiN. However, heating in N 2 atmosphere leads to isostructural carbonitrides, approximately TiC 0.2 N 0.8 in composition. The particle sizes of these materials range between 4-12 nm. Heating to a temperature that corresponds to the intermediate plateau in the TGA curve (450 deg. C) results in a black powder that is X-ray amorphous and is electrically conducting. The bulk chemical composition of this material is found to be TiC 0.22 N 1.01 H 0.07 , or Ti 3 (C 0.17 N 0.78 H 0.05 ) 3.96 , close to Ti 3 (C,N) 4 . Previous workers have suggested that the intermediate compound was an amorphous form of Ti 3 N 4 . TEM investigation of the material indicates the presence of nanocrystalline regions x (C,N) y crystalline phases

  19. Investigating the Role of Helicobacter pylori PriA Protein.

    Science.gov (United States)

    Singh, Aparna; Blaskovic, Dusan; Joo, Jungsoo; Yang, Zhen; Jackson, Sharon H; Coleman, William G; Yan, Ming

    2016-08-01

    In bacteria, PriA protein, a conserved DEXH-type DNA helicase, plays a central role in replication restart at stalled replication forks. Its unique DNA binding property allows it to recognize and stabilize stalled forks and the structures derived from them. PriA plays a very critical role in replication fork stabilization and DNA repair in E. coli and N. gonorrhoeae. In our in vivo expression technology screen, priA gene was induced in vivo when Helicobacter pylori infects mouse stomach. We decided to elucidate the role of H. pylori PriA protein in survival in mouse stomach, survival in gastric epithelial cells and macrophage cells, DNA repair, acid stress, and oxidative stress. The priA null mutant strain was unable to colonize mice stomach mucosa after long-term infections. Mouse colonization was observed after 1 week of infection, but the levels were much lower than the wild-type HpSS1 strain. PriA protein was found to be important for intracellular survival of epithelial cell-/macrophage cell-ingested H. pylori. Also, a priA null mutant was more sensitive to DNA-damaging agents and was much more sensitive to acid and oxidative stress as compared to the wild-type strain. These data suggest that the PriA protein is needed for survival and persistence of H. pylori in mice stomach mucosa. © 2016 John Wiley & Sons Ltd.

  20. Investigation of dietary fiber, protein, vitamin E and other nutritional ...

    African Journals Online (AJOL)

    USER

    banana flowers contained abundant dietary fiber (4.96-5.74 g/100g) and proteins (1.62-2.07 g/100 g). The major amino acids are glycine, ... as organic material and fertilizer in plantations in China until today (Yang et al., 2003). ..... banana flowers than in banana peel, in contrast to previous reports (Lima et al., 2008).

  1. A proteomic investigation of soluble olfactory proteins in Anopheles gambiae.

    Directory of Open Access Journals (Sweden)

    Guido Mastrobuoni

    Full Text Available Odorant-binding proteins (OBPs and chemosensory proteins (CSPs are small soluble polypeptides that bind semiochemicals in the lymph of insect chemosensilla. In the genome of Anopheles gambiae, 66 genes encode OBPs and 8 encode CSPs. Here we monitored their expression through classical proteomics (2D gel-MS analysis and a shotgun approach. The latter method proved much more sensitive and therefore more suitable for tiny biological samples as mosquitoes antennae and eggs. Females express a larger number and higher quantities of OBPs in their antennae than males (24 vs 19. OBP9 is the most abundant in the antennae of both sexes, as well as in larvae, pupae and eggs. Of the 8 CSPs, 4 were detected in antennae, while SAP3 was the only one expressed in larvae. Our proteomic results are in fairly good agreement with data of RNA expression reported in the literature, except for OBP4 and OBP5, that we could not identify in our analysis, nor could we detect in Western Blot experiments. The relatively limited number of soluble olfactory proteins expressed at relatively high levels in mosquitoes makes further studies on the coding of chemical messages at the OBP level more accessible, providing for few specific targets. Identification of such proteins in Anopheles gambiae might facilitate future studies on host finding behavior in this important disease vector.

  2. Structural investigation of membrane proteins by electron microscopy

    NARCIS (Netherlands)

    Moscicka, Katarzyna Beata

    2009-01-01

    Biological membranes are vital components of all living systems, forming the boundaries of cells and their organelles. They consist of a lipid bilayer and embedded proteins, which are nanomachines that fulfill key functions such as energy conversion, solute transport, secretion, and signal

  3. Investigation into ramie whisker reinforced arylated soy protein composites

    CSIR Research Space (South Africa)

    Kumar, R

    2010-03-01

    Full Text Available Reinforced Arylated Soy Protein Composites Rakesh Kumar1,2*, Lina Zhang2 1CSIR MSM, Port Elizabeth 6000, South Africa 2Department of Chemistry, Wuhan University, Wuhan 430072, China Abstract Whiskers were prepared from ramie fibers and were... of synthetic fibers and matrices the reuse of classical fibers reinforced composites are not possible. To get rid from these types of composites we use landfill disposable systems. Due to increasing population, lots of nonbiodegradable wastes are generated...

  4. A systematic investigation of the stability of green fluorescent protein fusion proteins.

    Science.gov (United States)

    Janczak, Monika; Bukowski, Michał; Górecki, Andrzej; Dubin, Grzegorz; Dubin, Adam; Wladyka, Benedykt

    2015-01-01

    X-ray crystallography provides important insights into structure-function relationship in biomolecules. However, protein crystals are usually hard to obtain which hinders our understanding of multiple important processes. Crystallization requires large amount of protein sample, whereas recombinant proteins are often unstable or insoluble. Green fluorescent protein (GFP) fusion is one of the approaches to increase protein synthesis, solubility and stability, facilitating crystallization. In this study we analyze the influence of the linker length, composition and the position of GFP relative to the fusion partner on the fusion protein production and stability. To this end, multiple constructs of enzymatically impaired variant of PemKSa toxin from Staphylococcus aureus CH91 fused to GFP were generated. Fusion protein production in Escherichia coli was evaluated. The proteins were purified and their stability tested. PemKSa-α14aa-GFP fusion provided best production and stability. Obtained results demonstrate the importance of optimization of fusion protein construct, including linker selection and the order of fusion partners, in obtaining high quantities of stable protein for crystallization.

  5. Investigation of the connection between the quality of protein, protein level and endogenous N excretion

    International Nuclear Information System (INIS)

    Koehler, R.; Gebhardt, G.

    1979-01-01

    The influence of various protein qualities as well as of different levels of protein on the amount of endogenous N excretion, metabolic fecal nitrogen (MFN) and endogenous urinary N (EUN) was determined in growing albino rats. The test rations were labelled with admixtures of 15 N-DL-methionine and 15 N-DL-lysine, respectively, or contained feed protein enriched with 15 N. EUN and MFN and their sum (the N maintenance requirement) showed the influence of the respective protein source and its dependence on the protein level. The endogenous N excretions showed an opposite tendency to the N balance; for high-quality protein feedstuffs with a high N balance (e.g. dried eggs) they are lower than for protein sources of inferior quality, with a low N-balance only (e.g. wheat gluten). Presumably this interaction of retention and maintenance is due to the complementary effect of exogenous and endogenous amino acids in the N and amino acid pool, respectively. Provided that the N dose and the live weight of the animals are comparable, the N balance appears to be more suitable as parameter for the description of the protein quality and the calculation of the protein utilisation than N retention, as the sum of N balance and the values of MFN and EUN (depending on the feedstuffs and the N level). (author)

  6. Solution-Phase Epitaxial Growth of Quasi-Monocrystalline Cuprous Oxide on Metal Nanowires

    Science.gov (United States)

    2014-01-01

    The epitaxial growth of monocrystalline semiconductors on metal nanostructures is interesting from both fundamental and applied perspectives. The realization of nanostructures with excellent interfaces and material properties that also have controlled optical resonances can be very challenging. Here we report the synthesis and characterization of metal–semiconductor core–shell nanowires. We demonstrate a solution-phase route to obtain stable core–shell metal–Cu2O nanowires with outstanding control over the resulting structure, in which the noble metal nanowire is used as the nucleation site for epitaxial growth of quasi-monocrystalline Cu2O shells at room temperature in aqueous solution. We use X-ray and electron diffraction, high-resolution transmission electron microscopy, energy dispersive X-ray spectroscopy, photoluminescence spectroscopy, and absorption spectroscopy, as well as density functional theory calculations, to characterize the core–shell nanowires and verify their structure. Metal–semiconductor core–shell nanowires offer several potential advantages over thin film and traditional nanowire architectures as building blocks for photovoltaics, including efficient carrier collection in radial nanowire junctions and strong optical resonances that can be tuned to maximize absorption. PMID:25233392

  7. Three-Dimensional ZnO Hierarchical Nanostructures: Solution Phase Synthesis and Applications

    Directory of Open Access Journals (Sweden)

    Xiaoliang Wang

    2017-11-01

    Full Text Available Zinc oxide (ZnO nanostructures have been studied extensively in the past 20 years due to their novel electronic, photonic, mechanical and electrochemical properties. Recently, more attention has been paid to assemble nanoscale building blocks into three-dimensional (3D complex hierarchical structures, which not only inherit the excellent properties of the single building blocks but also provide potential applications in the bottom-up fabrication of functional devices. This review article focuses on 3D ZnO hierarchical nanostructures, and summarizes major advances in the solution phase synthesis, applications in environment, and electrical/electrochemical devices. We present the principles and growth mechanisms of ZnO nanostructures via different solution methods, with an emphasis on rational control of the morphology and assembly. We then discuss the applications of 3D ZnO hierarchical nanostructures in photocatalysis, field emission, electrochemical sensor, and lithium ion batteries. Throughout the discussion, the relationship between the device performance and the microstructures of 3D ZnO hierarchical nanostructures will be highlighted. This review concludes with a personal perspective on the current challenges and future research.

  8. Tuning colloidal quantum dot band edge positions through solution-phase surface chemistry modification

    Science.gov (United States)

    Kroupa, Daniel M.; Vörös, Márton; Brawand, Nicholas P.; McNichols, Brett W.; Miller, Elisa M.; Gu, Jing; Nozik, Arthur J.; Sellinger, Alan; Galli, Giulia; Beard, Matthew C.

    2017-05-01

    Band edge positions of semiconductors determine their functionality in many optoelectronic applications such as photovoltaics, photoelectrochemical cells and light emitting diodes. Here we show that band edge positions of lead sulfide (PbS) colloidal semiconductor nanocrystals, specifically quantum dots (QDs), can be tuned over 2.0 eV through surface chemistry modification. We achieved this remarkable control through the development of simple, robust and scalable solution-phase ligand exchange methods, which completely replace native ligands with functionalized cinnamate ligands, allowing for well-defined, highly tunable chemical systems. By combining experiments and ab initio simulations, we establish clear relationships between QD surface chemistry and the band edge positions of ligand/QD hybrid systems. We find that in addition to ligand dipole, inter-QD ligand shell inter-digitization contributes to the band edge shifts. We expect that our established relationships and principles can help guide future optimization of functional organic/inorganic hybrid nanostructures for diverse optoelectronic applications.

  9. A facile solution-phase approach to transparent and conducting ITO nanocrystal assemblies.

    Science.gov (United States)

    Lee, Jonghun; Lee, Sunghwan; Li, Guanglai; Petruska, Melissa A; Paine, David C; Sun, Shouheng

    2012-08-15

    Monodisperse 11 nm indium tin oxide (ITO) nanocrystals (NCs) were synthesized by thermal decomposition of indium acetylacetonate, In(acac)(3), and tin bis(acetylacetonate)dichloride, Sn(acac)(2)Cl(2), at 270 °C in 1-octadecene with oleylamine and oleic acid as surfactants. Dispersed in hexane, these ITO NCs were spin-cast on centimeter-wide glass substrates, forming uniform ITO NC assemblies with root-mean-square roughness of 2.9 nm. The assembly thickness was controlled by ITO NC concentrations in hexane and rotation speeds of the spin coater. Via controlled thermal annealing at 300 °C for 6 h under Ar and 5% H(2), the ITO NC assemblies became conductive and transparent with the 146 nm-thick assembly showing 5.2 × 10(-3) Ω·cm (R(s) = 356 Ω/sq) resistivity and 93% transparency in the visible spectral range--the best values ever reported for ITO NC assemblies prepared from solution phase processes. The stable hexane dispersion of ITO NCs was also readily spin-cast on polyimide (T(g) ~360 °C), and the resultant ITO assembly exhibited a comparable conductivity and transparency to the assembly on a glass substrate. The reported synthesis and assembly provide a promising solution to the fabrication of transparent and conducting ITO NCs on flexible substrates for optoelectronic applications.

  10. Microscopic Investigation of Reversible Nanoscale Surface Size Dependent Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Michael A. Carpenter

    2009-05-01

    Full Text Available Aβ1-40 coated 20 nm gold colloidal nanoparticles exhibit a reversible color change as pH is externally altered between pH 4 and 10. This reversible process may contain important information on the initial reversible step reported for the fibrillogenesis of Aβ (a hallmark of Alzheimer’s disease. We examined this reversible color change by microscopic investigations. AFM images on graphite surfaces revealed the morphology of Aβ aggregates with gold colloids. TEM images clearly demonstrate the correspondence between spectroscopic features and conformational changes of the gold colloid.

  11. Investigation of the interaction of β-methylamino-L-alanine with eukaryotic and prokaryotic proteins.

    Science.gov (United States)

    Main, Brendan J; Italiano, Carly J; Rodgers, Kenneth J

    2017-12-12

    There is a strong body of evidence linking the non-protein amino acid (NPAA) β-methylamino-L-alanine (BMAA) to the development of a number of neurodegenerative diseases. BMAA has been found globally, is produced by a number of organisms including cyanobacteria, diatoms, and dinoflagellates; and has been shown to biomagnify through trophic levels. The role of BMAA in neurodegenerative disease is highlighted by its presence in the brains of a number of neurodegenerative disease patients, where it was found in a protein-bound form. We have previously shown that BMAA is bound to cell proteins, and results in the upregulation of the unfolded protein response, an endoplasmic reticulum stress response activated by the presence of misfolded proteins within the cell. Structurally aberrant proteins are features of a number of neurodegenerative diseases, and further investigation of how BMAA interacts with proteins is crucial to our understanding of its toxicity. Here we use radiolabelled BMAA to investigate the interaction and binding of BMAA to eukaryotic and prokaryotic proteins. We found differences in the presence and distribution of protein-bound BMAA between E. coli and neuroblastoma cells, with an increase in binding over time only seen in the eukaryotic cells. We also found that BMAA was unable to bind to pure proteins, or cell lysate in native or denaturing conditions, indicating that biological processing is required for BMAA to bind to proteins.

  12. MICROFLUIDIC MIXERS FOR THE INVESTIGATION OF PROTEIN FOLDING USING SYNCHROTRON RADIATION CIRCULAR DICHROISM SPECTROSCOPY

    International Nuclear Information System (INIS)

    Kane, A; Hertzog, D; Baumgartel, P; Lengefeld, J; Horsley, D; Schuler, B; Bakajin, O

    2006-01-01

    The purpose of this study is to design, fabricate and optimize microfluidic mixers to investigate the kinetics of protein secondary structure formation with Synchrotron Radiation Circular Dichroism (SRCD) spectroscopy. The mixers are designed to rapidly initiate protein folding reaction through the dilution of denaturant. The devices are fabricated out of fused silica, so that they are transparent in the UV. We present characterization of mixing in the fabricated devices, as well as the initial SRCD data on proteins inside the mixers

  13. Investigations on (photo) reactions of cosmetic UV filters towards skin proteins

    OpenAIRE

    Stiefel, Constanze

    2014-01-01

    Although UV filters are important, widespread used cosmetic ingredients, their reaction potential towards skin proteins has hardly been studied so far. Therefore, the aim of the present thesis was to investigate the reactivity of widespread UV filter substances towards skin proteins using increasingly complex protein and skin model systems and different analytical techniques. At first, the development of a rapid high-performance thin-layer chromatographic (HPTLC) screening method on an ami...

  14. Fluorescence Lifetime Imaging Microscopy (FLIM) as a Tool to Investigate Hypoxia-Induced Protein-Protein Interaction in Living Cells.

    Science.gov (United States)

    Schützhold, Vera; Fandrey, Joachim; Prost-Fingerle, Katrin

    2018-01-01

    Fluorescence resonance energy transfer (FRET) is widely used as a method to investigate protein-protein interactions in living cells. A FRET pair donor fluorophore in close proximity to an appropriate acceptor fluorophore transfers emission energy to the acceptor, resulting in a shorter lifetime of the donor fluorescence. When the respective FRET donor and acceptor are fused with two proteins of interest, a reduction in donor lifetime, as detected by fluorescence lifetime imaging microscopy (FLIM), can be taken as proof of close proximity between the fluorophores and therefore interaction between the proteins of interest. Here, we describe the usage of time-domain FLIM-FRET in hypoxia-related research when we record the interaction of the hypoxia-inducible factor-1 (HIF-1) subunits HIF-1α and HIF-1β in living cells in a temperature- and CO 2 -controlled environment under the microscope.

  15. Solution phase chemical synthesis of nano aluminium particles stabilized in poly(vinylpyrrolidone) and poly(methylmethacrylate) matrices.

    Science.gov (United States)

    Ghanta, Sekher Reddy; Muralidharan, Krishnamurthi

    2010-06-01

    The reduction of aluminium trichloride by lithium aluminium hydride in the presence of poly(vinylpyrrolidone) or poly(methylmethacrylate) in mesitylene yielded nano aluminium particles in the matrices of respective polymers. Solution phase synthesis methodology was used successfully to produce composites of various Al/polymer ratios. The composites were characterized by powder XRD patterns and 27Al-NMR with MAS spectroscopic study. The method was useful to produce up to 10 g of nano aluminium that were pure and stable.

  16. A nanobody-based toolset to investigate the role of protein localization and dispersal in Drosophila.

    Science.gov (United States)

    Harmansa, Stefan; Alborelli, Ilaria; Bieli, Dimitri; Caussinus, Emmanuel; Affolter, Markus

    2017-04-11

    The role of protein localization along the apical-basal axis of polarized cells is difficult to investigate in vivo, partially due to lack of suitable tools. Here, we present the GrabFP system, a collection of four nanobody-based GFP-traps that localize to defined positions along the apical-basal axis. We show that the localization preference of the GrabFP traps can impose a novel localization on GFP-tagged target proteins and results in their controlled mislocalization. These new tools were used to mislocalize transmembrane and cytoplasmic GFP fusion proteins in the Drosophila wing disc epithelium and to investigate the effect of protein mislocalization. Furthermore, we used the GrabFP system as a tool to study the extracellular dispersal of the Decapentaplegic (Dpp) protein and show that the Dpp gradient forming in the lateral plane of the Drosophila wing disc epithelium is essential for patterning of the wing imaginal disc.

  17. ToF-SIMS investigations of adsorbed proteins on dental titanium

    Energy Technology Data Exchange (ETDEWEB)

    Wald, J.; Ziegler, C. [Department of Physics and Research Centre OPTIMAS, University of Kaiserslautern (Germany); Institute for Surface and Thin Film Analysis (IFOS) GmbH and Research Centre OPTIMAS, Kaiserslautern (Germany); Mueller, C. [Department of Physics and Research Centre OPTIMAS, University of Kaiserslautern (Germany); Wahl, M.; Kopnarski, M. [Institute for Surface and Thin Film Analysis (IFOS) GmbH and Research Centre OPTIMAS, Kaiserslautern (Germany); Hoth-Hannig, W.; Hannig, M. [Department of Operative Dentistry and Periodontology, University Hospital of the Saarland, Homburg (Germany)

    2010-04-15

    Two model proteins, bovine serum albumin (BSA) and lysozyme (LSZ), were used to study adsorption behavior on dental titanium by time-of-flight secondary ion mass spectrometry (ToF-SIMS). Protein films were prepared as single component layers and as mixtures of the two proteins. Additionally, the behavior of consecutive adsorption of both proteins was investigated. The obtained data were analyzed by means of principal component analysis (PCA). Dental titanium samples with a layer consisting of simply one protein could be separated from each other by selecting amino acid related peaks and using PCA or samples coated with a mixture of both proteins, the differentiation was also possible. The partial displacement of LSZ molecules by BSA was shown in the case of simultaneous adsorption. The consecutive adsorption of BSA and subsequently LSZ resulted in layers with a bigger amount of LSZ than of BSA compared to the layers obtained by simultaneous adsorption. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  18. Investigation of atomic level patterns in protein--small ligand interactions.

    Directory of Open Access Journals (Sweden)

    Ke Chen

    Full Text Available BACKGROUND: Shape complementarity and non-covalent interactions are believed to drive protein-ligand interaction. To date protein-protein, protein-DNA, and protein-RNA interactions were systematically investigated, which is in contrast to interactions with small ligands. We investigate the role of covalent and non-covalent bonds in protein-small ligand interactions using a comprehensive dataset of 2,320 complexes. METHODOLOGY AND PRINCIPAL FINDINGS: We show that protein-ligand interactions are governed by different forces for different ligand types, i.e., protein-organic compound interactions are governed by hydrogen bonds, van der Waals contacts, and covalent bonds; protein-metal ion interactions are dominated by electrostatic force and coordination bonds; protein-anion interactions are established with electrostatic force, hydrogen bonds, and van der Waals contacts; and protein-inorganic cluster interactions are driven by coordination bonds. We extracted several frequently occurring atomic-level patterns concerning these interactions. For instance, 73% of investigated covalent bonds were summarized with just three patterns in which bonds are formed between thiol of Cys and carbon or sulfur atoms of ligands, and nitrogen of Lys and carbon of ligands. Similar patterns were found for the coordination bonds. Hydrogen bonds occur in 67% of protein-organic compound complexes and 66% of them are formed between NH- group of protein residues and oxygen atom of ligands. We quantify relative abundance of specific interaction types and discuss their characteristic features. The extracted protein-organic compound patterns are shown to complement and improve a geometric approach for prediction of binding sites. CONCLUSIONS AND SIGNIFICANCE: We show that for a given type (group of ligands and type of the interaction force, majority of protein-ligand interactions are repetitive and could be summarized with several simple atomic-level patterns. We summarize

  19. Investigating CFTR and KCa3.1 Protein/Protein Interactions.

    Directory of Open Access Journals (Sweden)

    Hélène Klein

    Full Text Available In epithelia, Cl- channels play a prominent role in fluid and electrolyte transport. Of particular importance is the cAMP-dependent cystic fibrosis transmembrane conductance regulator Cl- channel (CFTR with mutations of the CFTR encoding gene causing cystic fibrosis. The bulk transepithelial transport of Cl- ions and electrolytes needs however to be coupled to an increase in K+ conductance in order to recycle K+ and maintain an electrical driving force for anion exit across the apical membrane. In several epithelia, this K+ efflux is ensured by K+ channels, including KCa3.1, which is expressed at both the apical and basolateral membranes. We show here for the first time that CFTR and KCa3.1 can physically interact. We first performed a two-hybrid screen to identify which KCa3.1 cytosolic domains might mediate an interaction with CFTR. Our results showed that both the N-terminal fragment M1-M40 of KCa3.1 and part of the KCa3.1 calmodulin binding domain (residues L345-A400 interact with the NBD2 segment (G1237-Y1420 and C- region of CFTR (residues T1387-L1480, respectively. An association of CFTR and F508del-CFTR with KCa3.1 was further confirmed in co-immunoprecipitation experiments demonstrating the formation of immunoprecipitable CFTR/KCa3.1 complexes in CFBE cells. Co-expression of KCa3.1 and CFTR in HEK cells did not impact CFTR expression at the cell surface, and KCa3.1 trafficking appeared independent of CFTR stimulation. Finally, evidence is presented through cross-correlation spectroscopy measurements that KCa3.1 and CFTR colocalize at the plasma membrane and that KCa3.1 channels tend to aggregate consequent to an enhanced interaction with CFTR channels at the plasma membrane following an increase in intracellular Ca2+ concentration. Altogether, these results suggest 1 that the physical interaction KCa3.1/CFTR can occur early during the biogenesis of both proteins and 2 that KCa3.1 and CFTR form a dynamic complex, the formation of which

  20. Investigating the dynamics of recombinant protein secretion from a microalgal host.

    Science.gov (United States)

    Lauersen, Kyle J; Huber, Isabel; Wichmann, Julian; Baier, Thomas; Leiter, Andreas; Gaukel, Volker; Kartushin, Viktor; Rattenholl, Anke; Steinweg, Christian; von Riesen, Lena; Posten, Clemens; Gudermann, Frank; Lütkemeyer, Dirk; Mussgnug, Jan H; Kruse, Olaf

    2015-12-10

    Production of recombinant proteins with microalgae represents an alternative platform over plant- or bacterial-based expression systems for certain target proteins. Secretion of recombinant proteins allows accumulation of the target product physically separate from the valuable algal biomass. To date, there has been little investigation into the dynamics of recombinant protein secretion from microalgal hosts-the culture parameters that encourage secreted product accumulation and stability, while encouraging biomass production. In this work, the efficiency of recombinant protein production was optimized by adjusting cultivation parameters for a strain of Chlamydomonas reinhardtii previously engineered to secrete a functional recombinant Lolium perenne ice binding protein (LpIBP), which has applications as a frozen food texturing and cryopreservation additive, into its culture medium. Three media and several cultivation styles were investigated for effects on secreted LpIBP titres and culture growth. A combination of acetate and carbon dioxide feeding with illumination resulted in the highest overall biomass and recombinant protein titres up to 10mgL(-1) in the culture medium. Pure photoautotrophic production was possible using two media types, with recombinant protein accumulation in all cultivations correlating to culture cell density. Two different cultivation systems were used for scale-up to 10L cultivations, one of which produced yields of secreted recombinant protein up to 12mgL(-1) within six cultivation days. Functional ice recrystallization inhibition (IRI) of the LpIBP from total concentrated extracellular protein extracts was demonstrated in a sucrose solution used as a simplified ice cream model. IRI lasted up to 7 days, demonstrating the potential of secreted products from microalgae for use as food additives. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. Investigation of whey protein concentration by ultrafiltration elements designed for water treatment

    Directory of Open Access Journals (Sweden)

    Kukučka Miroslav Đ.

    2013-01-01

    Full Text Available Suitability of polysulfone ultrafiltration membranes (UFM commercial designed for water treatment have been investigated for separation of protein (PR from sweet whey. Ultrafiltration (UF of whey originated from dairy has been realized by self-made pilot plant which has been in service about one year. Influence of two whey temperatures (9 oC and 30 oC on efficiency of protein concentration has been examined. Application of investigated UF elements has given whey protein concentrate (WPC with 5 to 6 times excess amount of protein content in regard to starting one. In the same time the prevalent content of lactose has been removed to permeate. Better results have been occurred during the cold whey filtration. Besides the fact that molecular weight cut-off (MWCO of investigated membranes were 50-100 kDa, results showed very successful concentrating of whey proteins of dominantly lower molar weights than 50-100 kDa. Investigated membranes are beneficial for design and construction of UF plants for exploitation in small dairies.

  2. Proteomic Investigation of Falciparum and Vivax Malaria for Identification of Surrogate Protein Markers

    Science.gov (United States)

    Ray, Sandipan; Renu, Durairaj; Srivastava, Rajneesh; Gollapalli, Kishore; Taur, Santosh; Jhaveri, Tulip; Dhali, Snigdha; Chennareddy, Srinivasarao; Potla, Ankit; Dikshit, Jyoti Bajpai; Srikanth, Rapole; Gogtay, Nithya; Thatte, Urmila; Patankar, Swati; Srivastava, Sanjeeva

    2012-01-01

    This study was conducted to analyze alterations in the human serum proteome as a consequence of infection by malaria parasites Plasmodium falciparum and P. vivax to obtain mechanistic insights about disease pathogenesis, host immune response, and identification of potential protein markers. Serum samples from patients diagnosed with falciparum malaria (FM) (n = 20), vivax malaria (VM) (n = 17) and healthy controls (HC) (n = 20) were investigated using multiple proteomic techniques and results were validated by employing immunoassay-based approaches. Specificity of the identified malaria related serum markers was evaluated by means of analysis of leptospirosis as a febrile control (FC). Compared to HC, 30 and 31 differentially expressed and statistically significant (p<0.05) serum proteins were identified in FM and VM respectively, and almost half (46.2%) of these proteins were commonly modulated due to both of the plasmodial infections. 13 proteins were found to be differentially expressed in FM compared to VM. Functional pathway analysis involving the identified proteins revealed the modulation of different vital physiological pathways, including acute phase response signaling, chemokine and cytokine signaling, complement cascades and blood coagulation in malaria. A panel of identified proteins consists of six candidates; serum amyloid A, hemopexin, apolipoprotein E, haptoglobin, retinol-binding protein and apolipoprotein A-I was used to build statistical sample class prediction models. By employing PLS-DA and other classification methods the clinical phenotypic classes (FM, VM, FC and HC) were predicted with over 95% prediction accuracy. Individual performance of three classifier proteins; haptoglobin, apolipoprotein A-I and retinol-binding protein in diagnosis of malaria was analyzed using receiver operating characteristic (ROC) curves. The discrimination of FM, VM, FC and HC groups on the basis of differentially expressed serum proteins demonstrates

  3. Proteomic investigation of falciparum and vivax malaria for identification of surrogate protein markers.

    Directory of Open Access Journals (Sweden)

    Sandipan Ray

    Full Text Available This study was conducted to analyze alterations in the human serum proteome as a consequence of infection by malaria parasites Plasmodium falciparum and P. vivax to obtain mechanistic insights about disease pathogenesis, host immune response, and identification of potential protein markers. Serum samples from patients diagnosed with falciparum malaria (FM (n = 20, vivax malaria (VM (n = 17 and healthy controls (HC (n = 20 were investigated using multiple proteomic techniques and results were validated by employing immunoassay-based approaches. Specificity of the identified malaria related serum markers was evaluated by means of analysis of leptospirosis as a febrile control (FC. Compared to HC, 30 and 31 differentially expressed and statistically significant (p<0.05 serum proteins were identified in FM and VM respectively, and almost half (46.2% of these proteins were commonly modulated due to both of the plasmodial infections. 13 proteins were found to be differentially expressed in FM compared to VM. Functional pathway analysis involving the identified proteins revealed the modulation of different vital physiological pathways, including acute phase response signaling, chemokine and cytokine signaling, complement cascades and blood coagulation in malaria. A panel of identified proteins consists of six candidates; serum amyloid A, hemopexin, apolipoprotein E, haptoglobin, retinol-binding protein and apolipoprotein A-I was used to build statistical sample class prediction models. By employing PLS-DA and other classification methods the clinical phenotypic classes (FM, VM, FC and HC were predicted with over 95% prediction accuracy. Individual performance of three classifier proteins; haptoglobin, apolipoprotein A-I and retinol-binding protein in diagnosis of malaria was analyzed using receiver operating characteristic (ROC curves. The discrimination of FM, VM, FC and HC groups on the basis of differentially expressed serum proteins demonstrates

  4. Protein oligomerization equilibria and kinetics investigated by fluorescence correlation spectroscopy: a mathematical treatment.

    Science.gov (United States)

    Kanno, David M; Levitus, Marcia

    2014-10-30

    Fluorescence correlation spectroscopy (FCS) is a technique that is increasingly being used to investigate protein oligomerization equilibria and dynamics. Each individual FCS decay is characterized by its amplitude and a characteristic diffusion time, both of which are sensitive to the degree of dissociation of the protein. Here, we provide a mathematical treatment that relates these observables with the parameters of interest: the equilibrium constants of the different protein dissociation steps and their corresponding dissociation and association kinetic rate constants. We focused on the two most common types of protein homooligomers (dimers and tetramers) and on the experimental variables relevant for the design of the experiment (protein concentration, fractional concentration of labeled protein). The analysis of the theoretical expectations for proteins with different dissociation constants is a key aspect of experiment design and data analysis and cannot be performed without a physically accurate treatment of the system. In particular, we show that the analysis of FCS data using some commonly used empirical models may result in a serious misinterpretation of the experimental results.

  5. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    Science.gov (United States)

    Asafi, M. S.; Yildirim, A.; Tekpinar, M.

    2016-04-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated.

  6. Protein and Peptide Composition of Male Accessory Glands of Apis mellifera Drones Investigated by Mass Spectrometry

    Science.gov (United States)

    Gorshkov, Vladimir; Blenau, Wolfgang; Koeniger, Gudrun; Römpp, Andreas; Vilcinskas, Andreas; Spengler, Bernhard

    2015-01-01

    In honeybees, reproductive females usually mate early in their life with more than 10 males in free flight, often within 10 minutes, and then store male gametes for up to five years. Because of the extreme polyandry and mating in free flight special adaptations in males are most likely. We present here the results of an investigation of the protein content of four types of male reproductive glands from the Western honeybee (Apis mellifera) drone, namely seminal vesicles (secretion in ejaculate), as well as bulbus, cornua and mucus glands (secretions for the mating plug). Using high resolution and accuracy mass spectrometry and a combination of database searching and de novo sequencing techniques it was possible to identify 50 different proteins in total, inside all mentioned glands, except in the mucus gland. Most of the proteins are unique for a specific gland type, only one of them (H9KEY1/ATP synthase subunit O) was found in three glands, and 7 proteins were found in two types of glands. The identified proteins represent a wide variety of biological functions and can be assigned to several physiological classes, such as protection, energy generation, maintaining optimal conditions, associated mainly with vesicula seminalis; signaling, cuticle proteins, icarpin and apolipoproteins located mainly in the bulbus and cornua glands; and some other classes. Most of the discovered proteins were not found earlier during investigation of semen, seminal fluid and tissue of reproductive glands of the bee drone. Moreover, we provide here the origin of each protein. Thus, the presented data might shed light on the role of each reproductive gland. PMID:25955586

  7. Protein and Peptide Composition of Male Accessory Glands of Apis mellifera Drones Investigated by Mass Spectrometry.

    Science.gov (United States)

    Gorshkov, Vladimir; Blenau, Wolfgang; Koeniger, Gudrun; Römpp, Andreas; Vilcinskas, Andreas; Spengler, Bernhard

    2015-01-01

    In honeybees, reproductive females usually mate early in their life with more than 10 males in free flight, often within 10 minutes, and then store male gametes for up to five years. Because of the extreme polyandry and mating in free flight special adaptations in males are most likely. We present here the results of an investigation of the protein content of four types of male reproductive glands from the Western honeybee (Apis mellifera) drone, namely seminal vesicles (secretion in ejaculate), as well as bulbus, cornua and mucus glands (secretions for the mating plug). Using high resolution and accuracy mass spectrometry and a combination of database searching and de novo sequencing techniques it was possible to identify 50 different proteins in total, inside all mentioned glands, except in the mucus gland. Most of the proteins are unique for a specific gland type, only one of them (H9KEY1/ATP synthase subunit O) was found in three glands, and 7 proteins were found in two types of glands. The identified proteins represent a wide variety of biological functions and can be assigned to several physiological classes, such as protection, energy generation, maintaining optimal conditions, associated mainly with vesicula seminalis; signaling, cuticle proteins, icarpin and apolipoproteins located mainly in the bulbus and cornua glands; and some other classes. Most of the discovered proteins were not found earlier during investigation of semen, seminal fluid and tissue of reproductive glands of the bee drone. Moreover, we provide here the origin of each protein. Thus, the presented data might shed light on the role of each reproductive gland.

  8. A Molecular Biological and Biochemical Investigation on Mycobacterium tuberculosis MutT Protein.

    Science.gov (United States)

    Huang, Hsiu-Lin; Su, Ho-Ting; Wu, Chung-Hsiun Herbert; Tsai-Wu, Jyy-Jih

    2014-03-01

    Mycobacterium tuberculosis is a vicious microbe co-existing with the infected host. This pathogen exploited opportunities to spread during periods of urbanization and social upheaval, and got retreated with improved hygiene. This investigation was designed to clone and characterize M. tuberculosis mutT gene, a homologue of a DNA repair protein in Escherichia coli. The aim was to depict the possible role of this homologue in the virulent microbe. A DNA fragment of the mutT gene was amplified with PCR from the genomic DNA of strain H37Rv M. tuberculosis. The expression vector was transformed into E. coli strains BL21 (DE3) and MK602 (DE3) (mutT-). The protein activity assay was performed by biochemical methods. M. tuberculosis MutT shares 23% identity with the E. coli MutT protein. The mutT gene DNA fragment was subcloned into the expression vector pET28a(+) and the recombinant plasmid was overexpressed in E. coli. Purified and refolded M. tuberculosis MutT possesses a dGTPase activity, which is one of the most well-known preference nucleotidase activities of MutT in E. coli. This study also showed that the dGTPase activity of M. tuberculosis MutT was enhanced by magnesium and inhibited by Ni(2+) or EDTA. Endogenous MutT protein in M. tuberculosis lysate displayed a smear pattern in the Western blot, suggesting instability of this protein in the bacteria similar to the important proteins, such as P53 protein, tightly regulated by protein degradation. The cloned M. tuberculosis mutT gene and MutT protein were characterized. M. tuberculosis MutT has a dGTPase activity, which is one of the most well-known preference nucleotidase activities of MutT in E. coli. These findings provide further understanding about the vicious bacterium.

  9. Proteomic Investigation of Ram Spermatozoa and the Proteins Conferred by Seminal Plasma.

    Science.gov (United States)

    Pini, Taylor; Leahy, Tamara; Soleilhavoup, Clement; Tsikis, Guillaume; Labas, Valerie; Combes-Soia, Lucie; Harichaux, Gregoire; Rickard, Jessica P; Druart, Xavier; de Graaf, Simon P

    2016-10-07

    Sperm proteomes have emerged for several species; however, the extent of species similarity is unknown. Sheep are an important agricultural species for which a comprehensive sperm proteome has not been produced. In addition, potential proteomic factors from seminal plasma that may contribute to improved fertility after cervical insemination are yet to be explored. Here we use liquid chromatography-tandem mass spectrometry to investigate the proteome of ejaculated ram spermatozoa, with quantitative comparison to epididymal spermatozoa. We also present a comparison to published proteomes of five other species. We identified 685 proteins in ejaculated ram spermatozoa, with the most abundant proteins involved in metabolic pathways. Only 5% of ram sperm proteins were not detected in other species, which suggest highly conserved structures and pathways. Of the proteins present in both epididymal and ejaculated ram spermatozoa, 7% were more abundant in ejaculated spermatozoa. Only two membrane-bound proteins were detected solely in ejaculated sperm lysates: liver enriched gene 1 (LEG1/C6orf58) and epidermal growth factor-like repeats and discoidin I-like domains 3 (EDIL3). This is the first evidence that despite its relatively complex proteomic composition, seminal plasma exposure leads to few novel proteins binding tightly to the ram sperm plasma membrane.

  10. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    DEFF Research Database (Denmark)

    Celebioglu, Hilal Yilmaz

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers...... submaxillary mucin (BSM), a major salivary protein, were studied using high and low field Nuclear Magnetic Resonance (NMR), Dynamic Light Scattering (DLS), and Circular Dichroism (CD) spectroscopy. The zeta potentials of the proteins were also measured to provide information on the role of electrostatic forces...

  11. AN INVESTIGATION OF THE PROTONATION STATES OF HUMAN LACTOFERRIN IRON-BINDING PROTEIN

    Directory of Open Access Journals (Sweden)

    Lilia Anghel

    2015-06-01

    Full Text Available In this study, the protonation states of ionizable groups of human lactoferrin in various conformations were investigated theoretically, at physiological pH (7.365. These calculations show that the transition of the protein from a conformation to another one is accompanied by changes in the protonation state of specific amino acid residues. Analysis of the pKa calculatons underlined the importance of participation of two arginines and one lysine in the opening / closing of the protein. In addition, it was found that the mechanism of iron release depends on the protonation state of TYR-192. Protonated state of this residue in the closed form of lactoferrin will trigger the opening of protein and release of iron ions.

  12. Controlled in meso phase crystallization--a method for the structural investigation of membrane proteins.

    Directory of Open Access Journals (Sweden)

    Jan Kubicek

    Full Text Available We investigated in meso crystallization of membrane proteins to develop a fast screening technology which combines features of the well established classical vapor diffusion experiment with the batch meso phase crystallization, but without premixing of protein and monoolein. It inherits the advantages of both methods, namely (i the stabilization of membrane proteins in the meso phase, (ii the control of hydration level and additive concentration by vapor diffusion. The new technology (iii significantly simplifies in meso crystallization experiments and allows the use of standard liquid handling robots suitable for 96 well formats. CIMP crystallization furthermore allows (iv direct monitoring of phase transformation and crystallization events. Bacteriorhodopsin (BR crystals of high quality and diffraction up to 1.3 Å resolution have been obtained in this approach. CIMP and the developed consumables and protocols have been successfully applied to obtain crystals of sensory rhodopsin II (SRII from Halobacterium salinarum for the first time.

  13. Enhanced Open-Circuit Voltage in Colloidal Quantum Dot Photovoltaics via Reactivity-Controlled Solution-Phase Ligand Exchange

    KAUST Repository

    Jo, Jea Woong

    2017-10-09

    The energy disorder that arises from colloidal quantum dot (CQD) polydispersity limits the open-circuit voltage (VOC) and efficiency of CQD photovoltaics. This energy broadening is significantly deteriorated today during CQD ligand exchange and film assembly. Here, a new solution-phase ligand exchange that, via judicious incorporation of reactivity-engineered additives, provides improved monodispersity in final CQD films is reported. It has been found that increasing the concentration of the less reactive species prevents CQD fusion and etching. As a result, CQD solar cells with a VOC of 0.7 V (vs 0.61 V for the control) for CQD films with exciton peak at 1.28 eV and a power conversion efficiency of 10.9% (vs 10.1% for the control) is achieved.

  14. Enhanced Open-Circuit Voltage in Colloidal Quantum Dot Photovoltaics via Reactivity-Controlled Solution-Phase Ligand Exchange.

    Science.gov (United States)

    Jo, Jea Woong; Kim, Younghoon; Choi, Jongmin; de Arquer, F Pelayo García; Walters, Grant; Sun, Bin; Ouellette, Olivier; Kim, Junghwan; Proppe, Andrew H; Quintero-Bermudez, Rafael; Fan, James; Xu, Jixian; Tan, Chih Shan; Voznyy, Oleksandr; Sargent, Edward H

    2017-11-01

    The energy disorder that arises from colloidal quantum dot (CQD) polydispersity limits the open-circuit voltage (V OC ) and efficiency of CQD photovoltaics. This energy broadening is significantly deteriorated today during CQD ligand exchange and film assembly. Here, a new solution-phase ligand exchange that, via judicious incorporation of reactivity-engineered additives, provides improved monodispersity in final CQD films is reported. It has been found that increasing the concentration of the less reactive species prevents CQD fusion and etching. As a result, CQD solar cells with a V OC of 0.7 V (vs 0.61 V for the control) for CQD films with exciton peak at 1.28 eV and a power conversion efficiency of 10.9% (vs 10.1% for the control) is achieved. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  15. Investigation of selection methods im mutation breeding of barley for protein quantity and quality

    International Nuclear Information System (INIS)

    Ulonska, E.; Gaul, H.; Baumer, M.; Gesellschaft fuer Strahlen- und Umweltforschung m.b.H., Gruenbach

    1975-01-01

    This mutation breeding programme is investigating the qualification of micro-mutations for the selection of improved protein quality and quantity. Normally, improvement of protein content in micro-mutations is rather small. Therefore, it is important to develop methods and conditions of selection being (a) capable of measuring these small deviations in protein content and quality, and (b) simple to use. In two experiments carried out in 1971 and 1972 nitrogen fertilization was found to be the most important factor in the improvement of selection conditions. There is a highly significant negative correlation between crude protein content and the standard deviation; i.e. the higher the content of crude protein, the lower the variation coefficient. This in turn leads to an increase of genetic variation necessary for better selection progress. Nitrogen fertilization, especially during ear emergence, covers environmental influences - e.g., planting space, sowing rate, growing in different plots (6, 3, 2, 1 rows or in half-ear hills) - to a great extent. Thus, by applying high doses of nitrogen dressings comparable results can be achieved. In an overall selection experiment (testing the entire crossing and mutation material available at Weihenstephan in a stepwise selection from 1971 to 1973) and two selection experiments conducted in 1971 to 1973 with micro-mutants - variety Nota, 4 times X-rayed and the naked barley strain 1606 treated once with EMS - significant selection results were found. (author)

  16. Structural investigation of ribonuclease A conformational preferences using high pressure protein crystallography

    Energy Technology Data Exchange (ETDEWEB)

    Kurpiewska, Katarzyna, E-mail: kurpiews@chemia.uj.edu.pl [Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Protein Crystallography Group, Ingardena 3, 30-060 Kraków (Poland); Dziubek, Kamil; Katrusiak, Andrzej [Adam Mickiewicz University, Faculty of Chemistry, Department of Materials Chemistry, Umultowska 89b, 61-61 Poznań (Poland); Font, Josep [School of Medical Science, University of Sydney, NSW 2006 (Australia); Ribò, Marc; Vilanova, Maria [Universitat de Girona, Laboratorid’Enginyeria de Proteïnes, Departament de Biologia, Facultat de Ciències, Campus de Montilivi, 17071 Girona (Spain); Lewiński, Krzysztof [Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Protein Crystallography Group, Ingardena 3, 30-060 Kraków (Poland)

    2016-04-01

    Highlights: • A unique crystallographic studies of wild-type and mutated form of the same protein under high pressure. • Compressibility of RNase A molecule is significantly affected by a single amino acid substitution. • High pressure protein crystallography helps understanding protein flexibility and identify conformational substrates. - Abstract: Hydrostatic pressure in range 0.1–1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. The idea of the presented experiments is to examine the behaviour of RNase A molecule under high pressure before and after introduction of destabilizing mutation. For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. X-ray diffraction experiments at high pressure showed that the secondary structure of RNase A is well preserved even beyond 0.67 GPa at room temperature. Detailed structural analysis of ribonuclease A conformation observed under high pressure revealed that pressure influences hydrogen bonds pattern, cavity size and packing of molecule.

  17. A Simple Surfactant-Free Solution Phase Synthesis of Flower-like In2S3 Hierarchitectures and their Photocatalytic Activities

    Directory of Open Access Journals (Sweden)

    Rengaraj Selvaraj

    2015-02-01

    Full Text Available Flower-like In2S3 hierarchical nanostructures were successfully prepared via a facile solution-phase route, using thiacetamide as both sulfur source and capping agent. Our experimental results demonstrated that the morphology of these In2S3 nanostructures can be easily modified by changing the ratio of In(NO33/thiacetamide. With the ratio increasing from 1:1.5 to 1:6, the In2S3 crystals exhibited flower-like morphology of varying size. XRD and HRTEM of the flowers revealed the cubic structure of In2S3; morphological studies examined by SEM and TEM showed that the synthesized In2S3 nanostructure was a flower-like hierarchitecture assembled from nanoscale flakes. XPS and EDX analysis confirmed the stoichiometry of In2S3 nanoflowers. The optical properties were investigated by UV-vis DRS, which indicated that the In2S3 nanoflower samples possess a band gap from 1.90 to 1.97 eV. Furthermore, photocatalytic activity studies revealed that the prepared In2S3 nanoflowers exhibit an excellent photocatalytic performance, degrading rapidly the aqueous methylene blue dye solution under visible light irradiation. These results suggest that In2S3 nanoflowers will be a promising candidate for a photocatalyst working under the visible light range.

  18. In silico investigation of lactoferrin protein characterizations for the prediction of anti-microbial properties

    OpenAIRE

    Sohrabi, Seyyed Mohsen; Niazi, Ali; Chahardoli, Mahmood; Hortamani, Ali; Setoodeh, Payam

    2014-01-01

    Lactoferrin (Lf) is an iron-binding multi-functional glycoprotein which has numerous physiological functions such as iron transportation, anti-microbial activity and immune response. In this study, different in silico approaches were exploited to investigate Lf protein properties in a number of mammalian species. Results showed that the iron-binding site, DNA and RNA-binding sites, signal peptides and transferrin motifs in the Lf structure were highly conserved. Examined sequences showed thre...

  19. A Molecular Biological and Biochemical Investigation on Mycobacterium tuberculosis MutT Protein

    OpenAIRE

    Huang, Hsiu-Lin; Su, Ho-Ting; Wu, Chung-Hsiun Herbert; Tsai-Wu, Jyy-Jih

    2014-01-01

    Background: Mycobacterium tuberculosis is a vicious microbe co-existing with the infected host. This pathogen exploited opportunities to spread during periods of urbanization and social upheaval, and got retreated with improved hygiene. Objectives: This investigation was designed to clone and characterize M. tuberculosis mutT gene, a homologue of a DNA repair protein in Escherichia coli. The aim was to depict the possible role of this homologue in the virulent microbe. Materials and Methods: ...

  20. Investigating the Chaperone Properties of a Novel Heat Shock Protein, Hsp70.c, from Trypanosoma brucei

    Directory of Open Access Journals (Sweden)

    Adélle Burger

    2014-01-01

    Full Text Available The neglected tropical disease, African Trypanosomiasis, is fatal and has a crippling impact on economic development. Heat shock protein 70 (Hsp70 is an important molecular chaperone that is expressed in response to stress and Hsp40 acts as its co-chaperone. These proteins play a wide range of roles in the cell and they are required to assist the parasite as it moves from a cold blooded insect vector to a warm blooded mammalian host. A novel cytosolic Hsp70, from Trypanosoma brucei, TbHsp70.c, contains an acidic substrate binding domain and lacks the C-terminal EEVD motif. The ability of a cytosolic Hsp40 from Trypanosoma brucei J protein 2, Tbj2, to function as a co-chaperone of TbHsp70.c was investigated. The main objective was to functionally characterize TbHsp70.c to further expand our knowledge of parasite biology. TbHsp70.c and Tbj2 were heterologously expressed and purified and both proteins displayed the ability to suppress aggregation of thermolabile MDH and chemically denatured rhodanese. ATPase assays revealed a 2.8-fold stimulation of the ATPase activity of TbHsp70.c by Tbj2. TbHsp70.c and Tbj2 both demonstrated chaperone activity and Tbj2 functions as a co-chaperone of TbHsp70.c. In vivo heat stress experiments indicated upregulation of the expression levels of TbHsp70.c.

  1. Structural investigations of the Bacillus subtilis SPP1 phage G39P helicase inhibitor loading protein

    CERN Document Server

    Bailey, S

    2002-01-01

    The Bacillus subtilis SPPI phage encoded protein G39P is a loader and inhibitor of the phage G40P replicative helicase involved in the initiation of phage DNA replication. The 2.4A crystal structure of a C-terminal truncated variant of G39P was solved using multiple wavelength anomalous dispersion exploiting the anomalous signal of seleno- methionine substituted protein. Inspection of the electron density maps revealed the asymmetric unit contained three independent G39P monomers, composed of 3 alpha-helices and their connecting loops. However, the model only accounted for the first 67 residues of the protein, as there was no interpretable electron density for residues 68 to 112. A preliminary NMR investigation revealed the C-terminal region of the protein had rapid internal motion and formed no well-defined stable fold that involved immobilized side chains. This is consistent with the X-ray analysis that displayed no electron density for these residues. A detailed comparison of NMR spectra from the C-termina...

  2. Investigation of protein detection parameters using nanofunctionalized organic field-effect transistors.

    Science.gov (United States)

    Hammock, Mallory L; Knopfmacher, Oren; Naab, Benjamin D; Tok, Jeffrey B-H; Bao, Zhenan

    2013-05-28

    Biodetection using organic field-effect transistors (OFETs) is gaining increasing interest for applications as diverse as food security, environmental monitoring, and medical diagnostics. However, there still lacks a comprehensive, empirical study on the fundamental limits of OFET sensors. In this paper, we present a thorough study of the various parameters affecting biosensing using an OFET decorated with gold nanoparticle (AuNP) binding sites. These parameters include the spacing between receptors, pH of the buffer, and ionic strength of the buffer. To this end, we employed the thrombin protein and its corresponding DNA binding aptamer to form our model detection system. We demonstrate a detection limit of 100 pM for this protein with high selectivity over other proteases in situ. We describe herein a feasible approach for protein detection with OFETs and a thorough investigation of parameters governing biodetection events using OFETs. Our obtained results should provide important guidelines to tailor the sensor's dynamic range to suit other desired OFET-based biodetection applications.

  3. Investigation of protein and lipid metabolism in thyroid pathology using whole-body radiometry

    International Nuclear Information System (INIS)

    Gorobets, V.F.; Matveenko, E.G.

    1987-01-01

    Radiometry of the whole body and its organs was employed to study certain aspects of protein-aminoacid and lipid metabolism in patients with thyroid diseases. Metabolism of human serum 131 I-albumin was studied in 12 patients with neurocirculatory dystonia, in 13 patients with diffuse toxic goiter (in 10 before and after drug therapy) and in 9 controls. 75 Se-methionine aminoacid metabolism was investigated in 9 patients with toxic thyroid adenoma and in 13 controls. The body cell mass was determined in 82 patients with thyrotoxicosis by a measurable amount of 40 K. These data were compared with those of 249 healthy persons. An increase in catabolism of labeled albumin, intensification of labeled methionine metabolism at the tissue level, signs of a decrease in the total amount of metabolic albumin in the body were revealed. Intensification of protein metabolism resulted in a decrease in the body cell mass of these patients. After adequate therapy the above indices of protein metabolism in patients with thyrotoxicosis returned to normal. The assimilation of fatty acids and neutral fat was disturbed both in thyrotoxicosis and hypothyroidism

  4. Discovery of a thermally persistent h.c.p. solid-solution phase in the Ni-W system

    International Nuclear Information System (INIS)

    Kurz, S. J. B.; Leineweber, A.; Maisel, S. B.; Höfler, M.; Müller, S.; Mittemeijer, E. J.

    2014-01-01

    Although the accepted Ni-W phase diagram does not reveal the existence of h.c.p.-based phases, h.c.p.-like stacking sequences were observed in magnetron-co-sputtered Ni-W thin films at W contents of 20 to 25 at. %, by using transmission electron microscopy and X-ray diffraction. The occurrence of this h.c.p.-like solid-solution phase could be rationalized by first-principles calculations, showing that the vicinity of the system's ground-state line is populated with metastable h.c.p.-based superstructures in the intermediate concentration range from 20 to 50 at. % W. The h.c.p.-like stacking in Ni-W films was observed to be thermally persistent, up to temperatures as high as at least 850 K, as evidenced by extensive X-ray diffraction analyses on specimens before and after annealing treatments. The tendency of Ni-W for excessive planar faulting is discussed in the light of these new findings

  5. Investigating protein folding and unfolding in electrospray nanodrops upon rapid mixing using theta-glass emitters.

    Science.gov (United States)

    Mortensen, Daniel N; Williams, Evan R

    2015-01-20

    Theta-glass emitters are used to rapidly mix two solutions to induce either protein folding or unfolding during nanoelectrospray (nanoESI). Mixing acid-denatured myoglobin with an aqueous ammonium acetate solution to increase solution pH results in protein folding during nanoESI. A reaction time and upper limit to the droplet lifetime of 9 ± 2 μs is obtained from the relative abundance of the folded conformer in these rapid mixing experiments compared to that obtained from solutions at equilibrium and a folding time constant of 7 μs. Heme reincorporation does not occur, consistent with the short droplet lifetime and the much longer time constant for this process. Similar mixing experiments with acid-denatured cytochrome c and the resulting folding during nanoESI indicate a reaction time of between 7 and 25 μs depending on the solution composition. The extent of unfolding of holo-myoglobin upon rapid mixing with theta-glass emitters is less than that reported previously ( Fisher et al. Anal. Chem. 2014 , 86 , 4581 - 4588 ), a result that is attributed to the much smaller, ∼1.5 μm, average o.d. tips used here. These results indicate that the time frame during which protein folding or unfolding can occur during nanoESI depends both on the initial droplet size, which can be varied by changing the emitter tip diameter, and on the solution composition. This study demonstrates that protein folding or unfolding processes that occur on the ∼10 μs time scale can be readily investigated using rapid mixing with theta-glass emitters combined with mass spectrometry.

  6. Investigation of the reactions of histone protein hydroperoxides and their role in DNA damage

    International Nuclear Information System (INIS)

    Luxford, C.; Dean, R.T.; Davies, M.J.

    1998-01-01

    Free radical attack on DNA results in base changes, cross-linking and strand cleavage leading to mutations if unrepaired. Histone proteins are intimately involved in DNA packaging and are excellent candidates for investigating DNA damage arising from protein-OOH-derived radicals. This study aimed (i) to investigate the formation of hydroperoxide on the linker histone H1 via radical reactions in the presence of O 2 ; (ii) to examine the radicals formed from transition metal ion-catalyzed breakdown of histone H1-OOH and (iii) to determine whether histone H1-OOH-derived radicals can damage DNA and free bases. (i) Histone H1 solutions were γ-irradiated ( 60 Co source) in the presence of O 2 and histone H1-OOH concentrations determined using a manual iodometric assay. Formation ( histone H1-OOH was dose-dependent and, in the absence of light or transition metal ions these hydroperoxides were found to be very stable (half life of 24 hours at 4degC ). (ii) Electron Paramagnetic Resonance (EPR) spectroscopy and spin trapping was used t investigate the Cu + -catalyzed breakdown of histone H1-OOH to form histone H1 protein side chain and -backbone carbon-centred radicals. Further EPR/spin trapping experiments showed that histone H1-OOH-derived radicals can oxidise pyrimidine bases (eg. uridine with the resultant trapping of three radical species; two pyrimidine radicals, C5-yl and Ct yl adducts (via addition of histone H1-OOH-derived radicals to the C5-C6 double bond o the pyrimidine ring) and an acyl radical adduct, whose origin is currently unknown. (iii) Damage to DNA and 2'-deoxyguanosine after reaction of histone H1-OOH-derive radicals were detected and quantified using HPLC (with EC and UV detection). We have identified 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) as a significant product ( histone H1-OOH-derived oxidative DNA modification. Increasing histone H1-OOH concentrations resulted in a concomitant increase in the amount of 8-oxodG formed. Our studies show

  7. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  8. Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

    Science.gov (United States)

    Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

    2016-05-01

    The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

  9. Sensitizing curium luminescence through an antenna protein to investigate biological actinide transport mechanisms.

    Science.gov (United States)

    Sturzbecher-Hoehne, Manuel; Goujon, Christophe; Deblonde, Gauthier J-P; Mason, Anne B; Abergel, Rebecca J

    2013-02-20

    Worldwide stocks of actinides and lanthanide fission products produced through conventional nuclear spent fuel are increasing continuously, resulting in a growing risk of environmental and human exposure to these toxic radioactive metal ions. Understanding the biomolecular pathways involved in mammalian uptake, transport and storage of these f-elements is crucial to the development of new decontamination strategies and could also be beneficial to the design of new containment and separation processes. To start unraveling these pathways, our approach takes advantage of the unique spectroscopic properties of trivalent curium. We clearly show that the human iron transporter transferrin acts as an antenna that sensitizes curium luminescence through intramolecular energy transfer. This behavior has been used to describe the coordination of curium within the two binding sites of the protein and to investigate the recognition of curium-transferrin complexes by the cognate transferrin receptor. In addition to providing the first protein-curium spectroscopic characterization, these studies prove that transferrin receptor-mediated endocytosis is a viable mechanism of intracellular entry for trivalent actinides such as curium and provide a new tool utilizing the specific luminescence of curium for the determination of other biological actinide transport mechanisms.

  10. Root cause investigation of deviations in protein chromatography based on mechanistic models and artificial neural networks.

    Science.gov (United States)

    Wang, Gang; Briskot, Till; Hahn, Tobias; Baumann, Pascal; Hubbuch, Jürgen

    2017-09-15

    In protein chromatography, process variations, such as aging of column or process errors, can result in deviations of the product and impurity levels. Consequently, the process performance described by purity, yield, or production rate may decrease. Based on visual inspection of the UV signal, it is hard to identify the source of the error and almost unfeasible to determine the quantity of deviation. The problem becomes even more pronounced, if multiple root causes of the deviation are interconnected and lead to an observable deviation. In the presented work, a novel method based on the combination of mechanistic chromatography models and the artificial neural networks is suggested to solve this problem. In a case study using a model protein mixture, the determination of deviations in column capacity and elution gradient length was shown. Maximal errors of 1.5% and 4.90% for the prediction of deviation in column capacity and elution gradient length respectively demonstrated the capability of this method for root cause investigation. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

  11. Plastic protein microarray to investigate the molecular pathways of magnetic nanoparticle-induced nanotoxicity

    International Nuclear Information System (INIS)

    Liu Yingshuai; Li Xuelian; Bao Shujuan; Lu Zhisong; Li Changming; Li Qing

    2013-01-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) (about 15 nm) were synthesized via a hydrothermal method and characterized by field emission scanning electron microscopy, transmission electron microscopy, dynamic light scattering, x-ray diffraction, and vibrating sample magnetometer. The molecular pathways of SPIONs-induced nanotoxicity was further investigated by protein microarrays on a plastic substrate from evaluation of cell viability, reactive oxygen species (ROS) generation and cell apoptosis. The experimental results reveal that 50 μg ml −1 or higher levels of SPIONs cause significant loss of cell viability, considerable generation of ROS and cell apoptosis. It is proposed that high level SPIONs could induce cell apoptosis via a mitochondria-mediated intrinsic pathway by activation of caspase 9 and caspase 3, an increase of the Bax/Bcl-2 ratio, and down-regulation of HSP70 and HSP90 survivor factors. (paper)

  12. Plastic protein microarray to investigate the molecular pathways of magnetic nanoparticle-induced nanotoxicity

    Science.gov (United States)

    Liu, Yingshuai; Li, Xuelian; Bao, Shujuan; Lu, Zhisong; Li, Qing; Li, Chang Ming

    2013-05-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) (about 15 nm) were synthesized via a hydrothermal method and characterized by field emission scanning electron microscopy, transmission electron microscopy, dynamic light scattering, x-ray diffraction, and vibrating sample magnetometer. The molecular pathways of SPIONs-induced nanotoxicity was further investigated by protein microarrays on a plastic substrate from evaluation of cell viability, reactive oxygen species (ROS) generation and cell apoptosis. The experimental results reveal that 50 μg ml-1 or higher levels of SPIONs cause significant loss of cell viability, considerable generation of ROS and cell apoptosis. It is proposed that high level SPIONs could induce cell apoptosis via a mitochondria-mediated intrinsic pathway by activation of caspase 9 and caspase 3, an increase of the Bax/Bcl-2 ratio, and down-regulation of HSP70 and HSP90 survivor factors.

  13. The routine use of C-reactive protein in forensic investigations

    DEFF Research Database (Denmark)

    Astrup, B S; Thomsen, Jørgen Lange

    2007-01-01

    with special reference to the cause of death and survival time, Forensic Sci. Int. 130 (2002) 160-166; L. Uhlin-Hansen, C-reactive protein (CRP), a comparison of pre- and post-mortem blood levels, Forensic Sci. Int. 124 (2001) 32-35]. We have analysed the routine use of CRP in non-selected cases. Scarcity...... of blood available for analysis is a common problem in forensic investigation, and in response to this we have developed a method using liver as a source. In 50 consecutive autopsy cases, we have evaluated method, validated results and discussed their interpretation. In three cases the analysis......, and liver is a good post-mortem alternative when blood is not available. We conclude that CRP measurements are easy, viable and inexpensive in a forensic setting, and that the number of cases with CRP elevation is high in a non-selected forensic material. In cases of doubt, marked elevation of CRP...

  14. Protein supplements and adolescent athletes: A pilot study investigating the risk knowledge, motivations and prevalence of use.

    Science.gov (United States)

    Whitehouse, Gavin; Lawlis, Tanya

    2017-11-01

    Protein-based sports supplements are among the more common types of nutrition supplements consumed by athletes; however, there is currently limited data investigating the knowledge, motivations and occurrence of use among the adolescent population (13-18 years). This pilot study looks to obtain initial data regarding the use of protein supplements in this population. This study investigates the understanding and occurrence of protein supplement use in 87 adolescent athletes based in an Australian capital city who compete in a variety of sports. Sources of information, regularity of use, purchasing habits, associated risk knowledge and supplement beliefs were examined using a self-reported, written questionnaire. A total of 60% (n = 52) of athletes reported using protein supplements, with a positive relationship between age and use (P supplement consumption, with the most common risk reported as 'I don't know' (22%). Coaches were found to initiate protein supplement use more than other figures in the athlete's life (50%) and were the primary source of information regarding supplements (58%). It was found that 19% of adolescent athletes obtained information about protein supplements from the Internet, and 17% of all consumers purchase their supplements online. The evident lack of knowledge regarding protein supplements demonstrates a necessity for further education of athletes, coaches and families regarding the responsible purchasing and use of protein supplements in the current landscape of sports nutrition. Future research should further explore the role of the Internet in protein supplement purchase and education. © 2017 Dietitians Association of Australia.

  15. Investigating the fate of activated sludge extracellular proteins in sludge digestion using sodium dodecyl sulfate polyacrylamide gel electrophoresis.

    Science.gov (United States)

    Park, Chul; Helm, Richard F; Novak, John T

    2008-12-01

    The fate of activated sludge extracellular proteins in sludge digestion was investigated using three different cation-associated extraction methods and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Extraction methods used were the cation exchange resin (CER) method for extracting calcium (Ca2+) and magnesium (Mg2+), sulfide extraction for removing iron, and base treatment (pH 10.5) for dissolving aluminum. Extracellular polymeric substances extracted were then subjected to SDS-PAGE, and the resultant protein profiles were examined before and after sludge digestion. The SDS-PAGE results showed that three methods led to different SDS-PAGE profiles for both undigested and digested sludges. The results further revealed that CER-extracted proteins remained mainly undegraded in anaerobic digestion, but were degraded in aerobic digestion. While the fate of sulfide- and base-extracted proteins was not clear for aerobic digestion, their changes in anaerobic digestion were elucidated. Most sulfide-extracted proteins were removed by anaerobic digestion, while the increase in protein band intensity and diversity was observed for base-extracted proteins. These results suggest that activated sludge flocs contain different fractions of proteins that are distinguishable by their association with certain cations and that each fraction undergoes different fates in anaerobic and aerobic digestion. The proteins that were resistant to degradation and generated during anaerobic digestion were identified by liquid chromatography tandem mass spectrometry. Protein identification results and their putative roles in activated sludge and anaerobic digestion are discussed in this study.

  16. Scalable solution-phase epitaxial growth of symmetry-mismatched heterostructures on two-dimensional crystal soft template.

    Science.gov (United States)

    Lin, Zhaoyang; Yin, Anxiang; Mao, Jun; Xia, Yi; Kempf, Nicholas; He, Qiyuan; Wang, Yiliu; Chen, Chih-Yen; Zhang, Yanliang; Ozolins, Vidvuds; Ren, Zhifeng; Huang, Yu; Duan, Xiangfeng

    2016-10-01

    Epitaxial heterostructures with precisely controlled composition and electronic modulation are of central importance for electronics, optoelectronics, thermoelectrics, and catalysis. In general, epitaxial material growth requires identical or nearly identical crystal structures with small misfit in lattice symmetry and parameters and is typically achieved by vapor-phase depositions in vacuum. We report a scalable solution-phase growth of symmetry-mismatched PbSe/Bi 2 Se 3 epitaxial heterostructures by using two-dimensional (2D) Bi 2 Se 3 nanoplates as soft templates. The dangling bond-free surface of 2D Bi 2 Se 3 nanoplates guides the growth of PbSe crystal without requiring a one-to-one match in the atomic structure, which exerts minimal restriction on the epitaxial layer. With a layered structure and weak van der Waals interlayer interaction, the interface layer in the 2D Bi 2 Se 3 nanoplates can deform to accommodate incoming layer, thus functioning as a soft template for symmetry-mismatched epitaxial growth of cubic PbSe crystal on rhombohedral Bi 2 Se 3 nanoplates. We show that a solution chemistry approach can be readily used for the synthesis of gram-scale PbSe/Bi 2 Se 3 epitaxial heterostructures, in which the square PbSe (001) layer forms on the trigonal/hexagonal (0001) plane of Bi 2 Se 3 nanoplates. We further show that the resulted PbSe/Bi 2 Se 3 heterostructures can be readily processed into bulk pellet with considerably suppressed thermal conductivity (0.30 W/m·K at room temperature) while retaining respectable electrical conductivity, together delivering a thermoelectric figure of merit ZT three times higher than that of the pristine Bi 2 Se 3 nanoplates at 575 K. Our study demonstrates a unique epitaxy mode enabled by the 2D nanocrystal soft template via an affordable and scalable solution chemistry approach. It opens up new opportunities for the creation of diverse epitaxial heterostructures with highly disparate structures and functions.

  17. Investigation of two blood proteins binding to Cantharidin and Norcantharidin by multispectroscopic and chemometrics methods

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Rong; Cheng, Zhengjun, E-mail: ncczj1112@126.com; Li, Tian; Jiang, Xiaohui

    2015-01-15

    The interactions of Cantharidin/Norcantharidin (CTD/NCTD) with two blood proteins, i.e., bovine serum albumin (BSA) and bovine hemoglobin (BHb), have been investigated by the fluorescence, UV–vis absorption, and FT-IR spectra under imitated physiological condition. The binding characteristics between CTD/NCTD and BSA/BHb were determined by fluorescence emission and resonance light scattering (RLS) spectra. The quenching mechanism of two blood proteins with CTD/NCTD is a static quenching. Moreover, the experimental data were further analyzed based on multivariate curve resolution-alternating least squares (MCR-ALS) technique to obtain the concentration profiles and pure spectra for three species (BSA/BHb, CTD/NCTD and CTD/NCTD–BSA/BHb complexes) which existed in the interaction procedure. The number of binding sites n and binding constants K{sub b} were calculated at various temperatures. The thermodynamic parameters (such as, ΔG, ΔH, and ΔS) for BSA–CTD/NCTD and BHb–CTD/NCTD systems were calculated by the Van’t Hoff equation and also discussed. The distance r between CTD/NCTD and BSA/BHb were evaluated according to Förster no-radiation energy transfer theory. The results of Fourier transform infrared (FT-IR), synchronous fluorescence and three-dimensional fluorescence spectra showed that the conformations of BSA/BHb altered with the addition of CTD/NCTD. In addition, the effects of common ions on the binding constants of BSA–CTD/NCTD and BHb–CTD/NCTD systems were also discussed.

  18. Combining Surface Analytical and Computational Techniques to Investigate Orientation Effects of Immobilized Proteins

    Science.gov (United States)

    Harrison, Elisa Turla

    Controlling how proteins are immobilized (e.g. controlling their orientation and conformation) is essential for developing and optimizing the performance of in vitro protein-binding devices, such as enzyme-linked immunosorbent assays. The objective of this work is to develop new methodologies to study proteins and complex mixtures of proteins immobilized onto surfaces. The focus of this study was to control and characterize the orientation of protein G B1, an IgG antibody-binding domain of protein G, on well-defined surfaces as well as measure the effect of protein G B1 orientation on IgG antibody binding using a variety of surface analytical and computational techniques. The surface sensitivity of time-of-flight secondary ion mass spectrometry (ToF-SIMS) was used to distinguish between different proteins and their orientation by monitoring the changes in intensity of characteristic amino acid mass fragments. Amino acids distributed asymmetrically were used to calculate peak intensity ratios from ToF-SIMS data to determine the orientation of five different cysteine mutants of protein G B1 covalently attached to a maleimide surface. To study the effect of protein orientation on antibody binding, we formed multilayer protein films by binding IgG to protein G B1 films. Quartz crystal microbalance with dissipation monitoring (QCM-D) detected protein coverages of 69-130 ng/cm2 (theoretical mass of a monolayer of protein G B1 is 110-160 ng/cm2). QCM-D and X-ray photoelectron spectroscopy analysis revealed that packing density along with orientation affected the antibody binding process. Spectra from ToF-SIMS using large Ar gas cluster ion sources distinguished between different proteins in multilayer protein systems. A Monte Carlo algorithm was developed to predict protein orientation on surfaces. Two distinct orientations of protein G B1 adsorbed onto a hydrophobic surface were found and characterized as two mutually exclusive sets of amino acids on the outermost

  19. Solution-phase parallel synthesis of aryloxyimino amides via a novel multicomponent reaction among aromatic (Z)-chlorooximes, isocyanides, and electron-deficient phenols.

    Science.gov (United States)

    Mercalli, Valentina; Giustiniano, Mariateresa; Del Grosso, Erika; Varese, Monica; Cassese, Hilde; Massarotti, Alberto; Novellino, Ettore; Tron, Gian Cesare

    2014-11-10

    A library of 41 aryloxyimino amides was prepared via solution phase parallel synthesis by extending the multicomponent reaction of (Z)-chlorooximes and isocyanides to the use of electron-deficient phenols. The resulting aryloxyiminoamide derivatives can be used as intermediates for the synthesis of benzo[d]isoxazole-3-carboxamides, dramatically reducing the number of synthetic steps required by other methods reported in literature.

  20. Investigating the Efficacy of Nonlinear Dimensionality Reduction Schemes in Classifying Gene- and Protein-Expression Studies

    Science.gov (United States)

    Lee, George; Rodriguez, Carlos; Madabhushi, Anant

    2008-01-01

    The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. While some investigators are focused on identifying informative genes and proteins that play a role in specific diseases, other researchers have attempted instead to use patients based on their expression profiles to prognosticate disease status. A major limitation in the ability to accurate classify these high-dimensional datasets stems from the ‘curse of dimensionality’, occurring in situations where the number of genes or peptides significantly exceeds the total number of patient samples. Previous attempts at dealing with this issue have mostly centered on the use of a dimensionality reduction (DR) scheme, Principal Component Analysis (PCA), to obtain a low-dimensional projection of the high-dimensional data. However, linear PCA and other linear DR methods, which rely on Euclidean distances to estimate object similarity, do not account for the inherent underlying nonlinear structure associated with most biomedical data. While some researchers have begun to explore nonlinear DR methods for computer vision problems such as face detection and recognition, to the best of our knowledge, few such attempts have been made for classification and visualization of high-dimensional biomedical data. The motivation behind this work is to identify the appropriate DR methods for analysis of high-dimensional gene- and protein-expression studies. Towards this end, we empirically and rigorously compare three nonlinear (Isomap, Locally Linear Embedding, Laplacian Eigenmaps) and three linear DR schemes (PCA, Linear Discriminant Analysis, Multidimensional Scaling) with the intent of determining a reduced subspace representation in which the individual object classes are more easily discriminable. Owing to the to the inherent nonlinear

  1. Using Affinity Chromatography to Investigate Novel Protein-Protein Interactions in an Undergraduate Cell and Molecular Biology Lab Course

    Science.gov (United States)

    Belanger, Kenneth D.

    2009-01-01

    Inquiry-driven lab exercises require students to think carefully about a question, carry out an investigation of that question, and critically analyze the results of their investigation. Here, we describe the implementation and assessment of an inquiry-based laboratory exercise in which students obtain and analyze novel data that contribute to our…

  2. Synovial fluid protein adsorption on polymer-based artificial hip joint material investigated by MALDI-TOF mass spectrometry imaging

    Directory of Open Access Journals (Sweden)

    Sophie M. Fröhlich

    2014-09-01

    Full Text Available UHMW-PE (ultra-high molecular weight polyethylene, most frequently used material in acetabular cup replacement, is affected by the interaction with its surrounding synovial fluid. It is assumed that protein layer formation is of high importance for lubrication, however alters polymer characteristics. This study investigates in vitro protein adsorption on gamma-irradiated and Vitamin E doped UHMW-PE using synovia as modeling system. SDS-PAGE and MALDI-TOF mass spectrometry imaging showed adsorption of high abundance proteins in a mass range between 2 and 200 kDa. Protein layer formation was observed on planar UHMW-PE material, whereas morphologically modified UHMW-PE regions were highly affected by protein aggregation.

  3. Infrared Absorption Intensity Analysis as a New Tool for Investigation of Salt Effect on Proteins

    Science.gov (United States)

    Li, Heng; Xu, Yan-yan; Weng, Yu-xiang

    2009-12-01

    The native protein structures in buffer solution are maintained by the electrostatic force as well as the hydrophobic force, salt ions play an important role in maintaining the protein native structures, and their effect on the protein stability has attracted tremendous interests. Infrared spectroscopy has been generally used in molecular structure analysis due to its fingerprint resolution for different species including macromolecules as proteins. However spectral intensities have received much less attention than the vibrational frequencies. Here we report that the spectral intensities of protein amide I band, the finger prints for the protein secondary structures, are very sensitive to the local electric field known as Onsager reaction field caused by salt ions. IR absorbance thermal titrations have been conducted for a series of samples including simple water soluble amino acids, water soluble monomeric protein cytochrome c and dimeric protein DsbC and its single-site mutant G49R. We found that at lower temperature range (10-20 °C), there exists a thermal activated salting-in process, where the IR intensity increases with a rise in the temperature, corresponding to the ions binding of the hydrophobic surface of protein. This process is absent for the amino acids. When further raising the temperature, the IR intensity decreases, this is interpreted as the thermal activated breaking of the ion-protein surface binding. Applying Van't Hoff plot to the thermal titration curves, the thermodynamic parameters such as ΔH and ΔS for salting-in and ion unbinding processes can be derived for various protein secondary structural components, revealing quantitatively the extent of hydrophobic interaction as well as the strength of the ion-protein binding.

  4. Value of eight-amino-acid matches in predicting the allergenicity status of proteins: an empirical bioinformatic investigation

    Directory of Open Access Journals (Sweden)

    ThirumalaiswamySekhar Arvind

    2009-10-01

    Full Text Available Abstract The use of biotechnological techniques to introduce novel proteins into food crops (transgenic or GM crops has motivated investigation into the properties of proteins that favor their potential to elicit allergic reactions. As part of the allergenicity assessment, bioinformatic approaches are used to compare the amino-acid sequence of candidate proteins with sequences in a database of known allergens to predict potential cross reactivity between novel food proteins and proteins to which people have become sensitized. Two criteria commonly used for these queries are searches over 80-amino-acid stretches for >35% identity, and searches for 8-amino-acid contiguous matches. We investigated the added value provided by the 8-amino-acid criterion over that provided by the >35%-identity-over-80-amino-acid criterion, by identifying allergens pairs that only met the former criterion, but not the latter criterion. We found that the allergen-sequence pairs only sharing 8-amino-acid identity, but not >35% identity over 80 amino acids, were unlikely to be cross reactive allergens. Thus, the common search for 8-amino-acid identity between novel proteins and known allergens appears to be of little additional value in assessing the potential allergenicity of novel proteins.

  5. Investigation of phonon-like excitation in hydrated protein powders by neutron scattering

    Science.gov (United States)

    Chu, Xiang-Qiang (Rosie); Mamontov, Eugene; O'Neill, Hugh; Zhang, Qiu; Kolesnikov, Alexander

    2013-03-01

    Detecting the phonon dispersion relations in proteins is essential for understanding the intra-protein dynamical behavior. Such study has been attempted by X-ray in recent years. However, for such detections, neutrons have significant advantages in resolution and time-efficiency compare to X-rays. Traditionally the collective motions of atoms in protein molecules are hard to detect using neutrons, because of high incoherent scattering background from intrinsic hydrogen atoms in the protein molecules. The recent availability of a fully deuterated green fluorescent protein (GFP) synthesized by the Bio-deuteration Lab at ORNL opens new possibilities to probe collective excitations in proteins using inelastic neutron scattering. Using a direct time-of-flight Fermi chopper neutron spectrometer, we obtained a full map of the meV phonon-like excitations in the fully deuterated protein. The Q range of the observed excitations corresponds to the length scale close to the size of the secondary structures of proteins and reflects the collective intra-protein motions. Our results show that hydration of GFP seems to harden, not soften, the collective motions. This result is counterintuitive but in agreement with the observations by previous neutron scattering experiments. Sample preparation was supported by facilities operated by the Center for Structural Molecular Biology at ORNL which is supported by the U.S. DOE, Office of Science, Office of Biological and Environmental Research Project ERKP291.

  6. Electrochemical and spectroscopic investigations of immobilized de novo designed heme proteins on metal electrodes

    DEFF Research Database (Denmark)

    Albrecht, Tim; Li, WW; Ulstrup, Jens

    2005-01-01

    On the basis of rational design principles, template-assisted four-helix-bundle proteins that include two histidines for coordinative binding of a heme were synthesized. Spectroscopic and thermodynamic characterization of the proteins in solution reveals the expected bis-histidine coordinated heme...... methods. For all proteins, immobilization causes a decrease in protein stability and a loosening of the helix packing, as reflected by a partial dissociation of a histidine ligand in the ferrous state and very low redox potentials. For the covalently attached MOP-C, the overall interfacial redox process...

  7. Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank.

    Science.gov (United States)

    Abriata, Luciano Andres

    2013-04-01

    Protein X-ray structures with non-corrin cobalt(II)-containing sites, either natural or substituting another native ion, were downloaded from the Protein Data Bank and explored to (i) describe which amino acids are involved in their first ligand shells and (ii) analyze cobalt(II)-donor bond lengths in comparison with previously reported target distances, CSD data and EXAFS data. The set of amino acids involved in Co(II) binding is similar to that observed for catalytic Zn(II) sites, i.e. with a large fraction of carboxylate O atoms from aspartate and glutamate and aromatic N atoms from histidine. The computed Co(II)-donor bond lengths were found to depend strongly on structure resolution, an artifact previously detected for other metal-donor distances. Small corrections are suggested for the target bond lengths to the aromatic N atoms of histidines and the O atoms of water and hydroxide. The available target distance for cysteine (Scys) is confirmed; those for backbone O and other donors remain uncertain and should be handled with caution in refinement and modeling protocols. Finally, a relationship between both Co(II)-O bond lengths in bidentate carboxylates is quantified.

  8. Steady-State Fluorescence Anisotropy to Investigate Flavonoids Binding to Proteins

    Science.gov (United States)

    Ingersoll, Christine M.; Strollo, Christen M.

    2007-01-01

    The steady-state fluorescence anisotropy is employed to study the binding of protein of a model protein, human serum albumin, to a commonly used flavonoid, quercetin. The experiment describes the thermodynamics, as well as the biochemical interactions of such binding effectively.

  9. Investigating interactions between phospholipase B-Like 2 and antibodies during Protein A chromatography.

    Science.gov (United States)

    Tran, Benjamin; Grosskopf, Vanessa; Wang, Xiangdan; Yang, Jihong; Walker, Don; Yu, Christopher; McDonald, Paul

    2016-03-18

    Purification processes for therapeutic antibodies typically exploit multiple and orthogonal chromatography steps in order to remove impurities, such as host-cell proteins. While the majority of host-cell proteins are cleared through purification processes, individual host-cell proteins such as Phospholipase B-like 2 (PLBL2) are more challenging to remove and can persist into the final purification pool even after multiple chromatography steps. With packed-bed chromatography runs using host-cell protein ELISAs and mass spectrometry analysis, we demonstrated that different therapeutic antibodies interact to varying degrees with host-cell proteins in general, and PLBL2 specifically. We then used a high-throughput Protein A chromatography method to further examine the interaction between our antibodies and PLBL2. Our results showed that the co-elution of PLBL2 during Protein A chromatography is highly dependent on the individual antibody and PLBL2 concentration in the chromatographic load. Process parameters such as antibody resin load density and pre-elution wash conditions also influence the levels of PLBL2 in the Protein A eluate. Furthermore, using surface plasmon resonance, we demonstrated that there is a preference for PLBL2 to interact with IgG4 subclass antibodies compared to IgG1 antibodies. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. Synergistic Inhibition of Protein Fibrillation by Proline and Sorbitol: Biophysical Investigations.

    Directory of Open Access Journals (Sweden)

    Sinjan Choudhary

    Full Text Available We report here interesting synergistic effects of proline and sorbitol, two well-known chemical chaperones, in the inhibition of fibrillation of two proteins, insulin and lysozyme. A combination of many biophysical techniques has been used to understand the structural morphology and modes of interaction of the chaperones with the proteins during fibrillation. Both the chaperones establish stronger polar interactions in the elongation and saturation stages of fibrillation compared to that in the native stage. However, when presented as a mixture, we also see contribution of hydrophobic interactions. Thus, a co-operative adjustment of polar and hydrophobic interactions between the chaperones and the protein surface seems to drive the synergistic effects in the fibrillation process. In insulin, this synergy is quantitatively similar in all the stages of the fibrillation process. These observations would have significant implications for understanding protein folding concepts, in general, and for designing combination therapies against protein fibrillation, in particular.

  11. High pressure as a tool for investigating protein-ligand interactions

    International Nuclear Information System (INIS)

    Marchal, S; Lange, R; Tortora, P; Balny, C

    2004-01-01

    In recent years, the application of pressure on biological systems has gained increasing interest. Pressure-induced destabilization of electrostatic and hydrophobic interactions is currently exploited to study conformational protein stability and macromolecular assemblies of proteins. Due to links between severe human pathologies and ordered protein oligomerization into aggregates, which have become apparent, a better knowledge of the molecular and structural determinants that ensure the packing efficiency and stability of such complexes has taken on special importance. Here, we report the effect of pressure on the property of human ataxin-3 of aggregation. The results indicate the importance of its polyglutamine chain length in the stability and the tendency of the protein to form spheroids. Partial unfolding of the protein leading to solvent exposure of hydrophobic domains appears to be a prerequisite in the aggregation process of ataxin-3

  12. High pressure as a tool for investigating protein-ligand interactions

    Energy Technology Data Exchange (ETDEWEB)

    Marchal, S [INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cedex 5 (France); Lange, R [INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cedex 5 (France); Tortora, P [Dipartimento di Biotecnologie e Bioscienze, Universita di Milano-Bicocca, Piazza della Scienza 2, I-20126 Milan (Italy); Balny, C [INSERM U128, IFR 122, 1919 route de Mende, F-34293 Montpellier Cedex 5 (France)

    2004-04-14

    In recent years, the application of pressure on biological systems has gained increasing interest. Pressure-induced destabilization of electrostatic and hydrophobic interactions is currently exploited to study conformational protein stability and macromolecular assemblies of proteins. Due to links between severe human pathologies and ordered protein oligomerization into aggregates, which have become apparent, a better knowledge of the molecular and structural determinants that ensure the packing efficiency and stability of such complexes has taken on special importance. Here, we report the effect of pressure on the property of human ataxin-3 of aggregation. The results indicate the importance of its polyglutamine chain length in the stability and the tendency of the protein to form spheroids. Partial unfolding of the protein leading to solvent exposure of hydrophobic domains appears to be a prerequisite in the aggregation process of ataxin-3.

  13. Investigation on oxidative stress of nitric oxide synthase interacting protein from Clonorchis sinensis.

    Science.gov (United States)

    Bian, Meng; Xu, Qingxia; Xu, Yanquan; Li, Shan; Wang, Xiaoyun; Sheng, Jiahe; Wu, Zhongdao; Huang, Yan; Yu, Xinbing

    2016-01-01

    Numerous evidences indicate that excretory-secretory products (ESPs) from liver flukes trigger the generation of free radicals that are associated with the initial pathophysiological responses in host cells. In this study, we first constructed a Clonorchis sinensis (C. sinensis, Cs)-infected BALB/c mouse model and examined relative results respectively at 3, 5, 7, and 9 weeks postinfection (p.i.). Quantitative reverse transcription (RT)-PCR indicated that the transcriptional level of both endothelial nitric oxide synthase (eNOS) and superoxide dismutase (SOD) gradually decreased with lastingness of infection, while the transcriptional level of inducible NOS (iNOS) significantly increased. The level of malondialdehyde (MDA) in sera of infected mouse significantly increased versus the healthy control group. These results showed that the liver of C. sinensis-infected mouse was in a state with elevated levels of oxidation stress. Previously, C. sinensis NOS interacting protein coding gene (named CsNOSIP) has been isolated and recombinant CsNOSIP (rCsNOSIP) has been expressed in Escherichia coli, which has been confirmed to be a component present in CsESPs and confirmed to play important roles in immune regulation of the host. In the present paper, we investigated the effects of rCsNOSIP on the lipopolysaccharide (LPS)-induced activated RAW264.7, a murine macrophage cell line. We found that endotoxin-free rCsNOSIP significantly promoted the levels of nitric oxide (NO) and reactive oxygen species (ROS) after pretreated with rCsNOSIP, while the level of SOD decreased. Furthermore, rCsNOSIP could also increase the level of lipid peroxidation MDA. Taken together, these results suggested that CsNOSIP was a key molecule which was involved in the production of nitric oxide (NO) and its reactive intermediates, and played an important role in oxidative stress during C. sinensis infection.

  14. Thermodynamic investigations of protein's behaviour with ionic liquids in aqueous medium studied by isothermal titration calorimetry.

    Science.gov (United States)

    Bharmoria, Pankaj; Kumar, Arvind

    2016-05-01

    While a number of reports appear on ionic liquids-proteins interactions, their thermodynamic behaviour using suitable technique like isothermal titration calorimetry is not systematically presented. Isothermal titration calorimetry (ITC) is a key technique which can directly measure the thermodynamic contribution of IL binding to protein, particularly the enthalpy, heat capacities and binding stoichiometry. Ionic liquids (ILs), owing to their unique and tunable physicochemical properties have been the central area of scientific research besides graphene in the last decade, and growing unabated. Their encounter with proteins in the biological system is inevitable considering their environmental discharge though most of them are recyclable for a number of cycles. In this article we will cover the thermodynamics of proteins upon interaction with ILs as osmolyte and surfactant. The up to date literature survey of IL-protein interactions using isothermal titration calorimetry will be discussed and parallel comparison with the results obtained for such studies with other techniques will be highlighted to demonstrate the accuracy of ITC technique. Net stability of proteins can be obtained from the difference in the free energy (ΔG) of the native (folded) and denatured (unfolded) state using the Gibbs-Helmholtz equation (ΔG=ΔH-TΔS). Isothermal titration calorimetry can directly measure the heat changes upon IL-protein interactions. Calculation of other thermodynamic parameters such as entropy, binding constant and free energy depends upon the proper fitting of the binding isotherms using various fitting models. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. The Investigation of Virginiamycin-Added Fungal Fermentation on the Size and Immunoreactivity of Heat-Sensitive Soy Protein

    Directory of Open Access Journals (Sweden)

    Liyan Chen

    2015-01-01

    Full Text Available The usage of soy protein for young monogastric animals is restricted due to potential allergens and high molecular weight. The investigation of fungi fermentation effect on soy protein has been interrupted by substrate sterilization. Virginiamycin at 0.05% was added together with Aspergillus oryzae for solid state fermentation (SSF in unsterilized soy meal (SM. When compared to A. oryzae SSF alone, virginiamycin did not cause the interference of fungal fermentation but elucidated the protein degradation. SDS-PAGE results showed that both α and α′ subunits of β-conglycinin were degraded significantly. In addition, western blot results showed that the immunoreactive signals of soy protein were considerably reduced in virginiamycin-added fermentation with unsterilized SM. Furthermore, fungal fermentation increased total protein and essential amino acid contents, suggesting the value enhancement of SM products. Taken together, this study demonstrated for the first time that virginiamycin could help investigate fermentation effect on heat-sensitive soy protein. Fermented SM has several potential applications in feed industry.

  16. An Essential Protein Repair Enzyme: Investigation of the Molecular Recognition Mechanism of Methionine Sulfoxide Reductase A

    Science.gov (United States)

    2008-05-01

    18 Wild Type Staphylococcal Nuclease and Staph Nuclease T62P (SN T62P...Determination of Apparent Kd…………………………………………………...27 4 Protein-ligand Interactions of MsrA, ANS, and Reduced Staph Nuclease Peptide...28 Protein-ligand Interactions of MsrA, ANS, and Oxidized Staph Nuclease Peptide…..................………………………………....32 Protein-ligand

  17. Cysteine Specific Targeting of the Functionally Distinct Peroxiredoxin and Glutaredoxin Proteins by the Investigational Disulfide BNP7787

    Directory of Open Access Journals (Sweden)

    Aulma R. Parker

    2015-03-01

    Full Text Available Glutaredoxin (Grx, peroxiredoxin (Prx, and thioredoxin (Trx are redoxin family proteins that catalyze different types of chemical reactions that impact cell growth and survival through functionally distinct intracellular pathways. Much research is focused on understanding the roles of these redoxin proteins in the development and/or progression of human diseases. Grx and Prx are overexpressed in human cancers, including human lung cancers. BNP7787 is a novel investigational agent that has been evaluated in previous clinical studies, including non-small cell lung cancer (NSCLC studies. Herein, data from activity assays, mass spectrometry analyses, and X-ray crystallographic studies indicate that BNP7787 forms mixed disulfides with select cysteine residues on Grx and Prx and modulates their function. Studies of interactions between BNP7787 and Trx have been conducted and reported separately. Despite the fact that Trx, Grx, and Prx are functionally distinct proteins that impact oxidative stress, cell proliferation and disease processes through different intracellular pathways, BNP7787 can modify each protein and appears to modulate function through mechanisms that are unique to each target protein. Tumor cells are often genomically heterogeneous containing subpopulations of cancer cells that often express different tumor-promoting proteins or that have multiple dysregulated signaling pathways modulating cell proliferation and drug resistance. A multi-targeted agent that simultaneously modulates activity of proteins important in mediating cell proliferation by functionally distinct intracellular pathways could have many potentially useful therapeutic applications.

  18. Neutron scattering and molecular dynamics simulation: a conjugate approach to investigate the dynamics of electron transfer proteins

    International Nuclear Information System (INIS)

    Bizzarri, Anna Rita

    2004-01-01

    The neutron scattering technique is a relevant tool for studying the dynamical properties of electron transfer proteins. Macromolecular motions ranging in wide temporal and spatial windows can be investigated by separately analysing elastic, inelastic and quasielastic incoherent neutron scattering. The dynamical behaviour of the solvent surrounding a macromolecule can also be analysed. Neutron scattering is particularly rewarding when used in combination with molecular dynamics simulations. From the simulated atomic trajectories, physical quantities directly related to the neutron scattering technique can be calculated and compared with the corresponding experimental data. This article briefly introduces both the neutron scattering and molecular dynamics simulation methods applied to proteins, and reviews the biophysical studies of some electron transfer proteins. Both experimental and molecular dynamics results for these proteins and the surrounding solvent are also discussed in connection with their electron transfer properties. Possible developments are briefly outlined. (topical review)

  19. Theoretical Investigation of the Feasibility of PTD-Mediated Translocation of Proteins Across Artificial Membranes

    National Research Council Canada - National Science Library

    Kharkyanen, Valeriy N

    2006-01-01

    ...: The recent discovery of the ability of protein transduction domains (PTDs) and their synthetic analogues to transport high-molecular weight compounds through biological or artificial membranes is very promising for many applications...

  20. Investigation of the pH‐dependence of dye‐doped protein–protein interactions

    OpenAIRE

    Nudelman, Roman; Gloukhikh, Ekaterina; Rekun, Antonina; Richter, Shachar

    2016-01-01

    Proteins can dramatically change their conformation under environmental conditions such as temperature and pH. In this context, Glycoprotein's conformational determination is challenging. This is due to the variety of domains which contain rich chemical characters existing within this complex. Here we demonstrate a new, straightforward and efficient technique that uses the pH‐dependent properties of dyes‐doped Pig Gastric Mucin (PGM) for predicting and controlling protein–protein interaction ...

  1. Proteomics investigation reveals cell death-associated proteins of basidiomycete fungus Trametes versicolor treated with Ferruginol.

    Science.gov (United States)

    Chen, Yu-Han; Yeh, Ting-Feng; Chu, Fang-Hua; Hsu, Fu-Lan; Chang, Shang-Tzen

    2015-01-14

    Ferruginol has antifungal activity against wood-rot fungi (basidiomycetes). However, specific research on the antifungal mechanisms of ferruginol is scarce. Two-dimensional gel electrophoresis and fluorescent image analysis were employed to evaluate the differential protein expression of wood-rot fungus Trametes versicolor treated with or without ferruginol. Results from protein identification of tryptic peptides via liquid chromatography–electrospray ionization tandem mass spectrometry (LC–ESI-MS/MS) analyses revealed 17 protein assignments with differential expression. Downregulation of cytoskeleton β-tubulin 3 indicates that ferruginol has potential to be used as a microtubule-disrupting agent. Downregulation of major facilitator superfamily (MFS)–multiple drug resistance (MDR) transporter and peroxiredoxin TSA1 were observed, suggesting reduction in self-defensive capabilities of T. versicolor. In addition, the proteins involved in polypeptide sorting and DNA repair were also downregulated, while heat shock proteins and autophagy-related protein 7 were upregulated. These observations reveal that such cellular dysfunction and damage caused by ferruginol lead to growth inhibition and autophagic cell death of fungi.

  2. Investigating Structure and Dynamics of Proteins in Amorphous Phases Using Neutron Scattering

    Directory of Open Access Journals (Sweden)

    Maria Monica Castellanos

    Full Text Available In order to increase shelf life and minimize aggregation during storage, many biotherapeutic drugs are formulated and stored as either frozen solutions or lyophilized powders. However, characterizing amorphous solids can be challenging with the commonly available set of biophysical measurements used for proteins in liquid solutions. Therefore, some questions remain regarding the structure of the active pharmaceutical ingredient during freezing and drying of the drug product and the molecular role of excipients. Neutron scattering is a powerful technique to study structure and dynamics of a variety of systems in both solid and liquid phases. Moreover, neutron scattering experiments can generally be correlated with theory and molecular simulations to analyze experimental data. In this article, we focus on the use of neutron techniques to address problems of biotechnological interest. We describe the use of small-angle neutron scattering to study the solution structure of biological molecules and the packing arrangement in amorphous phases, that is, frozen glasses and freeze-dried protein powders. In addition, we discuss the use of neutron spectroscopy to measure the dynamics of glassy systems at different time and length scales. Overall, we expect that the present article will guide and prompt the use of neutron scattering to provide unique insights on many of the outstanding questions in biotechnology. Keywords: Neutron scattering, Protein structure, Protein dynamics, Freeze-dried proteins, Glasses, Frozen protein solutions, Molecular dynamics

  3. Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

    Science.gov (United States)

    Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

    2010-05-01

    Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

  4. Qualitative and quantitative changes in phospholipids and proteins investigated by spectroscopic techniques in animal depression model

    Science.gov (United States)

    Depciuch, J.; Sowa-Kucma, M.; Nowak, G.; Papp, M.; Gruca, P.; Misztak, P.; Parlinska-Wojtan, M.

    2017-04-01

    Depression becomes nowadays a high mortality civilization disease with one of the major causes being chronic stress. Raman, Fourier Transform Infra Red (FTIR) and Ultraviolet-Visible (UV-vis) spectroscopies were used to determine the changes in the quantity and structure of phospholipids and proteins in the blood serum of rats subjected to chronic mild stress, which is a common animal depression model. Moreover, the efficiency of the imipramine treatment was evaluated. It was found that chronic mild stress not only damages the structure of the phospholipids and proteins, but also decreases their level in the blood serum. A 5 weeks imipramine treatment did increase slightly the quantity of proteins, leaving the damaged phospholipids unchanged. Structural information from phospholipids and proteins was obtained by UV-vis spectroscopy combined with the second derivative of the FTIR spectra. Indeed, the structure of proteins in blood serum of stressed rats was normalized after imipramine therapy, while the impaired structure of phospholipids remained unaffected. These findings strongly suggest that the depression factor, which is chronic mild stress, may induce permanent (irreversible) damages into the phospholipid structure identified as shortened carbon chains. This study shows a possible new application of spectroscopic techniques in the diagnosis and therapy monitoring of depression.

  5. Structure and function of proteins investigated by crystallographic and spectroscopic time-resolved methods

    Science.gov (United States)

    Purwar, Namrta

    Biomolecules play an essential role in performing the necessary functions for life. The goal of this thesis is to contribute to an understanding of how biological systems work on the molecular level. We used two biological systems, beef liver catalase (BLC) and photoactive yellow protein (PYP). BLC is a metalloprotein that protects living cells from the harmful effects of reactive oxygen species by converting H2O2 into water and oxygen. By binding nitric oxide (NO) to the catalase, a complex was generated that mimics the Cat-H2O2 adduct, a crucial intermediate in the reaction promoted by the catalase. The Cat-NO complex is obtained by using a convenient NO generator (1-(N,N-diethylamino)diazen-1-ium-1,2-diolate). Concentrations up to 100˜200 mM are reached by using a specially designed glass cavity. With this glass apparatus and DEANO, sufficient NO occupation is achieved and structure determination of the catalase with NO bound to the heme iron becomes possible. Structural changes upon NO binding are minute. NO has a slightly bent geometry with respect to the heme normal, which results in a substantial overlap of the NO orbitals with the iron-porphyrin molecular orbitals. From the structure of the iron-NO complex, conclusions on the electronic properties of the heme iron can be drawn that ultimately lead to an insight into the catalytic properties of this enzyme. Enzyme kinetics is affected by additional parameters such as temperature and pH. Additionally, in crystallography, the absorbed X-ray dose may impair protein function. To address the effect of these parameters, we performed time-resolved crystallographic experiments on a model system, PYP. By collecting multiple time-series on PYP at increasing X-ray dose levels, we determined a kinetic dose limit up to which kinetically meaningful X-ray data sets can be collected. From this, we conclude that comprehensive time-series spanning up to 12 orders of magnitude in time can be collected from a single PYP

  6. Investigation of Pokemon-regulated proteins in hepatocellular carcinoma using mass spectrometry-based multiplex quantitative proteomics.

    Science.gov (United States)

    Bi, Xin; Jin, Yibao; Gao, Xiang; Liu, Feng; Gao, Dan; Jiang, Yuyang; Liu, Hongxia

    2013-01-01

    Pokemon is a transcription regulator involved in embryonic development, cellular differentiation and oncogenesis. It is aberrantly overexpressed in multiple human cancers including Hepatocellular carcinoma (HCC) and is considered as a promising biomarker for HCC. In this work, the isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics strategy was used to investigate the proteomic profile associated with Pokemon in human HCC cell line QGY7703 and human hepatocyte line HL7702. Samples were labeled with four-plex iTRAQ reagents followed by two-dimensional liquid chromatography coupled with tandem mass spectrometry analysis. A total of 24 differentially expressed proteins were selected as significant. Nine proteins were potentially up-regulated by Pokemon while 15 proteins were potentially down-regulated and many proteins were previously identified as potential biomarkers for HCC. Gene ontology (GO) term enrichment revealed that the listed proteins were mainly involved in DNA metabolism and biosynthesis process. The changes of glucose-6-phosphate 1-dehydrogenase (G6PD, up-regulated) and ribonucleoside-diphosphate reductase large sub-unit (RIM1, down-regulated) were validated by Western blotting analysis and denoted as Pokemon's function of oncogenesis. We also found that Pokemon potentially repressed the expression of highly clustered proteins (MCM3, MCM5, MCM6, MCM7) which played key roles in promoting DNA replication. Altogether, our results may help better understand the role of Pokemon in HCC and promote the clinical applications.

  7. Stable isotope labeling method for the investigation of protein haptenation by electrophilic skin sensitizers.

    Science.gov (United States)

    Parkinson, Erika; Boyd, Pete; Aleksic, Maja; Cubberley, Richard; O'Connor, David; Skipp, Paul

    2014-11-01

    The risk of contact sensitization is a major consideration in the development of new formulations for personal care products. However, developing a mechanistic approach for non-animal risk assessment requires further understanding of haptenation of skin proteins by sensitizing chemicals, which is the molecular initiating event causative of skin sensitization. The non-stoichiometric nature of protein haptenation results in relatively low levels of modification, often of low abundant proteins, presenting a major challenge for their assignment in complex biological matrices such as skin. Instrumental advances over the last few years have led to a considerable increase in sensitivity of mass spectrometry (MS) techniques. We have combined these advancements with a novel dual-labeling/LC-MS(E) approach to provide an in-depth direct comparison of human serum albumin (HSA), 2,4-dinitro-1-chlorobenzene (DNCB), 5-chloro-2-methyl-4-isothiazolin-3-one (MCI), trans-cinnamaldehyde, and 6-methyl coumarin. These data have revealed novel insights into the differences in protein haptenation between sensitizers with different reaction mechanisms and sensitizing potency; the extreme sensitizers DNCB and MCI were shown to modify a greater number of nucleophilic sites than the moderate sensitizer cinnamaldehyde; and the weak/non-sensitizer 6-methyl coumarin was restricted to only a single nucleophilic residue within HSA. The evaluation of this dual labeling/LC-MS(E) approach using HSA as a model protein has also demonstrated that this strategy could be applied to studying global haptenation in complex mixtures of skin-related proteins by different chemicals. © The Author 2014. Published by Oxford University Press on behalf of the Society of Toxicology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  8. Investigation of the protein osteocalcin of Camelops hesternus: Sequence, structure and phylogenetic implications

    Science.gov (United States)

    Humpula, James F.; Ostrom, Peggy H.; Gandhi, Hasand; Strahler, John R.; Walker, Angela K.; Stafford, Thomas W.; Smith, James J.; Voorhies, Michael R.; George Corner, R.; Andrews, Phillip C.

    2007-12-01

    Ancient DNA sequences offer an extraordinary opportunity to unravel the evolutionary history of ancient organisms. Protein sequences offer another reservoir of genetic information that has recently become tractable through the application of mass spectrometric techniques. The extent to which ancient protein sequences resolve phylogenetic relationships, however, has not been explored. We determined the osteocalcin amino acid sequence from the bone of an extinct Camelid (21 ka, Camelops hesternus) excavated from Isleta Cave, New Mexico and three bones of extant camelids: bactrian camel ( Camelus bactrianus); dromedary camel ( Camelus dromedarius) and guanaco ( Llama guanacoe) for a diagenetic and phylogenetic assessment. There was no difference in sequence among the four taxa. Structural attributes observed in both modern and ancient osteocalcin include a post-translation modification, Hyp 9, deamidation of Gln 35 and Gln 39, and oxidation of Met 36. Carbamylation of the N-terminus in ancient osteocalcin may result in blockage and explain previous difficulties in sequencing ancient proteins via Edman degradation. A phylogenetic analysis using osteocalcin sequences of 25 vertebrate taxa was conducted to explore osteocalcin protein evolution and the utility of osteocalcin sequences for delineating phylogenetic relationships. The maximum likelihood tree closely reflected generally recognized taxonomic relationships. For example, maximum likelihood analysis recovered rodents, birds and, within hominins, the Homo-Pan-Gorilla trichotomy. Within Artiodactyla, character state analysis showed that a substitution of Pro 4 for His 4 defines the Capra-Ovis clade within Artiodactyla. Homoplasy in our analysis indicated that osteocalcin evolution is not a perfect indicator of species evolution. Limited sequence availability prevented assigning functional significance to sequence changes. Our preliminary analysis of osteocalcin evolution represents an initial step towards a

  9. PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.

    Science.gov (United States)

    Li, Fei; Li, Peng; Xu, Wenjian; Peng, Yuxing; Bo, Xiaochen; Wang, Shengqi

    2010-01-15

    The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets. PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer. Supplementary data are available at Bioinformatics online.

  10. Investigating the Causal Relationship of C-Reactive Protein with 32 Complex Somatic and Psychiatric Outcomes

    DEFF Research Database (Denmark)

    Prins, Bram P; Abbasi, Ali; Wong, Anson

    2016-01-01

    BACKGROUND: C-reactive protein (CRP) is associated with immune, cardiometabolic, and psychiatric traits and diseases. Yet it is inconclusive whether these associations are causal. METHODS AND FINDINGS: We performed Mendelian randomization (MR) analyses using two genetic risk scores (GRSs) as inst...

  11. Differential dissociation micromethod for the investigation of binding of metandrostenolone (Nerobol) to plasma proteins

    International Nuclear Information System (INIS)

    Bojadzsieva, Milka; Kocsar, Laszlo; Kremmer, Tibor

    1985-01-01

    A micromethod was developed to determine the binding of anabolic streoids to plasma proteins. The new procedure combines precipitation with ammonium sulphate and differential dissociation. The binding parameters (association constant, specific binding capacity) are calculated on the basis of dissociation curves of sup(3)H-metandrostenolone from the precipitated sexual binding globuline. (L.E.)

  12. Differential dissociation micromethod for the investigation of binding of metandrostenolone (Nerobol) to plasma proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bojadzsieva, M.; Kocsar, L. (Orszagos Frederic Joliot-Curie Sugarbiologiai es Sugaregeszseguegyi Kutato Intezet, Budapest (Hungary)); Kremmer, T. (Orszagos Onkologiai Intezet, Budapest (Hungary))

    1985-01-01

    A micromethod was developed to determine the binding of anabolic steroids to plasma proteins. The new procedure combines precipitation with ammonium sulphate and differential dissociation. The binding parameters (association constant, specific binding capacity) are calculated on the basis of dissociation curves of sup(3)H-metandrostenolone from the precipitated sexual binding globuline.

  13. Single particle electron microscopy in combination with mass spectrometry to investigate novel complexes of membrane proteins

    NARCIS (Netherlands)

    Arteni, Ana A.; Nowaczyk, Marc; Lax, Julia; Rögner, Matthias; Boekema, Egbert J.; Kouril, R.; Rogner, M.

    2005-01-01

    Large data sets of molecular projections of the membrane proteins Photosystem I and Photosystem II from cyanobacteria were analyzed by single particle electron microscopy (EM). Analysis resulted in the averaging of 2D projections from the purified complexes but also in the simultaneous detection and

  14. Olefin cross-metathesis on proteins: investigation of allylic chalcogen effects and guiding principles in metathesis partner selection.

    Science.gov (United States)

    Lin, Yuya A; Chalker, Justin M; Davis, Benjamin G

    2010-12-01

    Olefin metathesis has recently emerged as a viable reaction for chemical protein modification. The scope and limitations of olefin metathesis in bioconjugation, however, remain unclear. Herein we report an assessment of various factors that contribute to productive cross-metathesis on protein substrates. Sterics, substrate scope, and linker selection are all considered. It was discovered during this investigation that allyl chalcogenides generally enhance the rate of alkene metathesis reactions. Allyl selenides were found to be exceptionally reactive olefin metathesis substrates, enabling a broad range of protein modifications not previously possible. The principles considered in this report are important not only for expanding the repertoire of bioconjugation but also for the application of olefin metathesis in general synthetic endeavors.

  15. Investigation of isolation conditions and ion-exchange purification of protein coagulation components from common bean seed

    Directory of Open Access Journals (Sweden)

    Antov Mirjana G.

    2007-01-01

    Full Text Available Investigation of an extraction procedure of protein coagulants from common bean seed regarding concentration of NaCl and pH was performed. High values of protein concentration and coagulation activity in crude extract (9.19 g/l and 23.9%, respectively were obtained when the extraction was performed using 0.5 mol/l NaCl and water as solvent, which represents an advantage for economic and environmental reasons. Crude extract of common bean seed was purified by precipitation at two different percentages of (NH42SO4 saturation, followed by batch ion-exchange chromatography. The highest obtained coagulation activity, 45%, was determined in fraction that was eluated at 1.75 mol/l NaCl from resin loaded with proteins precipitated upon 80-100% (NH42SO4 saturation. High values of coagulation activity showed by some eluates suggest their application as natural coagulant for water purification. .

  16. Investigation of basement membrane proteins in a case of granular cell ameloblastoma

    Science.gov (United States)

    Lapthanasupkul, Puangwan; Poomsawat, Sopee; Chindasombatjaroen, Jira

    2012-01-01

    Granular cell ameloblastoma is a rare, benign neoplasm of the odontogenic epithelium. A case of massive granular cell ameloblastoma in a 44-year-old Thai female is reported. Histopathological features displayed a follicular type of ameloblastoma with an accumulation of granular cells residing within the tumor follicles. After treatment by partial mandibulectomy, the patient showed a good prognosis without recurrence in a 2-year follow-up. To characterize the granular cells in ameloblastoma, we examined the expression of basement membrane (BM) proteins, including collagen type IV, laminins 1 and 5 and fibronectin using immunohistochemistry. Except for the granular cells, the tumor cells demonstrated a similar expression of BM proteins compared to follicular and plexiform ameloblastomas in our previous study, whereas the granular cells showed strong positivity to laminins 1 and 5 and fibronectin. The increased fibronectin expression in granular cells suggests a possibility of age-related transformation of granular cells in ameloblastoma. PMID:22361945

  17. Comparative study of protein dynamics in hydrated powders and in solutions: A neutron scattering investigation

    International Nuclear Information System (INIS)

    Marconi, M.; Cornicchi, E.; Onori, G.; Paciaroni, A.

    2008-01-01

    Neutron scattering spectroscopy on a time-of-flight spectrometer has been exploited to reveal the vibrational and relaxational spectral contributions of lysozyme in hydrated powder and solution states. The inelastic component of the dynamical structure factor seems to be quite similar for lysozyme in both the solid- and the liquid-state samples, particularly for energies higher than ∼4 meV. After the subtraction of this component, the quasielastic contribution is evaluated. In the case of hydrated lysozyme powder the quasielastic scattering follows a two-power law with a ballistic Gaussian decrease above ∼2 meV. The quasielastic scattering of lysozyme in solution exhibits a rather similar trend but a much larger intensity. This may be related to the increase of both the number and the amplitudes of the confined diffusive processes related to protein side-chains motions at the protein surface

  18. Investigation of the protective effect of whey proteins on lactococcal phages during heat treatment at various pH.

    Science.gov (United States)

    Geagea, Hany; Gomaa, Ahmed I; Remondetto, Gabriel; Moineau, Sylvain; Subirade, Muriel

    2015-10-01

    The incorporation of whey protein concentrates (WPC) into cheese is a risky process due to the potential contamination with thermo-resistant phages of lactic acid bacteria (LAB). Furthermore, whey proteins can protect phages during heat treatment, thereby increasing the above risk. The main objective of this work was to understand this protective effect in order to better control LAB phages and maximize whey recycling in the cheese industry. First, the inactivation of a previously characterized thermo-resistant lactococcal virulent phage (P1532) was investigated at 95 °C in WPC, in individual whey components β-lactoglobulin, α-lactalbumin, and bovine serum albumin as well as under different heat and pH conditions. The structural changes of the tested proteins were also monitored by transmission FTIR spectroscopy. Phage inactivation results indicated that the protective effect of whey proteins was pH and time dependent at 95 °C and was not restricted to one component. FTIR spectra suggest that the protection is related to protein molecular structures and to the level of protein aggregates, which was more pronounced in acidic conditions. Moreover, the molecular structure of the three proteins tested was differently influenced by pH and the duration of the heat treatment. This work confirms the protective effect of WPC on phages during heat treatment and offers the first hint to explain such phenomenon. Finding the appropriate treatment of WPC to reduce the phage risk is one of the keys to improving the cheese manufacturing process. Copyright © 2015 Elsevier B.V. All rights reserved.

  19. Surface Plasmon Resonance Investigations of Bioselective Element Based on the Recombinant Protein A for Immunoglobulin Detection

    Science.gov (United States)

    Bakhmachuk, A.; Gorbatiuk, O.; Rachkov, A.; Dons'koi, B.; Khristosenko, R.; Ushenin, I.; Peshkova, V.; Soldatkin, A.

    2017-02-01

    The developed surface plasmon resonance (SPR) biosensor based on the recombinant Staphylococcal protein A with an additional cysteine residue (SPA-Cys) used as a biorecognition component showed a good selectivity and sensitivity for the immunoglobulin detection. The developed biosensor with SPA-Cys-based bioselective element can also be used as a first step of immunosensor creation. The successful immobilization of SPA-Cys on the nanolayer gold sensor surface of the SPR spectrometer was performed. The efficiency of blocking nonspecific sorption sites on the sensor surface with milk proteins, gelatin, BSA, and HSA was studied, and a rather high efficiency of using gelatin was confirmed. The SPR biosensor selectively interacted with IgG and did not interact with the control proteins. The linear dependence of the sensor response on the IgG concentration in the range from 2 to 10 μg/ml was shown. Using the calibration curve, the IgG concentration was measured in the model samples. The determined concentrations are in good agreement ( r 2 = 0.97) with the given concentration of IgG.

  20. New environment-sensitive multichannel DNA fluorescent label for investigation of the protein-DNA interactions.

    Directory of Open Access Journals (Sweden)

    Alexandra A Kuznetsova

    Full Text Available Here, we report the study of a new multichannel DNA fluorescent base analogue 3-hydroxychromone (3HC to evaluate its suitability as a fluorescent reporter probe of structural transitions during protein-DNA interactions and its comparison with the current commercially available 2-aminopurine (aPu, pyrrolocytosine (Cpy and 1,3-diaza-2-oxophenoxazine (tCO. For this purpose, fluorescent base analogues were incorporated into DNA helix on the opposite or on the 5'-side of the damaged nucleoside 5,6-dihydrouridine (DHU, which is specifically recognized and removed by Endonuclease VIII. These fluorophores demonstrated different sensitivities to the DNA helix conformational changes. The highest sensitivity and the most detailed information about the conformational changes of DNA induced by protein binding and processing were obtained using the 3HC probe. The application of this new artificial fluorescent DNA base is a very useful tool for the studies of complex mechanisms of protein-DNA interactions. Using 3HC biosensor, the kinetic mechanism of Endonuclease VIII action was specified.

  1. New environment-sensitive multichannel DNA fluorescent label for investigation of the protein-DNA interactions.

    Science.gov (United States)

    Kuznetsova, Alexandra A; Kuznetsov, Nikita A; Vorobjev, Yuri N; Barthes, Nicolas P F; Michel, Benoît Y; Burger, Alain; Fedorova, Olga S

    2014-01-01

    Here, we report the study of a new multichannel DNA fluorescent base analogue 3-hydroxychromone (3HC) to evaluate its suitability as a fluorescent reporter probe of structural transitions during protein-DNA interactions and its comparison with the current commercially available 2-aminopurine (aPu), pyrrolocytosine (Cpy) and 1,3-diaza-2-oxophenoxazine (tCO). For this purpose, fluorescent base analogues were incorporated into DNA helix on the opposite or on the 5'-side of the damaged nucleoside 5,6-dihydrouridine (DHU), which is specifically recognized and removed by Endonuclease VIII. These fluorophores demonstrated different sensitivities to the DNA helix conformational changes. The highest sensitivity and the most detailed information about the conformational changes of DNA induced by protein binding and processing were obtained using the 3HC probe. The application of this new artificial fluorescent DNA base is a very useful tool for the studies of complex mechanisms of protein-DNA interactions. Using 3HC biosensor, the kinetic mechanism of Endonuclease VIII action was specified.

  2. Investigation of molecular mechanisms of action of chelating drugs on protein-lipid model membranes by X-ray fluorescence

    International Nuclear Information System (INIS)

    Novikova, N. N.; Zheludeva, S. I.; Koval'chuk, M. V.; Stepina, N. D.; Erko, A. I.; Yur'eva, E. A.

    2009-01-01

    Protein-lipid films based on the enzyme alkaline phosphatase were subjected to the action of chelating drugs, which are used for accelerating the removal of heavy metals from the human body, and the elemental composition of the resulting films was investigated. Total-reflection X-ray fluorescence measurements were performed at the Berlin Electron Storage Ring Company for Synchrotron Radiation (BESSY) in Germany. A comparative estimation of the protective effect of four drugs (EDTA, succimer, xydiphone, and mediphon) on membrane-bound enzymes damaged by lead ions was made. The changes in the elemental composition of the protein-lipid films caused by high doses of chelating drugs were investigated. It was shown that state-of-the-art X-ray techniques can, in principle, be used to develop new methods for the in vitro evaluation of the efficiency of drugs, providing differential data on their actions.

  3. Investigation of the functional role of CSLD proteins in plant cell wall deposition

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, Erik Etlar [Univ. of Michigan, Ann Arbor, MI (United States)

    2017-11-21

    The overall goal of this research proposal was to characterize the molecular machinery responsible for polarized secretion of cell wall components in Arabidopsis thaliana. We have used the polarized expansion that occurs during root hair cell growth to identify membrane trafficking pathways involved in polarized secretion of cell wall components to the expanding tips of these cells, and we have recently shown that CSLD3 is preferentially targeted to the apical plasma membranes in root hair cells, where it plays essential roles during cell wall deposition in these cells. The specific aims of the project are designed to answer the following objective: Identification of the cell wall polysaccharide class that CSLD proteins synthesize.

  4. Selective and extensive 13C labeling of a membrane protein for solid-state NMR investigations

    International Nuclear Information System (INIS)

    Hong, M.; Jakes, K.

    1999-01-01

    The selective and extensive 13C labeling of mostly hydrophobic amino acid residues in a 25 kDa membrane protein, the colicin Ia channel domain, is reported. The novel 13C labeling approach takes advantage of the amino acid biosynthetic pathways in bacteria and suppresses the synthesis of the amino acid products of the citric acid cycle. The selectivity and extensiveness of labeling significantly simplify the solid-state NMR spectra, reduce line broadening, and should permit the simultaneous measurement of multiple structural constraints. We show the assignment of most 13C resonances to specific amino acid types based on the characteristic chemical shifts, the 13C labeling pattern, and the amino acid composition of the protein. The assignment is partly confirmed by a 2D homonuclear double-quantum-filter experiment under magic-angle spinning. The high sensitivity and spectral resolution attained with this 13C-labeling protocol, which is termed TEASE for ten-amino acid selective and extensive labeling, are demonstrated

  5. Investigating the efficacy of nonlinear dimensionality reduction schemes in classifying gene and protein expression studies.

    Science.gov (United States)

    Lee, George; Rodriguez, Carlos; Madabhushi, Anant

    2008-01-01

    The recent explosion in procurement and availability of high-dimensional gene- and protein-expression profile datasets for cancer diagnostics has necessitated the development of sophisticated machine learning tools with which to analyze them. A major limitation in the ability to accurate classify these high-dimensional datasets stems from the 'curse of dimensionality', occurring in situations where the number of genes or peptides significantly exceeds the total number of patient samples. Previous attempts at dealing with this issue have mostly centered on the use of a dimensionality reduction (DR) scheme, Principal Component Analysis (PCA), to obtain a low-dimensional projection of the high-dimensional data. However, linear PCA and other linear DR methods, which rely on Euclidean distances to estimate object similarity, do not account for the inherent underlying nonlinear structure associated with most biomedical data. The motivation behind this work is to identify the appropriate DR methods for analysis of high-dimensional gene- and protein-expression studies. Towards this end, we empirically and rigorously compare three nonlinear (Isomap, Locally Linear Embedding, Laplacian Eigenmaps) and three linear DR schemes (PCA, Linear Discriminant Analysis, Multidimensional Scaling) with the intent of determining a reduced subspace representation in which the individual object classes are more easily discriminable.

  6. X-ray fluorescence methods for investigations of lipid/protein membrane models.

    Science.gov (United States)

    Novikova, Natalia N; Yurieva, Eleonora A; Zheludeva, Svetlana I; Kovalchuk, Michail V; Stepina, Nina D; Tolstikhina, Alla L; Gaynutdinov, Ratmir V; Urusova, Dariya V; Matkovskaya, Tatiana A; Rubtsov, Alexandr M; Lopina, Olga D; Erko, Alexsey I; Konovalov, Oleg V

    2005-07-01

    The protective effect of the bisphosphonate drug xydiphone (K,Na-ethidronate) on membrane-bound enzyme damaged by lead ions has been studied. A protein/lipid film of Ca-ATPase/phosphatedylethanolamine deposited on a silicon substrate was used as a model system. The position of lead ions within the molecular film before and after the xydiphone treatment was determined using the total-reflection X-ray fluorescence method. This technique is based on the simultaneous measurement of the X-ray reflection and the yield of the fluorescence radiation excited by X-ray inelastic scattering. The possibility of directly locating lead ions is the main advantage of this approach. Xydiphone has been found to effectively eliminate lead ions that have been incorporated into Ca-ATPase molecules during a preliminary incubation in lead acetate solution. The lead ions that were bound at the sites of the Ca-ATPase attachment to the phospholipid monolayer have proved to be inaccessible for xydiphone. A preliminary incubation of Ca-ATPase in the xydiphone solution precluded the incorporation of lead ions into the protein.

  7. Application of spectral deconvolution and inverse mechanistic modelling as a tool for root cause investigation in protein chromatography.

    Science.gov (United States)

    Brestrich, Nina; Hahn, Tobias; Hubbuch, Jürgen

    2016-03-11

    In chromatographic protein purification, process variations, aging of columns, or processing errors can lead to deviations of the expected elution behavior of product and contaminants and can result in a decreased pool purity or yield. A different elution behavior of all or several involved species leads to a deviating chromatogram. The causes for deviations are however hard to identify by visual inspection and complicate the correction of a problem in the next cycle or batch. To overcome this issue, a tool for root cause investigation in protein chromatography was developed. The tool combines a spectral deconvolution with inverse mechanistic modelling. Mid-UV spectral data and Partial Least Squares Regression were first applied to deconvolute peaks to obtain the individual elution profiles of co-eluting proteins. The individual elution profiles were subsequently used to identify errors in process parameters by curve fitting to a mechanistic chromatography model. The functionality of the tool for root cause investigation was successfully demonstrated in a model protein study with lysozyme, cytochrome c, and ribonuclease A. Deviating chromatograms were generated by deliberately caused errors in the process parameters flow rate and sodium-ion concentration in loading and elution buffer according to a design of experiments. The actual values of the three process parameters and, thus, the causes of the deviations were estimated with errors of less than 4.4%. Consequently, the established tool for root cause investigation is a valuable approach to rapidly identify process variations, aging of columns, or processing errors. This might help to minimize batch rejections or contribute to an increased productivity. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. LabVIEW-operated novel nanoliter osmometer for ice binding protein investigations.

    Science.gov (United States)

    Braslavsky, Ido; Drori, Ran

    2013-02-04

    Ice-binding proteins (IBPs), including antifreeze proteins, ice structuring proteins, thermal hysteresis proteins, and ice recrystallization inhibition proteins, are found in cold-adapted organisms and protect them from freeze injuries by interacting with ice crystals. IBPs are found in a variety of organism, including fish(1), plants(2, 3), arthropods(4, 5), fungi(6), and bacteria(7). IBPs adsorb to the surfaces of ice crystals and prevent water molecules from joining the ice lattice at the IBP adsorption location. Ice that grows on the crystal surface between the adsorbed IBPs develops a high curvature that lowers the temperature at which the ice crystals grow, a phenomenon referred to as the Gibbs-Thomson effect. This depression creates a gap (thermal hysteresis, TH) between the melting point and the nonequilibrium freezing point, within which ice growth is arrested(8-10), see Figure 1. One of the main tools used in IBP research is the nanoliter osmometer, which facilitates measurements of the TH activities of IBP solutions. Nanoliter osmometers, such as the Clifton instrument (Clifton Technical Physics, Hartford, NY,) and Otago instrument (Otago Osmometers, Dunedin, New Zealand), were designed to measure the osmolarity of a solution by measuring the melting point depression of droplets with nanoliter volumes. These devices were used to measure the osmolarities of biological samples, such as tears(11), and were found to be useful in IBP research. Manual control over these nanoliter osmometers limited the experimental possibilities. Temperature rate changes could not be controlled reliably, the temperature range of the Clifton instrument was limited to 4,000 mOsmol (about -7.5 °C), and temperature recordings as a function of time were not an available option for these instruments. We designed a custom-made computer-controlled nanoliter osmometer system using a LabVIEW platform (National Instruments). The cold stage, described previously(9, 10), contains a metal

  9. Fluorinated ionic liquids for protein drug delivery systems: Investigating their impact on the structure and function of lysozyme.

    Science.gov (United States)

    Alves, Márcia; Vieira, Nicole S M; Rebelo, Luís Paulo N; Araújo, João M M; Pereiro, Ana B; Archer, Margarida

    2017-06-30

    Since the approval of recombinant human insulin by FDA in 1982, more than 200 proteins are currently available for pharmaceutical use to treat a wide range of diseases. However, innovation is still required to develop effective approaches for drug delivery. Our aim is to investigate the potential use of fluorinated ionic liquids (FILs) as drug delivery systems (DDS) for therapeutic proteins. Some initial parameters need to be assessed before further studies can proceed. This work evaluates the impact of FILs on the stability, function, structure and aggregation state of lysozyme. Different techniques were used for this purpose, which included differential scanning fluorimetry (DSF), spectrophotometric assays, circular dichroism (CD), dynamic light scattering (DLS), and scanning and transmission electron microscopy (SEM/TEM). Ionic liquids composed of cholinium-, imidazolium- or pyridinium- derivatives were combined with different anions and analysed at different concentrations in aqueous solutions (below and above the critical aggregation concentration, CAC). The results herein presented show that the addition of ionic liquids had no significant effect on the stability and hydrolytic activity of lysozyme. Moreover, a distinct behaviour was observed in DLS experiments for non-surfactant and surfactant ionic liquids, with the latter encapsulating the protein at concentrations above the CAC. These results encourage us to further study ionic liquids as promising tools for DDS of protein drugs. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Investigation of the Maillard Reaction between Polysaccharides and Proteins from Longan Pulp and the Improvement in Activities.

    Science.gov (United States)

    Han, Miao-Miao; Yi, Yang; Wang, Hong-Xun; Huang, Fei

    2017-06-05

    The purpose of this study was to investigate the Maillard reaction between polysaccharides and proteins from longan pulp and the effects of reaction on their in vitro activities. The polysaccharide-protein mixtures of fresh longan pulp (LPPMs) were co-prepared by an alkali extraction-acid precipitation method. They were then dry-heated under controlled conditions for monitoring the characterization of the Maillard reaction by the measurement of the free amino group content, ultraviolet-visible spectrum, Fourier transform infrared spectrum and molecular weight distribution. All the physicochemical analyses indicated the development of the Maillard reaction between polysaccharides and proteins. The in vitro activity evaluation indicated that the Maillard reaction could effectively enhance the antioxidant, antitumor and immunostimulating activities of LPPMs. The enhancement of 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity and ferric reducing antioxidant power displayed both a positive correlation with the reaction time ( p Maillard-type intermacromolecular interaction is suggested to be an effective and controllable method for improving the functional activities of polysaccharides and proteins from longan pulp.

  11. Investigation of the Influence of Protein-Losing Enteropathy on Monoclonal Antibody Pharmacokinetics in Mice.

    Science.gov (United States)

    Yang, Yujie; Li, Tommy R; Balthasar, Joseph P

    2017-11-01

    Protein losing enteropathy (PLE), which is characterized by substantial loss of plasma proteins into the gastrointestinal (GI) tract, is a complication of a variety of GI diseases, including inflammatory bowel disease. Clinical studies have found that the clearance of monoclonal antibodies (mAb) is often increased in subjects with diseases known to cause PLE; however, direct relationships between PLE and mAb pharmacokinetics have not been demonstrated. This study employed a murine model of colitis to examine the influence of PLE on mAb pharmacokinetics. Mice were given dextran sodium sulfate (DSS, 2% w/v) supplemented tap water as drinking source for 6 days to induce colitis and PLE. Mice were then intravenously injected with 8C2, a murine IgG1 mAb. 8C2 plasma concentrations were measured up to 14 days post injection. Fecal alpha-1-antitrypsin (A1AT) clearance was measured as biomarker for PLE. DSS-treated mice developed PLE of clinically relevant severity. They also showed a transient increase in 8C2 plasma clearance and a decrease in 8C2 plasma exposure. The area under the 8C2 plasma concentration-time curve for the length of the study (AUC 0-14d ) reduced from 1368 ± 255 to 594 ± 224 day μg/ml following DSS treatment (p = 0.001). A quantitative relationship between A1AT clearance and 8C2 clearance was obtained via population pharmacokinetic modeling. DSS treatment substantially increased 8C2 clearance and reduced 8C2 exposure. Increased mAb plasma clearance was highly correlated with A1AT fecal clearance, suggesting the possible utility of A1AT fecal clearance as a mechanistic biomarker to predict the pharmacokinetics of therapeutic antibodies.

  12. One- and two-dimensional infrared spectroscopic studies of solution-phase homogeneous catalysis and spin-forbidden reactions

    Energy Technology Data Exchange (ETDEWEB)

    Sawyer, Karma Rae [Univ. of California, Berkeley, CA (United States)

    2008-12-01

    Understanding chemical reactions requires the knowledge of the elementary steps of breaking and making bonds, and often a variety of experimental techniques are needed to achieve this goal. The initial steps occur on the femto- through picosecond time-scales, requiring the use of ultrafast spectroscopic methods, while the rate-limiting steps often occur more slowly, requiring alternative techniques. Ultrafast one and two-dimensional infrared and step-scan FTIR spectroscopies are used to investigate the photochemical reactions of four organometallic complexes. The analysis leads to a detailed understanding of mechanisms that are general in nature and may be applicable to a variety of reactions.

  13. Immunochemical investigation of allergenic residues in experimental and commercially-available wines fined with egg white proteins.

    Science.gov (United States)

    Uberti, Francesca; Danzi, Roberta; Stockley, Creina; Peñas, Elena; Ballabio, Cinzia; Di Lorenzo, Chiara; Tarantino, Chiara; Restani, Patrizia

    2014-09-15

    Proteinaceous egg whites are widely used as a fining agent during the production of red wines. Residues of egg white in the final wine could present a risk for individuals allergic to eggs. This study investigated the presence of allergenic residues in both red and white wines fined with egg whites. Experimental and commercially available wines fined with egg whites, with or without subsequent bentonite fining, were studied. Unfined wines were used as negative controls. The physicochemical characteristics of each wine were determined to assess their possible role in enhancing or hindering the elimination of allergenic residues from wine. The amount of egg white protein residues was investigated both by a specifically developed/validated ELISA test and by immunoblotting. Both immunochemical tests used the same anti-total egg white protein antibody and were highly sensitive to the allergen. No egg white protein was detected in the wines studied in either immunochemical test, irrespective of the physicochemical characteristics of the wine, the type and dosage of the fining agent and the oenological process used. The risk of adverse reactions in egg-allergic individuals should therefore be considered negligible, but the exemption from labelling should be allowed only when the absence of residues is confirmed by analytical controls. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Biochip for Real-Time Monitoring of Hepatitis B Virus (HBV) by Combined Loop-Mediated Isothermal Amplification and Solution-Phase Electrochemical Detection

    Science.gov (United States)

    Tien, Bui Quang; Ngoc, Nguyen Thy; Loc, Nguyen Thai; Thu, Vu Thi; Lam, Tran Dai

    2017-06-01

    Accurate in situ diagnostic tests play a key role in patient management and control of most infectious diseases. To achieve this, use of handheld biochips that implement sample handling, sample analysis, and result readout together is an ideal approach. We present herein a fluid-handling biochip for real-time electrochemical monitoring of nucleic acid amplification based on loop-mediated isothermal amplification and real-time electrochemical detection on a microfluidic platform. Intercalation between amplifying DNA and free redox probe in solution phase was used to monitor the number of DNA copies. The whole diagnostic process is completed within 70 min. Our platform offers a fast and easy tool for quantification of viral pathogens in shorter time and with limited risk of all potential forms of cross-contamination. Such diagnostic tools have potential to make a huge difference to the lives of millions of people worldwide.

  15. The Influence of the Linker Geometry in Bis(3-hydroxy-N-methyl-pyridin-2-one) Ligands on Solution-Phase Uranyl Affinity

    Energy Technology Data Exchange (ETDEWEB)

    Szigethy, Geza; Raymond, Kenneth

    2010-08-12

    Seven water-soluble, tetradentate bis(3-hydroxy-N-methyl-pyridin-2-one) (bis-Me-3,2-HOPO) ligands were synthesized that vary only in linker geometry and rigidity. Solution phase thermodynamic measurements were conducted between pH 1.6 and pH 9.0 to determine the effects of these variations on proton and uranyl cation affinity. Proton affinity decreases by introduction of the solubilizing triethylene glycol group as compared to un-substituted reference ligands. Uranyl affinity was found to follow no discernable trends with incremental geometric modification. The butyl-linked 4Li-Me-3,2-HOPO ligand exhibited the highest uranyl affinity, consistent with prior in vivo decorporation results. Of the rigidly-linked ligands, the o-phenylene linker imparted the best uranyl affinity to the bis-Me-3,2-HOPO ligand platform.

  16. Investigation into the Effects of Boron on Liver Tissue Protein Carbonyl, MDA, and Glutathione Levels in Endotoxemia.

    Science.gov (United States)

    Balabanlı, Barbaros; Balaban, Tuba

    2015-10-01

    Endotoxin has been known to cause the formation and damage of free radical. The importance of boron for human life is increasing each passing day, and its consuming fields are continuing to expand due to the advances in science and technology. Therefore, in our study, we intended to investigate into the effects of boron on liver tissue oxidative events. Eighteen male Wistar albino rats were randomly separated into three equal groups in the experiments; control group, boron + endotoxin group, and endotoxin group. Dissolved in distilled water, boric acid (100 mg/kg) was administered to boron + endotoxin group via gavage procedure for 28 days. Only distilled water was administered to control and endotoxin groups via gavage procedure for 28 days. Then 4 mg/kg endotoxin (LPS; Escherichia coli 0111:B4) was intraperitoneally (ip) administered to boron + endotoxin and endotoxin groups on the 28th day. Sterile saline was injected into control group on the 28th day (ip). Malondialdehyde (MDA), which is the end product of lipid peroxidation in liver tissues, protein carbonyl compounds (PC), which are protein oxidization markers, and glutathione (GSH) levels were measured spectrophotometrically. The results were compared with Mann-Whitney U test. When boron + endotoxin group is compared with endotoxin group, PC levels of endotoxin group showed a significant increase. When GSH levels are compared, GSH level in boron + endotoxin group decreased according to endotoxin group. Variations among all groups in MDA levels were found to be statistically insignificant. We are of the opinion that endotoxin affects the proteins by forming free radicals, and boron may also cause the structural and/or functional changes in proteins in order to protect proteins from oxidization.

  17. Investigating the Bacterial Inactivation Potential of Purified Okra (Hibiscus esculentus Seed Proteins in Water Purification

    Directory of Open Access Journals (Sweden)

    Alfred N. Jones

    2017-02-01

    Full Text Available The ability of purified okra protein (POP as coagulant and as disinfectant material in comparison with aluminium sulphate (AS in water treatment was assessed. A laboratory jar test experiments and Colilert-18/Quanti-Tray method of bacterial analysis were conducted using POP as coagulant in treating river water. The results show an excellent dual performance function of POP against the conventional coagulant, AS in drinking water treatment. It was observed that a marked inactivation of approximately 100% of faecal and E-coli count in raw water was achieved with POP and zero regrowth of bacteria after 72-hour post treatment. However, there was regrowth in total coliform count as a result of the presence of other microbes other than E-coli and faecal coliform in the system. In all cases AS showed a reduced performance against the two indicator organisms achieving only 93% with remarkable regrowth of E-coli and faecal coliform after prolonged storage time in the clarified water. Turbidity removal was also noted to be approximately similar, 92% across all coagulants tested. Therefore, the use of POP in water treatment could improve access to clean water in developing countries and could help in reducing the import of water treatment chemicals.

  18. A roadmap for investigating the role of the prion protein in depression associated with neurodegenerative disease.

    Science.gov (United States)

    Beckman, Danielle; Linden, Rafael

    2016-03-03

    The physiological properties of the native, endogenous prion protein (PrP(C)) is a matter of concern, due to its pleiotropic functions and links to neurodegenerative disorders and cancer. In line with our hypothesis that the basic function of PrP(C) is to serve as a cell surface scaffold for the assembly of signaling modules, multiple interactions have been identified of PrP(C) with signaling molecules, including neurotransmitter receptors. We recently reported evidence that PrP(C) may modulate monoaminergic neurotransmission, as well as depressive-like behavior in mice. Here, we discuss how those results, together with a number of other studies, including our previous demonstration that both inflammatory and behavioral stress modulate PrP(C) content in neutrophils, suggest a distributed role of PrP(C) in clinical depression and inflammation associated with neurodegenerative diseases. An overarching understanding of the multiple interventions of PrP(C) upon physiological events may both shed light on the pathogenesis of, as well as help the identification of novel therapeutic targets for clinical depression, Prion and Alzheimer's Diseases.

  19. Investigational BET bromodomain protein inhibitors in early stage clinical trials for acute myelogenous leukemia (AML).

    Science.gov (United States)

    Braun, Thorsten; Gardin, Claude

    2017-07-01

    Acute myelogenous leukemia (AML) is a heterogeneous group of malignancies driven by genetic mutations and deregulated epigenetic control. Relapse/refractory disease remains frequent in younger patients and even more so in older patients, including treatment with epigenetic drugs in this age group, mainly with hypomethylating agents. New treatment strategies are urgently needed. The recent discovery that epigenetic readers of the bromodomain (BRD) and extraterminal (BET) protein family, are crucial for AML maintenance by transcription of oncogenic c-MYC lead to rapid development of BET inhibitors entering clinical trials. Areas covered: We provide a critical overview using main sources for the use of BET inhibitors in AML treatment. Limits of this treatment approach including resistance mechanisms and future directions including development of new generation BET inhibitors and combination strategies with other drugs are detailed. Expert opinion: BET inhibitors were expected to overcome limits of conventional treatment in patients as impressive in vitro data emerged recently in well-characterized AML subsets, including those associated with poor risk characteristics in the clinic. Nevertheless single activity of BET inhibitors appears to be modest and resistance mechanisms were already identified. BET inhibitors with alternative mechanisms of action and/or combination strategies with epigenetic drugs should be tested.

  20. Investigations of ultrafast ligand rebinding to heme and heme proteins using temperature and strong magnetic field perturbations

    Science.gov (United States)

    Zhang, Zhenyu

    This thesis is written to summarize investigations of the mechanisms that underlie the kinetics of diatomic ligand rebinding to the iron atom of the heme group, which is chelated inside heme proteins. The family of heme proteins is a major object of studies for several branches of scientific research activity. Understanding the ligand binding mechanisms and pathways is one of the major goals for biophysics. My interests mainly focus on the physics of this ligand binding process. Therefore, to investigate the problem, isolated from the influence of the protein matrix, Fe-protophorphyrin IX is chosen as the prototype system in my studies. Myoglobin, the most extensively and intensively studied protein, is another ideal system that allows coupling the protein polypeptide matrix into the investigation. A technique to synchro-lock two laser pulse trains electronically is applied to our pump-probe spectroscopic studies. Based on this technique, a two color, fs/ps pump-probe system is developed which extends the temporal window for our investigation to 13ns and fills a gap existing in previous pump-probe investigations. In order to apply this newly-developed pump-probe laser system to implement systematic studies on the kinetics of diatomic ligand (NO, CO, O2) rebinding to heme and heme proteins, several experimental setups are utilized. In Chapter 1, the essential background knowledge, which helps to understand the iron-ligand interaction, is briefly described. In Chapter 2, in addition to a description of the preparation protocols of protein samples and details of the method for data analysis, three home-made setups are described, which include: a picosecond laser regenerative amplifier, a pump-probe application along the bore (2-inch in diameter) of a superconducting magnet and a temperature-controllable cryostat for spinning sample cell. Chapter 3 presents high magnetic field studies of several heme-ligand or protein-ligand systems. Pump-probe spectroscopy is used to

  1. Solution Phase Exciton Diffusion Dynamics of a Charge-Transfer Copolymer PTB7 and a Homopolymer P3HT

    Energy Technology Data Exchange (ETDEWEB)

    Cho, Sung; Rolczynski, Brian S.; Xu, Tao; Yu, Luping; Chen, Lin X.

    2015-06-18

    Using ultrafast polarization-controlled transient absorption (TA) measurements, dynamics of the initial exciton states were investigated on the time scale of tens of femtoseconds to about 80 ps in two different types of conjugated polymers extensively used in active layers of organic photovoltaic devices. These polymers are poly(3-fluorothienothiophenebenzodithiophene) (PTB7) and poly-3-hexylthiophene (P3HT), which are charge-transfer polymers and homopolymers, respectively. In PTB7, the initial excitons with excess vibrational energy display two observable ultrafast time constants, corresponding to coherent exciton diffusion before the vibrational relaxation, and followed by incoherent exciton diffusion processes to a neighboring local state after the vibrational relaxation. In contrast, P3HT shows only one exciton diffusion or conformational motion time constant of 34 ps, even though its exciton decay kinetics are multiexponential. Based on the experimental results, an exciton dynamics mechanism is conceived taking into account the excitation energy and structural dependence in coherent and incoherent exciton diffusion processes, as well as other possible deactivation processes including the formation of the pseudo-charge-transfer and charge separate states, as well as interchain exciton hopping or coherent diffusion.

  2. Pharmacoinformatics approach for investigation of alternative potential hepatitis C virus nonstructural protein 5B inhibitors

    Directory of Open Access Journals (Sweden)

    Mirza MU

    2015-03-01

    Full Text Available Muhammad Usman Mirza,1 Noor-Ul-Huda Ghori,2 Nazia Ikram,3 Abdur Rehman Adil,4 Sadia Manzoor3 1Centre for Research in Molecular Medicine (CRiMM, The University of Lahore, Lahore, 2Atta-ur-Rehman School of Applied Biosciences (ASAB, National University of Science and Technology, Islamabad, 3Institute of Molecular Biology and Biotechnology (IMBB, The University of Lahore, Lahore, Pakistan; 4Centre for Excellence in Molecular Biology (CEMB, The University of Punjab, Lahore, Pakistan Abstract: Hepatitis C virus (HCV is one of the major viruses affecting the world today. It is a highly variable virus, having a rapid reproduction and evolution rate. The variability of genomes is due to hasty replication catalyzed by nonstructural protein 5B (NS5B which is also a potential target site for the development of anti-HCV agents. Recently, the US Food and Drug Administration approved sofosbuvir as a novel oral NS5B inhibitor for the treatment of HCV. Unfortunately, it is much highlighted for its pricing issues. Hence, there is an urgent need to scrutinize alternate therapies against HCV that are available at affordable price and do not have associated side effects. Such a need is crucial especially in underdeveloped countries. The search for various new bioactive compounds from plants is a key part of pharmaceutical research. In the current study, we applied a pharmacoinformatics-based approach for the identification of active plant-derived compounds against NS5B. The results were compared to docking results of sofosbuvir. The lead compounds with high-binding ligands were further analyzed for pharmacokinetic and pharmacodynamic parameters based on in silico absorption, distribution, metabolism, excretion, and toxicity (ADMET profile. The results showed the potential alternative lead compounds that can be developed into commercial drugs having high binding energy and promising ADMET properties. Keywords: hepatitis C, NS5B inhibitors, molecular docking, Auto

  3. A Molecular Dynamics Investigation of the Physical-Chemical Properties of Calicivirus Capsid Protein Adsorption to Fomites

    Science.gov (United States)

    Peeler, David; Matysiak, Silvina

    2013-03-01

    Any inanimate object with an exposed surface bears the possibility of hosting a virus and may therefore be labeled a fomite. This research hopes to distinguish which chemical-physical differences in fomite surface and virus capsid protein characteristics cause variations in virus adsorption through an alignment of in silico molecular dynamics simulations with in vitro measurements. The impact of surface chemistry on the adsorption of the human norovirus (HNV)-surrogate calicivirus capsid protein 2MS2 has been simulated for monomer and trimer structures and is reported in terms of protein-self assembled monolayer (SAM) binding free energy. The coarse-grained MARTINI forcefield was used to maximize spatial and temporal resolution while minimizing computational load. Future work will investigate the FCVF5 and SMSVS4 calicivirus trimers and will extend beyond hydrophobic and hydrophilic SAM surface chemistry to charged SAM surfaces in varying ionic concentrations. These results will be confirmed by quartz crystal microbalance experiments conducted by Dr. Wigginton at the University of Michigan. This should provide a novel method for predicting the transferability of viruses that cannot be studied in vitro such as dangerous foodborne and nosocomially-acquired viruses like HNV.

  4. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hua-xin, E-mail: h.x.zhang@yeah.net; Liu, E.

    2014-09-15

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔH{sup θ}), Gibbs free energy change (ΔG{sup θ}) and entropy change (ΔS{sup θ}) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of

  5. Investigations into the Sarcomeric Protein and Ca2+-Regulation Abnormalities Underlying Hypertrophic Cardiomyopathy in Cats (Felix catus

    Directory of Open Access Journals (Sweden)

    Andrew E. Messer

    2017-06-01

    Full Text Available Hypertrophic cardiomyopathy (HCM is the most common single gene inherited cardiomyopathy. In cats (Felix catus HCM is even more prevalent and affects 16% of the outbred population and up to 26% in pedigree breeds such as Maine Coon and Ragdoll. Homozygous MYBPC3 mutations have been identified in these breeds but the mutations in other cats are unknown. At the clinical and physiological level feline HCM is closely analogous to human HCM but little is known about the primary causative mechanism. Most identified HCM causing mutations are in the genes coding for proteins of the sarcomere. We therefore investigated contractile and regulatory proteins in left ventricular tissue from 25 cats, 18 diagnosed with HCM, including a Ragdoll cat with a homozygous MYBPC3 R820W, and 7 non-HCM cats in comparison with human HCM (from septal myectomy and donor heart tissue. Myofibrillar protein expression was normal except that we observed 20–44% MyBP-C haploinsufficiency in 5 of the HCM cats. Troponin extracted from 8 HCM and 5 non-HCM cat hearts was incorporated into thin filaments and studied by in vitro motility assay. All HCM cat hearts had a higher (2.06 ± 0.13 fold Ca2+-sensitivity than non-HCM cats and, in all the HCM cats, Ca2+-sensitivity was not modulated by troponin I phosphorylation. We were able to restore modulation of Ca2+-sensitivity by replacing troponin T with wild-type protein or by adding 100 μM Epigallocatechin 3-gallate (EGCG. These fundamental regulatory characteristics closely mimic those seen in human HCM indicating a common molecular mechanism that is independent of the causative mutation. Thus, the HCM cat is a potentially useful large animal model.

  6. Investigations into the Sarcomeric Protein and Ca2+-Regulation Abnormalities Underlying Hypertrophic Cardiomyopathy in Cats (Felix catus)

    Science.gov (United States)

    Messer, Andrew E.; Chan, Jasmine; Daley, Alex; Copeland, O'Neal; Marston, Steven B.; Connolly, David J.

    2017-01-01

    Hypertrophic cardiomyopathy (HCM) is the most common single gene inherited cardiomyopathy. In cats (Felix catus) HCM is even more prevalent and affects 16% of the outbred population and up to 26% in pedigree breeds such as Maine Coon and Ragdoll. Homozygous MYBPC3 mutations have been identified in these breeds but the mutations in other cats are unknown. At the clinical and physiological level feline HCM is closely analogous to human HCM but little is known about the primary causative mechanism. Most identified HCM causing mutations are in the genes coding for proteins of the sarcomere. We therefore investigated contractile and regulatory proteins in left ventricular tissue from 25 cats, 18 diagnosed with HCM, including a Ragdoll cat with a homozygous MYBPC3 R820W, and 7 non-HCM cats in comparison with human HCM (from septal myectomy) and donor heart tissue. Myofibrillar protein expression was normal except that we observed 20–44% MyBP-C haploinsufficiency in 5 of the HCM cats. Troponin extracted from 8 HCM and 5 non-HCM cat hearts was incorporated into thin filaments and studied by in vitro motility assay. All HCM cat hearts had a higher (2.06 ± 0.13 fold) Ca2+-sensitivity than non-HCM cats and, in all the HCM cats, Ca2+-sensitivity was not modulated by troponin I phosphorylation. We were able to restore modulation of Ca2+-sensitivity by replacing troponin T with wild-type protein or by adding 100 μM Epigallocatechin 3-gallate (EGCG). These fundamental regulatory characteristics closely mimic those seen in human HCM indicating a common molecular mechanism that is independent of the causative mutation. Thus, the HCM cat is a potentially useful large animal model. PMID:28642712

  7. Practical considerations for investigation of protein conformational dynamics by {sup 15}N R{sub 1ρ} relaxation dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Walinda, Erik [Kyoto University, Department of Molecular and Cellular Physiology, Graduate School of Medicine (Japan); Morimoto, Daichi; Shirakawa, Masahiro; Sugase, Kenji, E-mail: sugase@moleng.kyoto-u.ac.jp [Kyoto University, Department of Molecular Engineering, Graduate School of Engineering (Japan)

    2017-03-15

    It is becoming increasingly apparent that proteins are not static entities and that their function often critically depends on accurate sampling of multiple conformational states in aqueous solution. Accordingly, the development of methods to study conformational states in proteins beyond their ground-state structure (“excited states”) has crucial biophysical importance. Here we investigate experimental schemes for optimally probing chemical exchange processes in proteins on the micro- to millisecond timescale by {sup 15}N R{sub 1ρ} relaxation dispersion. The schemes use selective Hartmann–Hahn cross-polarization (CP) transfer for excitation, and derive peak integrals from 1D NMR spectra (Korzhnev et al. in J Am Chem Soc 127:713–721, 2005; Hansen et al. in J Am Chem Soc 131:3818–3819, 2009). Simulation and experiment collectively show that in such CP-based schemes care has to be taken to achieve accurate suppression of undesired off-resonance coherences, when using weak spin-lock fields. This then (i) ensures that relaxation dispersion profiles in the absence of chemical exchange are flat, and (ii) facilitates extraction of relaxation dispersion profiles in crowded regions of the spectrum. Further improvement in the quality of the experimental data is achieved by recording the free-induction decays in an interleaved manner and including a heating-compensation element. The reported considerations will particularly benefit the use of CP-based R{sub 1ρ} relaxation dispersion to analyze conformational exchange processes in larger proteins, where resonance line overlap becomes the main limiting factor.

  8. investigating acid production by Streptococcus mutans with a surface-displayed pH-sensitive green fluorescent protein.

    Directory of Open Access Journals (Sweden)

    Lihong Guo

    Full Text Available Acidogenicity and aciduricity are the main virulence factors of the cavity-causing bacterium Streptococcus mutans. Monitoring at the individual cell level the temporal and spatial distribution of acid produced by this important oral pathogen is central for our understanding of these key virulence factors especially when S. mutans resides in multi-species microbial communities. In this study, we explored the application of pH-sensitive green fluorescent proteins (pHluorins to investigate these important features. Ecliptic pHluorin was functionally displayed on the cell surface of S. mutans as a fusion protein with SpaP. The resulting strain (O87 was used to monitor temporal and spatial pH changes in the microenvironment of S. mutans cells under both planktonic and biofilm conditions. Using strain O87, we revealed a rapid pH drop in the microenviroment of S. mutans microcolonies prior to the decrease in the macro-environment pH following sucrose fermentation. Meanwhile, a non-uniform pH distribution was observed within S. mutans biofilms, reflecting differences in microbial metabolic activity. Furthermore, strain O87 was successfully used to monitor the S. mutans acid production profiles within dual- and multispecies oral biofilms. Based on these findings, the ecliptic pHluorin allows us to investigate in vivo and in situ acid production and distribution by the cariogenic species S. mutans.

  9. In-vitro Investigations of Skin Closure using Diode Laser and Protein Solder Containing Gold Nanoshells

    Directory of Open Access Journals (Sweden)

    Mohammad Sadegh Nourbakhsh

    2010-12-01

    Full Text Available Introduction: Laser tissue soldering is a new technique for repair of various tissues including the skin, liver, articular cartilage and nerves and is a promising alternative to suture. To overcome the problems of thermal damage to surrounding tissues and low laser penetration depth, some exogenous chromophores such as gold nanoshells, a new class of nanoparticles consisting of a dielectric core surrounded by a thin metal shell, are used. The aims of this study were to use two different concentrations of gold nanoshells as the exogenous material for skin tissue soldering and also to examine the effects of laser soldering parameters on the properties of the repaired skin. Material and Methods: Two mixtures of albumin solder and different concentrations of gold nanoshells were prepared. A full thickness incision of 2×20 mm2 was made on the surface and after placing 50 μl of the solder mixture on the incision, an 810 nm diode laser was used to irradiate it at different power densities. The changes of tensile strength, σt, due to temperature rise, number of scan (Ns, and scan velocity (Vs were investigated. Results: The results showed that the tensile strength of the repaired skin increased with increasing irradiance for both gold nanoshell concentrations. In addition, at constant laser irradiance (I, the tensile strength of the repaired incision increased with increasing Ns and decreasing Vs. In our case, this corresponded to st = 1610 g/cm2 at I ~ 60 Wcm-2, T ~ 65ºC, Ns = 10 and Vs = 0.2 mms-1. Discussion and Conclusion: Gold nanoshells can be used as an indocyanine green dye (ICG alterative for laser tissue soldering.  Although by increasing the laser power density, the tensile strength of the repaired skin increases, an optimum power density must be considered due to the resulting increase in tissue temperature.

  10. A protein diet score, including plant and animal protein, investigating the association with HbA1c and eGFR - the PREVIEW project

    DEFF Research Database (Denmark)

    Møller, Grith; Sluik, Diewertje; Ritz, Christian

    2017-01-01

    Higher-protein diets have been advocated for body-weight regulation for the past few decades. However, the potential health risks of these diets are still uncertain. We aimed to develop a protein score based on the quantity and source of protein, and to examine the association of the score...... with glycated haemoglobin (HbA1c) and estimated glomerular filtration rate (eGFR). Analyses were based on three population studies included in the PREVIEW project (PREVention of diabetes through lifestyle Intervention and population studies in Europe and around the World): NQplus, Lifelines, and the Young Finns...... Study. Cross-sectional data from food-frequency questionnaires (n = 76,777 subjects) were used to develop a protein score consisting of two components: 1) percentage of energy from total protein, and 2) plant to animal protein ratio. An inverse association between protein score and HbA1c (slope -0...

  11. Method of removing alkyl iodides or mixtures of iodine and alkyl iodides from a gas phase and an aqueous solution phase by utilizing ion exchange resins

    International Nuclear Information System (INIS)

    Shimizu, Hiroshi; Mizuuchi, Noboru; Yokoyama, Fumio.

    1967-01-01

    Alkyl iodides and mixtures of iodine and alkyl iodides are removed from a gas phase and an aquous solution phase by using solely an anion exchange resin containing a tertiary amine or together with an anion exchange resin containing quarternary ammonium compound. The resin containing the quarternary ammonium compound is employed mainly to remove iodine, and the resin containing the tertiary amine serves mainly to remove alkyl iodides. The method can be applied to collecting a majority of the methyl iodide as well as the radioactive iodine produced in the atmosphere of a reactor in case of a fuel accident. In embodiments, it is desirable to maintain the sufficient moisture content of the anion exchange resins at a sufficient moisture level so as not to reduce the migration speed of the iodine and alkyl iodides. The iodine and alkyl iodide can be produced with high efficiency and stability independently of the relative humidity of the gas phase. In examples, a solution which consists of 20.5 mg/l of iodine and 42.2mg/l of methyl iodide flew through a column of Amberite IRA-93 alone or blended with IRA-900 at a speed of 15 /hr. respectively. The resins were able to treat 400 times their equivalent in water. (Iwakiri, K.)

  12. Directly relating gas-phase cluster measurements to solution-phase hydrolysis, the absolute standard hydrogen electrode potential, and the absolute proton solvation energy.

    Science.gov (United States)

    Donald, William A; Leib, Ryan D; O'Brien, Jeremy T; Williams, Evan R

    2009-06-08

    Solution-phase, half-cell potentials are measured relative to other half-cell potentials, resulting in a thermochemical ladder that is anchored to the standard hydrogen electrode (SHE), which is assigned an arbitrary value of 0 V. A new method for measuring the absolute SHE potential is demonstrated in which gaseous nanodrops containing divalent alkaline-earth or transition-metal ions are reduced by thermally generated electrons. Energies for the reactions 1) M(H(2)O)(24)(2+)(g) + e(-)(g)-->M(H(2)O)(24)(+)(g) and 2) M(H(2)O)(24)(2+)(g) + e(-)(g)-->MOH(H(2)O)(23)(+)(g) + H(g) and the hydrogen atom affinities of MOH(H(2)O)(23)(+)(g) are obtained from the number of water molecules lost through each pathway. From these measurements on clusters containing nine different metal ions and known thermochemical values that include solution hydrolysis energies, an average absolute SHE potential of +4.29 V vs. e(-)(g) (standard deviation of 0.02 V) and a real proton solvation free energy of -265 kcal mol(-1) are obtained. With this method, the absolute SHE potential can be obtained from a one-electron reduction of nanodrops containing divalent ions that are not observed to undergo one-electron reduction in aqueous solution.

  13. Temperature-concentration oscillations of crystal-solution phase equilibria in the presence of trace impurities of surface-active agents

    Energy Technology Data Exchange (ETDEWEB)

    Kiryanova, E.V. [St. Petersburg State University, Crystallography Dept., 199034, University emb. 9, St. Petersburg (Russian Federation)

    2011-04-15

    Using the examples of aqueous salt solutions NaNO{sub 3}, KNO{sub 3}, RbNO{sub 3}, K{sub 2}SO{sub 4}, NaBr.2H{sub 2}O, KBr, and NH{sub 4}NO{sub 3}, it was experimentally proven that the new phenomena, i.e. temperature-concentration oscillations of crystal-solution phase equilibria detected previously in the range of 15-45 C remain in the presence of trace impurities (10{sup -4}-10{sup -3} wt. %) of ion-active organic matters. The signs of breaks transformation into pair oscillations of ''maximum-minimum'' type are established for the K{sub 2}SO{sub 4}, NaBr, KBr solutions. The efficiency of influence of trace impurities on phase equilibria sharply rises in the areas of the temperature-concentration oscillations (the saturation temperature ranges up to 10 K). The impurity efficiency is promoted by the presence of the amides in its content (as compared with the sulphates) and an increase in length of the hydrocarbon radical. The phenomenon is absent in case of an addition of ion-inactive compounds. (copyright 2011 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  14. Protein and Peptide Gas-phase Structure Investigation Using Collision Cross Section Measurements and Hydrogen Deuterium Exchange

    Science.gov (United States)

    Khakinejad, Mahdiar

    Protein and peptide gas-phase structure analysis provides the opportunity to study these species outside of their explicit environment where the interaction network with surrounding molecules makes the analysis difficult [1]. Although gas-phase structure analysis offers a unique opportunity to study the intrinsic behavior of these biomolecules [2-4], proteins and peptides exhibit very low vapor pressures [2]. Peptide and protein ions can be rendered in the gas-phase using electrospray ionization (ESI) [5]. There is a growing body of literature that shows proteins and peptides can maintain solution structures during the process of ESI and these structures can persist for a few hundred milliseconds [6-9]. Techniques for monitoring gas-phase protein and peptide ion structures are categorized as physical probes and chemical probes. Collision cross section (CCS) measurement, being a physical probe, is a powerful method to investigate gas-phase structure size [3, 7, 10-15]; however, CCS values alone do not establish a one to one relation with structure(i.e., the CCS value is an orientationally averaged value [15-18]. Here we propose the utility of gas-phase hydrogen deuterium exchange (HDX) as a second criterion of structure elucidation. The proposed approach incudes extensive MD simulations to sample biomolecular ion conformation space with the production of numerous, random in-silico structures. Subsequently a CCS can be calculated for these structures and theoretical CCS values are compared with experimental values to produce a pool of candidate structures. Utilizing a chemical reaction model based on the gas-phase HDX mechanism, the HDX kinetics behavior of these candidate structures are predicted and compared to experimental results to nominate the best in-silico structures which match (chemically and physically) with experimental observations. For the predictive approach to succeed, an extensive technique and method development is essential. To combine CCS

  15. Investigation of a Potential Scintigraphic Tracer for Imaging Apoptosis: Radioiodinated Annexin V-Kunitz Protease Inhibitor Fusion Protein

    Directory of Open Access Journals (Sweden)

    Mei-Hsiu Liao

    2011-01-01

    Full Text Available Radiolabeled annexin V (ANV has been widely used for imaging cell apoptosis. Recently, a novel ANV-Kunitz-type protease inhibitor fusion protein, ANV-6L15, was found to be a promising probe for improved apoptosis detection based on its higher affinity to phosphatidylserine (PS compared to native ANV. The present paper investigates the feasibility of apoptosis detection using radioiodinated ANV-6L15. Native ANV and ANV-6L15 were labeled with iodine-123 and iodine-125 using Iodogen method. The binding between the radioiodinated proteins and erythrocyte ghosts or chemical-induced apoptotic cells was examined. ANV-6L15 can be radioiodinated with high yield (40%−60% and excellent radiochemical purity (>95%. 123I-ANV-6L15 exhibited a higher binding ratio to erythrocyte ghosts and apoptotic cells compared to 123I-ANV. The biodistribution of 123I-ANV-6L15 in mice was also characterized. 123I-ANV-6L15 was rapidly cleared from the blood. High uptake in the liver and the kidneys may limit the evaluation of apoptosis in abdominal regions. Our data suggest that radiolabled ANV-6L15 may be a better scintigraphic tracer than native ANV for apoptosis detection.

  16. SANS investigation of the Self-organization behavior in Synthetic Resilin Gels: A Perfect Rubber-like protein

    International Nuclear Information System (INIS)

    Dutta, N.K.; Tran, N.D.; Roy Choudhury, N.; Hill, A.J.; Elvin, C.; Knott, Robert

    2005-01-01

    Full text: Elastic proteins are observed in a wide range of biological systems, from plants to invertebrates to humans, where they have evolved to fulfill precise biological function. The elasticity of resilins is exploited by animals in locomotion, through storing energy, especially in jumping and flight. Resilins are composed of naturally occurring protein polymers in which biological control of the polypeptide sequence made a material with mechanical and resilience characteristics superior to any synthetic and non-peptide natural polymer. We have successfully cloned, expressed and in vitro crosslinked insect pro-resilin to prepare resilin like polypeptide (Jaano-Resilin) with unusual viscoelastic characteristics with resilience characteristics more than 95% in preferred swollen gel state. The molecular basis of the unusual resilience characteristics of the resilin-gel is unknown but of significant scientific interest. In this research investigation Small angle neutron scattering (SANS) has be employed to explore the self-organisation behaviour of crosslinked resilin gel in equilibrium-swollen condition over a wide range of temperature (5 to 80 degrees C). The effect of drying and re-swelling on the organisational behaviour has been established. We also evaluate the viscoelastic characteristic of this resilin elastomer gels over a wide range of experimental conditions. The correlation between self-organisation and unique resilience behaviour will also be discussed. (authors)

  17. Cooking temperature is a key determinant of in vitro meat protein digestion rate: investigation of underlying mechanisms.

    Science.gov (United States)

    Bax, Marie-Laure; Aubry, Laurent; Ferreira, Claude; Daudin, Jean-Dominique; Gatellier, Philippe; Rémond, Didier; Santé-Lhoutellier, Véronique

    2012-03-14

    The present study aimed to evaluate the digestion rate and nutritional quality of pig muscle proteins in relation to different meat processes (aging, mincing, and cooking). Under our experimental conditions, aging and mincing had little impact on protein digestion. Heat treatments had different temperature-dependent effects on the meat protein digestion rate and degradation potential. At 70 °C, the proteins underwent denaturation that enhanced the speed of pepsin digestion by increasing enzyme accessibility to protein cleavage sites. Above 100 °C, oxidation-related protein aggregation slowed pepsin digestion but improved meat protein overall digestibility. The digestion parameters defined here open new insights on the dynamics governing the in vitro digestion of meat protein. However, the effect of cooking temperature on protein digestion observed in vitro needs to be confirmed in vivo.

  18. Laser-optical investigation of the effect of diamond nanoparticles on the structure and functional properties of proteins

    International Nuclear Information System (INIS)

    Perevedentseva, Elena V; Su, F.Y.; Su, T.H.; Lin, Y.C.; Cheng, C.L.; Karmenyan, A V; Priezzhev, A V; Lugovtsov, Andrei E

    2011-01-01

    Adsorption of such blood plasma proteins as albumin and g-globulin on diamond nanoparticles of size around 5 nm and around 100 nm is observed and studied using laser-optical methods. The adsorption of blood plasma proteins at physiological pH 7.4 is found weaker than that of enzyme protein lysozyme. The observed variations in the Fourier Transform Infrared (FTIR) spectra of proteins may be due to structural transformations of the adsorbed protein. Using the lysozyme as a test protein we show that the protein adsorption leading to observable changes in the FTIR spectrum (the band of Amide I) also induces a significant decrease in the protein functional activity. It is also found that the influence of ∼5-nm diamond nanoparticles on the protein structure and functions is more significant than that of ∼100-nm nanodiamonds. (application of lasers and laser-optical methods in life sciences)

  19. [Investigations on the relation between differentiation and the composition of soluble protein of tissue cultures and leaves of daucus carota].

    Science.gov (United States)

    Neumann, K H; Pauler, B

    1969-12-01

    The correlations between differentiation, the amino acid composition of total protein and of soluble protein, and the disc electrophoretic distribution of soluble protein of carrot tissue cultures and of carrot plants (leaves) were studied. In spite of pronounced and characteristic changes in the electrophoretic distribution of the components of soluble protein in various developmental stages of both bioassays, no significant differences in the amino acid composition of protein were observed. With progressive development of whole carrot plants and of carrot tissue cultures, the number of protein bands on disc electropherogramms increased.

  20. DbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications.

    Science.gov (United States)

    Lu, Cheng-Tsung; Huang, Kai-Yao; Su, Min-Gang; Lee, Tzong-Yi; Bretaña, Neil Arvin; Chang, Wen-Chi; Chen, Yi-Ju; Chen, Yu-Ju; Huang, Hsien-Da

    2013-01-01

    Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein-protein interaction and domain-domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.

  1. Protein Internal Dynamics Associated With Pre-System Glass Transition Temperature Endothermic Events: Investigation of Insulin and Human Growth Hormone by Solid State Hydrogen/Deuterium Exchange.

    Science.gov (United States)

    Fang, Rui; Grobelny, Pawel J; Bogner, Robin H; Pikal, Michael J

    2016-11-01

    Lyophilized proteins are generally stored below their glass transition temperature (T g ) to maintain long-term stability. Some proteins in the (pure) solid state showed a distinct endotherm at a temperature well below the glass transition, designated as a pre-T g endotherm. The pre-T g endothermic event has been linked with a transition in protein internal mobility. The aim of this study was to investigate the internal dynamics of 2 proteins, insulin and human growth hormone (hGH), both of which exhibit the pre-T g endothermic event with onsets at 50°C-60°C. Solid state hydrogen/deuterium (H/D) exchange of both proteins was characterized by Fourier transform infrared spectroscopy over a temperature range from 30°C to 80°C. A distinct sigmoidal transition in the extent of H/D exchange had a midpoint of 56.1 ± 1.2°C for insulin and 61.7 ± 0.9°C for hGH, suggesting a transition to greater mobility in the protein molecules at these temperatures. The data support the hypothesis that the pre-T g event is related to a transition in internal protein mobility associated with the protein dynamical temperature. Exceeding the protein dynamical temperature is expected to activate protein internal motion and therefore may have stability consequences. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

  2. Investigation the Response of Some Proteins That Involved in Cachexia Syndrome to Acute Resistance Exercise in Healthy Elderly People

    Directory of Open Access Journals (Sweden)

    Meysam Gholamali

    2015-01-01

    Full Text Available Objectives: The aim of this study was to investigate the response of plasma Myostatin and insulin growth factor like-1 (IGF-1, as two most important proteins that involved in Cachexia syndrome, to acute resistance exercise in healthy elderly people. Methods & Materials: Twelve healthy older men (Age=67±1.3 years, BMI=25±1.4 kg/m2 volunteered for participation in this study. 72 hours after the determination of muscular maximal strength (by 1-RM test, subjects participated in acute resistance exercises via 75% 1-RM. In this research, two blood samples were collected at before and immediately after the exercise from Antecubital vein. Plasma Myostatin and serum levels of IGF-1 were measured by ELISA methods. Paired T-Test used for statical analyses of research data. Significant level was set at P≤0.05. Results: The results of this study showed that plasma Myostatin significantly decreased in response to resistance exercise (P=0.0001. Also the serum levels of IGF-1 increased significantly in response to resistance exercise (P=0.0001. In turn, the results reveled that the IGF-1 to Myostatin ratio increased significantly in response to resistance exercise (P=0.001. Conclusion: The results of this study showed that resistance exercise through increases of IGF-1 and decreases of Myostatin causes increment of IGF-1 to Myostatin ratio. According to the results of this study it seems prescription of resistance exercise could positive changes in proteins that involved in Cachexia syndrome in elderly people. Presumably, through this way we can prevent from Cachexia and its many physiological and physical related dysfunctions in theses people. Although more study is needed to clear its mechanisms.

  3. Protein structural changes in keratin fibers induced by chemical modification using 2-iminothiolane hydrochloride: a Raman spectroscopic investigation.

    Science.gov (United States)

    Kuzuhara, Akio

    2005-11-01

    For the purpose of investigating in detail the influence of chemical modification using 2-iminothiolane hydrochloride (2-IT) on keratin fibers, the structure of cross-sections at various depths of white human hair, treated with 2-IT and then oxidized, was directly analyzed without isolating the cuticle and cortex, using Raman spectroscopy. In particular, the beta-sheet and/or random coil content (beta/R) and the alpha-helix (alpha) content in human hair fibers were estimated by amide I band analysis. The S-S band intensity, amide III (unordered) band intensity, and beta/R content existing from the cuticle region to the center of cortex region of virgin white human hair remarkably increased by performing the chemical modification using 2-IT. On the other hand, not only the S-S band intensity, but also S-O band intensity existing throughout the cortex region of the bleached (damaged) white human hair increased by performing chemical modification using 2-IT. In particular, beta/R content existing throughout the cortex region of the bleached white human hair decreased, while the skeletal C-C stretch (alpha) band intensity at 935 cm(-1) and the alpha content remarkably increased. This indicates a secondary structural change from the random coil form to the alpha-helix form in the proteins existing throughout the cortex region. From these experiments, we concluded that the formation of new disulfide (-SS-) groups resulting from chemical modification using 2-IT induced the secondary structural changes of proteins existing throughout the cortex region. Copyright 2005 Wiley Periodicals, Inc

  4. Proteomic investigation of Vibrio alginolyticus challenged Caenorhabditis elegans revealed regulation of cellular homeostasis proteins and their role in supporting innate immune system.

    Science.gov (United States)

    Durai, Sellegounder; Singh, Nirpendra; Kundu, Suman; Balamurugan, Krishnaswamy

    2014-08-01

    Caenorhabditis elegans has been the preferred model system for many investigators to study pathogenesis. In the present investigation, regulation of C. elegans proteome was explored against V. alginolyticus infection using quantitative proteomics approach. Proteins were separated using 2D-DIGE and the differentially regulated proteins were identified using PMF and MALDI TOF/TOF analysis. The results thus obtained were validated using Western blotting for candidate proteins. The corresponding transcriptional regulation was quantified subsequently using real-time PCR. Interaction network for candidate proteins was predicted using search tool for the retrieval of interacting genes/proteins (STRING) and functional validation was performed using respective mutant strains. Out of the 25 proteins identified, 21 proteins appeared to be upregulated while four were downregulated. Upregulated proteins included those involved in stress-response (PDI-2, HSP-6), immune-response (protein kinase -18, GST-8) and energy-production (ATP-2) while proteins involved in structural maintenance (IFB-2) and lipid metabolism (SODH-1) were downregulated. The roles of these players in the host system during Vibrio infection was analyzed in vivo using wild type and mutant C. elegans. Survival assays using mutants lacking pdi-2, ire-1, and xbp-1 displayed enhanced susceptibility to V. alginolyticus. Cellular stress generated by V. alginolyticus was determined using ROS assay. This is the first report of proteome changes in C. elegans against V. alginolyticus challenge and highlights the significance of unfolded protein response (UPR) pathway during bacterial infection. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. Investigation of protein distribution in solid lipid particles and its impact on protein release using coherent anti-Stokes Raman scattering microscopy

    DEFF Research Database (Denmark)

    Christophersen, Philip C.; Birch, Ditlev; Saarinen, Jukka

    2015-01-01

    The aim of this study was to gain new insights into protein distribution in solid lipid microparticles (SLMs) and subsequent release mechanisms using a novel label-free chemical imaging method, coherent anti-Stokes Raman scattering (CARS) microscopy. Lysozyme-loaded SLMs were prepared using...... in the solid lipid matrix, which required full lipolysis of the entire matrix to release lysozyme completely. Therefore, SLMs with lysozyme incorporated in an aqueous solution released lysozyme much faster than with lysozyme incorporated as a solid. In conclusion, CARS microscopy was an efficient and non......-destructive method for elucidating the distribution of lysozyme in SLMs. The interpretation of protein distribution and release during lipolysis enabled elucidation of protein release mechanisms. In future, CARS microscopy analysis could facilitate development of a wide range of protein-lipid matrices with tailor...

  6. Dietary intake of total, animal, and vegetable protein and risk of type 2 diabetes in the European Prospective Investigation into Cancer and Nutrition (EPIC)-NL study.

    Science.gov (United States)

    Sluijs, Ivonne; Beulens, Joline W J; van der A, Daphne L; Spijkerman, Annemieke M W; Grobbee, Diederick E; van der Schouw, Yvonne T

    2010-01-01

    Dietary recommendations are focused mainly on relative dietary fat and carbohydrate content in relation to diabetes risk. Meanwhile, high-protein diets may contribute to disturbance of glucose metabolism, but evidence from prospective studies is scarce. We examined the association among dietary total, vegetable, and animal protein intake and diabetes incidence and whether consuming 5 energy % from protein at the expense of 5 energy % from either carbohydrates or fat was associated with diabetes risk. A prospective cohort study was conducted among 38,094 participants of the European Prospective Investigation into Cancer and Nutrition (EPIC)-NL study. Dietary protein intake was measured with a validated food frequency questionnaire. Incident diabetes was verified against medical records. During 10 years of follow-up, 918 incident cases of diabetes were documented. Diabetes risk increased with higher total protein (hazard ratio 2.15 [95% CI 1.77-2.60] highest vs. lowest quartile) and animal protein (2.18 [1.80-2.63]) intake. Adjustment for confounders did not materially change these results. Further adjustment for adiposity measures attenuated the associations. Vegetable protein was not related to diabetes. Consuming 5 energy % from total or animal protein at the expense of 5 energy % from carbohydrates or fat increased diabetes risk. Diets high in animal protein are associated with an increased diabetes risk. Our findings also suggest a similar association for total protein itself instead of only animal sources. Consumption of energy from protein at the expense of energy from either carbohydrates or fat may similarly increase diabetes risk. This finding indicates that accounting for protein content in dietary recommendations for diabetes prevention may be useful.

  7. Conformational Flexibility of Proteins Involved in Ribosome Biogenesis: Investigations via Small Angle X-ray Scattering (SAXS

    Directory of Open Access Journals (Sweden)

    Dritan Siliqi

    2018-02-01

    Full Text Available The dynamism of proteins is central to their function, and several proteins have been described as flexible, as consisting of multiple domains joined by flexible linkers, and even as intrinsically disordered. Several techniques exist to study protein structures, but small angle X-ray scattering (SAXS has proven to be particularly powerful for the quantitative analysis of such flexible systems. In the present report, we have used SAXS in combination with X-ray crystallography to highlight their usefulness at characterizing flexible proteins, using as examples two proteins involved in different steps of ribosome biogenesis. The yeast BRCA2 and CDKN1A-interactig protein, Bcp1, is a chaperone for Rpl23 of unknown structure. We showed that it consists of a rigid, slightly elongated protein, with a secondary structure comprising a mixture of alpha helices and beta sheets. As an example of a flexible molecule, we studied the SBDS (Shwachman-Bodian-Diamond Syndrome protein that is involved in the cytoplasmic maturation of the 60S subunit and constitutes the mutated target in the Shwachman-Diamond Syndrome. In solution, this protein coexists in an ensemble of three main conformations, with the N- and C-terminal ends adopting different orientations with respect to the central domain. The structure observed in the protein crystal corresponds to an average of those predicted by the SAXS flexibility analysis.

  8. Hierarchical structure of the energy landscape of proteins revisited by time series analysis. II. Investigation of explicit solvent effects

    Science.gov (United States)

    Alakent, Burak; Camurdan, Mehmet C.; Doruker, Pemra

    2005-10-01

    Time series analysis tools are employed on the principal modes obtained from the Cα trajectories from two independent molecular-dynamics simulations of α-amylase inhibitor (tendamistat). Fluctuations inside an energy minimum (intraminimum motions), transitions between minima (interminimum motions), and relaxations in different hierarchical energy levels are investigated and compared with those encountered in vacuum by using different sampling window sizes and intervals. The low-frequency low-indexed mode relationship, established in vacuum, is also encountered in water, which shows the reliability of the important dynamics information offered by principal components analysis in water. It has been shown that examining a short data collection period (100ps) may result in a high population of overdamped modes, while some of the low-frequency oscillations (memory: future conformations are less dependent on previous conformations due to the lowering of energy barriers in hierarchical levels of the energy landscape. In short-time dynamics (sight contradicts. However, this comes about because water enhances the transitions between minima and forces the protein to reduce its already inherent inability to maintain oscillations observed in vacuum. Some of the frequencies lower than 10cm-1 are found to be overdamped, while those higher than 20cm-1 are slightly increased. As for the long-time dynamics in water, it is found that random-walk motion is maintained for approximately 200ps (about five times of that in vacuum) in the low-indexed modes, showing the lowering of energy barriers between the higher-level minima.

  9. Investigation of the somaclonal and mutagen induced variability in barley by the application of protein and DNA markers

    International Nuclear Information System (INIS)

    Atanassov, A.; Todorovska, E.; Trifonova, A.; Petrova, M.; Marinova, E.; Gramatikova, M.; Valcheva, D.; Zaprianov, S.; Mersinkov, N.

    1998-01-01

    Barley, Hordeum vulgare L., is one of the most important crop species for Bulgaria. The characterisation of the genetic pool is of great necessity for the Bulgarian barley breeding programme which is directed toward improving quantitative and qualitative traits. Molecular markers [protein, restriction fragment length polymorphisms (RFLP) and randomly amplified polymorphic DNA (RAPD)] have been applied to characterise the Bulgarian barley cultivars and their regenerants. The changes in DNA loci coding for 26S, 5.8S and 18S rRNA repeats, C hordein locus and mitochondrial DNA organisation have been investigated. The potential for ribosomal DNA length polymorphism in Bulgarian barley cultivars appear to be limited to three different repeat lengths (10.2, 9.5 and 9.0kb) and three plant rDNA phenotypes. Polymorphism was not observed in ribosomal DNA repeat units in somaclonal variants. Variation concerning C hordein electrophoretic pattern was observed in one line from cultivar Jubiley. Analysis of the HorI locus reveals RFLPs in sequences coding for C hordeins in this line. Mitochondrial molecular markers are convenient for detection of DNA polymorphisms in the variant germplasm as well as for the somaclonal variants derived from it. Two lines from Ruen revealed polymorphic bands after hybridisation with mitochondrial DNA probe. RAPD assays have been carried out by using 20 different 10-mer primers. Heritable polymorphism in several tissue culture derived (TCD) lines was observed. RAPD assay is a sensitive and representative approach to distinguish the variability created by tissue culture and mutagenesis

  10. A Versatile Strategy for Production of Membrane Proteins with Diverse Topologies: Application to Investigation of Bacterial Homologues of Human Divalent Metal Ion and Nucleoside Transporters.

    Science.gov (United States)

    Ma, Cheng; Hao, Zhenyu; Huysmans, Gerard; Lesiuk, Amelia; Bullough, Per; Wang, Yingying; Bartlam, Mark; Phillips, Simon E; Young, James D; Goldman, Adrian; Baldwin, Stephen A; Postis, Vincent L G

    2015-01-01

    Membrane proteins play key roles in many biological processes, from acquisition of nutrients to neurotransmission, and are targets for more than 50% of current therapeutic drugs. However, their investigation is hampered by difficulties in their production and purification on a scale suitable for structural studies. In particular, the nature and location of affinity tags introduced for the purification of recombinant membrane proteins can greatly influence their expression levels by affecting their membrane insertion. The extent of such effects typically depends on the transmembrane topologies of the proteins, which for proteins of unknown structure are usually uncertain. For example, attachment of oligohistidine tags to the periplasmic termini of membrane proteins often interferes with folding and drastically impairs expression in Escherichia coli. To circumvent this problem we have employed a novel strategy to enable the rapid production of constructs bearing a range of different affinity tags compatible with either cytoplasmic or periplasmic attachment. Tags include conventional oligohistidine tags compatible with cytoplasmic attachment and, for attachment to proteins with a periplasmic terminus, either tandem Strep-tag II sequences or oligohistidine tags fused to maltose binding protein and a signal sequence. Inclusion of cleavage sites for TEV or HRV-3C protease enables tag removal prior to crystallisation trials or a second step of purification. Together with the use of bioinformatic approaches to identify members of membrane protein families with topologies favourable to cytoplasmic tagging, this has enabled us to express and purify multiple bacterial membrane transporters. To illustrate this strategy, we describe here its use to purify bacterial homologues of human membrane proteins from the Nramp and ZIP families of divalent metal cation transporters and from the concentrative nucleoside transporter family. The proteins are expressed in E. coli in a

  11. Creation of model proteins to investigate the mechanism of aggregation of expanded-polyglutamine proteins. Insertion of polyglutamine tracts into the ß-lactamase BlaP

    OpenAIRE

    Scarafone, Natacha

    2012-01-01

    Polyglutamine (polyQ) diseases are characterized by the formation of intranuclear amyloid-like aggregates by proteins containing an expansion of a polyQ tract above a threshold length. These insoluble aggregates and/or some of their soluble precursors are thought to play a role in the pathogenesis of the diseases. The only known common point between the causative proteins is the expanded polyQ tract, suggesting that their aggregation critically depends on the expansion of the polyQ tract abov...

  12. Preliminary structural investigations of the Eut-L shell protein of the ethanolamine ammonia-lyase metabolosome of Escherichia coli

    International Nuclear Information System (INIS)

    Nikolakakis, Kiel; Ohtaki, Akashi; Newton, Keith; Chworos, Arkadiusz; Sagermann, Martin

    2009-01-01

    Preliminary X-ray analysis of crystals of the bacterial microcompartment shell protein Eut-L from Escherichia coli is reported. The ethanolamine ammonia-lyase microcompartment is composed of five different shell proteins that have been proposed to assemble into symmetrically shaped polyhedral particles of varying sizes. Here, preliminary X-ray analysis of crystals of the bacterial microcompartment shell protein Eut-L from Escherichia coli is reported. Cloning, overexpression and purification resulted in highly pure protein that crystallized readily under many different conditions. In all cases the protein forms thin hexagonal plate-shaped crystals belonging to space group P3 that are of unusually high stability against different solvent conditions. The crystals diffracted to a resolution of 2.0 Å using synchrotron radiation but proved to be radiation-sensitive. Preparations of heavy-atom-derivatized crystals for use in determining the three-dimensional structure are under way

  13. Evaluation of Neisseria Gonorrhoeae Opacity (Opa) Protein Loops as Targets for Passive Vaccination and Investigation of the Role of Opa Proteins During Infection of a Female Host

    Science.gov (United States)

    2009-08-24

    The disease gonorrhea can vary from asymptomatic to severe, however most infections with N. gonorrhoeae are uncomplicated lower urogenital tract ... infection , presumably to the HV regions, with detectable antibodies in serum and genital secretions from men and women with uncomplicated urogenital tract ...of CEACAMs during lower urogenital tract infection of women and indicate that another function for Opa proteins, perhaps complement resistance, may

  14. Identification of Novel G Protein-Coupled Receptor 143 Ligands as Pharmacologic Tools for Investigating X-Linked Ocular Albinism.

    Science.gov (United States)

    De Filippo, Elisabetta; Manga, Prashiela; Schiedel, Anke C

    2017-06-01

    GPR143 regulates melanosome biogenesis and organelle size in pigment cells. The mechanisms underlying receptor function remain unclear. G protein-coupled receptors (GPCRs) are excellent pharmacologic targets; thus, we developed and applied a screening approach to identify potential GPR143 ligands and chemical modulators. GPR143 interacts with β-arrestin; we therefore established a β-arrestin recruitment assay to screen for compounds that modulate activity. Because GPR143 is localized intracellularly, screening with the wild-type receptor would be restricted to agents absorbed by the cell. For the screen we used a mutant receptor, which shows similar basal activity as the wild type but traffics to the plasma membrane. We tested two compound libraries and investigated validated hits for their effects on melanocyte pigmentation. GPR143, which showed high constitutive activity in the β-arrestin assay, was inhibited by several compounds. The three validated inhibitors (pimozide, niclosamide, and ethacridine lactate) were assessed for impact on melanocytes. Pigmentation and expression of tyrosinase, a key melanogenic enzyme, were reduced by all compounds. Because GPR143 appears to be constitutively active, these compounds may turn off its activity. X-linked ocular albinism type I, characterized by developmental eye defects, results from GPR143 mutations. Identifying pharmacologic agents that modulate GPR143 activity will contribute significantly to our understanding of its function and provide novel tools with which to study GPCRs in melanocytes and retinal pigment epithelium. Pimozide, one of three GPR143 inhibitors identified in this study, maybe be a good lead structure for development of more potent compounds and provide a platform for design of novel therapeutic agents.

  15. Proteomic Investigation of Protein Profile Changes and Amino Acid Residue Level Modification in Cooked Lamb Meat: The Effect of Boiling.

    Science.gov (United States)

    Yu, Tzer-Yang; Morton, James D; Clerens, Stefan; Dyer, Jolon M

    2015-10-21

    Hydrothermal treatment (heating in water) is a common method of general food processing and preparation. For red-meat-based foods, boiling is common; however, how the molecular level effects of this treatment correlate to the overall food properties is not yet well-understood. The effects of differing boiling times on lamb meat and the resultant cooking water were here examined through proteomic evaluation. The longer boiling time was found to result in increased protein aggregation involving particularly proteins such as glyceraldehyde-3-phosphate dehydrogenase, as well as truncation in proteins such as in α-actinin-2. Heat-induced protein backbone cleavage was observed adjacent to aspartic acid and asparagine residues. Side-chain modifications of amino acid residues resulting from the heating, including oxidation of phenylalanine and formation of carboxyethyllysine, were characterized in the cooked samples. Actin and myoglobin bands from the cooked meat per se remained visible on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, even after significant cooking time. These proteins were also found to be the major source of observed heat-induced modifications. This study provides new insights into molecular-level modifications occurring in lamb meat proteins during boiling and a protein chemistry basis for better understanding the effect of this common treatment on the nutritional and functional properties of red-meat-based foods.

  16. Spectroscopic and theoretical investigation of conformational changes of proteins by synthesized pyrimidine derivative and its sensitivity towards FRET application

    Science.gov (United States)

    Ghosh, Swadesh; Singharoy, Dipti; Bhattacharya, Subhash Chandra

    2018-04-01

    Interest in synthesizing and characterizing (IR, NMR and HRMS spectroscopic methods) a pyrimidine based Schiff-base ligand, 2-(2-(Anthracen-9-ylmethylene) hydrazinyl)-4,6-dimethyl pyrimidine (ANHP) has been developed for its application to ascertain the conformational change of protein and sensitivity towards fluorescence resonance energy transfer (FRET) process. Location of ANHP in bovine serum albumin (BSA) and human serum albumin (HSA) proteins environment has been determined using different spectroscopic techniques. Weakly fluorescent ANHP have shown greater protein induced fluorescence enhancement (PIFE) in case of HSA than BSA, though in both cases energy transfer efficiency are almost same but difference in binding constant values encourages us to find the location of ANHP within the complex protein environment. From the FRET parameter and α-helicity change, it has been found that ANHP bound with Trp-214 of HSA and surface Trp-134 of BSA. Conformational changes of proteins have been observed more for HSA than BSA in presence of ANHP, which has confirmed the location of ANHP in both the protein environments. Coupled with experimental studies, molecular docking analysis has also been done to explain the locations and distance dependent FRET process of ANHP in both proteins.

  17. [Investigation of the abundance of proteins secreted by Fasciola hepatica, which is exposed to environmental change in experimental studies, with an advanced proteomic approach].

    Science.gov (United States)

    Haçarız, Orçun; Baykal, Ahmet Tarık

    2014-06-01

    Investigation of the abundance of proteins secreted by Fasciola hepatica, which is exposed to environmental change after it is removed from the main host, with an advanced proteomic approach. Adult Fasciola hepatica parasites, obtained from the main host, were directly placed in phosphate-buffered saline (PBS, at room temperature) and incubated at 37°C for 2 hours (after arrival at the Institute within 1 hour). After this, without applying extra procedures, such as washing the parasites, secreted parasite proteins in PBS were investigated using an advanced proteomic method [a mass spectrometry system with electrospray ionization and quadrupole time-of-flight source coupled to ultra performance liquid chromatography, nano UPLC-ESI-QTOF-MS] with a reviewed F. hepatica protein database (Universal Protein Resource; UniProt) and data-independent acquisition method. With the proteomic analysis of the PBS, after incubation with the parasites, cathepsin L protease 1, fatty acid-binding protein 1 and 2, thioredoxin peroxidase (TPx), and kunitz-type proteinase inhibitor were identified. The abundance of Fasciola hepatica TPx was approximately 2-6 times higher than that of the other proteins identified in this study (p<0.01). The stress on the parasite stem from environmental change could be associated with the stimulation of the secretion of TPx. The application of advanced proteomic approaches could provide useful data in the development of effective protective methods against the parasite.

  18. Investigating ER-Associated Degradation with RNAi Screening - and Searching for Model Proteins to Do It with

    DEFF Research Database (Denmark)

    Jensen, Njal Winther

    for cellular homeostasis. The aim of this thesis has been to gain insight into ERAD. The experimental approach was RNAi screening, which is a fast and efficient method for initial evaluation of a large pool of genes. Since relatively few proteins routinely are used as ERAD substrates, the first goal...... to possess the required properties. RNAi screening was then performed to identify proteins of the ERAD machinery that was needed for the successful degradation of a HA-tagged version of the ATP13A2 mutant (HA-ATP13A2). After a validation phase, one of the identified proteins, Sec61α was verified as being...

  19. Investigation of protein FTT1103 electroactivity using carbon and mercury electrodes. Surface-inhibition approach for disulfide oxidoreductases using silver amalgam powder.

    Science.gov (United States)

    Večerková, Renata; Hernychová, Lenka; Dobeš, Petr; Vrba, Jiří; Josypčuk, Bohdan; Bartošík, Martin; Vacek, Jan

    2014-06-09

    Recently, it was shown that electrochemical methods can be used for analysis of poorly water-soluble proteins and for study of their structural changes and intermolecular (protein-ligand) interactions. In this study, we focused on complex electrochemical investigation of recombinant protein FTT1103, a disulfide oxidoreductase with structural similarity to well described DsbA proteins. This thioredoxin-like periplasmic lipoprotein plays an important role in virulence of bacteria Francisella tularensis. For electrochemical analyses, adsorptive transfer (ex situ) square-wave voltammetry with pyrolytic graphite electrode, and alternating-current voltammetry and constant-current chronopotentiometric stripping analysis with mercury electrodes, including silver solid amalgam electrode (AgSAE) were used. AgSAE was used in poorly water-soluble protein analysis for the first time. In addition to basic redox, electrocatalytic and adsorption/desorption characterization of FTT1103, electrochemical methods were also used for sensitive determination of the protein at nanomolar level and study of its interaction with surface of AgSA microparticles. Proposed electrochemical protocol and AgSA surface-inhibition approach presented here could be used in future for biochemical studies focused on proteins associated with membranes as well as on those with disulfide oxidoreductase activity. Copyright © 2014 Elsevier B.V. All rights reserved.

  20. Investigating effects of sample pretreatment on protein stability using size-exclusion chromatography and high-resolution continuum source atomic absorption spectrometry.

    Science.gov (United States)

    Rakow, Tobias; El Deeb, Sami; Hahne, Thomas; El-Hady, Deia Abd; AlBishri, Hassan M; Wätzig, Hermann

    2014-09-01

    In this study, size-exclusion chromatography and high-resolution atomic absorption spectrometry methods have been developed and evaluated to test the stability of proteins during sample pretreatment. This especially includes different storage conditions but also adsorption before or even during the chromatographic process. For the development of the size exclusion method, a Biosep S3000 5 μm column was used for investigating a series of representative model proteins, namely bovine serum albumin, ovalbumin, monoclonal immunoglobulin G antibody, and myoglobin. Ambient temperature storage was found to be harmful to all model proteins, whereas short-term storage up to 14 days could be done in an ordinary refrigerator. Freezing the protein solutions was always complicated and had to be evaluated for each protein in the corresponding solvent. To keep the proteins in their native state a gentle freezing temperature should be chosen, hence liquid nitrogen should be avoided. Furthermore, a high-resolution continuum source atomic absorption spectrometry method was developed to observe the adsorption of proteins on container material and chromatographic columns. Adsorption to any container led to a sample loss and lowered the recovery rates. During the pretreatment and high-performance size-exclusion chromatography, adsorption caused sample losses of up to 33%. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry for the Investigation of Proteins and Peptides

    Science.gov (United States)

    Burnum, Kristin E.; Frappier, Sara L.; Caprioli, Richard M.

    2008-07-01

    Mass spectrometry (MS) is an excellent technology for molecular imaging because of its high data dimensionality. MS can monitor thousands of individual molecular data channels measured as mass-to-charge (m/z). We describe the use of matrix-assisted laser desorption/ionization (MALDI) MS for the image analysis of proteins, peptides, lipids, drugs, and metabolites in tissues. We discuss the basic instrumentation and sample preparation methods needed to produce high-resolution images and high image reproducibility. Matrix-addition protocols are briefly discussed along with normal operating procedures, and selected biological and medical applications of MALDI imaging MS are described. We give examples of both two- and three-dimensional imaging, including normal mouse embryo implantation, sperm maturation in mouse epididymis, protein distributions in brain sections, protein alterations as a result of drug administration, and protein changes in brain due to neurodegeneration and tumor formation. Advantages of this technology and future challenges for its improvement are discussed.

  2. Specific binding of tubeimoside-2 with proteins in hepatocarcinoma HepG2 cells: investigation by molecular spectroscopy

    Science.gov (United States)

    Yang, Sun; Shi-Sheng, Sun; Ying-Yong, Zhao; Jun, Fan

    2012-07-01

    In this study, we compared different binding interactions of TBMS2 with proteins both in hepatocarcinoma HepG2 cells and in normal embryo hepatic L02 cells by using fluorescence, absorption, and CD spectroscopy. The fluorescence data revealed that the fluorescence intensity of proteins in the HepG2 and L02 cells decreased in the presence of TBMS2 by 30.79% and 12.01%, respectively. Binding constants and thermodynamic parameters were obtained for systems of TBMS2 with the two kinds of cell proteins. The results indicated that HepG2 cell proteins had a higher TBMS2 binding activity than those in the L02 cells. Analysis of the TBMS2 cytotoxic activities showed that TBMS2 could selectively induce apoptosis of HepG2 cells by binding to them, while its apoptotic effect on L02 cells was relatively weaker.

  3. Effects of interferon gamma on Chlamydia trachomatis serovar A and L2 protein expression investigated by two-dimensional gel electrophoresis

    DEFF Research Database (Denmark)

    Shaw, A; Christiansen, Gunna; Birkelund, Svend

    1999-01-01

    ]methionine and two-dimensional gel electrophoresis with immobilized pH gradients in order to investigate changes in the protein expression of C. trachomatis serovar A and L2 caused by treatment with IFN-gamma. In contrast to what was observed in C. trachomatis L2, our results showed that, in C. trachomatis A, down...

  4. Photoionization and Electron Radical Recombination Dynamics in Photoactive Yellow Protein Investigated by Ultrafast Spectroscopy in the Visible and Near-Infrared Spectral Region

    NARCIS (Netherlands)

    Zhu, J.; Paparelli, L.; Hospes, M.; Arents, J.; Kennis, J.T.; van Stokkum, I.H.M.; Hellingwerf, K.J.; Groot, M.L.

    2013-01-01

    Photoinduced ionization of the chromophore inside photoactive yellow protein (PYP) was investigated by ultrafast spectroscopy in the visible and near-infrared spectral regions. An absorption band that extended from around 550 to 850 nm was observed and ascribed to solvated electrons, ejected from

  5. Molecular spectroscopic investigation on fractionation-induced changes on biomacromolecule of co-products from bioethanol processing to explore protein metabolism in ruminants

    Science.gov (United States)

    Zhang, Xuewei; Yan, Xiaogang; Beltranena, Eduardo; Yu, Peiqiang

    2014-03-01

    Fractionation processing is an efficient technology which is capable to redesign/redevelop a new food or feed product with a specified chemical and nutrient profile. This processing technique was able to produce four different fractions (called "A", "B", "C", "D" fractions/treatments) with different nutrient profile form a co-product of bioethanol processing [wheat dried distillers grains with soluble (DDGS)]. To date, there is no study on the effect of fractionation processing on inherent molecular structure of different fractions and how the processing-induced structural change affect the metabolic characteristics of protein and nutrient availability. The objectives of this experiment were to: (1) investigate the effect of fractionation processing on changes of protein functional groups (amide I, amide II, and their ratio) and molecular structure (modeled α-helix, β-sheet, and their ratio), and (2) study the relationship between the fractionation processing-induced changes of protein molecular structure and nutrients availability as well as the metabolic characteristics of protein. The hypothesis of this study was that the fractionation processing changes the molecular structure and such changes affect the metabolic characteristics of protein. The protein molecular structure spectral profile of the fractions A, B, C and D were identified by Fourier-transform infrared attenuated total reflection spectroscopy (FT/IR-ATR). The results showed that the fractionation processing significantly affected the protein molecular spectral profiles. The differences in amide I to amide II peak area and height ratios were strongly significant (P fractions, ranging from 4.98 to 6.33 and 3.28 to 4.00, respectively. The difference in the modeled protein α-helix to β-sheet ratio was also strongly significant (P fractions. Multivariate molecular spectral analysis with cluster (CLA) and principal component analyses (PCA) showed that there are no clear distinguished clusters and

  6. iTRAQ based investigation of plasma proteins in HIV infected and HIV/HBV coinfected patients - C9 and KLK are related to HIV/HBV coinfection.

    Science.gov (United States)

    Sun, Tao; Liu, Li; Wu, Ao; Zhang, Yujiao; Jia, Xiaofang; Yin, Lin; Lu, Hongzhou; Zhang, Lijun

    2017-10-01

    Human immunodeficiency virus (HIV) and hepatitis B virus (HBV) share similar routes of transmission, and rapid progression of hepatic and immunodeficiency diseases has been observed in coinfected individuals. Our main objective was to investigate the molecular mechanism of HIV/HBV coinfections. We selected HIV infected and HIV/HBV coinfected patients with and without Highly Active Antiretroviral Therapy (HAART). Low abundance proteins enriched using a multiple affinity removal system (MARS) were labeled with isobaric tags for relative and absolute quantitation (iTRAQ) kits and analyzed using liquid chromatography-mass spectrometry (LC-MS). The differential proteins were analyzed by Gene Ontology (GO) database. A total of 41 differential proteins were found in HIV/HBV coinfected patients as compared to HIV mono-infected patients with or without HAART treatment, including 7 common HBV-regulated proteins. The proteins involved in complement and coagulation pathways were significantly enriched, including plasma kallikrein (KLK) and complement component C9 (C9). C9 and KLK were verified to be down-regulated in HIV/HBV coinfected patients through ELISA analysis. The present iTRAQ based proteomic analyses identified 7 proteins that are related to HIV/HBV coinfection. HBV might influence hepatic and immune functions by deregulating complement and coagulation pathways. C9 and KLK could potentially be used as targets for the treatment of HIV/HBV coinfections. Copyright © 2017. Published by Elsevier Ltd.

  7. Investigation and Comparison of Leishmania major Promastigote and Amastigote Protein Content by Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis

    Directory of Open Access Journals (Sweden)

    S. Soleimanifard

    2013-04-01

    Full Text Available ntroduction & Objective: Leishmania is a protozoan of the trypanosomatidae family. This pro-tozoan has two stages in its life cycle, promastigote form in sand flies and amastigote form in macrophage of mammalian hosts. The purpose of this study was identification and compari-son of proteins of Leishmania amastigote and promastigote stages. Materials & Methods: The present study is a cross sectional study of two forms of Leishmania major. To culture promastigotes , L.major (MRHO/IR/75/ER from previously infected Balb/c mice was transferred to modified N.N.N medium with overlay of liquid BHI and then transferred to RPMI-1640 at 26oc ± 1 for mass production. After isolation and growth, pro-mastigotes were transferred to liquid cell culture medium RPMI-1640 with pH 5.5 and incu-bated at 5% CO2 at 37oc for 72 hours until promastigote to amastigote transformation. Elec-trophoresis was performed with SDS-PAGE method to find and compare the molecular weight of the antigens of two stages. Results: The molecular weights of the bands observed in both forms were as follows: 19, 36, 50, 63, 65, 80, 90, 94, 96, 110- 130 KDa. The proteins in the surface of only promastigote were 22, 28 and 46 KDa and special proteins in the surface of amastigote were 12 and 32 KDa. Conclusion : According to this study Leishmania parasite has stage specific proteins. Various studies have shown that axenic amastigotes and tissue amastigotes are similar in their protein content. Therefore, based on stage specific proteins ,effective drugs and vaccines can be de-signed against leishmaniasis. (Sci J Hamadan Univ Med Sci 2013; 20 (1:1-8

  8. A gradient-free method for the purification of infective dengue virus for protein-level investigations.

    Science.gov (United States)

    Jensen, Stephanie M; Nguyen, Celina T; Jewett, John C

    2016-09-01

    Dengue virus (DENV) is a mosquito-transmitted flavivirus that infects approximately 100 million people annually. Multi-day protocols for purification of DENV reduce the infective titer due to viral sensitivity to both temperature and pH. Herein we describe a 5-h protocol for the purification of all DENV serotypes, utilizing traditional gradient-free ultracentrifugation followed by selective virion precipitation. This protocol allows for the separation of DENV from contaminating proteins - including intact C6/36 densovirus, for the production of infective virus at high concentration for protein-level analysis. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Advanced fluidic handling and use of two-phase flow for high throughput structural investigation of proteins on a microfluidic sample preparation platform

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Snakenborg, Detlef; Møller, M.

    2010-01-01

    Research on the structure of proteins can bring forth a wealth of information about biological function and can be used to better understand the processes in living cells. This paper reports a new microfluidic sample preparation system for the structural investigation of proteins by Small Angle X......-ray Scattering (SAXS). The system includes hardware and software features for precise fluidic control, synchrotron beamline control, UV absorbance measurements and automated data analysis. The precise fluidic handling capabilities are used to transport and precisely position samples as small as 500 n...

  10. Automated microfluidic sample-preparation platform for high-throughput structural investigation of proteins by small-angle X-ray scattering

    DEFF Research Database (Denmark)

    Lafleur, Josiane P.; Snakenborg, Detlef; Nielsen, Søren Skou

    2011-01-01

    A new microfluidic sample-preparation system is presented for the structural investigation of proteins using small-angle X-ray scattering (SAXS) at synchrotrons. The system includes hardware and software features for precise fluidic control, sample mixing by diffusion, automated X-ray exposure...... control, UV absorbance measurements and automated data analysis. As little as 15 l of sample is required to perform a complete analysis cycle, including sample mixing, SAXS measurement, continuous UV absorbance measurements, and cleaning of the channels and X-ray cell with buffer. The complete analysis...... cycle can be performed in less than 3 min. Bovine serum albumin was used as a model protein to characterize the mixing efficiency and sample consumption of the system. The N2 fragment of an adaptor protein (p120-RasGAP) was used to demonstrate how the device can be used to survey the structural space...

  11. Diet as a system: an observational study investigating a multi-choice system of moderately restricted low-protein diets.

    Science.gov (United States)

    Piccoli, Giorgina Barbara; Nazha, Marta; Capizzi, Irene; Vigotti, Federica Neve; Scognamiglio, Stefania; Consiglio, Valentina; Mongilardi, Elena; Bilocati, Marilisa; Avagnina, Paolo; Versino, Elisabetta

    2016-12-07

    There is no single, gold-standard, low-protein diet (LPD) for CKD patients; the best compliance is probably obtained by personalization. This study tests the hypothesis that a multiple choice diet network allows patients to attain a good compliance level, and that, in an open-choice system, overall results are not dependent upon the specific diet, but upon the clinical characteristics of the patients. Observational study: Three LPD options were offered to all patients with severe or rapidly progressive CKD: vegan diets supplemented with alpha-ketoacids and essential aminoacids; protein-free food in substitution of normal bread and pasta; other (traditional, vegan non supplemented and tailored). Dialysis-free follow-up and survival were analyzed by Kaplan Meier curves according to diet, comorbidity and age. Compliance and metabolic control were estimated in 147 subjects on diet at March 2015, with recent complete data, prescribed protein intake 0.6 g/Kg/day. Protein intake was assessed by Maroni Mitch formula. Four hundreds and forty nine patients followed a LPD in December, 2007- March, 2015 (90% moderately restricted LPDs, 0.6 g/Kg/day of protein, 10% at lower targets); age (median 70 (19-97)) and comorbidity (Charlson index: 7) characterized our population as being in line with the usual CKD European population. Median e-GFR at start of the diet was 20 mL/min, 33.2% of the patients were diabetics. Baseline data differ significantly across diets: protein-free schemas are preferred by older, high-comorbidity patients (median age 76 years, Charlson index 8, GFR 20.5 mL/min, Proteinuria: 0.3 g/day), supplemented vegan diets by younger patients with lower GFR and higher proteinuria (median age 65 years, Charlson index 6, GFR 18.9 mL/min; Proteinuria: 1.2 g/day); other diets are chosen by an intermediate population (median age 71 years, Charlson index 6; GFR 22.5 mL/min; Proteinuria: 0.9 g/day); (p <0.001 for age, Charlson index, proteinuria, GFR

  12. High-throughput investigation of single and binary protein adsorption isotherms in anion exchange chromatography employing multivariate analysis.

    Science.gov (United States)

    Field, Nicholas; Konstantinidis, Spyridon; Velayudhan, Ajoy

    2017-08-11

    The combination of multi-well plates and automated liquid handling is well suited to the rapid measurement of the adsorption isotherms of proteins. Here, single and binary adsorption isotherms are reported for BSA, ovalbumin and conalbumin on a strong anion exchanger over a range of pH and salt levels. The impact of the main experimental factors at play on the accuracy and precision of the adsorbed protein concentrations is quantified theoretically and experimentally. In addition to the standard measurement of liquid concentrations before and after adsorption, the amounts eluted from the wells are measured directly. This additional measurement corroborates the calculation based on liquid concentration data, and improves precision especially under conditions of weak or moderate interaction strength. The traditional measurement of multicomponent isotherms is limited by the speed of HPLC analysis; this analytical bottleneck is alleviated by careful multivariate analysis of UV spectra. Copyright © 2017. Published by Elsevier B.V.

  13. Investigation of the immunogenicity of a protein drug using equilibrium dialysis and liquid chromatography tandem mass spectrometry detection.

    Science.gov (United States)

    Ji, Qin C; Rodila, Ramona; Morgan, Sherry J; Humerickhouse, Rod A; El-Shourbagy, Tawakol A

    2005-09-01

    Biotherapeutics such as protein and peptide drugs have attracted significant attention in the medical community and pharmaceutical industry in recent years. Immunogenicity is one of the major concerns in the development and application of biotherapeutics. Although great efforts have been put forth in reducing immunogenicity, monitoring the free ("active") drug concentration and the antibody formation is critical for preclinical and clinical studies. Currently, it is still a challenging task to have a standardized test method monitoring immunogenicity when biotherapeutic compounds such as proteins and peptides are administrated. Combined with liquid chromatography/tandem mass spectrometry detection, the equilibrium dialysis technique that is conventionally used for measuring the free and bound concentration of small organic molecules was extended to the application of measuring the free and bound concentrations of a protein drug with a relative molecular mass over 10,000 from plasma samples containing antibody. This novel approach could also be used for accurately measuring the antibody concentration when a reference standard of the antibody is available.

  14. Application of protein typing in molecular epidemiological investigation of nosocomial infection outbreak of aminoglycoside-resistant Pseudomonas aeruginosa.

    Science.gov (United States)

    Song, Min; Tang, Min; Ding, Yinghuan; Wu, Zecai; Xiang, Chengyu; Yang, Kui; Zhang, Zhang; Li, Baolin; Deng, Zhenghua; Liu, Jinbo

    2017-12-16

    Pseudomonas aeruginosan has emerged as an important pathogen elated to serious infections and nosocomial outbreaks worldwide. This study was conducted to understand the prevalence of aminoglycoside (AMG)-resistant P. aeruginosa in our hospital and to provide a scientific basis for control measures against nosocomial infections. Eighty-two strains of P. aeruginosa were isolated from clinical departments and divided into AMG-resistant strains and AMG-sensitive strains based on susceptibility test results. AMG-resistant strains were typed by drug resistance gene typing (DRGT) and protein typing. Five kinds of aminoglycoside-modifying enzyme (AME) genes were detected in the AMG-resistant group. AMG-resistant P. aeruginosa strains were classified into three types and six subtypes by DRGT. Four protein peaks, namely, 9900.02, 7600.04, 9101.25 and 10,372.87 Da, were significantly and differentially expressed between the two groups. AMG-resistant P. aeruginosa strains were also categorised into three types and six subtypes at the distance level of 10 by protein typing. AMG-resistant P. aeruginosa was cloned spread in our hospital; the timely implementation of nosocomial infection prevention and control strategies were needed in preventing outbreaks and epidemic of AMG-resistant P. aeruginosa. SELDI-TOF MS technology can be used for bacterial typing, which provides a new method of clinical epidemiological survey and nosocomial infection control.

  15. Investigation of two novel biochemical markers of inflammation, matrix metalloproteinase and cathepsin generated fragments of C-reactive protein, in patients with ankylosing spondylitis

    DEFF Research Database (Denmark)

    Skjøt-Arkil, Helene; Schett, Georg; Zhang, Chen

    2012-01-01

    Ankylosing spondylitis (AS) is a chronic inflammation of the spine and the sacroiliac joints. Current markers of inflammation, such as C-reactive protein (CRP), are reflecting the production of an acute phase reactant rather than tissue specific inflammation, but the use of CRP as a diagnostic an...... additional information on systemic inflammation as compared to that of full-length CRP. We investigated whether these CRP degradation products would provide additional diagnostic value in AS patients compared to full-length CRP....

  16. Quantitative changes in proteins responsible for flavonoid and anthocyanin biosynthesis in strawberry fruit at different ripening stages: A targeted quantitative proteomic investigation employing multiple reaction monitoring.

    Science.gov (United States)

    Song, Jun; Du, Lina; Li, Li; Kalt, Wilhelmina; Palmer, Leslie Campbell; Fillmore, Sherry; Zhang, Ying; Zhang, ZhaoQi; Li, XiHong

    2015-06-03

    To better understand the regulation of flavonoid and anthocyanin biosynthesis, a targeted quantitative proteomic investigation employing LC-MS with multiple reaction monitoring was conducted on two strawberry cultivars at three ripening stages. This quantitative proteomic workflow was improved through an OFFGEL electrophoresis to fractionate peptides from total protein digests. A total of 154 peptide transitions from 47 peptides covering 21 proteins and isoforms related to anthocyanin biosynthesis were investigated. The normalized protein abundance, which was measured using isotopically-labeled standards, was significantly changed concurrently with increased anthocyanin content and advanced fruit maturity. The protein abundance of phenylalanine ammonia-lyase; anthocyanidin synthase, chalcone isomerase; flavanone 3-hydroxylase; dihydroflavonol 4-reductase, UDP-glucose:flavonoid-3-O-glucosyltransferase, cytochrome c and cytochrome C oxidase subunit 2, was all significantly increased in fruit of more advanced ripeness. An interaction between cultivar and maturity was also shown with respect to chalcone isomerase. The good correlation between protein abundance and anthocyanin content suggested that a metabolic control point may exist for anthocyanin biosynthesis. This research provides insights into the process of anthocyanin formation in strawberry fruit at the level of protein concentration and reveals possible candidates in the regulation of anthocyanin formation during fruit ripening. To gain insight into the molecular mechanisms contributing to flavonoids and anthocyanin biosynthesis and regulation of strawberry fruit during ripening is challenging due to limited molecular biology tools and established hypothesis. Our targeted proteomic approach employing LC-MS/MS analysis and MRM technique to quantify proteins in relation to flavonoids and anthocyanin biosynthesis and regulation in strawberry fruit during fruit ripening is novel. The identification of peptides

  17. An investigation into the population abundance distribution of mRNAs, proteins, and metabolites in biological systems.

    Science.gov (United States)

    Lu, Chuan; King, Ross D

    2009-08-15

    Distribution analysis is one of the most basic forms of statistical analysis. Thanks to improved analytical methods, accurate and extensive quantitative measurements can now be made of the mRNA, protein and metabolite from biological systems. Here, we report a large-scale analysis of the population abundance distributions of the transcriptomes, proteomes and metabolomes from varied biological systems. We compared the observed empirical distributions with a number of distributions: power law, lognormal, loglogistic, loggamma, right Pareto-lognormal (PLN) and double PLN (dPLN). The best-fit for mRNA, protein and metabolite population abundance distributions was found to be the dPLN. This distribution behaves like a lognormal distribution around the centre, and like a power law distribution in the tails. To better understand the cause of this observed distribution, we explored a simple stochastic model based on geometric Brownian motion. The distribution indicates that multiplicative effects are causally dominant in biological systems. We speculate that these effects arise from chemical reactions: the central-limit theorem then explains the central lognormal, and a number of possible mechanisms could explain the long tails: positive feedback, network topology, etc. Many of the components in the central lognormal parts of the empirical distributions are unidentified and/or have unknown function. This indicates that much more biology awaits discovery.

  18. Investigation of the Copper Binding Site And the Role of Histidine As a Ligand in Riboflavin Binding Protein

    Energy Technology Data Exchange (ETDEWEB)

    Smith, S.R.; Bencze, K.Z.; Russ, K.A.; Wasiukanis, K.; Benore-Parsons, M.; Stemmler, T.L.

    2009-05-26

    Riboflavin Binding Protein (RBP) binds copper in a 1:1 molar ratio, forming a distinct well-ordered type II site. The nature of this site has been examined using X-ray absorption and pulsed electron paramagnetic resonance (EPR) spectroscopies, revealing a four coordinate oxygen/nitrogen rich environment. On the basis of analysis of the Cambridge Structural Database, the average protein bound copper-ligand bond length of 1.96 {angstrom}, obtained by extended x-ray absorption fine structure (EXAFS), is consistent with four coordinate Cu(I) and Cu(II) models that utilize mixed oxygen and nitrogen ligand distributions. These data suggest a Cu-O{sub 3}N coordination state for copper bound to RBP. While pulsed EPR studies including hyperfine sublevel correlation spectroscopy and electron nuclear double resonance show clear spectroscopic evidence for a histidine bound to the copper, inclusion of a histidine in the EXAFS simulation did not lead to any significant improvement in the fit.

  19. Molecular Investigation of the Mechanism of Non-Enzymatic Hydrolysis of Proteins and the Predictive Algorithm for Susceptibility.

    Science.gov (United States)

    Lauer, Timothy M; Wood, Geoffrey P F; Farkas, David; Sathish, Hasige A; Samra, Hardeep S; Trout, Bernhardt L

    2016-06-14

    A number of potential degradation routes can limit the shelf life of a biotherapeutic. While these are experimentally measurable, the tests to do so require a substantial investment in both time and material, resources rarely available early in the drug development process. To address the potential degradation route of non-enzymatic hydrolysis, we performed a molecular modeling analysis, together with an experimental study, to gain detailed insight into the reaction. On the basis of the mechanism, an algorithm for predicting the likely cleavage sites of a protein has been created. This algorithm measures four key properties during a molecular dynamics simulation, which relate to the key steps of the hydrolysis mechanism, in particular the rate-determining step (which can vary depending on the local environment). The first two properties include the secondary structure and the surface exposure of the amide bond, both of which help detect if the addition of the proton to the amide bond is possible. The second two properties relate to whether the side chain can cyclize and form a furane ring. These two properties are the orientation of the side chain relative to the amide bond and the number of hydrogen bonds between the side chain and the surrounding protein. Overall, the algorithm performs well at identifying reactive versus nonreactive bonds. The algorithm correctly classifies nearly 90% of all amide bonds following an aspartic or glutamic acid residue as reactive or nonreactive.

  20. An Investigation of Bacterial Protein Interactions as a Primary Research Project in a Sophomore-Level Molecular Biology Course

    Directory of Open Access Journals (Sweden)

    Jean A. Cardinale

    2011-09-01

    Full Text Available Longer term research activities that may be incorporated in undergraduate courses are a powerful tool for promoting student interest and learning, developing cognitive process skills, and allowing undergraduates to experience real research activities in which they may not otherwise have the opportunity to participate. The challenge to doing so in lower-level courses is that students may have not fully grasped the scientific concepts needed to undertake such research endeavors, and that they may be discouraged if activities are perceived to be too challenging. The paper describes how a bacterial protein:protein interaction detection system was adapted and incorporated into the laboratory component of a sophomore-level Molecular Cell Biology course. The project was designed to address multiple learning objectives connecting course content to the laboratory activities, as well as teach basic molecular biology laboratory skills and procedures in the context of a primary research activity. Pre- and posttesting and student surveys both suggest that the laboratory curriculum resulted in significant learning gains, as well as being well received and valued by the students.

  1. An investigation of bacterial protein interactions as a primary research project in a sophomore-level molecular biology course.

    Science.gov (United States)

    Cardinale, Jean A

    2011-01-01

    Longer term research activities that may be incorporated in undergraduate courses are a powerful tool for promoting student interest and learning, developing cognitive process skills, and allowing undergraduates to experience real research activities in which they may not otherwise have the opportunity to participate. The challenge to doing so in lower-level courses is that students may have not fully grasped the scientific concepts needed to undertake such research endeavors, and that they may be discouraged if activities are perceived to be too challenging. The paper describes how a bacterial protein:protein interaction detection system was adapted and incorporated into the laboratory component of a sophomore-level Molecular Cell Biology course. The project was designed to address multiple learning objectives connecting course content to the laboratory activities, as well as teach basic molecular biology laboratory skills and procedures in the context of a primary research activity. Pre- and posttesting and student surveys both suggest that the laboratory curriculum resulted in significant learning gains, as well as being well received and valued by the students.

  2. Antibodies directed to drug epitopes to investigate the structure of drug-protein photoadducts. Recognition of a common photobound substructure in tiaprofenic acid/ketoprofen cross-photoreactivity.

    Science.gov (United States)

    Lahoz, A; Hernández, D; Miranda, M A; Pérez-Prieto, J; Morera, I M; Castell, J V

    2001-11-01

    Drug-induced photoallergy is an immune adverse reaction to the combined effect of drugs and light. From the mechanistic point of view, it first involves covalent binding of drug to protein resulting in the formation of a photoantigen. Hence, determination of the structures of drug-protein photoadducts is of great relevance to understand the molecular basis of photoallergy and cross-immunoreactivity among drugs. Looking for new strategies to investigate the covalent photobinding of drugs to proteins, we generated highly specific antibodies to drug chemical substructures. The availability of such antibodies has allowed us to discriminate between the different modes by which tiaprofenic acid (TPA), suprofen (SUP), and ketoprofen (KTP) photobind to proteins. The finding that the vast majority of the TPA photoadduct can be accounted for by means of antibody anti-benzoyl strongly supports the view that the drug binds preferentially via the thiophene ring, leaving the benzene ring more accessible. By contrast, selective recognition of SUP-protein photoadducts by antibody anti-thenoyl evidences a preferential coupling via the benzene ring leaving the thiophene moiety more distant from the protein matrix. In the case of KTP, photoadducts are exclusively recognized by antibody anti-benzoyl, indicating that the benzene ring is again more accessible. As a result of this research, we have been able to identify a common substructure that is present in TPA-albumin and KTP-albumin photoadducts. This is remarkable since, at a first sight, the greatest structural similarities can be found between TPA and SUP as they share the same benzoylthiophene chromophore. These findings can explain the previously reported observations of cross-reactivity to KTP (or TPA) in patients photosensitized to TPA (or KTP).

  3. Investigations of the influence of the content of crude plant protein in the ration on the utilisation of urea in dairy cattle. 2

    International Nuclear Information System (INIS)

    Voigt, J.; Piatkowski, B.; Krawielitzki, R.; Adam, K.

    1984-01-01

    The metabolism of 15 N-urea in dairy cows was investigated in dependence on the crude protein content of the rations. With the energy concentration remaining unchanged, the rations contained 10.7(I), 13.7(II) and 17.1(III)% plant crude protein and, after the supplementation of 150 g urea per animal and day, a total of 13.8, 16.7 and 20.2% crude protein in the dry matter. The urea was intraruminally infused during the feeding in the morning and the evening. In the morning feeding of each 1st measuring day it was labelled with 27.5 atom-% 15 N-excess ( 15 N'). The degree of labelling with 15 N' of the N fraction of rumen fluid, contents of the duodenum, feces and milk, precipitable with trichloric acetic acid (TCA) decreased with the rising protein level of the ration. This effect was bigger than could be expected considering the low 15 N' quota in the total N of the ration. In the sequence I..III, 52.7, 32.2 and 30.6% of the 15 N' amount taken in passed the duodenal re-entrant cannula in TCA-precipitable form within 72 hours after 15 N application. 33.3, 21.9 and 22.6% were apparently absorbed in the intestines as TCA-precipitable N within 120 h after the 15 N' application. In the same period 31.7, 43.1 and 72.8% of the 15 N' taken in were excreted in urine. 12.3, 9.6 and 5.8% of the applied 15 N' were found in milk protein. One can conclude that the utilization of urea N decreases with the rising level of crude protein in the ration and that, however, urea N is still biochemically utilized when there is an excess of plant N in the ration. (author)

  4. Modulation of Calcium Oxalate Crystallization by Proteins and Small Molecules Investigated by In Situ Atomic Force Microscopy

    Science.gov (United States)

    Qiu, R.; Orme, C.; Cody, A. M.; Wierzbicki, A.; Hoyer, J.; Nancollas, G.; de Yoreo, J.

    2002-12-01

    Understanding the physical mechanisms by which biological inhibitors control nucleation and growth of inorganic crystals is a major focus of biomineral research. Calcium oxalate monohydrate (COM), which plays a functional role in plant physiology, is also a source of pathogenesis in humans where it causes kidney stone disease. Although a great deal of research has been carried out on the modulation COM by proteins and small molecules, the basic mechanism has not yet been understood. However, because the proteins that play a role in COM growth have been identified and sequenced, COM provides an excellent model system for research into biomineral growth. In this study, in situ atomic force microscopy (AFM) was used to monitor the COM surface under controlled growth conditions both from pure solutions and those doped with citrate and osteopontin (OPN) in order to determine their effects on surface morphology and growth dynamics at the molecular level. As with other solution-grown crystals such as calcite, COM grows on complex dislocation hillocks. In pure solution, while growth on the (010) face is isotropic, hillocks on the (-101) face exhibit anisotropic step kinetics. Steps of [-10-1] and orientation are clearly delineated with the [-10-1] being the fast growing direction. When citrate is added to the solution, both growth rate and morphology are drastically changed on (-101) face, especially along the [-10-1] direction. This results in isotropic disc-shaped hillocks a shape that is then reflected in the macroscopic growth habit. In contrast, no large growth changes were observed on the (010) facet. At the same time, molecular modeling predicts an excellent fit of the citrate ion into the (-101) plane and a poor fit to the (010) face. Here we propose a model that reconciles the step-specific interactions implied by the AFM results with the face-specific predictions of the calculations. Finally, we present the results of doping with aspartic acid as well as OPN, an

  5. Time-resolved methods in biophysics. 6. Time-resolved Laue crystallography as a tool to investigate photo-activated protein dynamics.

    Science.gov (United States)

    Bourgeois, Dominique; Schotte, Friedrich; Brunori, Maurizio; Vallone, Beatrice

    2007-10-01

    When polychromatic X-rays are shined onto crystalline material, they generate a Laue diffraction pattern. At third generation synchrotron radiation sources, a single X-ray pulse of approximately 100 ps duration is enough to produce interpretable Laue data from biomolecular crystals. Thus, by initiating biological turnover in a crystalline protein, structural changes along the reaction pathway may be filmed by ultra-fast Laue diffraction. Using laser-light as a trigger, transient species in photosensitive macromolecules can be captured at near atomic resolution with sub-nanosecond time-resolution. Such pump-probe Laue experiments have now reached an outstanding level of sophistication and have found a domain of excellence in the investigation of light-sensitive proteins undergoing cyclic photo-reactions and producing stiff crystals. The main theoretical concepts of Laue diffraction and the challenges associated with time-resolved experiments on biological crystals are recalled. The recent advances in the design of experiments are presented in terms of instrumental choices, data collection strategy and data processing, and some of the inherent difficulties of the method are highlighted. The discussion is based on the example of myoglobin, a protein that has traversed the whole history of pump-probe Laue diffraction, and for which a massive amount of data have provided considerable insight into the understanding of protein dynamics.

  6. Investigation of the Relationship between Lactococcal Host Cell Wall Polysaccharide Genotype and 936 Phage Receptor Binding Protein Phylogeny

    DEFF Research Database (Denmark)

    Mahony, Jennifer; Kot, Witold Piotr; Murphy, James

    2013-01-01

    Comparative genomics of 11 lactococcal 936-type phages combined with host range analysis allowed subgrouping of these phage genomes, particularly with respect to their encoded receptor binding proteins. The so-called pellicle or cell wall polysaccharide of Lactococcus lactis, which has been...... implicated as a host receptor of (certain) 936-type phages, is specified by a large gene cluster, which, among different lactococcal strains, contains highly conserved regions as well as regions of diversity. The regions of diversity within this cluster on the genomes of lactococcal strains MG1363, SK11, IL......1403, KF147, CV56, and UC509.9 were used for the development of a multiplex PCR system to identify the pellicle genotype of lactococcal strains used in this study. The resulting comparative analysis revealed an apparent correlation between the pellicle genotype of a given host strain and the host range...

  7. Is the pre-Tg DSC endotherm observed with solid state proteins associated with the protein internal dynamics? Investigation of bovine serum albumin by solid state hydrogen/deuterium exchange.

    Science.gov (United States)

    Mizuno, Masayasu; Pikal, Michael J

    2013-10-01

    DSC thermograms of solid state pure proteins often show a distinct endotherm at a temperature far below the glass transition temperature of the system (Tg). We hypothesized this endotherm represents enthalpy recovery associated with an internal mobility transition of the protein molecule. Although the existence of an internal transition has been postulated, whether this endotherm is associated with such a transition has not previously been discussed. The purpose of this study was to investigate the origin of the pre-Tg endotherm in lyophilized bovine serum albumin (BSA). Due to strong glass behavior, the system Tg was determined by extrapolating Tg data of disaccharide/BSA formulations to zero saccharide. A small pre-Tg endotherm around 40-60 °C was observed in amorphous BSA equilibrated at 11%RH. The apparent activation energy suggested the endotherm was "α-mobility"-related. A solid state hydrogen/deuterium exchange study using FTIR was conducted over a temperature range spanning the endotherm. We found a fast phase, followed by essentially a plateau level which is highly temperature dependent in the 40-60 °C range, suggesting enhanced internal protein motion as the system passes through the temperature range of the endotherm. These results suggest the pre-Tg endotherm is associated with a protein internal mobility transition. Copyright © 2013 Elsevier B.V. All rights reserved.

  8. Laboratory investigation of triple marking the parasitoid Gonatocerus ashmeadi (Hymenoptera: Mymaridae) with a fluorescent dye and two animal proteins

    Science.gov (United States)

    Gonatocerus ashmeadi Girault, a parasitoid of Homalodisca vitripennis (Germar), was used as a model insect to investigate triple marking a minute hymenopteran for potential use for monitoring dispersal patterns of natural enemies in the field. The triple mark contained egg albumin in chicken eggs, c...

  9. Investigation of metallodrug-protein interactions by size-exclusion chromatography coupled with inductively coupled plasma mass spectrometry (ICP-MS)

    International Nuclear Information System (INIS)

    Szpunar, J.; Makarov, A.; Pieper, T.; Keppler, B.K.; Lobinski, R.

    1999-01-01

    The coupling of size-exclusion HPLC with ICP-MS was developed for the studies of the kinetics of metallodrug binding to human serum proteins. Two platinum- and three ruthenium-based drugs were investigated. Various SEC columns (of different lengths and with different packings) were compared for the separation of the protein-bound and unbound fractions of a metallodrug prior to on-line detection of the metal (Ru or Pt). The approach developed offers considerable advantages over the methods based on ultrafiltration followed by the off-line metal determination in terms of speed, simplicity, precision and selectivity regarding the molecular weight of the complexes involved. (Copyright (c) 1999 Elsevier Science B.V., Amsterdam. All rights reserved.)

  10. Solid-State Nuclear Magnetic Resonance Investigation of the Structural Topology and Lipid Interactions of a Viral Fusion Protein Chimera Containing the Fusion Peptide and Transmembrane Domain.

    Science.gov (United States)

    Yao, Hongwei; Lee, Myungwoon; Liao, Shu-Yu; Hong, Mei

    2016-12-13

    The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of parainfluenza virus 5 (PIV5) fusion protein F using solid-state nuclear magnetic resonance. These studies provide structural information about the two domains when they are spatially well separated in the fusion process. To investigate how these two domains are structured relative to each other in the postfusion state, when the ectodomain forms a six-helix bundle that is thought to force the FP and TMD together in the membrane, we have now expressed and purified a chimera of the FP and TMD, connected by a Gly-Lys linker, and measured the chemical shifts and interdomain contacts of the protein in several lipid membranes. The FP-TMD chimera exhibits α-helical chemical shifts in all the membranes examined and does not cause strong curvature of lamellar membranes or membranes with negative spontaneous curvature. These properties differ qualitatively from those of the separate peptides, indicating that the FP and TMD interact with each other in the lipid membrane. However, no 13 C- 13 C cross peaks are observed in two-dimensional correlation spectra, suggesting that the two helices are not tightly associated. These results suggest that the ectodomain six-helix bundle does not propagate into the membrane to the two hydrophobic termini. However, the loosely associated FP and TMD helices are found to generate significant negative Gaussian curvature to membranes that possess spontaneous positive curvature, consistent with the notion that the FP-TMD assembly may

  11. Investigation of Filtration Membranes from the Dairy Protein Industry for Residual Fouling Using Infrared Spectroscopy and Chemometrics

    DEFF Research Database (Denmark)

    Jensen, Jannie Krog

    Ultrafiltration and microfiltration operations are applied intensively in the dairy and water cleaning industries. The main capacity limiting factors of such operations are the flux and efficiency decline by irreversible adsorption of foulants onto the membranes and the efficiency by which...... the reversible fouling can be removed/cleaned. The aim of this thesis is to investigate the residual fouling that is deposited on ultrafiltration and microfiltration membranes after usage. The membrane surfaces are investigated using infrared spectroscopy with an attenuated reflectance sampling unit...... fouling present at the center tube decreasing in concentration outwards in a flame-like shape. The relative concentration calculations are based on the height of the amide II peak (1500-1550 cm-1) which was chosen because it unlike the amide I band has no interference with adsorbed water and other...

  12. INVESTIGATION ON LACTOSE FERMENTING YEASTS ACTIVITY IN THE WHEY OBTAINED BY COAGULATION OF MILK PROTEINS BY BERRY COAGULANT

    Directory of Open Access Journals (Sweden)

    Olena GREK

    2017-06-01

    Full Text Available The results of biochemical activity of lactose fermenting yeasts in the wort based on whey, obtained by thermo acid coagulation of milk by berry raw material (sterilized black currant paste are shown. The extraction of black currant’ valuable components occur in the protein foundation and colored whey, which can be used in the production of fermented beverages with high biological and nutrition value. It was found from the analysis of lactose fermenting yeasts’ biomass accommodation that the biggest growth of yeasts in the wort based on colored whey was in the samples which are fermented by Zygosaccharomyces lactis 868-K – the general amount of cells was (78.1...79.9∙106 CFU/ml for 48 hours. The optimal fermentation temperature (30…32 °C was established by the parameters of fermentation activity: accumulation of ethyl alcohol and carbon dioxide in the wort, the total amount of yeasts cells.The obtained results were used in the technology development of non-alcocholic beverages based on colored whey.

  13. Cigarette smokers develop altered erythrocyte membrane composition: an investigation unmasking the role of membrane bound integral protein GLUT 1.

    Science.gov (United States)

    Sikdar, Jyotirmoy; Seal, Paromita; Roy, Amartya; Haldar, Rajen

    2017-04-01

    Erythrocytes in cigarette smokers are prone to oxidative damage. Here, we sought to elucidate the facts behind modifications and possible defense system developed in erythrocyte of cigarette smokers. We observed significant increase in stomatocytes and spherocytes, and osmotic fragility of erythrocyte, along with reduced level of protein thiol and increased fluorescence anisotropy in isolated membrane. Denaturing gel electrophoresis indicated alterations in band 3, band 4.2 and band 4.5. Among those, Glut 1 (i.e. band 4.5), which transports glucose (insulin independent) and dehydroascorbate (DHA), was selectively chosen for its long history in reducing reactive oxygen species (ROS). The increased Glut 1 level in smokers was confirmed by immunoblotting and immunocytochemistry. Furthermore, smokers showed significantly higher glucose uptake in whole blood. The intracellular (Ic) ROS (as indicated by 2',7'-dichlorofluorescin) was significantly higher in smokers as evidenced by flow cytometric assay. Glucose and DHA alone or together significantly reduced IcROS at higher rate in smokers. However, in presence of Glut 1 specific blocker, phloretin, neither glucose nor DHA could reduce IcROS in both non-smokers and smokers. This confirms that Glut 1 by transporting glucose or DHA attenuates IcROS. Therefore, we conclude that erythrocytes, although altered morphologically, also develop a defense system by upregulating Glut 1 to combat with enhanced Ic oxidative insult in cigarette smokers.

  14. Residue Modification and Mass Spectrometry for the Investigation of Structural and Metalation Properties of Metallothionein and Cysteine-Rich Proteins.

    Science.gov (United States)

    Irvine, Gordon W; Stillman, Martin J

    2017-04-26

    Structural information regarding metallothioneins (MTs) has been hard to come by due to its highly dynamic nature in the absence of metal-thiolate cluster formation and crystallization difficulties. Thus, typical spectroscopic methods for structural determination are limited in their usefulness when applied to MTs. Mass spectrometric methods have revolutionized our understanding of protein dynamics, structure, and folding. Recently, advances have been made in residue modification mass spectrometry in order to probe the hard-to-characterize structure of apo- and partially metalated MTs. By using different cysteine specific alkylation reagents, time dependent electrospray ionization mass spectrometry (ESI-MS), and step-wise "snapshot" ESI-MS, we are beginning to understand the dynamics of the conformers of apo-MT and related species. In this review we highlight recent papers that use these and similar techniques for structure elucidation and attempt to explain in a concise manner the data interpretations of these complex methods. We expect increasing resolution in our picture of the structural conformations of metal-free MTs as these techniques are more widely adopted and combined with other promising tools for structural elucidation.

  15. Almond or Mahaleb? Orthogonal Allergen Analysis During a Live Incident Investigation by ELISA, Molecular Biology, and Protein Mass Spectrometry.

    Science.gov (United States)

    Walker, Michael J; Burns, Malcolm; Quaglia, Milena; Nixon, Gavin; Hopley, Christopher J; Gray, Kirstin M; Moore, Victoria; Singh, Malvinder; Cowen, Simon

    2018-01-01

    It is now well known that an incident investigated in the United Kingdom in 2015 of cumin alleged to be contaminated with almond, a risk for people with almond allergy, was caused by the Prunus species, Prunus mahaleb. In the United Kingdom, the Government Chemist offers a route of technical appeal from official findings in the food control system. Findings of almond in two official samples, cumin and paprika, which had prompted action to exclude the consignments from the food chain, were so referred. Herein are described the approaches deployed to resolve the analytical issues during the investigation of the incidents. The cross-reactivity of ELISA to Prunus species was confirmed, and although this is useful in screening for the genus, orthogonal techniques are required to identify the species and confirm its presence. Two novel PCR assays were developed: one specific for P. mahaleb and the other a screening method capable of identifying common Prunus DNA. Peptides unique to almond and mahaleb were identified, permitting LC-tandem MS and criteria were developed for peptide identification to forensic standards. This work enables a staged approach to be taken to any future incident thought to involve Prunus species and provides a template for the investigation of similar incidents.

  16. Experimental oral iron administration: Histological investigations and expressions of iron handling proteins in rat retina with aging.

    Science.gov (United States)

    Kumar, Pankaj; Nag, Tapas Chandra; Jha, Kumar Abhiram; Dey, Sanjay Kumar; Kathpalia, Poorti; Maurya, Meenakshi; Gupta, Chandan Lal; Bhatia, Jagriti; Roy, Tara Sankar; Wadhwa, Shashi

    2017-12-01

    Iron is implicated in age-related macular degeneration (AMD). The aim of this study was to see if long-term, experimental iron administration with aging modifies retinal and choroidal structures and expressions of iron handling proteins, to understand some aspects of iron homeostasis. Male Wistar rats were fed with ferrous sulphate heptahydrate (500mg/kg body weight/week, oral; elemental iron availability: 20%) from 2 months of age onward until they were 19.5 month-old. At 8, 14 and 20 months of age, they were sacrificed and serum and retinal iron levels were detected by HPLC. Oxidative stress was analyzed by TBARS method. The retinas were examined for cell death (TUNEL), histology (electron microscopy) and the expressions of transferrin, transferrin receptor-1 [TFR-1], H- and L-ferritin. In control animals, at any age, there was no difference in the serum and retinal iron levels, but the latter increased significantly in 14- and 20 month-old iron-fed rats, indicating that retinal iron accumulation proceeds with progression of aging (>14 months). The serum and retinal TBARS levels increased significantly with progression of aging in experimental but not in control rats. There was significant damage to choriocapillaris, accumulation of phagosomes in retinal pigment epithelium and increased incidence of TUNEL+ cells in outer nuclear layer and vacuolation in inner nuclear layer (INL) of 20 month-aged experimental rats, compared to those in age-matched controls. Vacuolations in INL could indicate a long-term effect of iron accumulation in the inner retina. These events paralleled the increased expression of ferritins and transferrin and a decrease in the expression of TFR-1 in iron-fed rats with aging, thereby maintaining iron homeostasis in the retina. As some of these changes mimic with those happening in eyes with AMD, this model can be utilized to understand iron-induced pathophysiological changes in AMD. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. Real-time investigation of mannosyltransferase function of a Xylella fastidiosa recombinant GumH protein using QCM-D.

    Science.gov (United States)

    Alves, Claudia A; Pedroso, Mariele M; de Moraes, Marcela C; Souza, Dulce H F; Cass, Quezia B; Faria, Ronaldo C

    2011-05-20

    Xylella fastidiosa is a gram-negative bacterium that causes serious diseases in economically important crops, including grapevine, coffee, and citrus fruits. X. fastidiosa colonizes the xylem vessels of the infected plants, thereby blocking water and nutrient transport. The genome sequence of X. fastidiosa has revealed an operon containing nine genes possibly involved in the synthesis of an exopolisaccharide (EPS) named fastidian gum that can be related with the pathogenicity of this bacterium. The α-1,3-mannosyltransferase (GumH) enzyme from X. fastidiosa is involved in fastidian gum production. GumH is responsible for the transfer of mannose from guanosine diphosphate mannose (GDP-man) to the cellobiose-pyrophosphate-polyprenol carrier lipid (CPP-Lip) during the assembly and biosynthesis of EPS. In this work, a method for real-time detection of recombinant GumH enzymatic activity was successfully developed using a Quartz Crystal Microbalance with dissipation monitoring (QCM-D). The QCM-D transducer was strategically modified with CPP-Lip by using a solid-supported lipid bilayer that makes use of a self-assembled monolayer of 1-undecanethiol. Monitoring the real-time CPP-Lip QCM-D transducer in the presence of GDP-man and GumH enzyme shows a mass increase, indicating the transfer of mannose. The real-time QCM-D determination of mannosyltransferase function was validated by a High Performance Liquid Chromatography (LC) method developed for determination of GDP produced by enzymatic reaction. LC results confirmed the activity of recombinant GumH protein, which is the first enzyme involved in the biosynthesis of the EPS from X. fastidiosa enzymatically characterized. Copyright © 2011 Elsevier Inc. All rights reserved.

  18. Investigation of Filtration Membranes from the Dairy Protein Industry for Residual Fouling Using Infrared Spectroscopy and Chemometrics

    DEFF Research Database (Denmark)

    Jensen, Jannie Krog

    investigation (Paper I) describes the concentration development over the membrane leaves as a function of the distance from the feed inlet and the distance from the center permeate tube. A non-homogenous concentration distribution of residual fouling was observed with the highest concentration of residual...... the result showed that the MCR model needed three factors to describe the system, one describing the membrane material (polyethersulfone, PES), and two describing the residual fouling that is present on the membrane. The MCR method improved the interpretation of the models considerably compared to e.g. PCA...

  19. Preclinical investigation of the pharmacokinetics, metabolism, and protein and red blood cell binding of DRDE-07: a prophylactic agent against sulphur mustard

    Directory of Open Access Journals (Sweden)

    Pankaj Verma

    2014-10-01

    Full Text Available DRDE-07, a newly synthesized amifostine analog currently under clinical investigation in a phase I trial, is a potent antidote against sulfur mustard toxicity. The purpose of this research was to evaluate the pharmacokinetic profile of DRDE-07 in female Swiss Albino mice after a single oral dose of 400 or 600 mg/kg. The physicochemical properties of DRDE-07, including solubility, pKa, Log P, plasma protein binding and plasma/blood partitioning, were determined to support the pharmacokinetic characterization. DRDE-07 concentration was determined by an HPLC-UV method. The profile of plasma concentration versus time was analyzed using a non-compartmental model. Plasma protein binding was assessed using ultrafiltration. DRDE-07 appeared rapidly in plasma after oral administration with peak plasma levels (Cmax observed in less than 15 min. There was a rapid decline in the plasma levels followed by a smaller second peak about 90 min after dosing. The plasma protein binding of DRDE-07 was found to be less than 25% at all concentrations studied. Plasma clearance of DRDE-07 is expected to be ~1.5 fold higher than the blood clearance of DRDE-07. The probable metabolite of DRDE-07 was identified as phenyl-S-ethyl amine.

  20. Investigation of mercury-containing proteins by enriched stable isotopic tracer and size-exclusion chromatography hyphenated to inductively coupled plasma-isotope dilution mass spectrometry

    International Nuclear Information System (INIS)

    Shi Junwen; Feng Weiyue; Wang Meng; Zhang Fang; Li Bai; Wang Bing; Zhu Motao; Chai Zhifang

    2007-01-01

    In order to investigate trace mercury-containing proteins in maternal rat and their offspring, a method of enriched stable isotopic tracer ( 196 Hg and 198 Hg) combined with size-exclusion chromatography (SEC) coupled to inductively coupled plasma-isotope dilution mass spectrometry (ICP-IDMS) was developed. Prior to the analysis, 196 Hg- and 198 Hg-enriched methylmercury was administrated to the pregnant rats. Then the mercury-containing proteins in serum and brain cytosol of the dam and pup rats were separated by size-exclusion columns and the mercury was detected by ICP-MS. The ICP-MS spectrogram of the tracing samples showed significantly elevated 196 Hg and 198 Hg isotopic signals compared with the natural ones, indicating that the detection sensitivity could be increased by the tracer method. The contents of mercury in chromatographic fractions of the dam and pup rat brain cytosol were quantitatively estimated by post-column reverse ID-ICP-MS. The quantitative speciation differences of mercury in brain cytosol between the dam and pup rats were observed, indicating that such studies could be useful for toxicological estimation. Additionally, the isotopic ratio measurement of 198 Hg/ 202 Hg in the tracing samples could be used to identify the artifact mercury species caused in the analytical procedure. The study demonstrates that the tracer method combined with high-performance liquid chromatography (HPLC)-ICP-IDMS could provide reliably qualitative and quantitative information on mercury-containing proteins in organisms

  1. Surface aggregation of urinary proteins and aspartic acid-rich peptides on the faces of calcium oxalate monohydrate investigated by in situ force microscopy

    Energy Technology Data Exchange (ETDEWEB)

    Weaver, M L; Qiu, S R; Hoyer, J R; Casey, W H; Nancollas, G H; De Yoreo, J J

    2008-05-28

    The growth of calcium oxalate monohydrate in the presence of Tamm-Horsfall protein (THP), osteopontin (OPN), and the 27-residue synthetic peptides (DDDS){sub 6}DDD and (DDDG){sub 6}DDD [where D = aspartic acid and X = S (serine) or G (glycine)] was investigated via in situ atomic force microscopy (AFM). The results show that these three growth modulators create extensive deposits on the crystal faces. Depending on the modulator and crystal face, these deposits can occur as discrete aggregates, filamentary structures, or uniform coatings. These proteinaceous films can lead to either the inhibition or increase of the step speeds (with respect to the impurity-free system) depending on a range of factors that include peptide or protein concentration, supersaturation and ionic strength. While THP and the linear peptides act, respectively, to exclusively increase and inhibit growth on the (-101) face, both exhibit dual functionality on the (010) face, inhibiting growth at low supersaturation or high modulator concentration and accelerating growth at high supersaturation or low modulator concentration. Based on analyses of growth morphologies and dependencies of step speeds on supersaturation and protein or peptide concentration, we argue for a picture of growth modulation that accounts for the observations in terms of the strength of binding to the surfaces and steps and the interplay of electrostatic and solvent-induced forces at crystal surface.

  2. Investigation of gammaE-crystallin target protein binding to bovine lens alpha-crystallin by small-angle neutron scattering.

    Science.gov (United States)

    Clarke, M J; Artero, J B; Moulin, M; Callow, P; Carver, J A; Griffiths, P C; Haertlein, M; Harding, J J; Meek, K M; Timmins, P; Regini, J W

    2010-03-01

    alpha-Crystallin, one of the main constituent proteins in the crystalline lens, is an important molecular chaperone both within and outside the lens. Presently, the structural relationship between alpha-crystallin and its target proteins during chaperone action is poorly understood. It has been hypothesised that target proteins bind within a central cavity. Small-angle neutron-scattering (SANS) experiments in conjunction with isotopic substitution were undertaken to investigate the interaction of a target lens protein (gammaE-crystallin) with alpha-crystallin (alpha(H)) and to measure the radius of gyration (Rg) of the proteins and their binary complexes in solution under thermal stress. The size of the alpha(H) in D(2)O incubated at 65 degrees C increased from 69+/-3 to 81+/-5 A over 40 min, in good agreement with previously published small-angle X-ray scattering (SAXS) and SANS measurements. Deuterated gammaE-crystallin in H(2)O buffer (gammaE(D)/H(2)O) and hydrogenous gammaE-crystallin in D(2)O buffer (gammaE(H)/D(2)O) free in solution were of insufficient size and/or too dilute to provide any measurable scattering over the angular range used, which was selected primarily to investigate gammaE:alpha(H) complexes. The evolution of the aggregation size/shape as an indicator of alpha(H) chaperone action was monitored by recording the neutron scattering in different H:D solvent contrasts under thermally stressed conditions (65 degrees C) for binary mixtures of alpha(H), gammaE(H), and gammaE(D). It was found that Rg(alpha(H):gammaE(D)/D(2)O)>Rg(alpha(H):gammaE(H)/D(2)O)>Rg(alpha(H)/D(2)O) and that Rg(alpha(H):gammaE(H)/D(2)O) approximately Rg(alpha(H)/D(2)O). The relative sizes observed for the complexes weighted by the respective scattering powers of the various components imply that gammaE-crystallin binds in a central cavity of the alpha-crystallin oligomer, during chaperone action. Copyright (c) 2009 Elsevier B.V. All rights reserved.

  3. Structure-Activity Investigation of a G Protein-Biased Agonist Reveals Molecular Determinants for Biased Signaling of the D2 Dopamine Receptor

    Directory of Open Access Journals (Sweden)

    Lani S. Chun

    2018-02-01

    Full Text Available The dopamine D2 receptor (D2R is known to elicit effects through activating two major signaling pathways mediated by either G proteins (Gi/o or β-arrestins. However, the specific role of each pathway in physiological or therapeutic activities is not known with certainty. One approach to the dissection of these pathways is through the use of drugs that can selectively modulate one pathway vs. the other through a mechanism known as functional selectivity or biased signaling. Our laboratory has previously described a G protein signaling-biased agonist, MLS1547, for the D2R using a variety of in vitro functional assays. To further evaluate the biased signaling activity of this compound, we investigated its ability to promote D2R internalization, a process known to be mediated by β-arrestin. Using multiple cellular systems and techniques, we found that MLS1547 promotes little D2R internalization, which is consistent with its inability to recruit β-arrestin. Importantly, we validated these results in primary striatal neurons where the D2R is most highly expressed suggesting that MLS1547 will exhibit biased signaling activity in vivo. In an effort to optimize and further explore structure-activity relationships (SAR for this scaffold, we conducted an iterative chemistry campaign to synthesize and characterize novel analogs of MLS1547. The resulting analysis confirmed previously described SAR requirements for G protein-biased agonist activity and, importantly, elucidated new structural features that are critical for agonist efficacy and signaling bias of the MLS1547 scaffold. One of the most important determinants for G protein-biased signaling is the interaction of a hydrophobic moiety of the compound with a defined pocket formed by residues within transmembrane five and extracellular loop two of the D2R. These results shed new light on the mechanism of biased signaling of the D2R and may lead to improved functionally-selective molecules.

  4. CdS and Cd-Free Buffer Layers on Solution Phase Grown Cu2ZnSn(SxSe1- x)4 :Band Alignments and Electronic Structure Determined with Femtosecond Ultraviolet Photoemission Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Haight, Richard; Barkhouse, Aaron; Wang, Wei; Yu, Luo; Shao, Xiaoyan; Mitzi, David; Hiroi, Homare; Sugimoto, Hiroki

    2013-12-02

    The heterojunctions formed between solution phase grown Cu2ZnSn(SxSe1- x)4(CZTS,Se) and a number of important buffer materials including CdS, ZnS, ZnO, and In2S3, were studied using femtosecond ultraviolet photoemission spectroscopy (fs-UPS) and photovoltage spectroscopy. With this approach we extract the magnitude and direction of the CZTS,Se band bending, locate the Fermi level within the band gaps of absorber and buffer and measure the absorber/buffer band offsets under flatband conditions. We will also discuss two-color pump/probe experiments in which the band bending in the buffer layer can be independently determined. Finally, studies of the bare CZTS,Se surface will be discussed including our observation of mid-gap Fermi level pinning and its relation to Voc limitations and bulk defects.

  5. Uses and limitations of green fluorescent protein as a viability marker in Enterococcus faecalis: An observational investigation.

    Science.gov (United States)

    Hoogenkamp, Michel A; Crielaard, Wim; Krom, Bastiaan P

    2015-08-01

    Enterococci are capable of producing biofilms that are notoriously difficult to treat and remove, for instance in root canal infections. The tenacious nature of these organisms makes screening of known and novel antimicrobial compounds necessary. While traditionally growth and fluorescence-based screening methods have proven useful, these methods have their limitations when applied to enterococci (e.g. time consuming, no kinetic data, diffusion properties of the fluorescent dyes). The aim of this study was to develop and validate a GFP-based high-throughput screening system to assess the bactericidal activity of a broad range of antimicrobial agents on Enterococcus faecalis and its biofilms. The effect of antimicrobial compounds on cell viability and GFP fluorescence of enterococcal planktonic and biofilm cells was determined using colony forming unit counts, fluorescence spectrophotometry and real-time imaging devices. There was a linear correlation between cell viability and GFP fluorescence. The intensity of the GFP signal was effected by the extracellular pH. For a range of antimicrobials however, there was no correlation between these two parameters. In contrast, for oxidizing agents such as sodium hypochlorite, the antimicrobial of choice for root canal disinfection, there was a correlation between loss of fluorescence and loss of viability. To conclude, the use of a GFP-based system to monitor the antimicrobial activity of compounds on E. faecalis is possible despite significant limitations. This approach is useful for analysis of susceptibility to oxidizing agents. Using real-time measuring devices to follow GFP fluorescence it should be possible to investigate the mode of action and rate of diffusion of oxidizing agents in E. faecalis biofilm. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Photo-induced isomerization of ethylene-bridged azobenzene explored by ab initio based non-adiabatic dynamics simulation: A comparative investigation of the isomerization in the gas and solution phases

    Energy Technology Data Exchange (ETDEWEB)

    Cao Jun; Liu Lihong; Fang Weihai [Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875 (China); Xie Zhizhong [Department of Chemistry, School of Science, Wuhan University of Technology, Wuhan 430070 (China); Zhang Yong [Department of Chemistry, Chemical Biology, and Biomedical Engineering, Stevens Institute of Technology, Castle Point on Hudson, Hoboken, New Jersey 07030 (United States)

    2013-04-07

    Azobenzene is one of the most widely used photoactive units and recently an ethylene-bridged azobenzene (BAB) was reported to have greatly enhanced conversion efficiency, quantum yield, and other favorable properties. As the first step towards exploring its photo-switchable character in real systems, we report here a systematic study on the photoisomerization dynamics between trans (E) and cis (Z) isomers in the gas phase and the CH{sub 3}OH solution, using ab initio based surface hopping and molecular dynamics, which is the first report of dynamics simulation to reveal the environmental effects on BAB photoreactions. Results show that while the relatively faster S{sub 1} relaxation of the photo-induced E{yields}Z process is only mildly affected by the solvent effect, the relatively slower S{sub 1} relaxation of the reverse reaction becomes even slower in the solution compared to the gas phase. The subsequent S{sub 0} dynamics from the conical intersection between S{sub 1} and S{sub 0} (CI{sub E}) to Z is accelerated in solution compared to the gas phase because of avoided re-crossing to the S{sub 1} state, while the S{sub 0} dynamics from the conical intersection between S{sub 1} and S{sub 0} (CI{sub Z}) to E are basically the same in both phases. Overall, the solvent effect was found to enhance the back-and-forth photo-switch efficiency between the Z and E isomers compared to the gas phase, while the quantum yields are reduced. But the solution yields of both the forward and backward photoreactions are still around 0.4. Therefore, BAB may have good photo-responsive properties if used as a photoactive unit in real systems. These results will facilitate future experimental and theoretical studies in this area to help design new azobenzene derivatives as photoactive units in biological processes, nanoscale devices, and photo-responsive materials.

  7. Photo-induced isomerization of ethylene-bridged azobenzene explored by ab initio based non-adiabatic dynamics simulation: A comparative investigation of the isomerization in the gas and solution phases

    Science.gov (United States)

    Cao, Jun; Liu, Li-Hong; Fang, Wei-Hai; Xie, Zhi-Zhong; Zhang, Yong

    2013-04-01

    Azobenzene is one of the most widely used photoactive units and recently an ethylene-bridged azobenzene (BAB) was reported to have greatly enhanced conversion efficiency, quantum yield, and other favorable properties. As the first step towards exploring its photo-switchable character in real systems, we report here a systematic study on the photoisomerization dynamics between trans (E) and cis (Z) isomers in the gas phase and the CH3OH solution, using ab initio based surface hopping and molecular dynamics, which is the first report of dynamics simulation to reveal the environmental effects on BAB photoreactions. Results show that while the relatively faster S1 relaxation of the photo-induced E → Z process is only mildly affected by the solvent effect, the relatively slower S1 relaxation of the reverse reaction becomes even slower in the solution compared to the gas phase. The subsequent S0 dynamics from the conical intersection between S1 and S0 (CI_E) to Z is accelerated in solution compared to the gas phase because of avoided re-crossing to the S1 state, while the S0 dynamics from the conical intersection between S1 and S0 (CI_Z) to E are basically the same in both phases. Overall, the solvent effect was found to enhance the back-and-forth photo-switch efficiency between the Z and E isomers compared to the gas phase, while the quantum yields are reduced. But the solution yields of both the forward and backward photoreactions are still around 0.4. Therefore, BAB may have good photo-responsive properties if used as a photoactive unit in real systems. These results will facilitate future experimental and theoretical studies in this area to help design new azobenzene derivatives as photoactive units in biological processes, nanoscale devices, and photo-responsive materials.

  8. Investigations on the effect of forage source, grinding, and urea supplementation on ruminal fermentation and microbial protein flow in a semi-continuous rumen simulation system.

    Science.gov (United States)

    Hildebrand, Bastian; Boguhn, Jeannette; Rodehutscord, Markus

    2011-10-01

    The objective of the present study was to compare the effect of maize silage and grass silage on microbial fermentation and protein flow in a semi-continuous rumen simulation system (Rusitec) when milling screen size (MSS) during grinding was varied. Oven-dried silages were milled through screens of 1, 4 or 9 mm pore size and incubated for 48 h in a Rusitec system. Furthermore, the effect of N supplementation to maize silage (MSS: 4 mm) was investigated and single dose vs. continuous infusion of urea-N were compared. Degradation of organic matter (OM), crude protein (CP), fibre fractions and non-structural carbohydrates (NSC) as well as short-chain fatty acid production differed significantly between forage sources. Urea-N supplementation improved the degradation of NSC, but not that of fibre fractions in maize silage. The way of urea supply had only marginal effects on fermentation characteristics. An increase in MSS, and consequently in mean feed particle size, led to an improvement in the degradation of OM, CP and NSC, but efficiency of microbial net protein synthesis (EMPS; mg microbial N flow/g degraded OM) and the microbial amino acid profile were less affected. EMPS was higher in grass silage than in maize silage and was improved by urea-N supplementation in maize silage. This study indicates that fermentation of NSC as well as EMPS during incubation of maize silage was limited by availability of NH3-N. Furthermore, an increase in MSS above 1 mm seems to improve fermentation of silages in the Rusitec system.

  9. Analysis of active ricin and castor bean proteins in a ricin preparation, castor bean extract, and surface swabs from a public health investigation.

    Science.gov (United States)

    Schieltz, David M; McGrath, Sara C; McWilliams, Lisa G; Rees, Jon; Bowen, Michael D; Kools, John J; Dauphin, Leslie A; Gomez-Saladin, Eduardo; Newton, Bruce N; Stang, Heather L; Vick, Michael J; Thomas, Jerry; Pirkle, James L; Barr, John R

    2011-06-15

    In late February 2008, law enforcement officials in Las Vegas, Nevada, discovered in a hotel room, a copy of The Anarchist Cookbook, suspected castor beans and a "white powder" thought to be a preparation of ricin. Ricin is a deadly toxin from the seed of the castor bean plant (Ricinus communis). The United States regulates the possession, use, and transfer of ricin and it is the only substance considered a warfare agent in both the Chemical and the Biological Weapons Conventions. Six samples obtained from the hotel room were analyzed by laboratories at the Centers for Disease Control and Prevention using a panel of biological and mass spectrometric assays. The biological assays (real time-PCR, time resolved fluorescence and cytotoxicity) provided presumptive evidence of active ricin in each of the samples. This initial screen was followed by an in-depth analysis using a novel, state-of-the-art mass spectrometry-based ricin functional assay and high sensitivity tandem mass spectrometry for protein identification. Mass spectrometric analysis positively identified ricin and confirmed that in each of the samples it was enzymatically active. The tandem mass spectrometry analysis used here is the most selective method available to detect ricin toxin. In each sample, ricin was unequivocally identified along with other R. communis plant proteins, including the highly homologous protein RCA120. Although database searches using tandem mass spectra acquired from the samples indicated that additional controlled substances were not present in these samples, the mass spectrometric results did provide extensive detail about the sample contents. To the best of our knowledge following a review of the available literature, this report describes the most detailed analysis of a white powder for a public health or forensic investigation involving ricin. Published by Elsevier Ireland Ltd.

  10. Investigation of mercury-containing proteins by enriched stable isotopic tracer and size-exclusion chromatography hyphenated to inductively coupled plasma-isotope dilution mass spectrometry

    Energy Technology Data Exchange (ETDEWEB)

    Shi Junwen [Laboratory for Bio-Environmental Health Sciences of Nanoscale Materials and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)]|[Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Feng Weiyue [Laboratory for Bio-Environmental Health Sciences of Nanoscale Materials and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)]. E-mail: fengwy@mail.ihep.ac.cn; Wang Meng [Laboratory for Bio-Environmental Health Sciences of Nanoscale Materials and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)]|[Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Zhang Fang [Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Li Bai [Laboratory for Bio-Environmental Health Sciences of Nanoscale Materials and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China); Wang Bing; Zhu Motao [Laboratory for Bio-Environmental Health Sciences of Nanoscale Materials and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)]|[Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); Chai Zhifang [Laboratory for Bio-Environmental Health Sciences of Nanoscale Materials and Key Laboratory of Nuclear Analytical Techniques, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049 (China)]|[Institute of Nuclear Technology, Shenzhen University, Shenzhen 518060 (China)]|[Institute of Nanochemistry and Nanosafety, Shanghai University, Shanghai (China)

    2007-01-30

    In order to investigate trace mercury-containing proteins in maternal rat and their offspring, a method of enriched stable isotopic tracer ({sup 196}Hg and {sup 198}Hg) combined with size-exclusion chromatography (SEC) coupled to inductively coupled plasma-isotope dilution mass spectrometry (ICP-IDMS) was developed. Prior to the analysis, {sup 196}Hg- and {sup 198}Hg-enriched methylmercury was administrated to the pregnant rats. Then the mercury-containing proteins in serum and brain cytosol of the dam and pup rats were separated by size-exclusion columns and the mercury was detected by ICP-MS. The ICP-MS spectrogram of the tracing samples showed significantly elevated {sup 196}Hg and {sup 198}Hg isotopic signals compared with the natural ones, indicating that the detection sensitivity could be increased by the tracer method. The contents of mercury in chromatographic fractions of the dam and pup rat brain cytosol were quantitatively estimated by post-column reverse ID-ICP-MS. The quantitative speciation differences of mercury in brain cytosol between the dam and pup rats were observed, indicating that such studies could be useful for toxicological estimation. Additionally, the isotopic ratio measurement of {sup 198}Hg/{sup 202}Hg in the tracing samples could be used to identify the artifact mercury species caused in the analytical procedure. The study demonstrates that the tracer method combined with high-performance liquid chromatography (HPLC)-ICP-IDMS could provide reliably qualitative and quantitative information on mercury-containing proteins in organisms.

  11. Characterization of Caco-2 cells stably expressing the protein-based zinc probe eCalwy-5 as a model system for investigating intestinal zinc transport.

    Science.gov (United States)

    Maares, Maria; Keil, Claudia; Thomsen, Susanne; Günzel, Dorothee; Wiesner, Burkhard; Haase, Hajo

    2018-01-29

    Intestinal zinc resorption, in particular its regulation and mechanisms, are not yet fully understood. Suitable intestinal cell models are needed to investigate zinc uptake kinetics and the role of labile zinc in enterocytes in vitro. Therefore, a Caco-2 cell clone was produced, stably expressing the genetically encoded zinc biosensor eCalwy-5. The aim of the present study was to reassure the presence of characteristic enterocyte-specific properties in the Caco-2-eCalwy clone. Comparison of Caco-2-WT and Caco-2-eCalwy cells revealed only slight differences regarding subcellular localization of the tight junction protein occludin and alkaline phosphatase activity, which did not affect basic integrity of the intestinal barrier or the characteristic brush border membrane morphology. Furthermore, introduction of the additional zinc-binding protein in Caco-2 cells did not alter mRNA expression of the major intestinal zinc transporters (zip4, zip5, znt-1 and znt-5), but increased metallothionein 1a-expression and cellular resistance to higher zinc concentrations. Moreover, this study examines the effect of sensor expression level on its saturation with zinc. Fluorescence cell imaging indicated considerable intercellular heterogeneity in biosensor-expression. However, FRET-measurements confirmed that these differences in expression levels have no effect on fractional zinc-saturation of the probe. Copyright © 2018 Elsevier GmbH. All rights reserved.

  12. Investigations of the influence of the content of crude plant protein in the ration on the utilisation of urea in dairy cattle. 3

    International Nuclear Information System (INIS)

    Tarakanow, B.W.; Sommer, A.; Voigt, J.

    1984-01-01

    The rations contained 10.7 (I), 13.7 (II) and 17.1 (III)% plant crude protein and, after the supplementation of 150 g urea per animal and day, a total of 13.8 (I), 16.7 (II) and 20.2 (III)% crude protein in the dry matter. The starch content and the dry matter was 25.6, 19.6 and 13.4% from I to III. The urea was intraruminally infused during the feeding in the morning and the evening. In the morning feeding of each 1st measuring day it was labelled with 27.5 atom-% 15 N'. Samples were taken from the rumen up to 72 h after intake. 4, 8 and 12 hours after 15 N intake 100 ml rumen fluid contained 2.5, 3.3 and 3.0 (I), 3.1, 3.0 and 2.8 (II) and 4.1, 4.4 and 4.2 (III) g dry matter of the bacteria and 7.9, 9.0 and 5.9 (I), 3.8, 3.2 and 3.1 (II) and 2.1, 3.1 and 1.7 (III) g dry matter of the protozoa. In comparison to I the concentration of microbes in III decreased to 60-67%. The N level of the ration did not influence the N and carbohydrate content of the microbes as well as the amino acid composition of the microbial protein. Level and dynamics of 15 N incorporation differed between protozoa and bacteria. The latter were more intensively labelled and 15 N frequency increased more quickly. From I to III the maximum labelling degrees were 3.27, 3.09 and 1.98 for bacteria and 0.93, 0.82 and 0.80 atom-% 15 N excess. The apparent half life of 15 N on 10...12 h in the bacteria N and of 34...59 h in the protozoa N showed that 15 N metabolism in protozoa is distinctly slower. The 15 N frequency in the amino acids (AA) of the microbial protein revaled that urea N was included in the synthesis of all the 16 AA investigated, with big differences in the relative 15 N frequency in the AA both within the microbes and between the species of microbes. One can conclude that the decreasing utilization of 15 N from urea in comparison with that of the total N is caused by the reduction of the concentration of microbes in the rumen fluid and the relatively lower quota of the incorporation

  13. Investigating Molecular Structures of Bio-Fuel and Bio-Oil Seeds as Predictors To Estimate Protein Bioavailability for Ruminants by Advanced Nondestructive Vibrational Molecular Spectroscopy.

    Science.gov (United States)

    Ban, Yajing; L Prates, Luciana; Yu, Peiqiang

    2017-10-18

    This study was conducted to (1) determine protein and carbohydrate molecular structure profiles and (2) quantify the relationship between structural features and protein bioavailability of newly developed carinata and canola seeds for dairy cows by using Fourier transform infrared molecular spectroscopy. Results showed similarity in protein structural makeup within the entire protein structural region between carinata and canola seeds. The highest area ratios related to structural CHO, total CHO, and cellulosic compounds were obtained for carinata seeds. Carinata and canola seeds showed similar carbohydrate and protein molecular structures by multivariate analyses. Carbohydrate molecular structure profiles were highly correlated to protein rumen degradation and intestinal digestion characteristics. In conclusion, the molecular spectroscopy can detect inherent structural characteristics in carinata and canola seeds in which carbohydrate-relative structural features are related to protein metabolism and utilization. Protein and carbohydrate spectral profiles could be used as predictors of rumen protein bioavailability in cows.

  14. [Carriage of Streptococcus pyogenes in primary school children: M-protein types, pyrogenic toxin genes, and investigation of the clonal relationships between the isolates].

    Science.gov (United States)

    Otlu, Barış; Karakurt, Cemşit; Bayındır, Yaşar; Kayabaş, Üner; Yakupoğulları, Yusuf; Gözükara Bağ, Harika

    2015-07-01

    M-protein and pyrogenic toxins are the most important virulence factors of Streptococcus pyogenes, and they play significant role in the pathophysiology of acute rheumatoid fever and scarlet fever, respectively. In this study, the pharyngeal carriage of S.pyogenes of the primary school children, clonal relationship of the strains, M-protein types, and the presence of pyrogenic toxin genes were aimed to be investigated. A total of 668 throat cultures obtained from children (age range: 6-16 years) in two primary schools in our region, were included in the study. The clonal relationships of the isolated group A streptococci (GAS) strains were investigated by DiversiLab assay (BioMérieux, France), and the clonal relatedness was confirmed by pulsed-field gel electrophoresis (PFGE) method. M-protein (emm) typing was performed by DNA sequencing as suggested by Centers for Disease Control and Prevention (CDC). The genes encoding pyrogenic toxins, speA and speC, were investigated by an in-house multiplex polymerase chain reaction (PCR) method. S.pyogenes was isolated from 134 (20.05%) of the throat samples. The GAS carriage rate of the students aged ≥10 was statistically higher than those 7-9 years age group (%22 vs %16.4, pprotein gene could be characterized only among 123 isolates by DNA sequencing, and 20 different emm types were detected. The most frequent emm type was emm1 (n=38, 30.9%) followed by emm12 (n=18, 14.6%), emm89 (n=10, 8.1%), emm118 (n=9, 7.3%), and emm4 (n=7, 5.7%). Pyrogenic toxin genes were found in 25 (18.6%) of the isolates, including speA in 11 isolates (8.2%) and speC in 12 isolates (8.9%) and both genes were detected in 2 isolates (1.5%). Sixty-two different Rep (Repetitive extragenic palindromic)-PCR profiles were detected in 134 S.pyogenes isolates by DiversiLab method. Thirteen different clusters were formed by a total of clonally related 36 isolates revealing a strain clustering ratio of 26.9%. Clonal relationship of all isolates in the same

  15. Investigation on the Protein Degradation, Free Fatty Acid Content and Area Fraction of Poosti Cheese, Iranian Traditional Cheese Ripened in Skin

    Directory of Open Access Journals (Sweden)

    Mojgan Hemmatian

    2015-03-01

    Full Text Available Background and Objectives: In this study, the proteolysis and lipolysis of Poosti cheese produced from raw sheep milk in mountainous eastern regions of Iran were investigated during 90 days of ripening. Materials and Methods: Sodium dodecyl sulfate polyacrylamide gel electrophoresis for proteolysis (SDS-PAGE and gas chromatography (GC for free fatty acids (FFAs were applied to investigate the intensity of lipid degradation. To evaluate the Poosti cheese microstructural changes, the area fraction parameter of the scanning electron microscopy (SEM micrographs was also calculated by the Image J software. Results: The most alteration in protein profile was occurred in the first month of aging for high activity of the proteolytic microorganisms in this period. The amount of free fatty acids was depended on their length due to the variety of involved mechanisms. In addition, the microstructural parameter was considerably affected by the aging as a consequence of the effect of salt on the activity of raw milk and skin micro flora. Conclusions: The decline in proteolysis rate during the last stage of aging could be correlated with the inhibitory effects of salt on the engaged microorganisms, and increase in the pore fraction of the microstructure during the first month of Poosti cheese aging could be due to casein rearrangement and gas release by the fermentative activity of microorganisms. Keywords: Proteolysis, Lipolysis, Poosti cheese, Raw sheep milk.

  16. Experimental investigation of egg ovalbumin scaling on heated stainless steel surface and scale-removal compared with that of whey protein.

    Science.gov (United States)

    Li, Lin; Lv, Hui Ting; Deng, Ren Pan; Liao, Zhen Kai; Wu, Xue E; Chen, Xiao Dong

    2013-07-01

    Fouling and cleaning on a heat exchanger surface during milk processing have been studied extensively in the past due to their great importance in energy, product quality, and safety. However, little information is available for egg ovalbumin (OVA) fouling and cleaning behavior. In the present work, fouling and cleaning behaviors of OVA were investigated using a real-time monitoring system for heat transfer coefficient. A comparison was made between the behavior of whey protein concentrate (WPC) and that of OVA. WPC has been well studied which can be used as a benchmark. Ultrasonic cleaning was also applied to investigate the cleaning behavior of OVA fouling. Results have shown that OVA created more thermal resistance than WPC in the 2 h fouling process. It was also much more difficult to remove the OVA deposit than the WPC fouling. Different from what were observed from WPC deposit, there was no optimal cleaning rate for OVA deposit in the NaOH concentration range tested (0-2.0 wt%), while WPC fouling is known to have the highest cleaning rate around 0.5 wt% NaOH concentration at moderate temperatures. Copyright © 2013. Published by Elsevier B.V.

  17. Proteomic Investigation of Rhizoctonia solani AG 4 Identifies Secretome and Mycelial Proteins with roles in Plant Cell Wall Degradation and Virulence

    KAUST Repository

    Lakshman, Dilip

    2016-03-28

    Rhizoctonia solani AG 4 is a soilborne necrotrophic fungal plant pathogen that causes economically important diseases on agronomic crops worldwide. Here we used a proteomics approach to characterize both intracellular proteins and the secretome of R. solani AG 4 isolate Rs23A under several growth conditions; the secretome being highly important in pathogenesis. From over 500 total secretome and soluble intracellular protein spots from 2-D gels, 457 protein spots were analyzed and 318 proteins positively matched with fungal proteins of known function by comparison with available R. solani genome databases specific for anastomosis groups 1-IA, 1-IB, and 3. These proteins were categorized to possible cellular locations and functional groups; and for some proteins their putative roles in plant cell wall degradation and virulence. The majority of the secreted proteins were grouped to extracellular regions and contain hydrolase activity.

  18. Receptor oligomerization in family B1 of G-protein-coupled receptors: focus on BRET investigations and the link between GPCR oligomerization and binding cooperativity.

    Science.gov (United States)

    Roed, Sarah Norklit; Orgaard, Anne; Jorgensen, Rasmus; De Meyts, Pierre

    2012-01-01

    The superfamily of the seven transmembrane G-protein-coupled receptors (7TM/GPCRs) is the largest family of membrane-associated receptors. GPCRs are involved in the pathophysiology of numerous human diseases, and they constitute an estimated 30-40% of all drug targets. During the last two decades, GPCR oligomerization has been extensively studied using methods like bioluminescence resonance energy transfer (BRET) and today, receptor-receptor interactions within the GPCR superfamily is a well-established phenomenon. Evidence of the impact of GPCR oligomerization on, e.g., ligand binding, receptor expression, and signal transduction indicates the physiological and pharmacological importance of these receptor interactions. In contrast to the larger and more thoroughly studied GPCR subfamilies A and C, the B1 subfamily is small and comprises only 15 members, including, e.g., the secretin receptor, the glucagon receptor, and the receptors for parathyroid hormone (PTHR1 and PTHR2). The dysregulation of several family B1 receptors is involved in diseases, such as diabetes, chronic inflammation, and osteoporosis which underlines the pathophysiological importance of this GPCR subfamily. In spite of this, investigation of family B1 receptor oligomerization and especially its pharmacological importance is still at an early stage. Even though GPCR oligomerization is a well-established phenomenon, there is a need for more investigations providing a direct link between these interactions and receptor functionality in family B1 GPCRs. One example of the functional effects of GPCR oligomerization is the facilitation of allosterism including cooperativity in ligand binding to GPCRs. Here, we review the currently available data on family B1 GPCR homo- and heteromerization, mainly based on BRET investigations. Furthermore, we cover the functional influence of oligomerization on ligand binding as well as the link between oligomerization and binding cooperativity.

  19. A study protocol to investigate the relationship between dietary fibre intake and fermentation, colon cell turnover, global protein acetylation and early carcinogenesis: the FACT study

    Directory of Open Access Journals (Sweden)

    Croucher Lisa J

    2009-09-01

    Full Text Available Abstract Background A number of studies, notably EPIC, have shown a descrease in colorectal cancer risk associated with increased fibre consumption. Whilst the underlying mechanisms are likely to be multifactorial, production of the short-chain fatty-acid butyrate fro butyratye is frequently cited as a major potential contributor to the effect. Butyrate inhibits histone deacetylases, which work on a wide range of proteins over and above histones. We therefore hypothesized that alterations in the acetylated proteome may be associated with a cancer risk phenotype in the colorectal mucosa, and that such alterations are candidate biomarkers for effectiveness of fibre interventions in cancer prevention. Methods an design There are two principal arms to this study: (i a cross-sectional study (FACT OBS of 90 subjects recruited from gastroenterology clinics and; (ii an intervention trial in 40 subjects with an 8 week high fibre intervention. In both studies the principal goal is to investigate a link between fibre intake, SCFA production and global protein acetylation. The primary measure is level of faecal butyrate, which it is hoped will be elevated by moving subjects to a high fibre diet. Fibre intakes will be estimated in the cross-sectional group using the EPIC Food Frequency Questionnaire. Subsidiary measures of the effect of butyrate on colon mucosal function and pre-cancerous phenotype will include measures of apoptosis, apoptotic regulators cell cycle and cell division. Discussion This study will provide a new level of mechanistic data on alterations in the functional proteome in response to the colon microenvironment which may underwrite the observed cancer preventive effect of fibre. The study may yield novel candidate biomarkers of fibre fermentation and colon mucosal function. Trial Registration Trial Registration Number: ISRCTN90852168

  20. A study protocol to investigate the relationship between dietary fibre intake and fermentation, colon cell turnover, global protein acetylation and early carcinogenesis: the FACT study

    International Nuclear Information System (INIS)

    Corfe, Bernard M; Williams, Elizabeth A; Bury, Jonathan P; Riley, Stuart A; Croucher, Lisa J; Lai, Daphne YL; Evans, Caroline A

    2009-01-01

    A number of studies, notably EPIC, have shown a descrease in colorectal cancer risk associated with increased fibre consumption. Whilst the underlying mechanisms are likely to be multifactorial, production of the short-chain fatty-acid butyrate fro butyratye is frequently cited as a major potential contributor to the effect. Butyrate inhibits histone deacetylases, which work on a wide range of proteins over and above histones. We therefore hypothesized that alterations in the acetylated proteome may be associated with a cancer risk phenotype in the colorectal mucosa, and that such alterations are candidate biomarkers for effectiveness of fibre interventions in cancer prevention. There are two principal arms to this study: (i) a cross-sectional study (FACT OBS) of 90 subjects recruited from gastroenterology clinics and; (ii) an intervention trial in 40 subjects with an 8 week high fibre intervention. In both studies the principal goal is to investigate a link between fibre intake, SCFA production and global protein acetylation. The primary measure is level of faecal butyrate, which it is hoped will be elevated by moving subjects to a high fibre diet. Fibre intakes will be estimated in the cross-sectional group using the EPIC Food Frequency Questionnaire. Subsidiary measures of the effect of butyrate on colon mucosal function and pre-cancerous phenotype will include measures of apoptosis, apoptotic regulators cell cycle and cell division. This study will provide a new level of mechanistic data on alterations in the functional proteome in response to the colon microenvironment which may underwrite the observed cancer preventive effect of fibre. The study may yield novel candidate biomarkers of fibre fermentation and colon mucosal function. Trial Registration Number: ISRCTN90852168

  1. A simple solution-phase approach to synthesize high quality ternary AgInSe2 and band gap tunable quaternary AgIn(S1-xSe x)2 nanocrystals

    KAUST Repository

    Bai, Tianyu

    2014-01-01

    A facile solution-phase route for the preparation of AgInSe2 nanocrystals was developed by using silver nitrate, indium stearate, and oleylamine-selenium (OAm-Se) as precursors. The evolution process of the AgInSe2 nanocrystals is discussed in detail and different reaction conditions all have a great impact on the growth and morphology of the nanocrystals. Alloyed AgIn(S1-xSex)2 nanocrystals with controlled composition across the entire range (0 ≤ x ≤ 1) was also successfully prepared by modulating the S/Se reactant mole ratio. X-ray diffraction (XRD), energy dispersive X-ray (EDX), X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) were used to confirm that the alloyed AgIn(S1-xSex)2 nanocrystals are homogeneous. The UV-vis absorption spectra revealed that the band gap energies of the alloyed AgIn(S1-xSex)2 nanocrystals could be continuously tuned by increasing the Se content. © The Royal Society of Chemistry 2014.

  2. Design, synthesis, and evaluation of an alpha-helix mimetic library targeting protein-protein interactions.

    Science.gov (United States)

    Shaginian, Alex; Whitby, Landon R; Hong, Sukwon; Hwang, Inkyu; Farooqi, Bilal; Searcey, Mark; Chen, Jiandong; Vogt, Peter K; Boger, Dale L

    2009-04-22

    The design and solution-phase synthesis of an alpha-helix mimetic library as an integral component of a small-molecule library targeting protein-protein interactions are described. The iterative design, synthesis, and evaluation of the candidate alpha-helix mimetic was initiated from a precedented triaryl template and refined by screening the designs for inhibition of MDM2/p53 binding. Upon identifying a chemically and biologically satisfactory design and consistent with the screening capabilities of academic collaborators, the corresponding complete library was assembled as 400 mixtures of 20 compounds (20 x 20 x 20-mix), where the added subunits are designed to mimic all possible permutations of the naturally occurring i, i + 4, i + 7 amino acid side chains of an alpha-helix. The library (8000 compounds) was prepared using a solution-phase synthetic protocol enlisting acid/base liquid-liquid extractions for purification on a scale that insures its long-term availability for screening campaigns. Screening of the library for inhibition of MDM2/p53 binding not only identified the lead alpha-helix mimetic upon which the library was based, but also suggests that a digestion of the initial screening results that accompany the use of such a comprehensive library can provide insights into the nature of the interaction (e.g., an alpha-helix mediated protein-protein interaction) and define the key residues and their characteristics responsible for recognition.

  3. Protein Conformation and Supercharging with DMSO from Aqueous Solution

    Science.gov (United States)

    Sterling, Harry J.; Prell, James S.; Cassou, Catherine A.; Williams, Evan R.

    2011-07-01

    The efficacy of dimethyl sulfoxide (DMSO) as a supercharging reagent for protein ions formed by electrospray ionization from aqueous solution and the mechanism for supercharging were investigated. Addition of small amounts of DMSO to aqueous solutions containing hen egg white lysozyme or equine myoglobin results in a lowering of charge, whereas a significant increase in charge occurs at higher concentrations. Results from both near-UV circular dichroism spectroscopy and solution-phase hydrogen/deuterium exchange mass spectrometry indicate that DMSO causes a compaction of the native structure of these proteins at low concentration, but significant unfolding occurs at ~63% and ~43% DMSO for lysozyme and myoglobin, respectively. The DMSO concentrations required to denature these two proteins in bulk solution are ~3-5 times higher than the concentrations required for the onset of supercharging, consistent with a significantly increased concentration of this high boiling point supercharging reagent in the ESI droplet as preferential evaporation of water occurs. DMSO is slightly more basic than m-nitrobenzyl alcohol and sulfolane, two other supercharging reagents, based on calculated proton affinity and gas-phase basicity values both at the B3LYP and MP2 levels of theory, and all three of these supercharging reagents are significantly more basic than water. These results provide additional evidence that the origin of supercharging from aqueous solution is the result of chemical and/or thermal denaturation that occurs in the ESI droplet as the concentration of these supercharging reagents increases, and that proton transfer reactivity does not play a significant role in the charge enhancement observed.

  4. Metal-metallothioneins like proteins investigation by heteroatom-tagged proteomics in two different snails as possible sentinel organisms of metal contamination in freshwater ecosystems

    Energy Technology Data Exchange (ETDEWEB)

    Franca Maltez, Heloisa [Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julian Claveria 8, 33006 Oviedo (Spain); Villanueva Tagle, Margarita [Faculty of Chemistry, University of La Habana (Cuba); Rosario Fernandez de la Campa, Maria del [Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julian Claveria 8, 33006 Oviedo (Spain); Sanz-Medel, Alfredo, E-mail: asm@uniovi.es [Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julian Claveria 8, 33006 Oviedo (Spain)

    2009-09-21

    Metal speciation analysis in MLPs was carried out in two snails, Marisa cornuarietis and Pomacea bridgesi, in order to investigate them as possible sentinel organisms of heavy metal contamination. To carry out this study snails born in a non-contaminated environment were divided into two groups: a control group and a contaminated one with cadmium administered for 40 days. Subsequently, we investigated the speciation of the induced MLPs in exposed animals in relation to controls. In order to obtain the MLP fraction, cytosols from both snail species where subjected to size-exclusion fractionation, monitoring on-line the metal signal (Cd, Cu and Zn) by ICP-MS while protein elution was followed by on-line UV detection. MLP fraction was then separated by anion-exchange (AE)-FPLC using optimal chromatographic conditions for the separation of the different MLP isoforms in both snail species. Specific detection of separated metalloforms was carried out again by the hyphenation of the AE chromatographic system with ICP-MS. The determination of the amount of metal bound to MLPs was carried out by post-column isotope dilution analysis ICP-MS, finding that the snail M. cornuarietis accumulated higher concentrations of cadmium than P. bridgesi. Thus this first snail could therefore be a better candidate sentinel organism of pollution in natural waters. Identification and characterization of the isoforms separated in M. cornuarietis was carried out for the entire or intact isoforms by MALDI-TOF and then conventional triptic digestion was also carried out to identify the nature of the formed peptides. The presence identification of a MLP isoform of relatively low molecular weight in M. cornuarietis is reported.

  5. Metal-metallothioneins like proteins investigation by heteroatom-tagged proteomics in two different snails as possible sentinel organisms of metal contamination in freshwater ecosystems

    International Nuclear Information System (INIS)

    Franca Maltez, Heloisa; Villanueva Tagle, Margarita; Rosario Fernandez de la Campa, Maria del; Sanz-Medel, Alfredo

    2009-01-01

    Metal speciation analysis in MLPs was carried out in two snails, Marisa cornuarietis and Pomacea bridgesi, in order to investigate them as possible sentinel organisms of heavy metal contamination. To carry out this study snails born in a non-contaminated environment were divided into two groups: a control group and a contaminated one with cadmium administered for 40 days. Subsequently, we investigated the speciation of the induced MLPs in exposed animals in relation to controls. In order to obtain the MLP fraction, cytosols from both snail species where subjected to size-exclusion fractionation, monitoring on-line the metal signal (Cd, Cu and Zn) by ICP-MS while protein elution was followed by on-line UV detection. MLP fraction was then separated by anion-exchange (AE)-FPLC using optimal chromatographic conditions for the separation of the different MLP isoforms in both snail species. Specific detection of separated metalloforms was carried out again by the hyphenation of the AE chromatographic system with ICP-MS. The determination of the amount of metal bound to MLPs was carried out by post-column isotope dilution analysis ICP-MS, finding that the snail M. cornuarietis accumulated higher concentrations of cadmium than P. bridgesi. Thus this first snail could therefore be a better candidate sentinel organism of pollution in natural waters. Identification and characterization of the isoforms separated in M. cornuarietis was carried out for the entire or intact isoforms by MALDI-TOF and then conventional triptic digestion was also carried out to identify the nature of the formed peptides. The presence identification of a MLP isoform of relatively low molecular weight in M. cornuarietis is reported.

  6. Investigation into spatial distribution of macroelements in dried drops of albumins and proteins by the methods of atomic-emission multichannel spectrometry

    International Nuclear Information System (INIS)

    Chin', N.Kh.; Zazhogin, A.P.; Bulojchik, Zh.I.; Tanin, A.L.; Pashkovskaya, I.D.; Nechipurenko, N.I.

    2011-01-01

    Based on local analysis of the line intensities of Al, Ca, Mg, and Zn in spectra for the samples of dried drops of egg albumin, the possibility for estimation of the spatial elemental distribution by the drop diameter was demonstrated using the atomic-emission multichannel spectrometry method. It was found that with an increase in the concentration of the elements with a high diffusion coefficient (Ca) diffusion counteracts their carry-over to the boundary of evaporating drops, simultaneously displacing the salts of other elements (Al, Fe, Zn) to the drop periphery. This work shows that excitation of the analyzed surface of a dried protein drop by double laser pulses enables a semi-quantitative estimation of the distribution of essential elements by the drop radius. Such investigations look very promising in search for markers of various diseases and in the development of methods revealing the pathological processes at the preclinical stage, making it possible to look for the causes of the elemental unbalance, to realize a targeted selection of preparations and active additives, to correct the treatment course. (authors)

  7. QM/MM investigation of the reaction rates of substrates of 2,3-dimethylmalate lyase: A catabolic protein isolated from Aspergillus niger.

    Science.gov (United States)

    Chotpatiwetchkul, Warot; Jongkon, Nathjanan; Hannongbua, Supa; Gleeson, M Paul

    2016-07-01

    Aspergillus niger is an industrially important microorganism used in the production of citric acid. It is a common cause of food spoilage and represents a health issue for patients with compromised immune systems. Recent studies on Aspergillus niger have revealed details on the isocitrate lyase (ICL) superfamily and its role in catabolism, including (2R, 3S)-dimethylmalate lyase (DMML). Members of this and related lyase super families are of considerable interest as potential treatments for bacterial and fungal infections, including Tuberculosis. In our efforts to better understand this class of protein, we investigate the catalytic mechanism of DMML, studying five different substrates and two different active site metals configurations using molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. We show that the predicted barriers to reaction for the substrates show good agreement with the experimental kcat values. This results help to confirm the validity of the proposed mechanism and open up the possibility of developing novel mechanism based inhibitors specifically for this target. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. A conformational investigation of propeptide binding to the integral membrane protein γ-glutamyl carboxylase using nanodisc hydrogen exchange mass spectrometry

    DEFF Research Database (Denmark)

    Parker, Christine H; Morgan, Christopher R; Rand, Kasper Dyrberg

    2014-01-01

    Gamma (γ)-glutamyl carboxylase (GGCX) is an integral membrane protein responsible for the post-translational catalytic conversion of select glutamic acid (Glu) residues to γ-carboxy glutamic acid (Gla) in vitamin K-dependent (VKD) proteins. Understanding the mechanism of carboxylation and the rol...

  9. Investigation of protein FTT1103 electroactivity using carbon and mercury electrodes. Surface-inhibition approach for disulfide oxidoreductases using silver amalgam powder

    Czech Academy of Sciences Publication Activity Database

    Večerková, R.; Hernychová, L.; Dobeš, P.; Vrba, J.; Josypčuk, Bohdan; Bartošík, M.; Vacek, J.

    2014-01-01

    Roč. 830, JUN 2014 (2014), s. 23-32 ISSN 0003-2670 Institutional support: RVO:61388955 Keywords : Disulfide bond forming protein * Electrochemical sensing * Membrane proteins Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 4.513, year: 2014

  10. Investigation of in-situ poly(lactic acid)/soy protein concentrate composites: Composite preparation, properties and foam application development

    Science.gov (United States)

    Liu, Bo

    2011-12-01

    In this study, soy protein (SP), the residue of oil crushing, was used for preparation of value-added thermoplastics. Novel poly(lactic acid) (PLA)/soy protein concentrate (SPC) blends were investigated and foaming of the resulting blends was developed. PLA/SPC blends were prepared by twin-screw extrusion and test specimens by injection molding. Unlike the practice elsewhere SP was used as a filler in mixing with other polymers, SPC was processed as a plastic component in blending process in this work. Processing SPC as plastic component, water played an important role in terms of the deformability and the morphology of SP thus the properties of the blends. Plasticization of SP, compatibilization of the blends and structure-property relationship of the PLA/SPC blends were studied. In the literature water and glycerol were often used together in preparing SP plastics or plastic blends, but this study found that this traditional combination did not provide the best results in terms of morphology and mechanical properties. Water is only recommended in plasticizing SP in the blends. This study showed water as a plasticizer was a domain factor on control of morphology and properties of PLA/SPC blends. The due to the evaporation of water after extrusion, SP domain lost its deformability thus resulted in in-situ composites. Interconnected SPC phase structure was achieved by control water content in the pre-formulated SPC and SPC content in the blends. A novel dual compatibilization method was developed to improve the properties of PLA/SPC blends. Poly(2-ethyl-2-oxazoline) was used to improve the dispersion of SPC in the blending stage, and polymeric methylene diphenyl diisocyanate was used to improve the interfacial adhesion between SPC and PLA in the subsequent processing. The result showed excellent mechanical properties and improved thermal properties of PLA/SPC blends. Using processing aids is an effective way to decrease processing temperature and thermal degradation

  11. Investigating the Role of the Host Multidrug Resistance Associated Protein Transporter Family in Burkholderia cepacia Complex Pathogenicity Using a Caenorhabditis elegans Infection Model.

    Science.gov (United States)

    Tedesco, Pietro; Visone, Marco; Parrilli, Ermenegilda; Tutino, Maria Luisa; Perrin, Elena; Maida, Isabel; Fani, Renato; Ballestriero, Francesco; Santos, Radleigh; Pinilla, Clemencia; Di Schiavi, Elia; Tegos, George; de Pascale, Donatella

    2015-01-01

    This study investigated the relationship between host efflux system of the non-vertebrate nematode Caenorhabditis elegans and Burkholderia cepacia complex (Bcc) strain virulence. This is the first comprehensive effort to profile host-transporters within the context of Bcc infection. With this aim, two different toxicity tests were performed: a slow killing assay that monitors mortality of the host by intestinal colonization and a fast killing assay that assesses production of toxins. A Virulence Ranking scheme was defined, that expressed the toxicity of the Bcc panel members, based on the percentage of surviving worms. According to this ranking the 18 Bcc strains were divided in 4 distinct groups. Only the Cystic Fibrosis isolated strains possessed profound nematode killing ability to accumulate in worms' intestines. For the transporter analysis a complete set of isogenic nematode single Multidrug Resistance associated Protein (MRP) efflux mutants and a number of efflux inhibitors were interrogated in the host toxicity assays. The Bcc pathogenicity profile of the 7 isogenic C. elegans MRP knock-out strains functionality was classified in two distinct groups. Disabling host transporters enhanced nematode mortality more than 50% in 5 out of 7 mutants when compared to wild type. In particular mrp-2 was the most susceptible phenotype with increased mortality for 13 out 18 Bcc strains, whereas mrp-3 and mrp-4 knock-outs had lower mortality rates, suggesting a different role in toxin-substrate recognition. The use of MRP efflux inhibitors in the assays resulted in substantially increased (>40% on average) mortality of wild-type worms.

  12. Isolation, crystallization, and investigation of ribosomal protein S8 complexed with specific fragments of rRNA of bacterial or archaeal origin.

    Science.gov (United States)

    Tishchenko, S V; Vassilieva, J M; Platonova, O B; Serganov, A A; Fomenkova, N P; Mudrik, E S; Piendl, W; Ehresmann, C; Ehresmann, B; Garber, M B

    2001-09-01

    The core ribosomal protein S8 binds to the central domain of 16S rRNA independently of other ribosomal proteins and is required for assembling the 30S subunit. It has been shown with E. coli ribosomes that a short rRNA fragment restricted by nucleotides 588-602 and 636-651 is sufficient for strong and specific protein S8 binding. In this work, we studied the complexes formed by ribosomal protein S8 from Thermus thermophilus and Methanococcus jannaschii with short rRNA fragments isolated from the same organisms. The dissociation constants of the complexes of protein S8 with rRNA fragments were determined. Based on the results of binding experiments, rRNA fragments of different length were designed and synthesized in preparative amounts in vitro using T7 RNA-polymerase. Stable S8-RNA complexes were crystallized. Crystals were obtained both for homologous bacterial and archaeal complexes and for hybrid complexes of archaeal protein with bacterial rRNA. Crystals of the complex of protein S8 from M. jannaschii with the 37-nucleotide rRNA fragment from the same organism suitable for X-ray analysis were obtained.

  13. In silico investigation of intronless Rhodopsin-like G-protein coupled receptors (GPCR) in the human genome: features and classification.

    Science.gov (United States)

    Alem, K; Louhichi, A; Ladjama, A; Rebaï, A

    2007-01-01

    The G-protein coupled receptors (GPCRs) form a large protein family in the human genome that have been widely studied and classified into classes and phylogenetic subfamilies. However, there still exist orphan GPCRs that are not classified in any of the known subfamilies and new bioinformatics approaches are still needed to address this issue. One of the interesting features of GPCRs is that a large proportion of these proteins are encoded by intronless genes. In this work, we are interested in the study of Rhodpsin-like GPCRs proteins encoded by this kind of genes. After a manual validation of their gene structure, we studied some of their properties including the number of exons, chromosomal location and protein length. The same trend was found for intronless GPCRs as compared to total GPCRs, particularly the uneven chromosomal distribution with a large number (one third) of GPCRs on chromosomes 1 and 11. The proportion of intronless GPCRs among all Rhdopsin-like GPCRs was estimated to about 26% which is significantly less than previously reported. Significant differences in protein length were found between subfamilies. We then used composition properties of DNA and protein sequences to classify intronless Rhodopsin-like GPCRs. Principal component analysis was used to identify key variable and then a discriminant analysis was used to compute discriminant functions that best separates the phylogenetic subfamilies. We found that the most important features to separates the groups is the proportion of aromatic amino acids in protein sequence and the contrast between (A+T) versus (G+C) in coding sequence. These functions are finally used to classify fourteen putative or unclassified GPCRs.

  14. Robust high-yield methodologies for (2)H and (2)H/(15)N/(13)C labeling of proteins for structural investigations using neutron scattering and NMR.

    Science.gov (United States)

    Duff, Anthony P; Wilde, Karyn L; Rekas, Agata; Lake, Vanessa; Holden, Peter J

    2015-01-01

    We have developed a method that has proven highly reliable for the deuteration and triple labeling ((2)H/(15)N/(13)C) of a broad range of proteins by recombinant expression in Escherichia coli BL21. Typical biomass yields are 40-80g/L wet weight, yielding 50-500mg/L purified protein. This method uses a simple, relatively inexpensive defined medium, and routinely results in a high-yield expression without need for optimization. The key elements are very tight control of expression, careful starter culture adaptation steps, media composition, and strict maintenance of aerobic conditions ensuring exponential growth. Temperature is reduced as required to prevent biological oxygen demand exceeding maximum aeration capacity. Glycerol is the sole carbon source. We have not encountered an upper limit for the size of proteins that can be expressed, achieving excellent expression for proteins from 11 to 154kDa and the quantity produced at 1L scale ensures that no small-angle neutron scattering, nuclear magnetic resonance, or neutron crystallography experiment is limited by the amount of deuterated material. Where difficulties remain, these tend to be cases of altered protein solubility due to high protein concentration and a D2O-based environment. © 2015 Elsevier Inc. All rights reserved.

  15. Tau protein

    DEFF Research Database (Denmark)

    Frederiksen, Jette Lautrup Battistini; Kristensen, Kim; Bahl, Jmc

    2011-01-01

    Background: Tau protein has been proposed as biomarker of axonal damage leading to irreversible neurological impairment in MS. CSF concentrations may be useful when determining risk of progression from ON to MS. Objective: To investigate the association between tau protein concentration and 14......-3-3 protein in the cerebrospinal fluid (CSF) of patients with monosymptomatic optic neuritis (ON) versus patients with monosymptomatic onset who progressed to multiple sclerosis (MS). To evaluate results against data found in a complete literature review. Methods: A total of 66 patients with MS and/or ON from...... the Department of Neurology of Glostrup Hospital, University of Copenhagen, Denmark, were included. CSF samples were analysed for tau protein and 14-3-3 protein, and clinical and paraclinical information was obtained from medical records. Results: The study shows a significantly increased concentration of tau...

  16. An epidemiological investigation of a Forkhead box protein E3 founder mutation underlying the high frequency of sclerocornea, aphakia, and microphthalmia in a Mexican village.

    Science.gov (United States)

    Pantoja-Melendez, Carlos; Ali, Manir; Zenteno, Juan C

    2013-01-01

    To investigate the molecular epidemiological basis for the unusually high incidence of sclerocornea, aphakia, and microphthalmia in a village in the Tlaxcala province of central Mexico. A population census was performed in a village to identify all sclerocornea, aphakia, and microphthalmia cases. Molecular analysis of the previously identified Forkhead box protein E3 (FOXE3) mutation, c.292T>C (p.Y98H), was performed with PCR amplification and direct DNA sequencing. In addition, DNA from 405 randomly selected unaffected villagers was analyzed to establish the carrier frequency of the causal mutation. To identify the number of generations since the mutation arose in the village, 17 polymorphic markers distributed in a region of 6 Mb around the mutated locus were genotyped in the affected individuals, followed by DMLE software analysis to calculate mutation age. A total of 22 patients with sclerocornea, aphakia, and microphthalmia were identified in the village, rendering a disease prevalence of 2.52 cases per 1,000 habitants (1 in 397). The FOXE3 homozygous mutation was identified in all 17 affected subjects who consented to molecular analysis. Haplotype analysis indicated that the mutation arose 5.0-6.5 generations ago (approximately 106-138 years). Among the 405 unaffected villagers who were genotyped, ten heterozygote carriers were identified, yielding a population carrier frequency of approximately 1 in 40 and a predicted incidence of affected of 1 in 6,400 based on random marriages between two carriers in the village. This study demonstrates that a cluster of patients with sclerocornea, aphakia, and microphthalmia in a small Mexican village is due to a FOXE3 p.Y98H founder mutation that arose in the village just over a century ago at a time when a population migrated from a nearby village because of land disputes. The actual disease incidence is higher than the calculated predicted value and suggests non-random marriages (i.e., consanguinity) within the

  17. Salt effects on the picosecond dynamics of lysozyme hydration water investigated by terahertz time-domain spectroscopy and an insight into the Hofmeister series for protein stability and solubility.

    Science.gov (United States)

    Aoki, Katsuyoshi; Shiraki, Kentaro; Hattori, Toshiaki

    2016-06-01

    The addition of salts into protein aqueous solutions causes changes in protein solubility and stability, whose ability is known to be ordered in the Hofmeister series. We investigated the effects of Hofmeister salts on the picosecond dynamics of water around a lysozyme molecule using terahertz time-domain spectroscopy. The change in the absorption coefficient for 200 mg mL(-1) lysozyme aqueous solution by the addition of salts was found to depend on the salts used, whereas that for pure water was almost independent of salts. From the difference in the salt concentration dependence for various salts, it has been found that chaotropic anions make the dynamics of water around the lysozyme molecule slower, whereas kosmotropic anions make the dynamics faster. The ability of an anion to slow down the water dynamics was found to have the following order: SCN(-) > Cl(-) > H2PO4(-) > NO3(-) ≈ SO4(2-). This result indicates that the effects of anions on the dynamics of water around the lysozyme molecule are the opposite of those for bulk water. This finding agrees with a prediction from a molecular model proposed by Collins [K. D. Collins, Methods, 2004, 34, 300]. The results presented here are compared with the results from preferential interaction studies and the results from sum frequency generation spectroscopy. These discussions have led to the conclusion that the picosecond dynamics of protein hydration water strongly contributes to protein stability, whereas electrostatic interactions between protein molecules contribute to protein solubility.

  18. Investigations on early reactions of lymphocyte proteins on gamma irradiation of human blood and their dose dependence. Preconditions for the development of an individual radiobiological dosimeter

    International Nuclear Information System (INIS)

    Turtoi, Andrei

    2007-01-01

    The present thesis is concerned with the issues involved in obtaining reliable experimental data permitting a retrospective assessment of radiation-induced doses at the time of application or contamination. In order to provide prompt medical treatment of those injured in accidents with ionizing radiation, biological procedures that can be implemented swiftly and at an early stage are required both to determine the radiation dose originally received as well as to assess the course of the dosedependent biological reactions on the basis of individual sensitivity to radiation. To this end, in the present thesis the lymphocyte proteins (phosphoproteins and total proteins) in blood taken from test subjects who had been exposed to γ-radiation (applied dose: 0-4 Gy) were analysed just 15 minutes after completing irradiation by means of 2D gel electrophoresis. Only those early-response proteins (ERPROs) that displayed a significant radiation-induced change were identified by nano-HPLC-MS/MS. For validation purposes, the dose-dependent gene expression of some of these proteins was determined by RT-qPCR. The following ERPROs displayed pronounced early reactions in the form of changes of concentration in comparison to unirradiated control samples: talin-1, talin-2, β-actin, mutant β-actin, peroxin-1 and also the phosphoproteins annexin-A6, MHCbinding protein-2, zyxin-2, interleukin-17E and phosphoglycerate kinase-1. The majority of the lymphocyte ERPROs represent proteins responsible for changes to the cytoskeleton, proliferation and cell cycle, modulation of immunoreactions as well as protein degradation and energy production. Other cellular processes may not have been determined due to the sensitivity restrictions of the 2DPAGE and MS methods, but cannot be excluded. Gene expression studies revealed that a combination of methods, comprising RT-qPCR and 2D-PAGE as well as DNA microarray and Western blot, may in future be able to overcome these restrictions. The slopes of

  19. Synergic Investigation Of The Self-Assembly Structure And Mechanism Of Retroviral Capsid Proteins By Solid State NMR, Transmission Electron Microscopy And Multiscale simulation

    Science.gov (United States)

    2017-03-29

    manifestation of structural rearrangements, are likely a consequence of the localized large change of torsion angles of the loops between helices, interdomain...structures of native HIV-1 capsid protein reveal conformational variability, Science, 349 (2015) 99-103. [32] T.R. Gamble , S.H. Yoo, F.F. Vajdos, U.K

  20. Theoretical investigation on structural, functional and epitope of a 12 kDa excretory-secretory protein from Toxoplasma gondii

    Directory of Open Access Journals (Sweden)

    Tommy Yap Boon Wooi

    2012-11-01

    Full Text Available Abstract Background Toxoplasma gondii is an intracellular coccidian parasite that causes toxoplasmosis. It was estimated that more than one third of the world population is infected by T. gondii, and the disease is critical in fetuses and immunosuppressed patients. Thus, early detection is crucial for disease diagnosis and therapy. However, the current available toxoplasmosis diagnostic tests vary in their accuracy and the better ones are costly. Results An earlier published work discovered a highly antigenic 12 kDa excretory-secretory (ES protein of T. gondii which may potentially be used for the development of an antigen detection test for toxoplasmosis. However, the three-dimensional structure of the protein is unknown. Since epitope identification is important prior to designing of a specific antibody for an antigen-detection based diagnostic test, the structural elucidation of this protein is essential. In this study, we constructed a three dimensional model of the 12 kDa ES protein. The built structure possesses a thioredoxin backbone which consists of four α-helices flanking five β-strands at the center. Three potential epitopes (6–8 residues which can be combined into one “single” epitope have been identified from the built structure as the most potential antibody binding site. Conclusion Together with specific antibody design, this work could contribute towards future development of an antigen detection test for toxoplasmosis.

  1. Metabolic studies with L-(1-/sup 14/C)tyrosine for the investigation of a kinetic model to measure protein synthesis rates with PET

    Energy Technology Data Exchange (ETDEWEB)

    Ishiwata, K.; Vaalburg, W.; Elsinga, P.H.; Paans, A.M.; Woldring, M.G.

    1988-04-01

    To evaluate a kinetic model for measuring protein synthesis rates by positron emission tomography (PET) in neoplastic and normal tissue, metabolic studies with L-(1-14C)tyrosine were carried out. As an animal model, rats bearing Walker 256 carcinosarcoma were used. Within 60 min after injection, several metabolic parameters were measured. The highest radioactivity uptake, expressed as the differential absorption ratio, was found in pancreas, followed by liver, tumor, and brain. A rapid decarboxylation was observed during the first 15 min. After 60 min, 7.4% of the total injected 14C was expired as 14CO2. In plasma a significant amount of (14C)bicarbonate was detected, but in tissue the amount was negligible. Protein incorporation increased with time. The incorporation rate was the highest in the liver followed by pancreas, tumor, and brain tissues. At 60 min after injection, more than approximately 80% of the 14C in tissue was protein bound. In plasma after a rapid clearance during the first 15 min, the total 14C level increased rapidly and paralleled the increase of protein-bound 14C. As nonprotein (14C)metabolites, in plasma, tumor and brain tissues, p-hydroxyphenylpyruvic acid, p-hydroxyphenyllactic acid, and unidentified metabolites were observed by high performance liquid chromatography. The formation of 14C-labeled 3,4-dihydroxyphenylalanine was found to be negligible. The total amount of these nonprotein metabolites increased with time. At 60 min after injection the percentages of the total nonprotein metabolites and (14C)bicarbonate were only 5.0%, 1.9%, and 3.7% in plasma, tumor and brain tissue, respectively. From our data it is concluded that (11C)carboxylic-labeled tyrosine would be a suitable radiopharmaceutical for measuring protein synthesis rates in neoplastic and normal tissue by PET.

  2. Investigation on the effects of dietary protein reduction with constant ratio of digestible sulfur amino acids and threonine to lysine on performance, egg quality and protein retention in two strains of laying hens

    Directory of Open Access Journals (Sweden)

    Farhad Foroudi

    2013-01-01

    Full Text Available An experiment was conducted to determine the possibility of using various levels of crude protein (CP by providing laying hens with constant levels of digestible sulfur amino acid, threonine and lysine to improve performance and egg quality. The experiment was conducted as a completely randomized block design in a factorial arrangement (4 × 2 with 8 replicates of 10 hens in each. Factors included 4 levels of CP (18.5%, 17.5%, 16.5% and 15.5% and 2 strains (LSL and Hy-Line W-36 of laying hens. Hens were fed experimental diets from 25 to 33 weeks of age. Production performance was measured for eight weeks and egg quality characteristics were determined at 29 and 33 weeks of age. Protein reduction decreased egg weight, egg mass and hen body weight linearly (P≤0.01. Egg production was not affected by protein reduction but feed efficiency, and average daily feed intake increased significantly (P≤0.01. Lohmann Selected Leghorn laying hens showed significantly higher egg production, egg weight, egg mass, weight gain, feed efficiency and feed intake compared to the W-36 laying hens (P≤0.01. Shell thickness increased linearly as protein levels decreased (P≤0.05. There were significant differences between two strains on the egg quality characteristics (P≤0.01. Significant (P≤0.05 CP × strain interactions were observed for hen weight, albumen height, Haugh units, yolk and shell percentage. Based on the results of this experiment, a reduction in dietary protein level (from 18.5% to 15.5%, without any alteration in digestible TSAA and Thr: Lys ratio, led to inferior egg mass and feed conversion ratio during the peak production period.

  3. Attenuated Total Reflection Fourier Transform Infrared (ATR FT-IR) Spectroscopy as an Analytical Method to Investigate the Secondary Structure of a Model Protein Embedded in Solid Lipid Matrices.

    Science.gov (United States)

    Zeeshan, Farrukh; Tabbassum, Misbah; Jorgensen, Lene; Medlicott, Natalie J

    2018-02-01

    Protein drugs may encounter conformational perturbations during the formulation processing of lipid-based solid dosage forms. In aqueous protein solutions, attenuated total reflection Fourier transform infrared (ATR FT-IR) spectroscopy can investigate these conformational changes following the subtraction of spectral interference of solvent with protein amide I bands. However, in solid dosage forms, the possible spectral contribution of lipid carriers to protein amide I band may be an obstacle to determine conformational alterations. The objective of this study was to develop an ATR FT-IR spectroscopic method for the analysis of protein secondary structure embedded in solid lipid matrices. Bovine serum albumin (BSA) was chosen as a model protein, while Precirol AT05 (glycerol palmitostearate, melting point 58 ℃) was employed as the model lipid matrix. Bovine serum albumin was incorporated into lipid using physical mixing, melting and mixing, or wet granulation mixing methods. Attenuated total reflection FT-IR spectroscopy and size exclusion chromatography (SEC) were performed for the analysis of BSA secondary structure and its dissolution in aqueous media, respectively. The results showed significant interference of Precirol ATO5 with BSA amide I band which was subtracted up to 90% w/w lipid content to analyze BSA secondary structure. In addition, ATR FT-IR spectroscopy also detected thermally denatured BSA solid alone and in the presence of lipid matrix indicating its suitability for the detection of denatured protein solids in lipid matrices. Despite being in the solid state, conformational changes occurred to BSA upon incorporation into solid lipid matrices. However, the extent of these conformational alterations was found to be dependent on the mixing method employed as indicated by area overlap calculations. For instance, the melting and mixing method imparted negligible effect on BSA secondary structure, whereas the wet granulation mixing method promoted

  4. Computational Approaches for Designing Protein/Inhibitor Complexes and Membrane Protein Variants

    Science.gov (United States)

    Vijayendran, Krishna Gajan

    Drug discovery of small-molecule protein inhibitors is a vast enterprise that involves several scientific disciplines (i.e. genomics, cell biology, x-ray crystallography, chemistry, computer science, statistics), with each discipline focusing on a particular aspect of the process. In this thesis, I use computational and experimental approaches to explore the most fundamental aspect of drug discovery: the molecular interactions of small-molecules inhibitors with proteins. In Part I (Chapters I and II), I describe how computational docking approaches can be used to identify structurally diverse molecules that can inhibit multiple protein targets in the brain. I illustrate this approach using the examples of microtubule-stabilizing agents and inhibitors of cyclooxygenase(COX)-I and 5-lipoxygenase (5-LOX). In Part II (Chapters III and IV), I focus on membrane proteins, which are notoriously difficult to work with due to their low natural abundances, low yields for heterologous over expression, and propensities toward aggregation. I describe a general approach for designing water-soluble variants of membrane proteins, for the purpose of developing cell-free, label-free, detergent-free, solution-phase studies of protein structure and small-molecule binding. I illustrate this approach through the design of a water-soluble variant of the membrane protein Smoothened, wsSMO. This wsSMO stands to serve as a first-step towards developing membrane protein analogs of this important signaling protein and drug target.

  5. Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L..

    Directory of Open Access Journals (Sweden)

    Mukesh Kumar Meena

    Full Text Available Calcium ion (Ca2+ is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

  6. Investigation of genes encoding calcineurin B-like protein family in legumes and their expression analyses in chickpea (Cicer arietinum L.).

    Science.gov (United States)

    Meena, Mukesh Kumar; Ghawana, Sanjay; Sardar, Atish; Dwivedi, Vikas; Khandal, Hitaishi; Roy, Riti; Chattopadhyay, Debasis

    2015-01-01

    Calcium ion (Ca2+) is a ubiquitous second messenger that transmits various internal and external signals including stresses and, therefore, is important for plants' response process. Calcineurin B-like proteins (CBLs) are one of the plant calcium sensors, which sense and convey the changes in cytosolic Ca2+-concentration for response process. A search in four leguminous plant (soybean, Medicago truncatula, common bean and chickpea) genomes identified 9 to 15 genes in each species that encode CBL proteins. Sequence analyses of CBL peptides and coding sequences (CDS) suggested that there are nine original CBL genes in these legumes and some of them were multiplied during whole genome or local gene duplication. Coding sequences of chickpea CBL genes (CaCBL) were cloned from their cDNAs and sequenced, and their annotations in the genome assemblies were corrected accordingly. Analyses of protein sequences and gene structures of CBL family in plant kingdom indicated its diverse origin but showed a remarkable conservation in overall protein structure with appearance of complex gene structure in the course of evolution. Expression of CaCBL genes in different tissues and in response to different stress and hormone treatment were studied. Most of the CaCBL genes exhibited high expression in flowers. Expression profile of CaCBL genes in response to different abiotic stresses and hormones related to development and stresses (ABA, auxin, cytokinin, SA and JA) at different time intervals suggests their diverse roles in development and plant defence in addition to abiotic stress tolerance. These data not only contribute to a better understanding of the complex regulation of chickpea CBL gene family, but also provide valuable information for further research in chickpea functional genomics.

  7. Investigation of the effect of recombinant Neutrophil activating protein (Hp-NapA of helicobacter pylori on proliferation and viability by peritoneal macrophage from BALB/c mice

    Directory of Open Access Journals (Sweden)

    Soleimani N

    2015-04-01

    Full Text Available Abstract Background: The neutrophil-activating protein (HP-NAP of Helicobacter pylori is a protective antigen and a major virulence factor of this bacteria. Stimulating the immune system for helicobacter infection treatment could have an important role. The aim of study is to assess the effect of recombinant Neutrophil activating protein (Hp-NapA of helicobacter pylori on proliferation and viability of peritoneal macrophages from BALB/c mice. Materials and Methods: In this experimental study, recombinant Hp-NapA of helicobacter pylori was produced in vitro. Mice peritoneal macrophages were purified and cultured. Different concentrations of recombinant Hp-NapA was used for macrophages stimulation. MTT assay was performed to assess the viability and proliferation of macrophages. Results: The results elucidated that the increasing effect of stimulation with recombinant Hp-NapA was significant at the dose of 30 µg/ml(p=0.01. The rate of viabitity was significantly higher than control group at the doses of 30 and 60 µg/ml and in the concurrency series of recombinant protein with lipopolysaccharid, there was a statistically significarit increase in proliferation at just these doses. Conclusion: According to our findings, recombinant Hp-NapA has a positive effect on proliferation, viability and function of peritoneal macrophages. Therefore, it is proposed that recombinant Hp-NapA can be studied as an immunomodulator for immunotherapy.

  8. Investigating possible biological targets of Bj-CRP, the first cysteine-rich secretory protein (CRISP) isolated from Bothrops jararaca snake venom.

    Science.gov (United States)

    Lodovicho, Marina E; Costa, Tássia R; Bernardes, Carolina P; Menaldo, Danilo L; Zoccal, Karina F; Carone, Sante E; Rosa, José C; Pucca, Manuela B; Cerni, Felipe A; Arantes, Eliane C; Tytgat, Jan; Faccioli, Lúcia H; Pereira-Crott, Luciana S; Sampaio, Suely V

    2017-01-04

    Cysteine-rich secretory proteins (CRISPs) are commonly described as part of the protein content of snake venoms, nevertheless, so far, little is known about their biological targets and functions. Our study describes the isolation and characterization of Bj-CRP, the first CRISP isolated from Bothrops jararaca snake venom, also aiming at the identification of possible targets for its actions. Bj-CRP was purified using three chromatographic steps (Sephacryl S-200, Source 15Q and C18) and showed to be an acidic protein of 24.6kDa with high sequence identity to other snake venom CRISPs. This CRISP was devoid of proteolytic, hemorrhagic or coagulant activities, and it did not affect the currents from 13 voltage-gated potassium channel isoforms. Conversely, Bj-CRP induced inflammatory responses characterized by increase of leukocytes, mainly neutrophils, after 1 and 4h of its injection in the peritoneal cavity of mice, also stimulating the production of IL-6. Bj-CRP also acted on the human complement system, modulating some of the activation pathways and acting directly on important components (C3 and C4), thus inducing the generation of anaphylatoxins (C3a, C4a and C5a). Therefore, our results for Bj-CRP open up prospects for better understanding this class of toxins and its biological actions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  9. Investigations on the use of graphite electrodes using a Hull-type growth cell for the electrochemically-assisted protein crystallization

    Science.gov (United States)

    Espinoza-Montero, Patricio J.; Moreno-Narváez, María Esther; Frontana-Uribe, Bernardo A.; Stojanoff, Vivian; Moreno, Abel

    2012-01-01

    This paper describes the use of an electrochemical Hull type cell adapted for protein crystallization evaluating three inclination angles (45°, 60° and 90°). For optimization experiments, classical platinum wire electrodes were used and once the best geometry was known, they were replaced with 0.5 mm diameter low-cost graphite automatic pencil leads. Using Pt and graphite, the cell with electrodes fitted at 90° showed the most favorable geometry for promoting the growth of lysozyme crystals with enough size for protein crystallography (between 200–250 μm in solution, and between 500–650 μm in gel). The crystalline quality (mosaicity and I/σ(I) ratio) of crystals obtained at different current values, was studied using these graphite electrodes and was compared with those protein crystals grown using platinum wire electrodes in solution as well as in gel experiments. These studies showed that it is possible to efficiently substitute the platinum electrodes by the low-cost graphite electrodes. This cell could be a first approach to a disposable cell for a large-scale use of electrochemically-assisted crystal growth method. PMID:24659923

  10. Analysis of high school students’ conceptual maps to investigate their understanding of DNA-RNA protein relation after accessing the GenBank

    Directory of Open Access Journals (Sweden)

    Rosane Teresinha Nascimento da Rosa

    2013-08-01

    Full Text Available This article presents an analysis of conceptual maps elaborated by high school students during the application of a didactic unit (DU about synthesis of protein. One of the activities in this DU involved the supervised access to the GenBank, a database for genes and DNA sequences available, at the National Center Biotechnology Information (NCBI, website. The purpose of this study was to check the students’ understanding of DNA-RNA-protein relation through the elaboration of conceptual maps. These maps were developed at the end of the DU by six volunteer students from grade 10 at the Militar School (CMSM, in Santa Maria, RS, Brazil. This DU was developed, outside of regular, school activities time. For the analysis of the conceptual maps, a score table proposed by Novak and Gowin (1996 was used. The model conceptual map had 52 points; in our study, two students got score 41, others three got 26, 10, 2 points and only one had no score. In the quantitative and in the qualitative analyses it was possible to indentify a significant improvement in these students´ conceptual relations about protein synthesis. The data suggest that the access to the GenBank, used as a didactic strategy in the DU, has made this improvement possible.

  11. Functional investigation of the plant-specific long coiled-coil proteins PAMP-INDUCED COILED-COIL (PICC and PICC-LIKE (PICL in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Sowmya Venkatakrishnan

    Full Text Available We have identified and characterized two Arabidopsis long coiled-coil proteins PAMP-INDUCED COILED-COIL (PICC and PICC-LIKE (PICL. PICC (147 kDa and PICL (87 kDa are paralogs that consist predominantly of a long coiled-coil domain (expanded in PICC, with a predicted transmembrane domain at the immediate C-terminus. Orthologs of PICC and PICL were found exclusively in vascular plants. PICC and PICL GFP fusion proteins are anchored to the cytoplasmic surface of the endoplasmic reticulum (ER membrane by a C-terminal transmembrane domain and a short tail domain, via a tail-anchoring mechanism. T-DNA-insertion mutants of PICC and PICL as well as the double mutant show an increased sensitivity to the plant abiotic stress hormone abscisic acid (ABA in a post-germination growth response. PICC, but not PICL gene expression is induced by the bacterial pathogen-associated molecular pattern (PAMP flg22. T-DNA insertion alleles of PICC, but not PICL, show increased susceptibility to the non-virulent strain P. syringae pv. tomato DC3000 hrcC, but not to the virulent strain P. syringae pv. tomato DC3000. This suggests that PICC mutants are compromised in PAMP-triggered immunity (PTI. The data presented here provide first evidence for the involvement of a plant long coiled-coil protein in a plant defense response.

  12. Functional investigation of the plant-specific long coiled-coil proteins PAMP-INDUCED COILED-COIL (PICC) and PICC-LIKE (PICL) in Arabidopsis thaliana.

    Science.gov (United States)

    Venkatakrishnan, Sowmya; Mackey, David; Meier, Iris

    2013-01-01

    We have identified and characterized two Arabidopsis long coiled-coil proteins PAMP-INDUCED COILED-COIL (PICC) and PICC-LIKE (PICL). PICC (147 kDa) and PICL (87 kDa) are paralogs that consist predominantly of a long coiled-coil domain (expanded in PICC), with a predicted transmembrane domain at the immediate C-terminus. Orthologs of PICC and PICL were found exclusively in vascular plants. PICC and PICL GFP fusion proteins are anchored to the cytoplasmic surface of the endoplasmic reticulum (ER) membrane by a C-terminal transmembrane domain and a short tail domain, via a tail-anchoring mechanism. T-DNA-insertion mutants of PICC and PICL as well as the double mutant show an increased sensitivity to the plant abiotic stress hormone abscisic acid (ABA) in a post-germination growth response. PICC, but not PICL gene expression is induced by the bacterial pathogen-associated molecular pattern (PAMP) flg22. T-DNA insertion alleles of PICC, but not PICL, show increased susceptibility to the non-virulent strain P. syringae pv. tomato DC3000 hrcC, but not to the virulent strain P. syringae pv. tomato DC3000. This suggests that PICC mutants are compromised in PAMP-triggered immunity (PTI). The data presented here provide first evidence for the involvement of a plant long coiled-coil protein in a plant defense response.

  13. Functional Investigation of the Plant-Specific Long Coiled-Coil Proteins PAMP-INDUCED COILED-COIL (PICC) and PICC-LIKE (PICL) in Arabidopsis thaliana

    Science.gov (United States)

    Venkatakrishnan, Sowmya; Mackey, David; Meier, Iris

    2013-01-01

    We have identified and characterized two Arabidopsis long coiled-coil proteins PAMP-INDUCED COILED-COIL (PICC) and PICC-LIKE (PICL). PICC (147 kDa) and PICL (87 kDa) are paralogs that consist predominantly of a long coiled-coil domain (expanded in PICC), with a predicted transmembrane domain at the immediate C-terminus. Orthologs of PICC and PICL were found exclusively in vascular plants. PICC and PICL GFP fusion proteins are anchored to the cytoplasmic surface of the endoplasmic reticulum (ER) membrane by a C-terminal transmembrane domain and a short tail domain, via a tail-anchoring mechanism. T-DNA-insertion mutants of PICC and PICL as well as the double mutant show an increased sensitivity to the plant abiotic stress hormone abscisic acid (ABA) in a post-germination growth response. PICC, but not PICL gene expression is induced by the bacterial pathogen-associated molecular pattern (PAMP) flg22. T-DNA insertion alleles of PICC, but not PICL, show increased susceptibility to the non-virulent strain P. syringae pv. tomato DC3000 hrcC, but not to the virulent strain P. syringae pv. tomato DC3000. This suggests that PICC mutants are compromised in PAMP-triggered immunity (PTI). The data presented here provide first evidence for the involvement of a plant long coiled-coil protein in a plant defense response. PMID:23451199

  14. What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae?

    OpenAIRE

    Ekman, Diana; Light, Sara; Bj?rklund, ?sa K; Elofsson, Arne

    2006-01-01

    Background Most proteins interact with only a few other proteins while a small number of proteins (hubs) have many interaction partners. Hub proteins and non-hub proteins differ in several respects; however, understanding is not complete about what properties characterize the hubs and set them apart from proteins of low connectivity. Therefore, we have investigated what differentiates hubs from non-hubs and static hubs (party hubs) from dynamic hubs (date hubs) in the protein-protein interact...

  15. Protein Foods

    Science.gov (United States)

    ... Text Size: A A A Listen En Español Protein Foods Foods high in protein such as fish, ... for the vegetarian proteins, whether they have carbohydrate. Protein Choices Plant-Based Proteins Plant-based protein foods ...

  16. Investigation of free fatty acid associated recombinant membrane receptor protein expression in HEK293 cells using Raman spectroscopy, calcium imaging, and atomic force microscopy.

    Science.gov (United States)

    Lin, Juqiang; Xu, Han; Wu, Yangzhe; Tang, Mingjie; McEwen, Gerald D; Liu, Pin; Hansen, Dane R; Gilbertson, Timothy A; Zhou, Anhong

    2013-02-05

    G-protein-coupled receptor 120 (GPR120) is a previously orphaned G-protein-coupled receptor that apparently functions as a sensor for dietary fat in the gustatory and digestive systems. In this study, a cDNA sequence encoding a doxycycline (Dox)-inducible mature peptide of GPR120 was inserted into an expression vector and transfected in HEK293 cells. We measured Raman spectra of single HEK293 cells as well as GPR120-expressing HEK293-GPR120 cells at a 48 h period following the additions of Dox at several concentrations. We found that the spectral intensity of HEK293-GPR120 cells is dependent upon the dose of Dox, which correlates with the accumulation of GPR120 protein in the cells. However, the amount of the fatty acid activated changes in intracellular calcium (Ca(2+)) as measured by ratiometric calcium imaging was not correlated with Dox concentration. Principal components analysis (PCA) of Raman spectra reveals that the spectra from different treatments of HEK293-GPR120 cells form distinct, completely separated clusters with the receiver operating characteristic (ROC) area of 1, while those spectra for the HEK293 cells form small overlap clusters with the ROC area of 0.836. It was also found that expression of GPR120 altered the physiochemical and biomechanical properties of the parental cell membrane surface, which was quantitated by atomic force microscopy (AFM). These findings demonstrate that the combination of Raman spectroscopy, calcium imaging, and AFM may provide new tools in noninvasive and quantitative monitoring of membrane receptor expression induced alterations in the biophysical and signaling properties of single living cells.

  17. Infants and children with cow milk allergy/intolerance. Investigation of the uptake of cow milk protein and activation of the complement system

    DEFF Research Database (Denmark)

    Husby, S; Høst, A; Teisner, B

    1990-01-01

    and up to 24 h after the start of the challenge. The cow milk protein beta-lactoglobulin (BLG) was determined in serum with ELISA (lower detection limit 0.3 micrograms/l). BLG was detectable in five children at low levels (below 2 micrograms/l). Analysis of the size distribution of the BLG by size......Seventeen children with challenge-verified cow milk allergy/intolerance (CMAI), age 3-78 months, median 12 months, were re-challenged with cow milk in increasing doses. All subjects developed symptoms, such as bronchospasm, rhinitis, diarrhoea, erythema or eczema. Blood samples were taken before...

  18. Investigation on Secondary Structure Perturbations of Proteins Embedded in Solid Lipid Matrices as a Novel Indicator of their Biological Activity upon In Vitro Release

    DEFF Research Database (Denmark)

    Zeeshan, Farrukh; Tabbassum, Misbah; Jorgensen, Lene

    2018-01-01

    encased in solid lipid matrices as a novel indicator of their stability upon in vitro release. Model proteins namely catalase and lysozyme were incorporated into lipid namely Precirol® AT05 (glycerol palmitostearate, melting point 58°C) at 30% w/w loading using melting and mixing and wet granulation...... aggregation for catalase which was increased using wet granulation. The biological activity of catalase was statistically different from that of control and was affected by the incorporation method and was found to be in alignment with ATR spectral changes and extent of aggregation. In conclusion, ATR...

  19. Infants and children with cow milk allergy/intolerance. Investigation of the uptake of cow milk protein and activation of the complement system

    DEFF Research Database (Denmark)

    Husby, S; Høst, A; Teisner, B

    1990-01-01

    Seventeen children with challenge-verified cow milk allergy/intolerance (CMAI), age 3-78 months, median 12 months, were re-challenged with cow milk in increasing doses. All subjects developed symptoms, such as bronchospasm, rhinitis, diarrhoea, erythema or eczema. Blood samples were taken before...... and up to 24 h after the start of the challenge. The cow milk protein beta-lactoglobulin (BLG) was determined in serum with ELISA (lower detection limit 0.3 micrograms/l). BLG was detectable in five children at low levels (below 2 micrograms/l). Analysis of the size distribution of the BLG by size...

  20. Crystallization and preliminary X-ray crystallographic investigations on a βγ-crystallin domain of absent in melanoma 1 (AIM1), a protein from Homo sapiens

    Energy Technology Data Exchange (ETDEWEB)

    Aravind, Penmatsa; Rajini, Bheemreddy; Sharma, Yogendra; Sankaranarayanan, Rajan, E-mail: sankar@ccmb.res.in [Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500 007 (India)

    2006-03-01

    The crystallization and preliminary X-ray diffraction analysis of AIM1g1, a βγ-crystallin domain of absent in melanoma (AIM1) protein from H. sapiens, is reported. AIM1g1 is a single βγ-crystallin domain from the protein absent in melanoma 1 (AIM1), which appears to play a role in the suppression of melanomas. This domain is known to bind calcium and its structure would help in identifying calcium-coordinating sites in vertebrate crystallins, which have hitherto been believed to have lost this ability during evolution. Crystallization of this domain was performed by the hanging-drop vapour-diffusion method. Crystals diffracted to a maximum resolution of 1.86 Å and were found to belong to space group P6{sub 1} or P6{sub 5}, with unit-cell parameters a = b = 54.98, c = 59.73 Å. Solvent-content analysis indicated the presence of one monomer per asymmetric unit.

  1. Investigation of the interaction between Tc85-11 protein and antibody anti-T. cruzi by AFM and amperometric measurements

    Energy Technology Data Exchange (ETDEWEB)

    Ferreira, A.A.P. [UNESP, Institute of Chemistry, CP 355, 14801-970 Araraquara, SP (Brazil); Colli, W. [USP, Institute of Chemistry, Av. Prof. Lineu Prestes 748, 05508-900 Sao Paulo, SP (Brazil); Alves, M.J.M. [USP, Institute of Chemistry, Av. Prof. Lineu Prestes 748, 05508-900 Sao Paulo, SP (Brazil); Oliveira, D.R. [USP, Institute of Chemistry, Av. Prof. Lineu Prestes 748, 05508-900 Sao Paulo, SP (Brazil); Costa, P.I. [UNESP, Faculty of Pharmaceutical Sciences, Rodovia Araraquara/Jau Km 1, 14801-902 Araraquara, SP (Brazil); Gueell, A.G. [CBEN, University of Barcelona, Scientific Park of Barcelona, C/ Josep Samitier 1-5, 08028 Barcelona (Spain); Sanz, F. [CBEN, University of Barcelona, Scientific Park of Barcelona, C/ Josep Samitier 1-5, 08028 Barcelona (Spain); Benedetti, A.V. [UNESP, Institute of Chemistry, CP 355, 14801-970 Araraquara, SP (Brazil); Yamanaka, H. [UNESP, Institute of Chemistry, CP 355, 14801-970 Araraquara, SP (Brazil)]. E-mail: hidekoy@iq.unesp.br

    2006-07-15

    This present work reports on development of an amperometric immunosensor for the diagnosis of Chagas' disease using a specific glycoprotein of the trypomastigote surface, which belongs to the Tc85-11 protein family of Trypanosoma cruzi (T. cruzi). An atomically flat gold surface on a silicon substrate and gold screen-printed electrodes were functionalized with cystamine and later activated with glutaraldehyde (GA), which was used to form covalent bonds with the purified recombinant antigen (Tc85-11). The antigen reacts with the antibody from the serum, and the affinity reaction was monitored directly using atomic force microscopy or amperometry through a secondary antibody tagged to peroxidase (HRP). Surface imaging allowed to us to differentiate the modification steps and antigen-antibody interaction allowed to distinguish the affinity reactions. In the amperometric immunosensor, peroxidase catalyses the L{sub 2} formation in the presence of hydrogen peroxide and potassium iodide, and the reduction current intensity was measured at a given potential with screen-printed electrodes. The immunosensor was applied to sera of chagasic patients and patients having different systemic diseases.

  2. Inverse association between intelligence quotient and urinary retinol binding protein in Chinese school-age children with low blood lead levels: results from a cross-sectional investigation.

    Science.gov (United States)

    Sun, Hong; Chen, Wen; Wang, Dongyue; Jin, Yinlong; Chen, Xiaodong; Xu, Yan; Huang, Lei

    2015-06-01

    Examine the relationship between blood lead concentration and children's intelligence quotient (IQ) in Chinese children 8-12 years old. This is a cross-sectional study, and participants included 446 children from three primary schools in Jiangsu, China. We collected environmental and genetic information from questionnaires. Blood lead (Pb), manganese (Mn), cadmium (Cd) and selenium (Se) concentrations were measured using inductively coupled plasma mass spectrometry (ICP-MS). IQ was assessed using the Combined Raven's Test and then converted to a standard IQ score according to Chinese children's norm. Morning urine samples were collected to measure retinol binding protein (RBP). The average blood lead concentration was 33.13 μg L(-1) (geometric mean), and the blood lead concentration (BoxCox transform) was inversely and significantly associated with IQ (r=-0.11, p=0.02). The geometric mean of blood Mn, Cd and Se was 7.02 μg L(-1), 0.18 μg L(-1) and 94.77 μg L(-1), respectively. Blood Mn, Cd and Se showed no association with IQ, but all of them associated with urinary RBP. Urinary RBP was identified as a new factor associated with IQ (β=-6.49, p=0.011). Urinary RBP was recognized as a new indicated factor associated with children's IQ. Mn, Cd and Se exposure might affect urinary RBP concentration and further IQ. Findings also support that blood lead concentrations in 8-12 years old children, even IQ. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Investigation of Fasciculation and Elongation Protein ζ-1 (FEZ1 in Peripheral Blood Reveals Differences in Gene Expression in Patients with Schizophrenia

    Directory of Open Access Journals (Sweden)

    Vachev T.I.

    2015-06-01

    Full Text Available Schizophrenia (SZ is a chronic neuropsychiatric disorder characterized by affective, neuromorphological and cognitive impairment, deteriorated social functioning and psychosis with underlying molecular abnormalities, including gene expression changes. Observations have suggested that fasciculation and elongation protein ζ-1 (FEZ1 may be implicated in the pathogenesis of schizophrenia. Nevertheless, our current knowledge of the expression of FEZ1 in peripheral blood of schizophrenia patients remains unclear. The purpose of this study was to identify the characteristic gene expression patterns of FEZ1 in peripheral blood samples from schizophrenia patients. We performed quantitative reverse-transcriptase (qRT-PCR analysis using peripheral blood from drug-free schizophrenia patients (n = 29 and age and gender-matched general population controls (n = 24. For the identification of FEZ1 gene expression patterns, we applied a comparative threshold cycle (CT method. A statistically significant difference of FEZ1 mRNA level was revealed in schizophrenia subjects compared to healthy controls (p = 0.0034. To the best of our knowledge, this study is the first describing a down-regulation of FEZ1 gene expression in peripheral blood of patients with schizophrenia. Our results suggested a possible functional role of FEZ1 in the pathogenesis of schizophrenia and confirmed the utility of peripheral blood samples for molecular profiling of psychiatric disorders including schizophrenia. The current study describes FEZ1 gene expression changes in peripheral blood of patients with schizophrenia with significantly down-regulation of FEZ1 mRNA. Thus, our results provide support for a model of SZ pathogenesis that includes the effects of FEZ1 expression.

  4. Investigation of gene expressions in differentiated cell derived bone marrow stem cells during bone morphogenetic protein-4 treatments with Fourier transform infrared spectroscopy

    Science.gov (United States)

    Zafari, Jaber; Jouni, Fatemeh Javani; Ahmadvand, Ali; Abdolmaleki, Parviz; Soodi, Malihe; Zendehdel, Rezvan

    2017-02-01

    A model was set up to predict the differentiation patterns based on the data extracted from FTIR spectroscopy. For this reason, bone marrow stem cells (BMSCs) were differentiated to primordial germ cells (PGCs). Changes in cellular macromolecules in the time of 0, 24, 48, 72, and 96 h of differentiation, as different steps of the differentiation procedure were investigated by using FTIR spectroscopy. Also, the expression of pluripotency (Oct-4, Nanog and c-Myc) and specific genes (Mvh, Stella and Fragilis) were investigated by real-time PCR. However, the expression of genes in five steps of differentiation was predicted by FTIR spectroscopy. FTIR spectra showed changes in the template of band intensities at different differentiation steps. There are increasing changes in the stepwise differentiation procedure for the ratio area of CH2, which is symmetric to CH2 asymmetric stretching. An ensemble of expert methods, including regression tree (RT), boosting algorithm (BA), and generalized regression neural network (GRNN), was the best method to predict the gene expression by FTIR spectroscopy. In conclusion, the model was able to distinguish the pattern of different steps from cell differentiation by using some useful features extracted from FTIR spectra.

  5. Protein-protein interactions

    DEFF Research Database (Denmark)

    Byron, Olwyn; Vestergaard, Bente

    2015-01-01

    Responsive formation of protein:protein interaction (PPI) upon diverse stimuli is a fundament of cellular function. As a consequence, PPIs are complex, adaptive entities, and exist in structurally heterogeneous interplays defined by the energetic states of the free and complexed protomers......, are reported. The aim is to depict how the elucidation of the interplay of structures requires the interplay of methods....

  6. Evaluation of energy spectral information in nuclear imaging and investigation of protein binding of radiogallium. Progress report, October 1, 1980-September 30, 1981

    International Nuclear Information System (INIS)

    Hoffer, P.B.

    1981-01-01

    Most of the planned modifications on the gamma camera-computer interface are completed. These modifications will allow to determine the contribution of scatter radiation to inaccuracies in cardiac volume and ejection fraction determinations and allow for correction of these inaccuracies. The modifications will also allow testing of the weighted window imaging concept. Specific accomplishments include construction of an energy interface between ZLC-75 camera and DEC gamma 11/34 computer and development and testing of new programs to allow region of interest energy analysis and determination of photopeak and scatter contributions. A new type of converging collimator was built and is being tested which corrects for tissue attenuation at the average cardiac ventricular depth and may prove useful in cardiac chamber volume estimates. A new generator system using a /sup 195m/Hg parent to produce a /sup 195m/Au daughter which will be useful for cardiac studies is being evaluated. The mechanisms by which Ga-67 localizes in abscess and tumor were further elucidated by demonstrating that Ga-67 can transfer from transferrin to ferritin directly. This transfer is facilitated by certain mediators, especially the organic phosphates and does not appear to be energy dependent. A method of labelling viable bacteria with 111 In oxine was developed, and the exact role of siderophores in Ga-67 uptake in bacteria and also Ga-67 uptake in monocytes are being investigated

  7. Molecular characterization of insulin-like androgenic gland hormone-binding protein gene from the oriental river prawn Macrobrachium nipponense and investigation of its transcriptional relationship with the insulin-like androgenic gland hormone gene.

    Science.gov (United States)

    Li, Fajun; Bai, Hongkun; Xiong, Yiwei; Fu, Hongtuo; Jiang, Sufei; Jiang, Fengwei; Jin, Shubo; Sun, Shengming; Qiao, Hui; Zhang, Wenyi

    2015-05-15

    Insulin-like androgenic gland hormone-binding protein (IAGBP) has been investigated in crustaceans in vitro. However, the relationship between IAGBP and its putative binding protein partner insulin-like androgenic gland hormone (IAG) has not been studied at the transcriptional level in vivo. In the current study, we cloned the full-length cDNA of IAGBP from the oriental river prawn Macrobrachium nipponense (Mn-IAGBP) and investigated the transcriptional patterns of Mn-IAGBP and the M. nipponense IAG gene (Mn-IAG) at different developmental stages and in different tissues. Mn-IAGBP mRNA was detected in all examined tissues from adult male prawns, with the highest transcriptional levels in the testis. Mn-IAG mRNA was detected in the androgenic gland and hepatopancreas. The genomic sequences of Mn-IAGBP and Mn-IAG were isolated by genome walking and two gene copies were found in both Mn-IAGBP and Mn-IAG. The relationship between Mn-IAGBP and Mn-IAG at the transcriptional level was studied by RNA interference. Injection of Mn-IAGBP double-stranded RNA (dsRNA) significantly reduced the transcription of Mn-IAG, while injection of Mn-IAG dsRNA significantly reduced the transcription of Mn-IAGBP in testis, muscle, androgenic gland, and hepatopancreas. These results demonstrate the involvement of the IAGBP gene in IAG signaling in M. nipponense. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Evaluation of energy spectral information in nuclear imaging and investigation of protein binding of cationic radionuclides by lactoferrin. Comprehensive progress report, October 1, 1977-September 30, 1980

    Energy Technology Data Exchange (ETDEWEB)

    Hoffer, P. B.

    1980-06-10

    Construction of an Anger camera-computer system which allows collection of both the position and energy signals from events detected by the scintillation camera has been completed. The system allows correction of energy response non-uniformity of the detector and facilitates research related to effects of energy discrimination in radionuclide scintigraphy. The system consists of electronic hardware to transmit and digitize the energy signal, software to record and process that signal in conjunction with spatial positioning signals, and additional hardware for recording the processed images so that they can be evaluated by observers. Preliminary results indicate that the system is useful in evaluating clinical images. Assymetric (eccentric) energy windows do improve image quality and are of value in improving detection of lesions on liver scintigraphs. The mechanisms by which Ga-67 is taken up in infection and tumor has been elucidated, and the uptake of radiogallium in microorganisms as a function of its interaction with siderophores was also studied. The primary function of these low molecular weight compounds is to trap ferric ion. However, gallium may be substituted for ferric ion and becomes trapped within the microorganism. The uptake of radiogallium by neutrophils and the role that lactoferrin plays in both intracellular localization of radiogallium and subsequent deposition of the radionuclide at sites of infection were also studied. Investigation of ferric ion analogs reveals definate differences in the affinity of these metals for binding molecules which helps explain their biologic activity. While ferric ion has the strongest affinity for such molecules, gallium has very high affinity for siderophores, moderate affinity for lactoferrin, and lower affinity for transferrin. The relative affinity of indium for these molecules is in approximately the reverse order.

  9. Investigation of reference gene expression during human herpesvirus 6B infection indicates peptidylprolyl isomerase A as a stable reference gene and TATA box binding protein as a gene up-regulated by this virus.

    Science.gov (United States)

    Engdahl, Elin; Dunn, Nicky; Fogdell-Hahn, Anna

    2016-01-01

    When using relative gene expression for quantification of RNA it is crucial that the reference genes used for normalization do not change with the experimental condition. We aimed at investigating the expressional stability of commonly used reference genes during Human herpesvirus 6B (HHV-6B) infection. Expression of eight commonly used reference genes were investigated with quantitative PCR in a T-cell line infected with HHV-6B. The stability of genes was investigated using the 2(-ΔΔCT) method and the algorithms BestKeeper, GeNorm and NormFinder. Our results indicate that peptidylprolyl isomerase A (PPIA) is the most stably expressed gene while TATA box binding protein (TBP) is the least stably expressed gene during HHV-6B infection. In a confirmatory experiment, TBP was demonstrated to be dose and time dependently upregulated by HHV-6B. The stability of PPIA is in line with other studies investigating different herpesvirus infections whereas the finding that HHV-6B significantly upregulates TBP is novel and most likely specific to HHV-6B. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. A high protein diet (3.4 g/kg/d) combined with a heavy resistance training program improves body composition in healthy trained men and women--a follow-up investigation.

    Science.gov (United States)

    Antonio, Jose; Ellerbroek, Anya; Silver, Tobin; Orris, Steve; Scheiner, Max; Gonzalez, Adriana; Peacock, Corey A

    2015-01-01

    The consumption of a high protein diet (>4 g/kg/d) in trained men and women who did not alter their exercise program has been previously shown to have no significant effect on body composition. Thus, the purpose of this investigation was to determine if a high protein diet in conjunction with a periodized heavy resistance training program would affect indices of body composition, performance and health. Forty-eight healthy resistance-trained men and women completed this study (mean ± SD; Normal Protein group [NP n = 17, four female and 13 male]: 24.8 ± 6.9 yr; 174.0 ± 9.5 cm height; 74.7 ± 9.6 kg body weight; 2.4 ± 1.7 yr of training; High Protein group [HP n = 31, seven female and 24 male]: 22.9 ± 3.1 yr; 172.3 ± 7.7 cm; 74.3 ± 12.4 kg; 4.9 ± 4.1 yr of training). Moreover, all subjects participated in a split-routine, periodized heavy resistance-training program. Training and daily diet logs were kept by each subject. Subjects in the NP and HP groups were instructed to consume their baseline (~2 g/kg/d) and >3 g/kg/d of dietary protein, respectively. Subjects in the NP and HP groups consumed 2.3 and 3.4 g/kg/day of dietary protein during the treatment period. The NP group consumed significantly (p body weight (change: +1.3 ± 1.3 kg NP, -0.1 ± 2.5 HP), fat mass (change: -0.3 ± 2.2 kg NP, -1.7 ± 2.3 HP), and % body fat (change: -0.7 ± 2.8 NP, -2.4 ± 2.9 HP). The NP group gained significantly more body weight than the HP group; however, the HP group experienced a greater decrease in fat mass and % body fat. There was a significant time effect for FFM; however, there was a non-significant time by group effect for FFM (change: +1.5 ± 1.8 NP, +1.5 ± 2.2 HP). Furthermore, a significant time effect (p ≤ 0.05) was seen in both groups vis a vis improvements in maximal strength (i.e., 1-RM squat and bench) vertical jump and pull-ups; however, there were no

  11. Interfacial photochemistry of retinal proteins

    Science.gov (United States)

    Hong, Felix T.

    1999-09-01

    Retinal proteins are membrane-bound protein pigments that contain vitamin A aldehyde (retinal) as the chromophore. They include the visual pigment rhodopsin and four additional ones in the plasma membrane of Halobacterium salinarium (formerly Halobacterium halobium). These proteins maintain a fixed and asymmetric orientation in the membranes, and respond to a light stimulus by generating vectorial charge movement, which can be detected as an electric potential across the membrane or an electric current through the membrane. These phenomena are collectively called the photoelectric effects, which defy a rigorous quantitative treatment by means of either conventional (solution phase) photochemistry or conventional electrophysiology. As an alternative to the mainstream approach, we utilize the analytic tools of electrochemical surface science and electrophysiology to analyze two molecular models of light-induced charge separation and recombination. Being tutorial in nature, this article demands no prior knowledge about the subject. A parsimonious equivalent circuit model is developed. Data obtained from reconstituted bacteriorhodopsin membranes are used to validate the theoretical model and the analytical approach. Data generated and used by critics to refute our approach is shown to actually support it. The present analysis is sufficiently general to be applicable to other pigment-containing membranes, such as the visual photoreceptor membrane and the chlorophyll-based photosynthetic membranes. It provides a coherent description of a wide range of light-induced phenomena associated with various pigment-containing membranes. In contrast, the mainstream approach has been plagued with self-contradictions and paradoxes. Last, but not least, the alternative bioelectrochemical approach also exhibits a predictive power that has hitherto been generally lacking. Comparison of the photoelectric effects is made with regard to bacteriorhodopsin, rhodopsin, and the chlorophyll

  12. Protein-carbohydrate supplements improve muscle protein balance in muscular dystrophy patients after endurance exercise

    DEFF Research Database (Denmark)

    Andersen, Grete; Ørngreen, Mette C; Preisler, Nicolai

    2015-01-01

    In healthy individuals, postexercise protein supplementation increases muscle protein anabolism. In patients with muscular dystrophies, aerobic exercise improves muscle function, but the effect of exercise on muscle protein balance is unknown. Therefore, we investigated 1) muscle protein balance ...

  13. [Advances in the investigation of structure and function of G protein-coupled receptors (by awarding the Nobel Prize for Chemistry in 2012 to Robert Lefkowitz and Bryan Kobilka)].

    Science.gov (United States)

    Shpakov, A O

    2013-01-01

    The Nobel Prize for Chemistry in 2012 was awarded to Robert Lefkowitz and Bryan Kobilka "for studies in G-protein-coupled receptors" (GPCR). In this review the most important discoveries of these Nobel Prize winners dealing with investigation of the structure and functions of GPCR were discussed and analyzed. In the 1980s, they were the first in the world to clone GPCR--the 32-adrenergic receptor. After 20 years, the team led by B. Kobilka for the first time prepared this receptor in the crystalline form and established its three-dimensional structure. In these studies, unique approaches for purification and crystallization of other receptors were developed. In 1980s, R. Lefkowitz and his colleagues discovered beta-arrestins that regulate signal transduction occurring via GPCR. Later they revealed that beta-arrestins were the most important members of signal transduction and were responsible for the signal transduction from the hormone-activated receptor to intracellular signaling cascades independently of heterotrimeric G-proteins. These and other outstanding discoveries of R. Lefkowitz and B. Kobilka have become the basis for the novel area of molecular biology and pharmacology--the molecular endocrinology of GPCR.

  14. The clinical expression of hereditary protein C and protein S deficiency: : a relation to clinical thrombotic risk-factors and to levels of protein C and protein S

    NARCIS (Netherlands)

    Henkens, C. M. A.; van der Meer, J.; Hillege, J. L.; Bom, V. J. J.; Halie, M. R.; van der Schaaf, W.

    We investigated 103 first-degree relatives of 13 unrelated protein C or protein S deficient patients to assess the role of additional thrombotic risk factors and of protein C and protein S levels in the clinical expression of hereditary protein C and protein S deficiency. Fifty-seven relatives were

  15. A randomized, Phase IIb study investigating oliceridine (TRV130), a novel µ-receptor G-protein pathway selective (μ-GPS) modulator, for the management of moderate to severe acute pain following abdominoplasty.

    Science.gov (United States)

    Singla, Neil; Minkowitz, Harold S; Soergel, David G; Burt, David A; Subach, Ruth Ann; Salamea, Monica Y; Fossler, Michael J; Skobieranda, Franck

    2017-01-01

    Oliceridine (TRV130), a novel μ-receptor G-protein pathway selective (μ-GPS) modulator, was designed to improve the therapeutic window of conventional opioids by activating G-protein signaling while causing low β-arrestin recruitment to the μ receptor. This randomized, double-blind, patient-controlled analgesia Phase IIb study was conducted to investigate the efficacy, safety, and tolerability of oliceridine compared with morphine and placebo in patients with moderate to severe pain following abdominoplasty (NCT02335294; oliceridine is an investigational agent not yet approved by the US Food and Drug Administration). Patients were randomized to receive postoperative regimens of intravenous oliceridine (loading/patient-controlled demand doses [mg/mg]: 1.5/0.10 [regimen A]; 1.5/0.35 [regimen B]), morphine (4.0/1.0), or placebo with treatment initiated within 4 hours of surgery and continued as needed for 24 hours. Two hundred patients were treated (n=39, n=39, n=83, and n=39 in the oliceridine regimen A, oliceridine regimen B, morphine, and placebo groups, respectively). Patients were predominantly female (n=198 [99%]) and had a mean age of 38.2 years, weight of 71.2 kg, and baseline pain score of 7.7 (on 11-point numeric pain rating scale). Patients receiving the oliceridine regimens had reductions in average pain scores (model-based change in time-weighted average versus placebo over 24 hours) of 2.3 and 2.1 points, respectively ( P =0.0001 and P =0.0005 versus placebo); patients receiving morphine had a similar reduction (2.1 points; P opioids; no serious AEs were reported with oliceridine. These results suggest that oliceridine may provide effective, rapid analgesia in patients with moderate to severe postoperative pain, with an acceptable safety/tolerability profile and potentially wider therapeutic window than morphine.

  16. Oligomeric protein structure networks: insights into protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Brinda KV

    2005-12-01

    Full Text Available Abstract Background Protein-protein association is essential for a variety of cellular processes and hence a large number of investigations are being carried out to understand the principles of protein-protein interactions. In this study, oligomeric protein structures are viewed from a network perspective to obtain new insights into protein association. Structure graphs of proteins have been constructed from a non-redundant set of protein oligomer crystal structures by considering amino acid residues as nodes and the edges are based on the strength of the non-covalent interactions between the residues. The analysis of such networks has been carried out in terms of amino acid clusters and hubs (highly connected residues with special emphasis to protein interfaces. Results A variety of interactions such as hydrogen bond, salt bridges, aromatic and hydrophobic interactions, which occur at the interfaces are identified in a consolidated manner as amino acid clusters at the interface, from this study. Moreover, the characterization of the highly connected hub-forming residues at the interfaces and their comparison with the hubs from the non-interface regions and the non-hubs in the interface regions show that there is a predominance of charged interactions at the interfaces. Further, strong and weak interfaces are identified on the basis of the interaction strength between amino acid residues and the sizes of the interface clusters, which also show that many protein interfaces are stronger than their monomeric protein cores. The interface strengths evaluated based on the interface clusters and hubs also correlate well with experimentally determined dissociation constants for known complexes. Finally, the interface hubs identified using the present method correlate very well with experimentally determined hotspots in the interfaces of protein complexes obtained from the Alanine Scanning Energetics database (ASEdb. A few predictions of interface hot

  17. The association between Mediterranean Diet Score and glucokinase regulatory protein gene variation on the markers of cardiometabolic risk: an analysis in the European Prospective Investigation into Cancer (EPIC)-Norfolk study.

    Science.gov (United States)

    Sotos-Prieto, Mercedes; Luben, Robert; Khaw, Kay-Tee; Wareham, Nicholas J; Forouhi, Nita G

    2014-07-14

    Consumption of a Mediterranean diet (MD) and genetic variation in the glucokinase regulatory protein (GCKR) gene have been reported to be associated with TAG and glucose metabolism. It is uncertain whether there is any interaction between these factors. Therefore, the aims of the present study were to test the association of adherence to a MD and rs780094 (G>A) SNP in the GCKR gene with the markers of cardiometabolic risk, and to investigate the interaction between genetic variation and MD adherence. We studied 20 986 individuals from the European Prospective Investigation into Cancer (EPIC)-Norfolk study. The relative Mediterranean Diet Score (rMED: range 0-18) was used to assess MD adherence. Linear regression was used to estimate the association between the rMED, genotype and cardiometabolic continuous traits, adjusting for potential confounders. In adjusted analyses, we observed independent associations of MD adherence and genotype with cardiometabolic risk, with the highest risk group (AA genotype; lowest rMED) having higher concentrations of TAG, total cholesterol and apoB (12·5, 2·3 and 3·1%, respectively) v. those at the lowest risk (GG genotype; highest rMED). However, the associations of MD adherence with metabolic markers did not differ by genotype, with no significant gene-diet interactions for lipids or for glycated Hb. In conclusion, we found independent associations of the rMED and of the GCKR genotype with cardiometabolic profile, but found no evidence of interaction between them.

  18. Protein solubility modeling

    Science.gov (United States)

    Agena, S. M.; Pusey, M. L.; Bogle, I. D.

    1999-01-01

    A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

  19. (Ba1-x Bi x )(Ti1-x Ni0.5x Sn0.5x )O3 Solid Solution: Phase Evolution, Microstructure, Dielectric Properties, and Impedance Analysis

    Science.gov (United States)

    Chen, Xiuli; Li, Xiaoxia; Yan, Xiao; Liu, Gaofeng; Zhou, Huanfu

    2018-02-01

    (Ba1-x Bi x )(Ti1-x Ni0.5x Sn0.5x )O3 (BBTNS, 0.02 ≤ x ≤ 0.1) samples have been synthesized by traditional solid-state reaction technique and their structural transformation and dielectric properties investigated. X-ray diffraction (XRD) analysis revealed that BBTNS could form a homogeneous solid solution, and the transformation from tetragonal to pseudocubic phase occurred at 0.04 ≤ &!nbsp;x ≤ 0.06. Optimized properties with stable ɛ r (˜ 1829 to 1838), small Δɛ/ɛ 25°C values (± 15%) over a broad temperature range from -60°C to 140°C, and low tan Δ (≤ 0.02) from 4°C to 194°C were obtained at x = 0.1. The relaxation and conduction process in the high-temperature region are attributed to thermal activation, and oxygen vacancies may be the ionic charge carriers in perovskite ferroelectrics.

  20. Solution phase photophysics of 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one: Analysing the lineaments of a new fluorosensor to probe different micro-environments

    Energy Technology Data Exchange (ETDEWEB)

    Mitra, Amrit Krishna [Department of Clinical and Experimental Pharmacology, School of Tropical Medicine, Kolkata 700073 (India); Ghosh, Sujay; Sau, Abhishek [Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata 700064 (India); Saha, Chandan [Department of Clinical and Experimental Pharmacology, School of Tropical Medicine, Kolkata 700073 (India); Basu, Samita, E-mail: samita.basu@saha.ac.in [Chemical Sciences Division, Saha Institute of Nuclear Physics, Kolkata 700064 (India)

    2015-11-15

    We present here a detailed photophysical study of a newly synthesised fluorophore 5,7-dimethoxy-2,3,4,9-tetrahydro-1H-carbazol-1-one (KTHC-57). Spectroscopic investigation of the compound has been carried out in 14 different protic and aprotic solvents, as well as in different binary solvent mixtures, using absorption, steady-state and time-resolved fluorescence techniques. The spectral behaviour of this compound is found to be extremely sensitive to the polarity and hydrogen bonding nature of the solvent. When considered in micelles, reverse micelles and β-cyclodextrin, KTHC-57 behaves as a reporter of its immediate microenvironment. Extent of hypsochromic shift varies as we move from cationic surfactant cetyltrimethylammonium bromide (~40 nm) to anionic surfactant sodium dodecyl sulphate (~23 nm) to non-ionic surfactant Triton X-100 (~37 nm). In case of anionic reverse micellar nanocavities composed of sodium bis(2-ethylhexyl) sulfosuccinate (AOT)/heptane with increasing water contents, a bathochromic shift of ~50 nm is observed. A quantitative assessment of the emission intensity data on Benesi–Hildebrand equation reveals a 1:1 stoichiometry for KTHC-57:β-CD complex. Triethylamine (TEA) is a simple aliphatic organic molecule that interacts with KTHC-57 in polar aprotic medium. Within β-CD environment, fluorescence quenching takes place along with a bathochromic shift. Interaction of (TEA) with KTHC-57 in β-CD nano-confinement is studied using absorption spectroscopy, steady-state as well as time-resolved fluorescence spectroscopy and laser flash photolysis in conjunction with an external magnetic field. - Highlights: • Excited state properties of KTHC-57 vary with its H-bonding environment. • KTHC-57 interacts differently in various microheterogeneous environments. • Benesi–Hildebrand equation reveals a 1:1 stoichiometry for KTHC-57:β-CD complex. • Organic base TEA quench KTHC-57 fluorescence in polar aprotic solvents. • PET takes place from

  1. Protein Colloidal Aggregation Project

    Science.gov (United States)

    Oliva-Buisson, Yvette J. (Compiler)

    2014-01-01

    To investigate the pathways and kinetics of protein aggregation to allow accurate predictive modeling of the process and evaluation of potential inhibitors to prevalent diseases including cataract formation, chronic traumatic encephalopathy, Alzheimer's Disease, Parkinson's Disease and others.

  2. Interfacial Protein-Protein Associations

    OpenAIRE

    Langdon, Blake B.; Kastantin, Mark; Walder, Robert; Schwartz, Daniel K.

    2013-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for ...

  3. A randomized, Phase IIb study investigating oliceridine (TRV130, a novel µ-receptor G-protein pathway selective (µ-GPS modulator, for the management of moderate to severe acute pain following abdominoplasty

    Directory of Open Access Journals (Sweden)

    Singla N

    2017-10-01

    Full Text Available Neil Singla,1 Harold S Minkowitz,2 David G Soergel,3 David A Burt,3 Ruth Ann Subach,3 Monica Y Salamea,3 Michael J Fossler,3 Franck Skobieranda3 1Lotus Clinical Research, Pasadena, CA, 2Memorial Hermann Memorial City Medical Center, Houston, TX, 3Trevena, Inc, King of Prussia, PA, USA Background: Oliceridine (TRV130, a novel µ-receptor G-protein pathway selective (µ-GPS modulator, was designed to improve the therapeutic window of conventional opioids by activating G-protein signaling while causing low β-arrestin recruitment to the µ receptor. This randomized, double-blind, patient-controlled analgesia Phase IIb study was conducted to investigate the efficacy, safety, and tolerability of oliceridine compared with morphine and placebo in patients with moderate to severe pain following abdominoplasty (NCT02335294; oliceridine is an investigational agent not yet approved by the US Food and Drug Administration. Methods: Patients were randomized to receive postoperative regimens of intravenous oliceridine (loading/patient-controlled demand doses [mg/mg]: 1.5/0.10 [regimen A]; 1.5/0.35 [regimen B], morphine (4.0/1.0, or placebo with treatment initiated within 4 hours of surgery and continued as needed for 24 hours. Results: Two hundred patients were treated (n=39, n=39, n=83, and n=39 in the oliceridine regimen A, oliceridine regimen B, morphine, and placebo groups, respectively. Patients were predominantly female (n=198 [99%] and had a mean age of 38.2 years, weight of 71.2 kg, and baseline pain score of 7.7 (on 11-point numeric pain rating scale. Patients receiving the oliceridine regimens had reductions in average pain scores (model-based change in time-weighted average versus placebo over 24 hours of 2.3 and 2.1 points, respectively (P=0.0001 and P=0.0005 versus placebo; patients receiving morphine had a similar reduction (2.1 points; P<0.0001 versus placebo. A lower prevalence of adverse events (AEs related to nausea, vomiting, and respiratory

  4. Protein Crystal Malic Enzyme

    Science.gov (United States)

    1992-01-01

    Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

  5. Investigation of the effects of experimental autolysis on the detection of abnormal prion protein in lymphoid and central nervous system tissues from elk and sheep using the Western blotting method.

    Science.gov (United States)

    Huang, Hongsheng; Soutyrine, Andrei; Rendulich, Jasmine; O'Rourke, Katherine; Balachandran, Aru

    2011-01-01

    Tissues unsuitable for standard immunohistochemical and histopathological examinations for chronic wasting disease (CWD) in cervids and for scrapie in sheep are frequently submitted for testing. This study investigated the effects of experimental autolysis on the detection of abnormal prion protein (PrPsc) in lymphoid and central nervous system (CNS) tissues from elk and sheep. The PrPsc was detected using a Western blotting (WB) test following PrPsc enrichment using sodium phosphotungstic acid (PTA) precipitation (PTA-WB). A commercial enzyme-linked immunosorbent assay (ELISA) was used as a reference test for quantitative measurement. This study showed that the amount of PrPsc in lymphoid and CNS tssues from elk and sheep decreased gradually as a result of autolysis, but PrPsc was still detectable after 5 and 15 d incubation at 37°C by PTA-WB for all lymphoid and CNS samples. The results of the ELISA supported those of PTA-WB, particularly for CNS tissues. In conclusion, autolysis at 37°C for 15 d would not significantly affect the detection of PrPsc in lymphoid and CNS tissues by WB and ELISA and, particularly, PTA-WB is a valuable and alternative confirmatory test to detect PrPsc in autolyzed lymphoid and CNS samples.

  6. Real-time HD Exchange Kinetics of Proteins from Buffered Aqueous Solution with Electrothermal Supercharging and Top-Down Tandem Mass Spectrometry

    Science.gov (United States)

    Going, Catherine C.; Xia, Zijie; Williams, Evan R.

    2016-06-01

    Electrothermal supercharging (ETS) with electrospray ionization produces highly charged protein ions from buffered aqueous solutions in which proteins have native folded structures. ETS increases the charge of ribonuclease A by 34%, whereas only a 6% increase in charge occurs for a reduced-alkylated form of this protein, which is unfolded and its structure is ~66% random coil in this solution. These results indicate that protein denaturation that occurs in the ESI droplets is the primary mechanism for ETS. ETS does not affect the extent of solution-phase hydrogen-deuterium exchange (HDX) that occurs for four proteins that have significantly different structures in solution, consistent with a droplet lifetime that is considerably shorter than observable rates of HDX. Rate constants for HDX of ubiquitin are obtained with a spatial resolution of ~1.3 residues with ETS and electron transfer dissociation of the 10+ charge-state using a single capillary containing a few μL of protein solution in which HDX continuously occurs. HDX protection at individual residues with ETS HDX is similar to that with reagent supercharging HDX and with solution-phase NMR, indicating that the high spray potentials required to induce ETS do not lead to HD scrambling.

  7. Non-Catalytic Self Healing Composite Material Solution, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Fiber reinforce polymer (FRP) composite materials are seeing increasing use in the construction of a wide variety of aerospace structures. However, uncertainties...

  8. Isomerization Intermediates In Solution Phase Photochemistry Of Stilbenes

    Science.gov (United States)

    Doany, F. E.; Hochstrasser, R. M.; Greene, B. I.

    1985-04-01

    Picosecond and subpicosecond spectroscopic studies have revealed evidence for an isomerization intermediate between cis and trans in the photoinduced isomerism of both stilbene and biindanyledene ("stiff" stilbene). In stiff stilbene, a transient absorption at 351 nm displays time evolution and viscosity dependence consistent with absorption by a twisted intermediate ("phantom" state) with a lOps lifetime. An analagous bottleneck state with a life-time of 4ps is also consistent with the ground state recovery dynamics of t-stilbene following excitation of c-stilbene when monitored with 0.1ps resolution.

  9. Selected topics in solution-phase biomolecular NMR spectroscopy

    Science.gov (United States)

    Kay, Lewis E.; Frydman, Lucio

    2017-05-01

    Solution bio-NMR spectroscopy continues to enjoy a preeminent role as an important tool in elucidating the structure and dynamics of a range of important biomolecules and in relating these to function. Equally impressive is how NMR continues to 'reinvent' itself through the efforts of many brilliant practitioners who ask increasingly demanding and increasingly biologically relevant questions. The ability to manipulate spin Hamiltonians - almost at will - to dissect the information of interest contributes to the success of the endeavor and ensures that the NMR technology will be well poised to contribute to as yet unknown frontiers in the future. As a tribute to the versatility of solution NMR in biomolecular studies and to the continued rapid advances in the field we present a Virtual Special Issue (VSI) that includes over 40 articles on various aspects of solution-state biomolecular NMR that have been published in the Journal of Magnetic Resonance in the past 7 years. These, in total, help celebrate the achievements of this vibrant field.

  10. A Sustainable Spacecraft Component Database Solution, Phase I

    Data.gov (United States)

    National Aeronautics and Space Administration — Numerous spacecraft component databases have been developed to support NASA, DoD, and contractor design centers and design tools. Despite the clear utility of...

  11. Heterogeneous Ferroelectric Solid Solutions Phases and Domain States

    CERN Document Server

    Topolov, Vitaly

    2012-01-01

    The book deals with perovskite-type ferroelectric solid solutions for modern materials science and applications, solving problems of complicated heterophase/domain structures near the morphotropic phase boundary and applications to various systems with morphotropic phases. In this book domain state–interface diagrams are presented for the interpretation of heterophase states in perovskite-type ferroelectric solid solutions. It allows to describe the stress relief in the presence of polydomain phases, the behavior of unit-cell parameters of coexisting phases and the effect of external electric fields. The novelty of the book consists in (i) the first systematization of data about heterophase states and their evolution in ferroelectric solid solutions (ii) the general interpretation of heterophase and domain structures at changing temperature, composition or electric field (iii) the complete analysis of interconnection domain structures, unit-cell parameters changes, heterophase structures and stress relief.

  12. Photoisomerization of ethyl ferulate: A solution phase transient absorption study

    Science.gov (United States)

    Horbury, Michael D.; Baker, Lewis A.; Rodrigues, Natércia D. N.; Quan, Wen-Dong; Stavros, Vasilios G.

    2017-04-01

    Ethyl ferulate (ethyl 4-hydroxy-3-methoxycinnamate) is currently used as a sunscreening agent in commercial sunscreen blends. Recent time-resolved gas-phase measurements have demonstrated that it possesses long-lived (>ns) electronic excited states, counterintuitive to what one might anticipate for an effective sunscreening agent. In the present work, the photodynamics of ethyl ferulate in cyclohexane, are explored using time-resolved transient electronic absorption spectroscopy, upon photoexcitation to the 11ππ∗ and 21ππ∗ states. We demonstrate that ethyl ferulate undergoes efficient non-radiative decay to repopulate the electronic ground state, mediated by trans-cis isomerization. These results strongly suggest that even mild perturbations induced by a non-polar solvent, as may be found in a closer-to-market sunscreen blend, may contribute to our understanding of ethyl ferulate's role as a sunscreening agent.

  13. Mapping a Noncovalent Protein-Peptide Interface by Top-Down FTICR Mass Spectrometry Using Electron Capture Dissociation

    Science.gov (United States)

    Clarke, David J.; Murray, Euan; Hupp, Ted; Mackay, C. Logan; Langridge-Smith, Pat R. R.

    2011-08-01

    Noncovalent protein-ligand and protein-protein complexes are readily detected using electrospray ionization mass spectrometry (ESI MS). Furthermore, recent reports have demonstrated that careful use of electron capture dissociation (ECD) fragmentation allows covalent backbone bonds of protein complexes to be dissociated without disruption of noncovalent protein-ligand interactions. In this way the site of protein-ligand interfaces can be identified. To date, protein-ligand complexes, which have proven tractable to this technique, have been mediated by ionic electrostatic interactions, i.e., ion pair interactions or salt bridging. Here we extend this methodology by applying ECD to study a protein-peptide complex that contains no electrostatics interactions. We analyzed the complex between the 21 kDa p53-inhibitor protein anterior gradient-2 and its hexapeptide binding ligand (PTTIYY). ECD fragmentation of the 1:1 complex occurs with retention of protein-peptide binding and analysis of the resulting fragments allows the binding interface to be localized to a C-terminal region between residues 109 and 175. These finding are supported by a solution-phase competition assay, which implicates the region between residues 108 and 122 within AGR2 as the PTTIYY binding interface. Our study expands previous findings by demonstrating that top-down ECD mass spectrometry can be used to determine directly the sites of peptide-protein interfaces. This highlights the growing potential of using ECD and related top-down fragmentation techniques for interrogation of protein-protein interfaces.

  14. Proteins engineering

    International Nuclear Information System (INIS)

    2000-01-01

    At the - Departement d'Ingenierie et d'etudes de proteines (Deip) of the CEA more than seventy researchers are working hard to understand the function of proteins. For that they use the molecular labelling technique (F.M.)

  15. Total protein

    Science.gov (United States)

    ... page: //medlineplus.gov/ency/article/003483.htm Total protein To use the sharing features on this page, please enable JavaScript. The total protein test measures the total amount of two classes ...

  16. Investigative psychology

    OpenAIRE

    Canter, David V.

    2010-01-01

    The domain of Investigative Psychology covers all aspects of psychology that are relevant to the conduct of criminal or civil investigations. Its focus is on the ways in which criminal activities may be examined and understood in order for the detection of crime to be effective and legal proceedings to be appropriate. As such Investigative Psychology is concerned with psychological input to the full range of issues that relate to the management, investigation and prosecution of crime

  17. Dairy Proteins and Energy Balance

    DEFF Research Database (Denmark)

    Bendtsen, Line Quist

    High protein diets affect energy balance beneficially through decreased hunger, enhanced satiety and increased energy expenditure. Dairy products are a major source of protein. Dairy proteins are comprised of two classes, casein (80%) and whey proteins (20%), which are both of high quality......, but casein is absorbed slowly and whey is absorbed rapidly. The present PhD study investigated the effects of total dairy proteins, whey, and casein, on energy balance and the mechanisms behind any differences in the effects of the specific proteins. The results do not support the hypothesis that dairy...... proteins, whey or casein are more beneficial than other protein sources in the regulation of energy balance, and suggest that dairy proteins, whey or casein seem to play only a minor role, if any, in the prevention and treatment of obesity....

  18. Smoking interacts with HLA-DRB1 shared epitope in the development of anti-citrullinated protein antibody-positive rheumatoid arthritis: results from the Malaysian Epidemiological Investigation of Rheumatoid Arthritis (MyEIRA).

    Science.gov (United States)

    Too, Chun Lai; Yahya, Abqariyah; Murad, Shahnaz; Dhaliwal, Jasbir Singh; Larsson, Per Tobias; Muhamad, Nor Asiah; Abdullah, Nor Aini; Mustafa, Amal Nasir; Klareskog, Lars; Alfredsson, Lars; Padyukov, Leonid; Bengtsson, Camilla

    2012-04-26

    Rheumatoid arthritis (RA) is a multifactorial autoimmune disease in which genetic and environmental factors interact in the etiology. In this study, we investigated whether smoking and HLA-DRB1 shared-epitope (SE) alleles interact differently in the development of the two major subgroups of rheumatoid arthritis (RA), anti-citrullinated proteins antibody (ACPA)-positive and ACPA-negative disease, in a multiethnic population of Asian descent. A case-control study comprising early diagnosed RA cases was carried out in Malaysia between 2005 and 2009. In total, 1,076 cases and 1,612 matched controls participated in the study. High-resolution HLA-DRB1 genotyping was performed for shared-epitope (SE) alleles. All participants answered a questionnaire on a broad range of issues, including smoking habits. The odds ratio (OR) of developing ACPA-positive and ACPA-negative disease was calculated for smoking and the presence of any SE alleles separately. Potential interaction between smoking history (defined as "ever" and "never" smoking) and HLA-DRB1 SE alleles also was calculated. In our multiethnic study, both the SE alleles and smoking were associated with an increased risk of developing ACPA-positive RA (OR SE alleles, 4.7; 95% confidence interval (CI), 3.6 to 6.2; OR smoking, 4.1; 95% CI, 1.9 to 9.2). SE-positive smokers had an odds ratio of ACPA-positive RA of 25.6 (95% CI, 10.4 to 63.4), compared with SE-negative never-smokers. The interaction between smoking and SE alleles was significant (attributable proportion due to interaction (AP) was 0.7 (95% CI, 0.5 to 1.0)). The HLA-DRB1*04:05 SE allele, which is common in Asian populations, but not among Caucasians, was associated with an increased risk of ACPA-positive RA, and this allele also showed signs of interaction with smoking (AP, 0.4; 95% CI, -0.1 to 0.9). Neither smoking nor SE alleles nor their combination was associated with an increased risk of ACPA-negative RA. The risk of developing ACPA-positive RA is

  19. Protein Extractability

    African Journals Online (AJOL)

    Results showed that protein extractability was dependent on pH, type of salt, salt concentrations and extraction time. Salts extracted more proteins from the moringa seed flour than water. Maximum extraction of protein was. 85.06% and 84.72% with 0.5 M CaCl and 0.75 M NaCl respectively. On varying the pH, maximum ...

  20. Fire investigation

    Science.gov (United States)

    Gomberg, A.

    There was considerable progress made on several fronts of fire investigation in the United States in recent years. Progress was made in increasing the quantity of fire investigation and reporting, through efforts to develop the National Fire Incident Reporting System. Improving overall quality of fire investigation is the objective of efforts such as the Fire Investigation Handbook, which was developed and published by the National Bureau of Standards, and the upgrading and expanding of the ""dictionary'' of fire investigation and reporting, the NFPA 901, Uniform Coding for Fire Protection, system. The science of fire investigation as furthered also by new approaches to post fire interviews being developed at the University of Washington, and by in-depth research into factors involved in several large loss fires, including the MGM Grand Hotel in Las Vegas. Finally, the use of special study fire investigations - in-depth investigations concentrating on specific fire problems - is producing new glimpses into the nature of the national fire problem. A brief description of the status of efforts in each of these areas is discussed.

  1. Event Investigation

    International Nuclear Information System (INIS)

    Korosec, D.

    2000-01-01

    The events in the nuclear industry are investigated from the license point of view and from the regulatory side too. It is well known the importance of the event investigation. One of the main goals of such investigation is to prevent the circumstances leading to the event and the consequences of the event. The protection of the nuclear workers against nuclear hazard, and the protection of general public against dangerous effects of an event could be achieved by systematic approach to the event investigation. Both, the nuclear safety regulatory body and the licensee shall ensure that operational significant events are investigated in a systematic and technically sound manner to gather information pertaining to the probable causes of the event. One of the results should be appropriate feedback regarding the lessons of the experience to the regulatory body, nuclear industry and general public. In the present paper a general description of systematic approach to the event investigation is presented. The systematic approach to the event investigation works best where cooperation is present among the different divisions of the nuclear facility or regulatory body. By involving management and supervisors the safety office can usually improve their efforts in the whole process. The end result shall be a program which serves to prevent events and reduce the time and efforts solving the root cause which initiated each event. Selection of the proper method for the investigation and an adequate review of the findings and conclusions lead to the higher level of the overall nuclear safety. (author)

  2. Automated SDS Depletion for Mass Spectrometry of Intact Membrane Proteins though Transmembrane Electrophoresis.

    Science.gov (United States)

    Kachuk, Carolyn; Faulkner, Melissa; Liu, Fang; Doucette, Alan A

    2016-08-05

    Membrane proteins are underrepresented in proteome analysis platforms because of their hydrophobic character, contributing to decreased solubility. Sodium dodecyl sulfate is a favored denaturant in proteomic workflows, facilitating cell lysis and protein dissolution; however, SDS impedes MS detection and therefore must be removed prior to analysis. Although strategies exist for SDS removal, they provide low recovery, purity, or reproducibility. Here we present a simple automated device, termed transmembrane electrophoresis (TME), incorporating the principles of membrane filtration, but with an applied electric current to ensure near-complete (99.9%) removal of the surfactant, including protein-bound SDS. Intact proteins are recovered in solution phase in high yield (90-100%) within 1 h of operation. The strategy is applied to protein standards and proteome mixtures, including an enriched membrane fraction from E. coli, resulting in quality MS spectra free of SDS adducts. The TME platform is applicable to both bottom-up MS/MS as well as LC-ESI-MS analysis of intact proteins. SDS-depleted fractions reveal a similar number of protein identifications (285) compared wit a non-SDS control (280), being highly correlated in terms of protein spectral counts. This fully automated approach to SDS removal presents a viable tool for proteome sample processing ahead of MS analysis. Data are available via ProteomeXchange, identifier PXD003941.

  3. Legibility Investigations

    DEFF Research Database (Denmark)

    Beier, Sofie

    2013-01-01

    One frequent problem in legibility investigations is that the tested typefaces vary on too many variables. In an investigation which compares typefaces that – at the same time – vary on letter width, weight, contrast and skeleton, it will be difficult to determine precisely why the findings come....... One is the master typeface; three of the remaining typefaces have one stylistic feature that differs from the master (skeleton, weight, and width); and three have two stylistic features that differ from the master (weight/skeleton, weight/contrast and weight/width). In an experimental investigation...

  4. Protein politics

    NARCIS (Netherlands)

    Vijver, Marike

    2005-01-01

    This study is part of the program of the interdisciplinary research group Profetas (protein foods, environment, technology and society). Profetas consists of technological, environmental and socio-economic research projects on protein food systems which result in the development of scenarios and

  5. Whey Protein

    Science.gov (United States)

    ... Fraction de Lactosérum, Fraction de Petit-Lait, Goat Milk Whey, Goat Whey, Isolat de Protéine de Lactosérum, Isolat de Protéine de Petit-Lait, Lactosérum de Lait de Chèvre, MBP, Milk Protein, Milk Protein Isolate, Mineral Whey Concentrate, Proteínas ...

  6. Protein adhesives

    Science.gov (United States)

    Charles R. Frihart; Linda F. Lorenz

    2018-01-01

    Nature uses a wide variety of chemicals for providing adhesion internally (e.g., cell to cell) and externally (e.g., mussels to ships and piers). This adhesive bonding is chemically and mechanically complex, involving a variety of proteins, carbohydrates, and other compounds.Consequently,the effect of protein structures on adhesive properties is only partially...

  7. Clinical Investigations

    Science.gov (United States)

    1977-09-30

    Unit No. 77/20 (FY77, 0) An Analysis of Ameloblastic Fibro- odontoma ....................... 27 Department of Medicine Nork Unit No, 69/338 (FY69, T...Ar, Analysis of Ameiloblastic Fibro- odontoma ,IRK UNIT NO: 77/20 PRINCIPAL INVESTIGATOR: COL George J Tsagaris, DC ASSOCIATE INVESTIGATORS: OBJECTIVES...The coals of this research study are to report upon and analyze cases of ameloblastic fibro- odontoma and to correlate these findinas with those of

  8. Investigating the function of Fc -specific binding of IgM to Plasmodium falciparum erythrocyte membrane protein 1 mediating erythrocyte rosetting

    DEFF Research Database (Denmark)

    Stevenson, Liz; Huda, Pie; Jeppesen, Anine

    2015-01-01

    of opsonized infected erythrocytes (IEs) without compromising the placental IE adhesion mediated by this PfEMP1 type. IgM also binds via Fc to several other PfEMP1 proteins, where it has been proposed to facilitate rosetting (binding of uninfected erythrocytes to a central IE). To further dissect...

  9. Polymers for Protein Conjugation

    Directory of Open Access Journals (Sweden)

    Gianfranco Pasut

    2014-01-01

    Full Text Available Polyethylene glycol (PEG at the moment is considered the leading polymer for protein conjugation in view of its unique properties, as well as to its low toxicity in humans, qualities which have been confirmed by its extensive use in clinical practice. Other polymers that are safe, biodegradable and custom-designed have, nevertheless, also been investigated as potential candidates for protein conjugation. This review will focus on natural polymers and synthetic linear polymers that have been used for protein delivery and the results associated with their use. Genetic fusion approaches for the preparation of protein-polypeptide conjugates will be also reviewed and compared with the best known chemical conjugation ones.

  10. Protein-Protein Interaction Databases

    DEFF Research Database (Denmark)

    Szklarczyk, Damian; Jensen, Lars Juhl

    2015-01-01

    of research are explored. Here we present an overview of the most widely used protein-protein interaction databases and the methods they employ to gather, combine, and predict interactions. We also point out the trade-off between comprehensiveness and accuracy and the main pitfall scientists have to be aware...

  11. Severity investigation

    NARCIS (Netherlands)

    Rooij, M.R. de; Godart, B.

    2013-01-01

    From the confirmation inspection and its subsequent test results the presence of AAR has either been confirmed or eliminated. Assuming the first outcome, the next step is to investigate the severity of the situation, see Figure 23. One should keep in mind that it is possible that some evidence of

  12. Investigating Corruption

    OpenAIRE

    Prendergast, Canice

    2000-01-01

    Agency theory has had little to say about the control of bureaucratic corruption, perhaps the greatest agency problem that exists. The author considers the role of incentive contracting in reducing corruption through the use of independent investigations-a common way to monitor corruption. In simple settings, bureaucratic corruption can be suppressed by rewarding and penalizing bureaucrats...

  13. Protein deamidation

    OpenAIRE

    Robinson, Noah E.

    2002-01-01

    A completely automatic computerized technique for the quantitative estimation of the deamidation rates of any protein for which the three-dimensional structure is known has been developed. Calculations of the specific deamidation rates of 170,014 asparaginyl residues in 13,335 proteins have been carried out. The calculated values have good quantitative reliability when compared with experimental measurements. These rates demonstrate that deamidation may be a biologically ...

  14. Protein-Protein Interaction on Lysozyme Crystallization Revealed by Rotational Diffusion Analysis

    OpenAIRE

    Takahashi, Daisuke; Nishimoto, Etsuko; Murase, Tadashi; Yamashita, Shoji

    2008-01-01

    Intermolecular interactions between protein molecules diffusing in various environments underlie many biological processes as well as control protein crystallization, which is a crucial step in x-ray protein structure determinations. Protein interactions were investigated through protein rotational diffusion analysis. First, it was confirmed that tetragonal lysozyme crystals containing fluorescein-tagged lysozyme were successfully formed with the same morphology as that of native protein. Usi...

  15. Docking and Molecular Dynamics Calculations of Some Previously Studied and newly Designed Ligands to Catalytic Core Domain of HIV-1 Integrase and an Investigation to Effects of Conformational Changes of Protein on Docking Results

    Directory of Open Access Journals (Sweden)

    Selami Ercan

    2016-10-01

    Full Text Available Nowadays, AIDS still remains as a worldwide pandemic and continues to cause many death which arise from HIV-1 virus. For nearly 35 years, drugs that target various steps of virus life cycle have been developed. HIV-1 integrase is the one of these steps which is essential for virus life cycle. Computer aided drug design is being used in many drug design studies as also used in development of the first HIV-1 integrase inhibitor Raltegravir. In this study 3 ligands which are used as HIV-1 integrase inhibitors and 4 newly designed ligands were docked to catalytic core domain of HIV-1 integrase. Each of ligands docked to three different conformations of protein. Prepared complexes (21 item were carried out by 50 ns MD simulations and results were analyzed. Finally, the binding free energies of ligands were calculated. Hereunder, it was determined that designed ligands L01 and L03 gave favorable results. The questions about the ligands which have low docking scores in a conformation of protein could give better scores in another conformation of protein and if the MD simulations carry the different oriented and different localized ligands in same position at the end of simulation were answered.

  16. Geotechnical Investigations

    Science.gov (United States)

    2001-01-01

    assessment are discussed in Construction Site Environmental Survey and Clearance Procedures Manual (Draft), EM 1110-1-4000, Walker (1988), and Borrelli ...EM 1110-1-1804 1 January 2001 US Army Corps of Engineers ENGINEER MANUAL Geotechnical Investigations ENGINEERING AND DESIGN Report Documentation Page...for all official USACE engineer regulations, circulars, manuals , and other documents originating from HQUSACE. Publications are provided in portable

  17. Disease specific protein corona

    Science.gov (United States)

    Rahman, M.; Mahmoudi, M.

    2015-03-01

    It is now well accepted that upon their entrance into the biological environments, the surface of nanomaterials would be covered by various biomacromolecules (e.g., proteins and lipids). The absorption of these biomolecules, so called `protein corona', onto the surface of (nano)biomaterials confers them a new `biological identity'. Although the formation of protein coronas on the surface of nanoparticles has been widely investigated, there are few reports on the effect of various diseases on the biological identity of nanoparticles. As the type of diseases may tremendously changes the composition of the protein source (e.g., human plasma/serum), one can expect that amount and composition of associated proteins in the corona composition may be varied, in disease type manner. Here, we show that corona coated silica and polystyrene nanoparticles (after interaction with in the plasma of the healthy individuals) could induce unfolding of fibrinogen, which promotes release of the inflammatory cytokines. However, no considerable releases of inflammatory cytokines were observed for corona coated graphene sheets. In contrast, the obtained corona coated silica and polystyrene nanoparticles from the hypofibrinogenemia patients could not induce inflammatory cytokine release where graphene sheets do. Therefore, one can expect that disease-specific protein coronas can provide a novel approach for applying nanomedicine to personalized medicine, improving diagnosis and treatment of different diseases tailored to the specific conditions and circumstances.

  18. Protein production and purification.

    Science.gov (United States)

    Gräslund, Susanne; Nordlund, Pär; Weigelt, Johan; Hallberg, B Martin; Bray, James; Gileadi, Opher; Knapp, Stefan; Oppermann, Udo; Arrowsmith, Cheryl; Hui, Raymond; Ming, Jinrong; dhe-Paganon, Sirano; Park, Hee-won; Savchenko, Alexei; Yee, Adelinda; Edwards, Aled; Vincentelli, Renaud; Cambillau, Christian; Kim, Rosalind; Kim, Sung-Hou; Rao, Zihe; Shi, Yunyu; Terwilliger, Thomas C; Kim, Chang-Yub; Hung, Li-Wei; Waldo, Geoffrey S; Peleg, Yoav; Albeck, Shira; Unger, Tamar; Dym, Orly; Prilusky, Jaime; Sussman, Joel L; Stevens, Ray C; Lesley, Scott A; Wilson, Ian A; Joachimiak, Andrzej; Collart, Frank; Dementieva, Irina; Donnelly, Mark I; Eschenfeldt, William H; Kim, Youngchang; Stols, Lucy; Wu, Ruying; Zhou, Min; Burley, Stephen K; Emtage, J Spencer; Sauder, J Michael; Thompson, Devon; Bain, Kevin; Luz, John; Gheyi, Tarun; Zhang, Fred; Atwell, Shane; Almo, Steven C; Bonanno, Jeffrey B; Fiser, Andras; Swaminathan, Sivasubramanian; Studier, F William; Chance, Mark R; Sali, Andrej; Acton, Thomas B; Xiao, Rong; Zhao, Li; Ma, Li Chung; Hunt, John F; Tong, Liang; Cunningham, Kellie; Inouye, Masayori; Anderson, Stephen; Janjua, Heleema; Shastry, Ritu; Ho, Chi Kent; Wang, Dongyan; Wang, Huang; Jiang, Mei; Montelione, Gaetano T; Stuart, David I; Owens, Raymond J; Daenke, Susan; Schütz, Anja; Heinemann, Udo; Yokoyama, Shigeyuki; Büssow, Konrad; Gunsalus, Kristin C

    2008-02-01

    In selecting a method to produce a recombinant protein, a researcher is faced with a bewildering array of choices as to where to start. To facilitate decision-making, we describe a consensus 'what to try first' strategy based on our collective analysis of the expression and purification of over 10,000 different proteins. This review presents methods that could be applied at the outset of any project, a prioritized list of alternate strategies and a list of pitfalls that trip many new investigators.

  19. Random protein association analyses of MALDI-TOF mass spectra of two- and three-component protein systems using binomial and multinomial distribution

    Science.gov (United States)

    Lee, Bao-Shiang; Krishnanchettiar, Sangeeth; Lateef, Syed Salman; Li, Chun-Ting; Gupta, Shalini

    2006-07-01

    The phenomenon of protein randomly associating among themselves during MALDI-TOF mass spectrometric measurements is manifest on all the proteins tested here. The magnitude of this random association seems to be protein-dependent. However, a detailed mathematical analysis of this process has not been reported so far. Here, binomial and multinomial equations are used to analyze the relative populations of multimer ions formed by random protein association during MALDI-TOF mass spectrometric measurements. Hemoglobin A (which consists of two [alpha]-globins and two [beta]-globins) and biotinylated insulin (which contains intact, singly biotinylated, and doubly biotinylated insulin) are used as the test cases for two- and three-component protein systems, respectively. MALDI-TOF spectra are acquired using standard MALDI-TOF techniques and equipment. The binomial distribution matches the relative populations of multimer ions of Hb A perfectly. For biotinylated insulin sample, taking lesser relative populations for doubly biotinylated insulin and intact insulin compared with singly biotinylated insulin into account, the relative populations of multimer ions of the biotinylated insulin confirms the prediction of multinomial equation. The pairs of unrelated proteins such as myoglobin, avidin, and lysozyme show lesser intensities for heteromultimers than for homomultimers, indicating weaker propensities to associate between different proteins during MALDI-TOF mass spectrometric measurements. Contrary to the suggestion that the multimer ions are formed in the solution phase prior to MALDI-TOF mass spectrometric measurement through multistage sequential reactions of the aggregation of protein molecules, we postulate that multimer ions of proteins are formed after the protein molecules have been vaporized into the gas phase through the assistance of the laser and matrix.

  20. Protein Crystallizability.

    Science.gov (United States)

    Smialowski, Pawel; Wong, Philip

    2016-01-01

    Obtaining diffracting quality crystals remains a major challenge in protein structure research. We summarize and compare methods for selecting the best protein targets for crystallization, construct optimization and crystallization condition design. Target selection methods are divided into algorithms predicting the chance of successful progression through all stages of structural determination (from cloning to solving the structure) and those focusing only on the crystallization step. We tried to highlight pros and cons of different approaches examining the following aspects: data size, redundancy and representativeness, overfitting during model construction, and results evaluation. In summary, although in recent years progress was made and several sequence properties were reported to be relevant for crystallization, the successful prediction of protein crystallization behavior and selection of corresponding crystallization conditions continue to challenge structural researchers.

  1. Crosshole investigations

    International Nuclear Information System (INIS)

    Olsson, O.; Pihl, J.

    1987-09-01

    The analysis of the radar and seismic data has given a consistent description of the fracture zones at the Crosshole site in agreement with geological and other geophysical observations made in the boreholes. The hydraulic investigations within the Crosshole project have yielded substantial progress in assessing the hydrogeology of fractured granitic rocks. The crosshole hydraulic testing concentrated on measuring the distribution of hydraulic properties within the extensive fractured zones identified by geophysics. A new analysis involving the 'dimension' of the flow test has been developed to analyse the results of the crosshole sinusoidal testing. The combined analysis of the geophysical and the hydraulic data set has shown that groundwater flow is concentrated within a few major features which have been identified by the geophysical methods. (orig./DG)

  2. Laboratory investigations

    International Nuclear Information System (INIS)

    Handin, J.

    1980-01-01

    Our task is to design mined-repository systems that will adequately secure high-level nuclear waste for at least 10,000 yr and that will be mechanically stable for 50 to 100-yr periods of retrievability during which mistakes could be corrected and a valuable source of energy could be reclaimed, should national policy on the reprocessing of spent fuel ever change. The only credible path for the escape of radionuclides from the repository to the biosphere is through ground-water, and in hard rock, bulk permeability is largely governed by natural and artificial fracture systems. Catastrophic failure of an excavation in hard rock is likely to occur at the weakest links - the discontinuities in the rock mass that is perturbed first by mining and then by radiogenic heating. The laboratory can contribute precise measurements of the pertinent thermomechanical, hydrological and chemical properties and improve our understanding of the fundamental processes through careful experiments under well controlled conditions that simulate the prototype environment. Thus laboratory investigations are necessary, but they are not sufficient, for conventional sample sizes are small relative to natural defects like joints - i.e., the rock mass is not a continuum - and test durations are short compared to those that predictive modeling must take into account. Laboratory investigators can contribute substantially more useful data if they are provided facilities for testing large specimens(say one cubic meter) and for creep testing of all candidate host rocks. Even so, extrapolations of laboratory data to the field in neither space nor time are valid without the firm theoretical foundations yet to be built. Meanwhile in-situ measurements of structure-sensitive physical properties and access to direct observations of rock-mass character will be absolutely necessary

  3. Duchenne Muscular Dystrophy (DMD) Protein-Protein Interaction Mapping.

    Science.gov (United States)

    Rezaei Tavirani, Mostafa; OkHOVATIAN, Farshad; Zamanian Azodi, Mona; Rezaei Tavirani, Majid

    2017-01-01

    Duchenne muscular dystrophy (DMD) is one of the mortal diseases, subjected to study in terms of molecular investigation. In this study, the protein interaction map of this muscle-wasting condition was generated to gain a better knowledge of interactome profile of DMD. Applying Cytoscape and String Database, the protein-protein interaction network was constructed and the gene ontology of the constructed network was analyzed for biological process, molecular function, and cellular component annotations. Among 100 proteins related to DMD, dystrophin, utrophin, caveolin 3, and myogenic differentiation 1 play key roles in DMD network. In addition, the gene ontology analysis showed that regulation processes, kinase activity, and sarcoplasmic reticulum were the highlighted biological processes, molecular function, and cell component enrichments respectively for the proteins related to DMD. The central proteins and the enriched ontologies can be suggested as possible prominent agents in DMD; however, the validation studies may be required.

  4. Protein Polymers and Amyloids

    DEFF Research Database (Denmark)

    Risør, Michael Wulff

    2014-01-01

    Several human disorders are caused by a common general disease mechanism arising from abnormal folding and aggregation of the underlying protein. These include the prevalent dementias like Alzheimer’s and Parkinson’s, where accumulation of protein fibrillar structures, known as amyloid fibrils...... that inhibits its target protease through a large conformational change but mutations compromise this function and cause premature structural collapse into hyperstable polymers. Understanding the conformational disorders at a molecular level is not only important for our general knowledge on protein folding......, underlining the importance of understanding this relationship. The monomeric C-36 peptide was investigated by liquid-state NMR spectroscopy and found to be intrinsically disordered with minor propensities towards β-sheet structure. The plasticity of such a peptide makes it suitable for a whole range...

  5. Human neuronal stargazin-like proteins, γ2, γ3 and γ4; an investigation of their specific localization in human brain and their influence on CaV2.1 voltage-dependent calcium channels expressed in Xenopus oocytes.

    Directory of Open Access Journals (Sweden)

    Dolphin Annette C

    2003-09-01

    Full Text Available Abstract Background Stargazin (γ2 and the closely related γ3, and γ4 transmembrane proteins are part of a family of proteins that may act as both neuronal voltage-dependent calcium channel (VDCC γ subunits and transmembrane α-amino-3-hydroxy-5-methyl-4-isoxazoleproponinc (AMPA receptor regulatory proteins (TARPs. In this investigation, we examined the distribution patterns of the stargazin-like proteins γ2, γ3, and γ4 in the human central nervous system (CNS. In addition, we investigated whether human γ2 or γ4 could modulate the electrophysiological properties of a neuronal VDCC complex transiently expressed in Xenopus oocytes. Results The mRNA encoding human γ2 is highly expressed in cerebellum, cerebral cortex, hippocampus and thalamus, whereas γ3 is abundant in cerebral cortex and amygdala and γ4 in the basal ganglia. Immunohistochemical analysis of the cerebellum determined that both γ2 and γ4 are present in the molecular layer, particularly in Purkinje cell bodies and dendrites, but have an inverse expression pattern to one another in the dentate cerebellar nucleus. They are also detected in the interneurons of the granule cell layer though only γ2 is clearly detected in granule cells. The hippocampus stains for γ2 and γ4 throughout the layers of the every CA region and the dentate gyrus, whilst γ3 appears to be localized particularly to the pyramidal and granule cell bodies. When co-expressed in Xenopus oocytes with a CaV2.1/β4 VDCC complex, either in the absence or presence of an α2δ2 subunit, neither γ2 nor γ4 significantly modulated the VDCC peak current amplitude, voltage-dependence of activation or voltage-dependence of steady-state inactivation. Conclusion The human γ2, γ3 and γ4 stargazin-like proteins are detected only in the CNS and display differential distributions among brain regions and several cell types in found in the cerebellum and hippocampus. These distribution patterns closely resemble those

  6. Vibrational spectroscopy of proteins

    International Nuclear Information System (INIS)

    Schwaighofer, A.

    2013-01-01

    Two important steps for the development of a biosensor are the immobilization of the biological component (e.g. protein) on a surface and the enhancement of the signal to improve the sensitivity of detection. To address these subjects, the present work describes Fourier transform infrared (FTIR) investigations of several proteins bound to the surface of an attenuated total reflection (ATR) crystal. Furthermore, new nanostructured surfaces for signal enhancement were developed for use in FTIR microscopy. The mitochondrial redox-protein cytochrome c oxidase (CcO) was incorporated into a protein-tethered bilayer lipid membrane (ptBLM) on an ATR crystal featuring a roughened two-layer gold surface for signal enhancement. Electrochemical excitation by periodic potential pulses at different modulation frequencies was followed by time-resolved FTIR spectroscopy. Phase sensitive detection was used for deconvolution of the IR spectra into vibrational components. A model based on protonation-dependent chemical reaction kinetics could be fitted to the time evolution of IR bands attributed to several different redox centers of the CcO. Further investigations involved the odorant binding protein 14 (OBP14) of the honey bee (Apis mellifera), which was studied using ATR-FTIR spectroscopy and circular dichroism. OBP14 was found to be thermally stable up to 45 °C, thus permitting the potential application of this protein for the fabrication of biosensors. Thermal denaturation measurements showed that odorant binding increases the thermal stability of the OBP-odorant complex. In another project, plasmonic nanostructures were fabricated that enhance the absorbance in FTIR microscopy measurements. The nanostructures are composed of an array of round-shaped insulator and gold discs on top of a continuous gold layer. Enhancement factors of up to ⁓125 could be observed with self-assembled monolayers of dodecanethiol molecules immobilized on the gold surface (author) [de

  7. Heterogeneity in recombinant protein production

    DEFF Research Database (Denmark)

    Schalén, Martin; Johanson, Ted; Lundin, Luisa

    2012-01-01

    contribute to make a population in a fermenter heterogeneous, resulting in cell-to-cell variation in physiological parameters of the microbial culture. Our study aims at investigating how population heterogeneity and recombinant protein production is affected by environmental gradients in bioreactors....... For this purpose, a Saccharomyces cerevisiae strain, that functions as a protein production reporter, has been developed. A heterologous protein has been tagged with a fluorescent protein providing a way to measure the amount of heterologous protein produced by the cells on single cell level. Gradients...... are simulated in small bioreactors and the population heterogeneity can be visualised by analysing single cells with flow cytometry. This can give new insights to cell physiology and recombinant protein production at the industrial scale....

  8. NMR Studies of Protein Hydration and Protein-Ligand Interactions

    Science.gov (United States)

    Chong, Yuan

    Water on the surface of a protein is called hydration water. Hydration water is known to play a crucial role in a variety of biological processes including protein folding, enzymatic activation, and drug binding. Although the significance of hydration water has been recognized, the underlying mechanism remains far from being understood. This dissertation employs a unique in-situ nuclear magnetic resonance (NMR) technique to study the mechanism of protein hydration and the role of hydration in alcohol-protein interactions. Water isotherms in proteins are measured at different temperatures via the in-situ NMR technique. Water is found to interact differently with hydrophilic and hydrophobic groups on the protein. Water adsorption on hydrophilic groups is hardly affected by the temperature, while water adsorption on hydrophobic groups strongly depends on the temperature around 10 C, below which the adsorption is substantially reduced. This effect is induced by the dramatic decrease in the protein flexibility below 10 C. Furthermore, nanosecond to microsecond protein dynamics and the free energy, enthalpy, and entropy of protein hydration are studied as a function of hydration level and temperature. A crossover at 10 C in protein dynamics and thermodynamics is revealed. The effect of water at hydrophilic groups on protein dynamics and thermodynamics shows little temperature dependence, whereas water at hydrophobic groups has stronger effect above 10 C. In addition, I investigate the role of water in alcohol binding to the protein using the in-situ NMR detection. The isotherms of alcohols are first measured on dry proteins, then on proteins with a series of controlled hydration levels. The free energy, enthalpy, and entropy of alcohol binding are also determined. Two distinct types of alcohol binding are identified. On the one hand, alcohols can directly bind to a few specific sites on the protein. This type of binding is independent of temperature and can be

  9. Protein nanoparticles for therapeutic protein delivery.

    Science.gov (United States)

    Herrera Estrada, L P; Champion, J A

    2015-06-01

    Therapeutic proteins can face substantial challenges to their activity, requiring protein modification or use of a delivery vehicle. Nanoparticles can significantly enhance delivery of encapsulated cargo, but traditional small molecule carriers have some limitations in their use for protein delivery. Nanoparticles made from protein have been proposed as alternative carriers and have benefits specific to therapeutic protein delivery. This review describes protein nanoparticles made by self-assembly, including protein cages, protein polymers, and charged or amphipathic peptides, and by desolvation. It presents particle fabrication and delivery characterization for a variety of therapeutic and model proteins, as well as comparison of the features of different protein nanoparticles.

  10. Modeling Mercury in Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Smith, Jeremy C [ORNL; Parks, Jerry M [ORNL

    2016-01-01

    Mercury (Hg) is a naturally occurring element that is released into the biosphere both by natural processes and anthropogenic activities. Although its reduced, elemental form Hg(0) is relatively non-toxic, other forms such as Hg2+ and, in particular, its methylated form, methylmercury, are toxic, with deleterious effects on both ecosystems and humans. Microorganisms play important roles in the transformation of mercury in the environment. Inorganic Hg2+ can be methylated by certain bacteria and archaea to form methylmercury. Conversely, bacteria also demethylate methylmercury and reduce Hg2+ to relatively inert Hg(0). Transformations and toxicity occur as a result of mercury interacting with various proteins. Clearly, then, understanding the toxic effects of mercury and its cycling in the environment requires characterization of these interactions. Computational approaches are ideally suited to studies of mercury in proteins because they can provide a detailed picture and circumvent issues associated with toxicity. Here we describe computational methods for investigating and characterizing how mercury binds to proteins, how inter- and intra-protein transfer of mercury is orchestrated in biological systems, and how chemical reactions in proteins transform the metal. We describe quantum chemical analyses of aqueous Hg(II), which reveal critical factors that determine ligand binding propensities. We then provide a perspective on how we used chemical reasoning to discover how microorganisms methylate mercury. We also highlight our combined computational and experimental studies of the proteins and enzymes of the mer operon, a suite of genes that confers mercury resistance in many bacteria. Lastly, we place work on mercury in proteins in the context of what is needed for a comprehensive multi-scale model of environmental mercury cycling.

  11. Recombinant protein production technology

    Science.gov (United States)

    Recombinant protein production is an important technology for antibody production, biochemical activity study, and structural determination during the post-genomic era. Limiting factors in recombinant protein production include low-level protein expression, protein precipitation, and loss of protein...

  12. Kinetics of protein unfolding at interfaces

    International Nuclear Information System (INIS)

    Yano, Yohko F

    2012-01-01

    The conformation of protein molecules is determined by a balance of various forces, including van der Waals attraction, electrostatic interaction, hydrogen bonding, and conformational entropy. When protein molecules encounter an interface, they are often adsorbed on the interface. The conformation of an adsorbed protein molecule strongly depends on the interaction between the protein and the interface. Recent time-resolved investigations have revealed that protein conformation changes during the adsorption process due to the protein-protein interaction increasing with increasing interface coverage. External conditions also affect the protein conformation. This review considers recent dynamic observations of protein adsorption at various interfaces and their implications for the kinetics of protein unfolding at interfaces. (topical review)

  13. Protein aggregation and degradation during iodine labeling and its consequences for protein adsorption to biomaterials

    DEFF Research Database (Denmark)

    Holmberg, Maria; Jensen, Karin Bagger Stibius; Ndoni, Sokol

    2007-01-01

    Protein adsorption on modified and unmodified polymer surfaces investigated through radiolabeling experiments showed a tendency for higher than expected albumin and immunoglobulin G (IgG) adsorption. Possible enhanced protein aggregation and degradation caused by the iodine labeling method used...

  14. Raapzaadeiwitconcentraat en erwteneiwitconcentraat in biologisch biggenvoer = Canola protein concentrate and pea protein concentratrate in diets for organically housed piglets

    NARCIS (Netherlands)

    Peet-Schwering, van der C.M.C.; Binnendijk, G.P.; Diepen, van J.T.M.

    2011-01-01

    At the Experimental Farm Raalte it was investigated whether canola protein concentrate and pea protein concentrate are suitable protein-rich feedstuffs for organically housed piglets. It is concluded that both protein concentrates are suitable protein-rich feedstuffs for piglets. Feed intake and

  15. Advantages of isotopic depletion of proteins for hydrogen/deuterium exchange experiments monitored by mass spectrometry.

    Science.gov (United States)

    Bou-Assaf, George M; Chamoun, Jean E; Emmett, Mark R; Fajer, Piotr G; Marshall, Alan G

    2010-04-15

    Solution-phase hydrogen/deuterium exchange (HDX) monitored by mass spectrometry is an excellent tool to study protein-protein interactions and conformational changes in biological systems, especially when traditional methods such as X-ray crystallography or nuclear magnetic resonance are not feasible. Peak overlap among the dozens of proteolytic fragments (including those from autolysis of the protease) can be severe, due to high protein molecular weight(s) and the broad isotopic distributions due to multiple deuterations of many peptides. In addition, different subunits of a protein complex can yield isomeric proteolytic fragments. Here, we show that depletion of (13)C and/or (15)N for one or more protein subunits of a complex can greatly simplify the mass spectra, increase the signal-to-noise ratio of the depleted fragment ions, and remove ambiguity in assignment of the m/z values to the correct isomeric peptides. Specifically, it becomes possible to monitor the exchange progress for two isobaric fragments originating from two or more different subunits within the complex, without having to resort to tandem mass spectrometry techniques that can lead to deuterium scrambling in the gas phase. Finally, because the isotopic distribution for a small to medium-size peptide is essentially just the monoisotopic species ((12)C(c)(1)H(h)(14)N(n)(16)O(o)(32)S(s)), it is not necessary to deconvolve the natural abundance distribution for each partially deuterated peptide during HDX data reduction.

  16. Protein function prediction using neighbor relativity in protein-protein interaction network.

    Science.gov (United States)

    Moosavi, Sobhan; Rahgozar, Masoud; Rahimi, Amir

    2013-04-01

    There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called "Neighbor Relativity Coefficient" (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network. Copyright © 2012 Elsevier Ltd. All rights reserved.

  17. Protein Adsorption in Three Dimensions

    Science.gov (United States)

    Vogler, Erwin A.

    2011-01-01

    Recent experimental and theoretical work clarifying the physical chemistry of blood-protein adsorption from aqueous-buffer solution to various kinds of surfaces is reviewed and interpreted within the context of biomaterial applications, especially toward development of cardiovascular biomaterials. The importance of this subject in biomaterials surface science is emphasized by reducing the “protein-adsorption problem” to three core questions that require quantitative answer. An overview of the protein-adsorption literature identifies some of the sources of inconsistency among many investigators participating in more than five decades of focused research. A tutorial on the fundamental biophysical chemistry of protein adsorption sets the stage for a detailed discussion of the kinetics and thermodynamics of protein adsorption, including adsorption competition between two proteins for the same adsorbent immersed in a binary-protein mixture. Both kinetics and steady-state adsorption can be rationalized using a single interpretive paradigm asserting that protein molecules partition from solution into a three-dimensional (3D) interphase separating bulk solution from the physical-adsorbent surface. Adsorbed protein collects in one-or-more adsorbed layers, depending on protein size, solution concentration, and adsorbent surface energy (water wettability). The adsorption process begins with the hydration of an adsorbent surface brought into contact with an aqueous-protein solution. Surface hydration reactions instantaneously form a thin, pseudo-2D interface between the adsorbent and protein solution. Protein molecules rapidly diffuse into this newly-formed interface, creating a truly 3D interphase that inflates with arriving proteins and fills to capacity within milliseconds at mg/mL bulk-solution concentrations CB. This inflated interphase subsequently undergoes time-dependent (minutes-to-hours) decrease in volume VI by expulsion of either-or-both interphase water and

  18. Noninvasive imaging of protein-protein interactions in living animals

    Science.gov (United States)

    Luker, Gary D.; Sharma, Vijay; Pica, Christina M.; Dahlheimer, Julie L.; Li, Wei; Ochesky, Joseph; Ryan, Christine E.; Piwnica-Worms, Helen; Piwnica-Worms, David

    2002-05-01

    Protein-protein interactions control transcription, cell division, and cell proliferation as well as mediate signal transduction, oncogenic transformation, and regulation of cell death. Although a variety of methods have been used to investigate protein interactions in vitro and in cultured cells, none can analyze these interactions in intact, living animals. To enable noninvasive molecular imaging of protein-protein interactions in vivo by positron-emission tomography and fluorescence imaging, we engineered a fusion reporter gene comprising a mutant herpes simplex virus 1 thymidine kinase and green fluorescent protein for readout of a tetracycline-inducible, two-hybrid system in vivo. By using micro-positron-emission tomography, interactions between p53 tumor suppressor and the large T antigen of simian virus 40 were visualized in tumor xenografts of HeLa cells stably transfected with the imaging constructs. Imaging protein-binding partners in vivo will enable functional proteomics in whole animals and provide a tool for screening compounds targeted to specific protein-protein interactions in living animals.

  19. Modular protein switches derived from antibody mimetic proteins.

    Science.gov (United States)

    Nicholes, N; Date, A; Beaujean, P; Hauk, P; Kanwar, M; Ostermeier, M

    2016-02-01

    Protein switches have potential applications as biosensors and selective protein therapeutics. Protein switches built by fusion of proteins with the prerequisite input and output functions are currently developed using an ad hoc process. A modular switch platform in which existing switches could be readily adapted to respond to any ligand would be advantageous. We investigated the feasibility of a modular protein switch platform based on fusions of the enzyme TEM-1 β-lactamase (BLA) with two different antibody mimetic proteins: designed ankyrin repeat proteins (DARPins) and monobodies. We created libraries of random insertions of the gene encoding BLA into genes encoding a DARPin or a monobody designed to bind maltose-binding protein (MBP). From these libraries, we used a genetic selection system for β-lactamase activity to identify genes that conferred MBP-dependent ampicillin resistance to Escherichia coli. Some of these selected genes encoded switch proteins whose enzymatic activity increased up to 14-fold in the presence of MBP. We next introduced mutations into the antibody mimetic domain of these switches that were known to cause binding to different ligands. To different degrees, introduction of the mutations resulted in switches with the desired specificity, illustrating the potential modularity of these platforms. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  20. Protein recognition using synthetic small-molecular binders toward optical protein sensing in vitro and in live cells.

    Science.gov (United States)

    Kubota, Ryou; Hamachi, Itaru

    2015-07-07

    Chemical sensing of amino acids, peptides, and proteins provides fruitful information to understand their biological functions, as well as to develop the medical and technological applications. To detect amino acids, peptides, and proteins in vitro and in vivo, vast kinds of chemical sensors including small synthetic binders/sensors, genetically-encoded fluorescent proteins and protein-based semisynthetic biosensors have been intensely investigated. This review deals with concepts, strategies, and applications of protein recognition and sensing using small synthetic binders/sensors, which are now actively studied but still in the early stage of investigation. The recognition strategies for peptides and proteins can be divided into three categories: (i) recognition of protein substructures, (ii) protein surface recognition, and (iii) protein sensing through protein-ligand interaction. Here, we overview representative examples of protein recognition and sensing, and discuss biological or diagnostic applications such as potent inhibitors/modulators of protein-protein interactions.

  1. Aquaporin Protein-Protein Interactions

    Directory of Open Access Journals (Sweden)

    Jennifer Virginia Roche

    2017-10-01

    Full Text Available Aquaporins are tetrameric membrane-bound channels that facilitate transport of water and other small solutes across cell membranes. In eukaryotes, they are frequently regulated by gating or trafficking, allowing for the cell to control membrane permeability in a specific manner. Protein–protein interactions play crucial roles in both regulatory processes and also mediate alternative functions such as cell adhesion. In this review, we summarize recent knowledge about aquaporin protein–protein interactions; dividing the interactions into three types: (1 interactions between aquaporin tetramers; (2 interactions between aquaporin monomers within a tetramer (hetero-tetramerization; and (3 transient interactions with regulatory proteins. We particularly focus on the structural aspects of the interactions, discussing the small differences within a conserved overall fold that allow for aquaporins to be differentially regulated in an organism-, tissue- and trigger-specific manner. A deep knowledge about these differences is needed to fully understand aquaporin function and regulation in many physiological processes, and may enable design of compounds targeting specific aquaporins for treatment of human disease.

  2. Protein-stabilized magnetic fluids

    Energy Technology Data Exchange (ETDEWEB)

    Soenen, S.J.H. [Interdisciplinary Research Center, Katholieke Universiteit Leuven-Campus Kortrijk, University Campus, B-8500 Kortrijk (Belgium); Hodenius, M.; Schmitz-Rode, T. [Helmholtz Institute, Applied Medical Engineering, RWTH Aachen University, Aachen (Germany); De Cuyper, M. [Interdisciplinary Research Center, Katholieke Universiteit Leuven-Campus Kortrijk, University Campus, B-8500 Kortrijk (Belgium)], E-mail: Marcel.DeCuyper@KULeuven-Kortrijk.be

    2008-03-15

    The adsorption of bovine serum albumin (BSA) and egg yolk phosvitin on magnetic fluid particles was investigated. Incubation mixtures were prepared by mixing an alkaline suspension of tetramethylammonium-coated magnetite cores with protein solutions at various protein/Fe{sub 3}O{sub 4} ratios, followed by dialysis against a 5 mM TES buffer (pH 7.0), after which separation of bound and non-bound protein by high-gradient magnetophoresis was executed. Both the kinetic profiles as well as the isotherms of adsorption strongly differed for both proteins. In case of the spherical BSA, initially, abundant adsorption occurred, then it decreased and-at high protein concentrations-it slowly raised again. In contrast, with the highly phosphorylated phosvitin, binding slowly started and the extent of protein adsorption remained unchanged both as a function of time and phosvitin concentration. Competition binding studies, using binary protein mixtures composed of equal weight amounts of BSA and phosvitin, showed that binding of the latter protein is 'unrealistically' high. Based on the geometry of the two proteins, putative pictures on their orientation on the particle's surface in the various experimental conditions were deduced.

  3. Dynamics of hydration water and coupled protein sidechains around a polymerase protein surface

    Science.gov (United States)

    Qin, Yangzhong; Yang, Yi; Wang, Lijuan; Zhong, Dongping

    2017-09-01

    Water-protein coupled interactions are essential to the protein structural stability, flexibility and dynamic functions. The ultimate effects of the hydration dynamics on the protein fluctuations remain substantially unexplored. Here, we investigated the dynamics of both hydration water and protein sidechains at 13 different sites around the polymerase β protein surface using a tryptophan scan with femtosecond spectroscopy. Three types of hydration-water relaxations and two types of protein sidechain motions were determined, reflecting a highly dynamic water-protein interactions fluctuating on the picosecond time scales. The hydration-water dynamics dominate the coupled interactions with higher flexibility.

  4. Non-food applications of Jatropha protein

    OpenAIRE

    Lestari, D.

    2012-01-01

    The aim of this thesis is to explore how to gain more value per hectare Jatropha curcas by utilizing Jatropha protein for various applications. Specifically, this research investigated the extractability and functional properties of Jatropha protein for non-food/technical applications. Jatropha press cake and leaves are the potential sources of protein. Jatropha proteins can be extracted from Jatropha seed press cake or leaves, with or without detoxification to remove the toxic phorbol esters...

  5. Protein immobilization strategies for protein biochips

    NARCIS (Netherlands)

    Rusmini, F.; Rusmini, Federica; Zhong, Zhiyuan; Feijen, Jan

    2007-01-01

    In the past few years, protein biochips have emerged as promising proteomic and diagnostic tools for obtaining information about protein functions and interactions. Important technological innovations have been made. However, considerable development is still required, especially regarding protein

  6. Soliton/exciton transport in proteins.

    Science.gov (United States)

    Sinkala, Zachariah

    2006-08-21

    The study of electron/proton transport in alpha-helix sections of proteins have illustrated the existence of soliton-like mechanisms. Recently, Ciblis and Cosic extended investigation to the existence of possible like soliton-type mechanisms in other parts of the protein. They used Quantum Hamiltonian analysis to investigate. In this paper, we investigate the same problem but we use Classical Hamiltonian analysis in our investigation.

  7. Metabolism of biologics: biotherapeutic proteins.

    Science.gov (United States)

    Hamuro, Lora L; Kishnani, Narendra S

    2012-01-01

    Recombinant therapeutic protein drugs have now been in clinical use for nearly three decades and have advanced considerably in complexity over this time period. Regulatory approvals of some early pioneering protein drugs did not require characterization of metabolism, but more recently regulatory expectations and guidance have appropriately evolved. Sponsors may now be expected to investigate metabolism of newer biologics as the structural complexity of proteins has increased markedly, particularly with the introduction of conjugated and modified proteins. This review discusses the value and need for metabolite characterization of some therapeutic proteins by presenting select examples. Regulatory expectations will undoubtedly evolve further with the development of other novel macromolecular biologic therapeutics based on modified nucleic acids, novel conjugated lipids and polysaccharides.

  8. Advances in organometallic and protein chemistry

    OpenAIRE

    Ryan, C. P.

    2010-01-01

    This thesis describes two areas of scientific investigation. The first contains a description of a study on the synthesis of biotinylated and fluoresceinylated bromomaleimide based reagents. Upon synthesis, the ability of these reagents to add reversibly to cysteine containing proteins is investigated by a series of LCMS experiments. A single point mutant (L111C) of the SH2 domain of the Grb2 adaptor protein, containing a single cysteine residue, is chosen as an ideal protein for study. Thus ...

  9. Secretory proteins of the pulmonary extracellular lining

    International Nuclear Information System (INIS)

    Gupta, R.P.; Patton, S.E.; Eddy, M.; Smits, H.L.; Jetten, A.M.; Nettesheim, P.; Hook, G.E.R.

    1986-01-01

    The objective of this investigation was to identify proteins in the pulmonary extracellular lining (EL) that are secreted by cells of the pulmonary epithelium. Pulmonary lavage effluents from the lungs of rabbits were centrifuged to remove all cells and particulate materials. Serum proteins were removed by repeatedly passing concentrated lavage effluent fluid through an affinity column containing IgG fraction of goat anti-rabbit (whole serum) antiserum bound to Sepharose-4B. Nonserum proteins accounted for 21.3 +/- 10.3% of the total soluble proteins in pulmonary lavage effluents. Serum free lavage effluents (SFL) contained 25 identifiable proteins as determined by using SDS-PAGE under reducing conditions. Of these proteins approximately 73% was accounted for by a single protein with MW of 66 kd. The secretory nature of the proteins present in SFL was investigated by studying the incorporation of 35 S-methionine into proteins released by lung slices and trachea followed by SDS-PAGE and autoradiography. Many, but not all proteins present in SFL were identified as proteins secreted by pulmonary tissues. The major secretory proteins appeared to have MWs of 59, 53, 48, 43, 24, 14, and 6 kd under reducing conditions. These data demonstrate the presence of several proteins in the pulmonary extracellular lining that appear to be secreted by the pulmonary epithelium

  10. Influence of protein abundance on high-throughput protein-protein interaction detection.

    Directory of Open Access Journals (Sweden)

    Joseph Ivanic

    2009-06-01

    Full Text Available Experimental protein-protein interaction (PPI networks are increasingly being exploited in diverse ways for biological discovery. Accordingly, it is vital to discern their underlying natures by identifying and classifying the various types of deterministic (specific and probabilistic (nonspecific interactions detected. To this end, we have analyzed PPI networks determined using a range of high-throughput experimental techniques with the aim of systematically quantifying any biases that arise from the varying cellular abundances of the proteins. We confirm that PPI networks determined using affinity purification methods for yeast and Escherichia coli incorporate a correlation between protein degree, or number of interactions, and cellular abundance. The observed correlations are small but statistically significant and occur in both unprocessed (raw and processed (high-confidence data sets. In contrast, the yeast two-hybrid system yields networks that contain no such relationship. While previously commented based on mRNA abundance, our more extensive analysis based on protein abundance confirms a systematic difference between PPI networks determined from the two technologies. We additionally demonstrate that the centrality-lethality rule, which implies that higher-degree proteins are more likely to be essential, may be misleading, as protein abundance measurements identify essential proteins to be more prevalent than nonessential proteins. In fact, we generally find that when there is a degree/abundance correlation, the degree distributions of nonessential and essential proteins are also disparate. Conversely, when there is no degree/abundance correlation, the degree distributions of nonessential and essential proteins are not different. However, we show that essentiality manifests itself as a biological property in all of the yeast PPI networks investigated here via enrichments of interactions between essential proteins. These findings provide

  11. Influence of protein abundance on high-throughput protein-protein interaction detection.

    Science.gov (United States)

    Ivanic, Joseph; Yu, Xueping; Wallqvist, Anders; Reifman, Jaques

    2009-06-05

    Experimental protein-protein interaction (PPI) networks are increasingly being exploited in diverse ways for biological discovery. Accordingly, it is vital to discern their underlying natures by identifying and classifying the various types of deterministic (specific) and probabilistic (nonspecific) interactions detected. To this end, we have analyzed PPI networks determined using a range of high-throughput experimental techniques with the aim of systematically quantifying any biases that arise from the varying cellular abundances of the proteins. We confirm that PPI networks determined using affinity purification methods for yeast and Escherichia coli incorporate a correlation between protein degree, or number of interactions, and cellular abundance. The observed correlations are small but statistically significant and occur in both unprocessed (raw) and processed (high-confidence) data sets. In contrast, the yeast two-hybrid system yields networks that contain no such relationship. While previously commented based on mRNA abundance, our more extensive analysis based on protein abundance confirms a systematic difference between PPI networks determined from the two technologies. We additionally demonstrate that the centrality-lethality rule, which implies that higher-degree proteins are more likely to be essential, may be misleading, as protein abundance measurements identify essential proteins to be more prevalent than nonessential proteins. In fact, we generally find that when there is a degree/abundance correlation, the degree distributions of nonessential and essential proteins are also disparate. Conversely, when there is no degree/abundance correlation, the degree distributions of nonessential and essential proteins are not different. However, we show that essentiality manifests itself as a biological property in all of the yeast PPI networks investigated here via enrichments of interactions between essential proteins. These findings provide valuable insights

  12. An insert-based enzymatic cell culture system to rapidly and reversibly induce hypoxia: investigations of hypoxia-induced cell damage, protein expression and phosphorylation in neuronal IMR-32 cells

    Directory of Open Access Journals (Sweden)

    Ying Huang

    2013-11-01

    Ischemia-reperfusion injury and tissue hypoxia are of high clinical relevance because they are associated with various pathophysiological conditions such as myocardial infarction and stroke. Nevertheless, the underlying mechanisms causing cell damage are still not fully understood, which is at least partially due to the lack of cell culture systems for the induction of rapid and transient hypoxic conditions. The aim of the study was to establish a model that is suitable for the investigation of cellular and molecular effects associated with transient and long-term hypoxia and to gain insights into hypoxia-mediated mechanisms employing a neuronal culture system. A semipermeable membrane insert system in combination with the hypoxia-inducing enzymes glucose oxidase and catalase was employed to rapidly and reversibly generate hypoxic conditions in the culture medium. Hydrogen peroxide assays, glucose measurements and western blotting were performed to validate the system and to evaluate the effects of the generated hypoxia on neuronal IMR-32 cells. Using the insert-based two-enzyme model, hypoxic conditions were rapidly induced in the culture medium. Glucose concentrations gradually decreased, whereas levels of hydrogen peroxide were not altered. Moreover, a rapid and reversible (onoff generation of hypoxia could be performed by the addition and subsequent removal of the enzyme-containing inserts. Employing neuronal IMR-32 cells, we showed that 3 hours of hypoxia led to morphological signs of cellular damage and significantly increased levels of lactate dehydrogenase (a biochemical marker of cell damage. Hypoxic conditions also increased the amounts of cellular procaspase-3 and catalase as well as phosphorylation of the pro-survival kinase Akt, but not Erk1/2 or STAT5. In summary, we present a novel framework for investigating hypoxia-mediated mechanisms at the cellular level. We claim that the model, the first of its kind, enables researchers to rapidly and

  13. Learning about Proteins

    Science.gov (United States)

    ... Videos for Educators Search English Español Learning About Proteins KidsHealth / For Kids / Learning About Proteins What's in ... from the foods you eat. Different Kinds of Protein Protein from animal sources, such as meat and ...

  14. Protein intake does not increase vastus lateralis muscle protein synthesis during cycling

    DEFF Research Database (Denmark)

    Hulston, CJ; Wolsk, Emil; Grøndahl, Thomas Sahl

    2011-01-01

    that consuming protein during prolonged bicycle exercise does not increase protein synthesis within highly active leg muscles. However, protein intake may have stimulated protein synthesis within less active leg muscles and/or other nonmuscle leg tissue. Finally, protein supplementation, during exercise......PURPOSE: This study aimed to investigate the effect of protein ingestion on leg protein turnover and vastus lateralis muscle protein synthesis during bicycle exercise and recovery. METHODS: Eight healthy males participated in two experiments in which they ingested either a carbohydrate solution...... (CHO) providing 0.49 g·kg(-1)·h(-1), or a carbohydrate and protein solution (CHO + P) providing 0.49 and 0.16 g·kg(-1)·h(-1), during 3 h of bicycle exercise and 3 h of recovery. Leg protein turnover was determined from stable isotope infusion (l-[ring-C6]phenylalanine), femoral-arterial venous blood...

  15. Preserved skeletal muscle protein anabolic response to acute exercise and protein intake in well-treated rheumatoid arthritis patients

    DEFF Research Database (Denmark)

    Mikkelsen, Ulla Ramer; Dideriksen, Kasper; Andersen, Mads Bisgaard

    2015-01-01

    INTRODUCTION: Rheumatoid arthritis (RA) is often associated with diminished muscle mass, reflecting an imbalance between protein synthesis and protein breakdown. To investigate the anabolic potential of both exercise and nutritional protein intake we investigated the muscle protein synthesis rate...... and in combination with physical exercise in patients with well-treated RA to a similar extent as in healthy individuals. This indicates that moderately inflamed RA patients have maintained their muscle anabolic responsiveness to physical activity and protein intake....

  16. Prion Protein and Aging

    Directory of Open Access Journals (Sweden)

    Lisa eGasperini

    2014-08-01

    Full Text Available The cellular prion protein (PrPC has been widely investigated ever since its conformational isoform, the prion (or PrPSc, was identified as the etiological agent of prion disorders. The high homology shared by the PrPC-encoding gene among mammals, its high turnover rate and expression in every tissue strongly suggest that PrPC may possess key physiological functions. Therefore, defining PrPC roles, properties and fate in the physiology of mammalian cells would be fundamental to understand its pathological involvement in prion diseases. Since the incidence of these neurodegenerative disorders is enhanced in aging, understanding PrPC functions in this life phase may be of crucial importance. Indeed, a large body of evidence suggests that PrPC plays a neuroprotective and antioxidant role. Moreover, it has been suggested that PrPC is involved in Alzheimer disease, another neurodegenerative pathology that develops predominantly in the aging population. In prion diseases, PrPC function is likely lost upon protein aggregation occurring in the course of the disease. Additionally, the aging process may alter PrPC biochemical properties, thus influencing its propensity to convert into PrPSc. Both phenomena may contribute to the disease development and progression. In Alzheimer disease, PrPC has a controversial role because its presence seems to mediate β-amyloid toxicity, while its down-regulation correlates with neuronal death. The role of PrPC in aging has been investigated from different perspectives, often leading to contrasting results. The putative protein functions in aging have been studied in relation to memory, behavior and myelin maintenance. In aging mice, PrPC changes in subcellular localization and post-translational modifications have been explored in an attempt to relate them to different protein roles and propensity to convert into PrPSc. Here we provide an overview of the most relevant studies attempting to delineate PrPC functions and

  17. Proteomic Investigations into Hemodialysis Therapy

    Science.gov (United States)

    Bonomini, Mario; Sirolli, Vittorio; Pieroni, Luisa; Felaco, Paolo; Amoroso, Luigi; Urbani, Andrea

    2015-01-01

    The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(in)compatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research. PMID:26690416

  18. Proteomic Investigations into Hemodialysis Therapy

    Directory of Open Access Journals (Sweden)

    Mario Bonomini

    2015-12-01

    Full Text Available The retention of a number of solutes that may cause adverse biochemical/biological effects, called uremic toxins, characterizes uremic syndrome. Uremia therapy is based on renal replacement therapy, hemodialysis being the most commonly used modality. The membrane contained in the hemodialyzer represents the ultimate determinant of the success and quality of hemodialysis therapy. Membrane’s performance can be evaluated in terms of removal efficiency for unwanted solutes and excess fluid, and minimization of negative interactions between the membrane material and blood components that define the membrane’s bio(incompatibility. Given the high concentration of plasma proteins and the complexity of structural functional relationships of this class of molecules, the performance of a membrane is highly influenced by its interaction with the plasma protein repertoire. Proteomic investigations have been increasingly applied to describe the protein uremic milieu, to compare the blood purification efficiency of different dialyzer membranes or different extracorporeal techniques, and to evaluate the adsorption of plasma proteins onto hemodialysis membranes. In this article, we aim to highlight investigations in the hemodialysis setting making use of recent developments in proteomic technologies. Examples are presented of why proteomics may be helpful to nephrology and may possibly affect future directions in renal research.

  19. Competitive Protein Adsorption - Multilayer Adsorption and Surface Induced Protein Aggregation

    DEFF Research Database (Denmark)

    Holmberg, Maria; Hou, Xiaolin

    2009-01-01

    and that the outcome of IgG adsorption is much more sensitive to surface characteristics than the outcome of albumin adsorption. Using high concentrations of protein solution and hydrophobic polymer surfaces during adsorption can induce IgG aggregation, which is observed as extremely high IgG adsorptions. Besides......In this study, competitive adsorption of albumin and IgG (immunoglobulin G) from human serum solutions and protein mixtures onto polymer surfaces is studied by means of radioactive labeling. By using two different radiolabels (125I and 131I), albumin and IgG adsorption to polymer surfaces...... is monitored simultaneously and the influence from the presence of other human serum proteins on albumin and IgG adsorption, as well as their mutual influence during adsorption processes, is investigated. Exploring protein adsorption by combining analysis of competitive adsorption from complex solutions...

  20. Plant protein for food: opportunities and bottlenecks

    Directory of Open Access Journals (Sweden)

    Chardigny Jean-Michel

    2016-07-01

    Full Text Available Dietary proteins represent a key issue for the future regarding worldwide food security. Besides animal sources, plant proteins represent an opportunity to mainly contribute to protein demand. Whether some plant protein sources could appear as deficient in some essential amino acids, mixtures from different sources could represent opportunities to further propose adapted supply regarding specific demand. Such opportunities includes legumes as well as by-products of oil processing, i.e. canola and sunflower cakes. The nutritional benefits of such new sources are still under investigation considering benefits and limits like allergenicity. Finally, consumer behavior and acceptability remains the final bottleneck for developing new protein sources.

  1. Fusion-protein-assisted protein crystallization.

    Science.gov (United States)

    Kobe, Bostjan; Ve, Thomas; Williams, Simon J

    2015-07-01

    Fusion proteins can be used directly in protein crystallization to assist crystallization in at least two different ways. In one approach, the `heterologous fusion-protein approach', the fusion partner can provide additional surface area to promote crystal contact formation. In another approach, the `fusion of interacting proteins approach', protein assemblies can be stabilized by covalently linking the interacting partners. The linker connecting the proteins plays different roles in the two applications: in the first approach a rigid linker is required to reduce conformational heterogeneity; in the second, conversely, a flexible linker is required that allows the native interaction between the fused proteins. The two approaches can also be combined. The recent applications of fusion-protein technology in protein crystallization from the work of our own and other laboratories are briefly reviewed.

  2. Membrane bending by protein-protein crowding.

    Science.gov (United States)

    Stachowiak, Jeanne C; Schmid, Eva M; Ryan, Christopher J; Ann, Hyoung Sook; Sasaki, Darryl Y; Sherman, Michael B; Geissler, Phillip L; Fletcher, Daniel A; Hayden, Carl C

    2012-09-01

    Curved membranes are an essential feature of dynamic cellular structures, including endocytic pits, filopodia protrusions and most organelles. It has been proposed that specialized proteins induce curvature by binding to membranes through two primary mechanisms: membrane scaffolding by curved proteins or complexes; and insertion of wedge-like amphipathic helices into the membrane. Recent computational studies have raised questions about the efficiency of the helix-insertion mechanism, predicting that proteins must cover nearly 100% of the membrane surface to generate high curvature, an improbable physiological situation. Thus, at present, we lack a sufficient physical explanation of how protein attachment bends membranes efficiently. On the basis of studies of epsin1 and AP180, proteins involved in clathrin-mediated endocytosis, we propose a third general mechanism for bending fluid cellular membranes: protein-protein crowding. By correlating membrane tubulation with measurements of protein densities on membrane surfaces, we demonstrate that lateral pressure generated by collisions between bound proteins drives bending. Whether proteins attach by inserting a helix or by binding lipid heads with an engineered tag, protein coverage above ~20% is sufficient to bend membranes. Consistent with this crowding mechanism, we find that even proteins unrelated to membrane curvature, such as green fluorescent protein (GFP), can bend membranes when sufficiently concentrated. These findings demonstrate a highly efficient mechanism by which the crowded protein environment on the surface of cellular membranes can contribute to membrane shape change.

  3. EDITORIAL: Precision proteins Precision proteins

    Science.gov (United States)

    Demming, Anna

    2010-06-01

    Since the birth of modern day medicine, during the times of Hippocrates in ancient Greece, the profession has developed from the rudimentary classification of disease into a rigorous science with an inspiring capability to treat and cure. Scientific methodology has distilled clinical diagnostic tools from the early arts of prognosis, which used to rely as much on revelation and prophecy, as intuition and judgement [1]. Over the past decade, research into the interactions between proteins and nanosystems has provided some ingenious and apt techniques for delving into the intricacies of anatomical systems. In vivo biosensing has emerged as a vibrant field of research, as much of medical diagnosis relies on the detection of substances or an imbalance in the chemicals in the body. The inherent properties of nanoscale structures, such as cantilevers, make them well suited to biosensing applications that demand the detection of molecules at very low concentrations. Measurable deflections in cantilevers functionalised with antibodies provide quantitative indicators of the presence of specific antigens when the two react. Such developments have roused mounting interest in the interactions of proteins with nanostructures, such as carbon nanotubes [3], which have demonstrated great potential as generic biomarkers. Plasmonic properties are also being exploited in sensing applications, such as the molecular sentinel recently devised by researchers in the US. The device uses the plasmonic properties of a silver nanoparticle linked to a Raman labelled hairpin DNA probe to signal changes in the probe geometry resulting from interactions with substances in the environment. Success stories so far include the detection of two specific genes associated with breast cancer [4]. A greater understanding of how RNA interference regulates gene expression has highlighted the potential of using this natural process as another agent for combating disease in personalized medicine. However, the

  4. Characterization and quantification of intact 26S proteasome proteins by real-time measurement of intrinsic fluorescence prior to top-down mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Jason D Russell

    Full Text Available Quantification of gas-phase intact protein ions by mass spectrometry (MS is impeded by highly-variable ionization, ion transmission, and ion detection efficiencies. Therefore, quantification of proteins using MS-associated techniques is almost exclusively done after proteolysis where peptides serve as proxies for estimating protein abundance. Advances in instrumentation, protein separations, and informatics have made large-scale sequencing of intact proteins using top-down proteomics accessible to the proteomics community; yet quantification of proteins using a top-down workflow has largely been unaddressed. Here we describe a label-free approach to determine the abundance of intact proteins separated by nanoflow liquid chromatography prior to MS analysis by using solution-phase measurements of ultraviolet light-induced intrinsic fluorescence (UV-IF. UV-IF is measured directly at the electrospray interface just prior to the capillary exit where proteins containing at least one tryptophan residue are readily detected. UV-IF quantification was demonstrated using commercially available protein standards and provided more accurate and precise protein quantification than MS ion current. We evaluated the parallel use of UV-IF and top-down tandem MS for quantification and identification of protein subunits and associated proteins from an affinity-purified 26S proteasome sample from Arabidopsis thaliana. We identified 26 unique proteins and quantified 13 tryptophan-containing species. Our analyses discovered previously unidentified N-terminal processing of the β6 (PBF1 and β7 (PBG1 subunit - such processing of PBG1 may generate a heretofore unknown additional protease active site upon cleavage. In addition, our approach permitted the unambiguous identification and quantification both isoforms of the proteasome-associated protein DSS1.

  5. PSAIA – Protein Structure and Interaction Analyzer

    Directory of Open Access Journals (Sweden)

    Vlahoviček Kristian

    2008-04-01

    Full Text Available Abstract Background PSAIA (Protein Structure and Interaction Analyzer was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites.

  6. Gas-phase hydrogen/deuterium exchange in a traveling wave ion guide for the examination of protein conformations.

    Science.gov (United States)

    Rand, Kasper D; Pringle, Steven D; Murphy, James P; Fadgen, Keith E; Brown, Jeff; Engen, John R

    2009-12-15

    Accumulating evidence suggests that solution-phase conformations of small globular proteins and large molecular protein assemblies can be preserved for milliseconds after electrospray ionization. Thus, the study of proteins in the gas phase on this time scale is highly desirable. Here we demonstrate that a traveling wave ion guide (TWIG) of a Synapt mass spectrometer offers a highly suitable environment for rapid and efficient gas-phase hydrogen/deuterium exchange (HDX). Gaseous ND(3) was introduced into either the source TWIG or the TWIG located just after the ion mobility cell, such that ions underwent HDX as they passed through the ND(3) on the way to the time-of-flight analyzer. The extent of deuterium labeling could be controlled by varying the quantity of ND(3) or the speed of the traveling wave. The gas-phase HDX of model peptides corresponded to labeling of primarily fast exchanging sites due to the short labeling times (ranging from 0.1 to 10 ms). In addition to peptides, gas-phase HDX of ubiquitin, cytochrome c, lysozyme, and apomyoglobin were examined. We conclude that HDX of protein ions in a TWIG is highly sensitive to protein conformation, enables the detection of conformers present on submilliseconds time scales, and can readily be combined with ion mobility spectrometry.

  7. Conserved cysteine residues provide a protein-protein interaction surface in dual oxidase (DUOX) proteins.

    Science.gov (United States)

    Meitzler, Jennifer L; Hinde, Sara; Bánfi, Botond; Nauseef, William M; Ortiz de Montellano, Paul R

    2013-03-08

    Intramolecular disulfide bond formation is promoted in oxidizing extracellular and endoplasmic reticulum compartments and often contributes to protein stability and function. DUOX1 and DUOX2 are distinguished from other members of the NOX protein family by the presence of a unique extracellular N-terminal region. These peroxidase-like domains lack the conserved cysteines that confer structural stability to mammalian peroxidases. Sequence-based structure predictions suggest that the thiol groups present are solvent-exposed on a single protein surface and are too distant to support intramolecular disulfide bond formation. To investigate the role of these thiol residues, we introduced four individual cysteine to glycine mutations in the peroxidase-like domains of both human DUOXs and purified the recombinant proteins. The mutations caused little change in the stabilities of the monomeric proteins, supporting the hypothesis that the thiol residues are solvent-exposed and not involved in disulfide bonds that are critical for structural integrity. However, the ability of the isolated hDUOX1 peroxidase-like domain to dimerize was altered, suggesting a role for these cysteines in protein-protein interactions that could facilitate homodimerization of the peroxidase-like domain or, in the full-length protein, heterodimeric interactions with a maturation protein. When full-length hDUOX1 was expressed in HEK293 cells, the mutations resulted in decreased H2O2 production that correlated with a decreased amount of the enzyme localized to the membrane surface rather than with a loss of activity or with a failure to synthesize the mutant proteins. These results support a role for the cysteine residues in intermolecular disulfide bond formation with the DUOX maturation factor DUOXA1.

  8. Protein docking prediction using predicted protein-protein interface

    Directory of Open Access Journals (Sweden)

    Li Bin

    2012-01-01

    Full Text Available Abstract Background Many important cellular processes are carried out by protein complexes. To provide physical pictures of interacting proteins, many computational protein-protein prediction methods have been developed in the past. However, it is still difficult to identify the correct docking complex structure within top ranks among alternative conformations. Results We present a novel protein docking algorithm that utilizes imperfect protein-protein binding interface prediction for guiding protein docking. Since the accuracy of protein binding site prediction varies depending on cases, the challenge is to develop a method which does not deteriorate but improves docking results by using a binding site prediction which may not be 100% accurate. The algorithm, named PI-LZerD (using Predicted Interface with Local 3D Zernike descriptor-based Docking algorithm, is based on a pair wise protein docking prediction algorithm, LZerD, which we have developed earlier. PI-LZerD starts from performing docking prediction using the provided protein-protein binding interface prediction as constraints, which is followed by the second round of docking with updated docking interface information to further improve docking conformation. Benchmark results on bound and unbound cases show that PI-LZerD consistently improves the docking prediction accuracy as compared with docking without using binding site prediction or using the binding site prediction as post-filtering. Conclusion We have developed PI-LZerD, a pairwise docking algorithm, which uses imperfect protein-protein binding interface prediction to improve docking accuracy. PI-LZerD consistently showed better prediction accuracy over alternative methods in the series of benchmark experiments including docking using actual docking interface site predictions as well as unbound docking cases.

  9. Shotgun protein sequencing.

    Energy Technology Data Exchange (ETDEWEB)

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  10. Our interests in protein-protein interactions

    Indian Academy of Sciences (India)

    protein interactions. Evolution of P-P partnerships. Evolution of P-P structures. Evolutionary dynamics of P-P interactions. Dynamics of P-P interaction network. Host-pathogen interactions. CryoEM mapping of gigantic protein assemblies.

  11. Investigation of dietary fiber, protein, vitamin E and other nutritional ...

    African Journals Online (AJOL)

    The nutritional composition of banana flowers of two cultivars [cvs. Baxijiao (AAA) and Paradisical (AAB)] grown in Hainan of China has been studied. Flower samples were collected and extracted according to methods of Association of Official Analytical Chemists (AOAC). Results showed that banana flowers contained ...

  12. Investigation of protein binding of radiogallium. Progress report

    International Nuclear Information System (INIS)

    Hoffer, P.B.

    1985-01-01

    The main objective of the contract is to study aspects of the localization of gallium-67 in tumor are reported and compared with a new tumor imaging agent, specifically radiolabeled monoclonal tumor antibody. Our studies have demonstrated that phosphate compounds used in bone imaging do not significantly influence gallium-67 localization, that the adenosine triphosphate cannot be used to enhance gallium-67 uptake in malignant tissue, and that gallium-67 has higher affinity than radiolabeled anti-p97 for melanoma, even in tumors which produce significant amounts of p97 antigen on their cell surface. 23 refs., 17 figs., 5 tabs

  13. Raman spectroscopy as a tool for investigating lipid protein interactions

    DEFF Research Database (Denmark)

    Petersen, Frederic Nicolas Rønne; Helix Nielsen, Claus

    2009-01-01

    Raman spectroscopy is a very well-established technique for noninvasive probing of chemical compounds. The fad that Raman scattering is an inherently weak effect has prompted many new developments in sample signal enhancement and techniques (such as surface-enhancement Raman spectroscopy [SERS]) ...

  14. Diffusivities of lysozyme in aqueous MgCl2 solutions from dynamic light-scattering data:  Effect of protein and salt concentrations

    Energy Technology Data Exchange (ETDEWEB)

    Grigsby, J. J. [Univ. of California, Berkeley, CA (United States); Blanch, H. W. [Univ. of California, Berkeley, CA (United States); Prausnitz, J. M. [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2000-03-25

    Dynamic light-scattering (DLS) studies are reported for lysozyme in aqueous magnesium chloride solutions at ionic strengths 0.6, 0.8, and 1.0 M for a temperature range 10–30 °C at pH 4.0. The diffusion coefficient of lysozyme was calculated as a function of protein concentration, salt concentration, temperature, and scattering angle. A Zimm-plot analysis provided the infinitely-dilute diffusion coefficient and the protein-concentration dependence of the diffusion coefficient. The hydrodynamic radius of a lysozyme monomer was obtained from the Stokes–Einstein equation; it is 18.6 ± 1.0 Å. The difference (1.4 Å) between the hydrodynamic and the crystal-structure radius is attributed to binding of Mg2+ ions to the protein surface and subsequent water structuring. The effect of protein concentration on the diffusion coefficient indicates that attractive interactions increase as the temperature falls at fixed salt concentration. However, when plotted against ionic strength, attractive interactions exhibit a maximum at ionic strength 0.84 M, probably because Mg2+protein binding and water structuring become increasingly important as the concentration of magnesium ion rises. Finally, the present work suggests that inclusion of ion binding and water structuring at the protein surface in a pair-potential model is needed to achieve accurate predictions of protein-solution phase behavior.

  15. Nano-Bio Interactions of Porous and Nonporous Silica Nanoparticles of Varied Surface Chemistry: A Structural, Kinetic, and Thermodynamic Study of Protein Adsorption from RPMI Culture Medium.

    Science.gov (United States)

    Lehman, Sean E; Mudunkotuwa, Imali A; Grassian, Vicki H; Larsen, Sarah C

    2016-01-26

    Understanding complex chemical changes that take place at nano-bio interfaces is of great concern for being able to sustainably implement nanomaterials in key applications such as drug delivery, imaging, and environmental remediation. Typical in vitro assays use cell viability as a proxy to understanding nanotoxicity but often neglect how the nanomaterial surface can be altered by adsorption of solution-phase components in the medium. Protein coronas form on the nanomaterial surface when incubated in proteinaceous solutions. Herein, we apply a broad array of techniques to characterize and quantify protein corona formation on silica nanoparticle surfaces. The porosity and surface chemistry of the silica nanoparticles have been systematically varied. Using spectroscopic tools such as FTIR and circular dichroism, structural changes and kinetic processes involved in protein adsorption were evaluated. Additionally, by implementing thermogravimetric analysis, quantitative protein adsorption measurements allowed for the direct comparison between samples. Taken together, these measurements enabled the extraction of useful chemical information on protein binding onto nanoparticles in solution. Overall, we demonstrate that small alkylamines can increase protein adsorption and that even large polymeric molecules such as poly(ethylene glycol) (PEG) cannot prevent protein adsorption in these systems. The implications of these results as they relate to further understanding nano-bio interactions are discussed.

  16. Evolution of protein-protein interactions

    Indian Academy of Sciences (India)

    Evolution of protein-protein interactions · Our interests in protein-protein interactions · Slide 3 · Slide 4 · Slide 5 · Slide 6 · Slide 7 · Slide 8 · Slide 9 · Slide 10 · Slide 11 · Slide 12 · Slide 13 · Slide 14 · Slide 15 · Slide 16 · Slide 17 · Slide 18 · Slide 19 · Slide 20.

  17. Development of a system for the study of protein-protein interactions in planta: characterization of a TATA-box binding protein complex in Oryza sativa.

    Science.gov (United States)

    Zhong, Jingping; Haynes, Paul A; Zhang, Shiping; Yang, Xinping; Andon, Nancy L; Eckert, Donna; Yates, John R; Wang, Xun; Budworth, Paul

    2003-01-01

    We describe a simple, rapid method for protein complex purification in planta. Using a biotin peptide as an affinity tag with TATA-box binding protein (TBP), 86 unique proteins present in the purified complex were identified by tandem mass spectrometry. We identified proteins known to be associated with TBP, and many other proteins involved in pre-mRNA processing and chromatin remodeling. The identification of these novel protein-protein associations will upon further investigations provide new insights into the mechanisms of mRNA transcription and pre-mRNA processing.

  18. Ontological visualization of protein-protein interactions

    Directory of Open Access Journals (Sweden)

    Hill David P

    2005-02-01

    Full Text Available Abstract Background Cellular processes require the interaction of many proteins across several cellular compartments. Determining the collective network of such interactions is an important aspect of understanding the role and regulation of individual proteins. The Gene Ontology (GO is used by model organism databases and other bioinformatics resources to provide functional annotation of proteins. The annotation process provides a mechanism to document the binding of one protein with another. We have constructed protein interaction networks for mouse proteins utilizing the information encoded in the GO annotations. The work reported here presents a methodology for integrating and visualizing information on protein-protein interactions. Results GO annotation at Mouse Genome Informatics (MGI captures 1318 curated, documented interactions. These include 129 binary interactions and 125 interaction involving three or more gene products. Three networks involve over 30 partners, the largest involving 109 proteins. Several tools are available at MGI to visualize and analyze these data. Conclusions Curators at the MGI database annotate protein-protein interaction data from experimental reports from the literature. Integration of these data with the other types of data curated at MGI places protein binding data into the larger context of mouse biology and facilitates the generation of new biological hypotheses based on physical interactions among gene products.

  19. 24-hour urine protein

    Science.gov (United States)

    Urine protein - 24 hour; Chronic kidney disease - urine protein; Kidney failure - urine protein ... Heart failure High blood pressure during pregnancy ( preeclampsia ) Kidney disease caused by diabetes, high blood pressure, autoimmune disorders, ...

  20. Protein-losing enteropathy

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/007338.htm Protein-losing enteropathy To use the sharing features on this page, please enable JavaScript. Protein-losing enteropathy is an abnormal loss of protein ...

  1. Protein in diet

    Science.gov (United States)

    Diet - protein ... Protein foods are broken down into parts called amino acids during digestion. The human body needs a ... to eat animal products to get all the protein you need in your diet. Amino acids are ...

  2. Intricate knots in proteins: Function and evolution.

    Directory of Open Access Journals (Sweden)

    Peter Virnau

    2006-09-01

    Full Text Available Our investigation of knotted structures in the Protein Data Bank reveals the most complicated knot discovered to date. We suggest that the occurrence of this knot in a human ubiquitin hydrolase might be related to the role of the enzyme in protein degradation. While knots are usually preserved among homologues, we also identify an exception in a transcarbamylase. This allows us to exemplify the function of knots in proteins and to suggest how they may have been created.

  3. Analyzing Protein Dynamics Using Dimensionality Reduction

    OpenAIRE

    Eryol, Atahan

    2015-01-01

    This thesis investigates dimensionality reduction for analyzing the dynamics ofprotein simulations, particularly disordered proteins which do not fold into a xedshape but are thought to perform their functions through their movements. Ratherthan analyze the movement of the proteins in 3D space, we use dimensionalityreduction to project the molecular structure of the proteins into a target space inwhich each structure is represented as a point. All that is needed to do this arethe pairwise dis...

  4. Protein Sequencing with Tandem Mass Spectrometry

    Science.gov (United States)

    Ziady, Assem G.; Kinter, Michael

    The recent introduction of electrospray ionization techniques that are suitable for peptides and whole proteins has allowed for the design of mass spectrometric protocols that provide accurate sequence information for proteins. The advantages gained by these approaches over traditional Edman Degradation sequencing include faster analysis and femtomole, sometimes attomole, sensitivity. The ability to efficiently identify proteins has allowed investigators to conduct studies on their differential expression or modification in response to various treatments or disease states. In this chapter, we discuss the use of electrospray tandem mass spectrometry, a technique whereby protein-derived peptides are subjected to fragmentation in the gas phase, revealing sequence information for the protein. This powerful technique has been instrumental for the study of proteins and markers associated with various disorders, including heart disease, cancer, and cystic fibrosis. We use the study of protein expression in cystic fibrosis as an example.

  5. Molecular mechanisms of spatial protein quality control.

    Science.gov (United States)

    Alberti, Simon

    2012-01-01

    Evidence is now accumulating that damaged proteins are not randomly distributed but often concentrated in microscopically visible and functionally distinct inclusion bodies. How misfolded proteins are organized into these compartments, however, is still unknown. We have recently begun to investigate stress-inducible protein quality control (PQC) bodies in yeast cells. Surprisingly, we found that protein misfolding and aggregation were not sufficient to trigger body formation under mild heat stress conditions. Rather, compartment assembly also required the concerted action of molecular chaperones, protein-sorting factors and protein-sequestration factors, thus defining a minimal machinery for spatial PQC. Expression of this machinery was limited to times of acute stress through rapid changes in mRNA abundance and a proteasomal feedback mechanism. These findings demonstrate that yeast cells can control the amount of soluble misfolded proteins through regulated phase transitions in the cytoplasm, thus allowing them to rapidly adapt to changing environmental conditions.

  6. Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation

    Directory of Open Access Journals (Sweden)

    Wang Yong

    2011-10-01

    Full Text Available Abstract Background With the development of genome-sequencing technologies, protein sequences are readily obtained by translating the measured mRNAs. Therefore predicting protein-protein interactions from the sequences is of great demand. The reason lies in the fact that identifying protein-protein interactions is becoming a bottleneck for eventually understanding the functions of proteins, especially for those organisms barely characterized. Although a few methods have been proposed, the converse problem, if the features used extract sufficient and unbiased information from protein sequences, is almost untouched. Results In this study, we interrogate this problem theoretically by an optimization scheme. Motivated by the theoretical investigation, we find novel encoding methods for both protein sequences and protein pairs. Our new methods exploit sufficiently the information of protein sequences and reduce artificial bias and computational cost. Thus, it significantly outperforms the available methods regarding sensitivity, specificity, precision, and recall with cross-validation evaluation and reaches ~80% and ~90% accuracy in Escherichia coli and Saccharomyces cerevisiae respectively. Our findings here hold important implication for other sequence-based prediction tasks because representation of biological sequence is always the first step in computational biology. Conclusions By considering the converse problem, we propose new representation methods for both protein sequences and protein pairs. The results show that our method significantly improves the accuracy of protein-protein interaction predictions.

  7. Protein surface shielding agents in protein crystallization

    International Nuclear Information System (INIS)

    Hašek, J.

    2011-01-01

    The crystallization process can be controlled by protein surface shielding agents blocking undesirable competitive adhesion modes during non-equilibrium processes of deposition of protein molecules on the surface of growing crystalline blocks. The hypothesis is based on a number of experimental proofs from diffraction experiments and also retrieved from the Protein Data Bank. The molecules adhering temporarily on the surface of protein molecules change the propensity of protein molecules to deposit on the crystal surface in a definite position and orientation. The concepts of competitive adhesion modes and protein surface shielding agents acting on the surface of molecules in a non-equilibrium process of protein crystallization provide a useful platform for the control of crystallization. The desirable goal, i.e. a transient preference of a single dominating adhesion mode between protein molecules during crystallization, leads to uniform deposition of proteins in a crystal. This condition is the most important factor for diffraction quality and thus also for the accuracy of protein structure determination. The presented hypothesis is a generalization of the experimentally well proven behaviour of hydrophilic polymers on the surface of protein molecules of other compounds

  8. Non-food applications of Jatropha protein

    NARCIS (Netherlands)

    Lestari, D.

    2012-01-01

    The aim of this thesis is to explore how to gain more value per hectare Jatropha curcas by utilizing Jatropha protein for various applications. Specifically, this research investigated the extractability and functional properties of Jatropha protein for non-food/technical applications. Jatropha

  9. Fibril assembly in whey protein mixtures

    NARCIS (Netherlands)

    Bolder, S.G.

    2007-01-01

    The objective of this thesis was to study fibril assembly in mixtures of whey proteins. The effect of the composition of the protein mixture on the structures and the resulting phase behaviour was investigated. The current work has shown that beta-lactoglobulin is responsible for the fibril assembly

  10. Regulatory protein modification: techniques and protocols

    National Research Council Canada - National Science Library

    Hemmings, Hugh C

    1997-01-01

    ... important roles in cellular regulation. The techniques used to analyze various forms of posttranslational protein modification are described, along with current protocols, discussion of the methodological limitations, and relevant examples from recent publications. This collection should be of use to investigators of protein modification who work i...

  11. Origins of Protein Functions in Cells

    Science.gov (United States)

    Seelig, Burchard; Pohorille, Andrzej

    2011-01-01

    In modern organisms proteins perform a majority of cellular functions, such as chemical catalysis, energy transduction and transport of material across cell walls. Although great strides have been made towards understanding protein evolution, a meaningful extrapolation from contemporary proteins to their earliest ancestors is virtually impossible. In an alternative approach, the origin of water-soluble proteins was probed through the synthesis and in vitro evolution of very large libraries of random amino acid sequences. In combination with computer modeling and simulations, these experiments allow us to address a number of fundamental questions about the origins of proteins. Can functionality emerge from random sequences of proteins? How did the initial repertoire of functional proteins diversify to facilitate new functions? Did this diversification proceed primarily through drawing novel functionalities from random sequences or through evolution of already existing proto-enzymes? Did protein evolution start from a pool of proteins defined by a frozen accident and other collections of proteins could start a different evolutionary pathway? Although we do not have definitive answers to these questions yet, important clues have been uncovered. In one example (Keefe and Szostak, 2001), novel ATP binding proteins were identified that appear to be unrelated in both sequence and structure to any known ATP binding proteins. One of these proteins was subsequently redesigned computationally to bind GTP through introducing several mutations that introduce targeted structural changes to the protein, improve its binding to guanine and prevent water from accessing the active center. This study facilitates further investigations of individual evolutionary steps that lead to a change of function in primordial proteins. In a second study (Seelig and Szostak, 2007), novel enzymes were generated that can join two pieces of RNA in a reaction for which no natural enzymes are known

  12. Nanotechnologies in protein microarrays.

    Science.gov (United States)

    Krizkova, Sona; Heger, Zbynek; Zalewska, Marta; Moulick, Amitava; Adam, Vojtech; Kizek, Rene

    2015-01-01

    Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.

  13. Self-assembling peptide and protein nanodiscs for studies of membrane proteins

    DEFF Research Database (Denmark)

    Midtgaard, Søren Roi

    investigations of membrane proteins by traditional X-ray crystallography have proved a difficult challenge, and a surprisingly small amount of membrane proteins has been crystalized so far. This implies that development of lipoproteins as a platform for studying membrane proteins is much needed. In this thesis......Particles containing both lipids and proteins (so-called lipoproteins) are vital to study. They are selfassembling particles that, in the human body, are responsible for the transport of lipids and cholesterol. Due to the increasing problems of obesity and related illnesses in the world, obtaining...... for working with lipoprotein particles are their potential in the study membrane proteins. Membrane proteins are responsible for most of the transport in and out of cells and signaling between cells. As an example G-protein coupled receptors, a class of membrane proteins, are the third largest class...

  14. Viscosity Analysis of Dual Variable Domain Immunoglobulin Protein Solutions: Role of Size, Electroviscous Effect and Protein-Protein Interactions.

    Science.gov (United States)

    Raut, Ashlesha S; Kalonia, Devendra S

    2016-01-01

    Increased solution viscosity results in difficulties in manufacturing and delivery of therapeutic protein formulations, increasing both the time and production costs, and leading to patient inconvenience. The solution viscosity is affected by the molecular properties of both the solute and the solvent. The purpose of this work was to investigate the effect of size, charge and protein-protein interactions on the viscosity of Dual Variable Domain Immunoglobulin (DVD-Ig(TM)) protein solutions. The effect of size of the protein molecule on solution viscosity was investigated by measuring intrinsic viscosity and excluded volume calculations for monoclonal antibody (mAb) and DVD-Ig(TM) protein solutions. The role of the electrostatic charge resulting in electroviscous effects for DVD-Ig(TM) protein was assessed by measuring zeta potential. Light scattering measurements were performed to detect protein-protein interactions affecting solution viscosity. DVD-Ig(TM) protein exhibited significantly higher viscosity compared to mAb. Intrinsic viscosity and excluded volume calculations indicated that the size of the molecule affects viscosity significantly at higher concentrations, while the effect was minimal at intermediate concentrations. Electroviscous contribution to the viscosity of DVD-Ig(TM) protein varied depending on the presence or absence of ions in the solution. In buffered solutions, negative k D and B 2 values indicated the presence of attractive interactions which resulted in high viscosity for DVD-Ig(TM) protein at certain pH and ionic strength conditions. Results show that more than one factor contributes to the increased viscosity of DVD-Ig(TM) protein and interplay of these factors modulates the overall viscosity behavior of the solution, especially at higher concentrations.

  15. Stretching of macromolecules and proteins

    International Nuclear Information System (INIS)

    Strick, T R; Dessinges, M-N; Charvin, G; Dekker, N H; Allemand, J-F; Bensimon, D; Croquette, V

    2003-01-01

    In this paper we review the biophysics revealed by stretching single biopolymers. During the last decade various techniques have emerged allowing micromanipulation of single molecules and simultaneous measurements of their elasticity. Using such techniques, it has been possible to investigate some of the interactions playing a role in biology. We shall first review the simplest case of a non-interacting polymer and then present the structural transitions in DNA, RNA and proteins that have been studied by single-molecule techniques. We shall explain how these techniques permit a new approach to the protein folding/unfolding transition

  16. Protein sequence comparison and protein evolution

    Energy Technology Data Exchange (ETDEWEB)

    Pearson, W.R. [Univ. of Virginia, Charlottesville, VA (United States). Dept. of Biochemistry

    1995-12-31

    This tutorial was one of eight tutorials selected to be presented at the Third International Conference on Intelligent Systems for Molecular Biology which was held in the United Kingdom from July 16 to 19, 1995. This tutorial examines how the information conserved during the evolution of a protein molecule can be used to infer reliably homology, and thus a shared proteinfold and possibly a shared active site or function. The authors start by reviewing a geological/evolutionary time scale. Next they look at the evolution of several protein families. During the tutorial, these families will be used to demonstrate that homologous protein ancestry can be inferred with confidence. They also examine different modes of protein evolution and consider some hypotheses that have been presented to explain the very earliest events in protein evolution. The next part of the tutorial will examine the technical aspects of protein sequence comparison. Both optimal and heuristic algorithms and their associated parameters that are used to characterize protein sequence similarities are discussed. Perhaps more importantly, they survey the statistics of local similarity scores, and how these statistics can both be used to improve the selectivity of a search and to evaluate the significance of a match. They them examine distantly related members of three protein families, the serine proteases, the glutathione transferases, and the G-protein-coupled receptors (GCRs). Finally, the discuss how sequence similarity can be used to examine internal repeated or mosaic structures in proteins.

  17. Novel methods for tendon investigations

    DEFF Research Database (Denmark)

    Kjær, Michael; Langberg, Henning; Bojsen-Møller, J.

    2008-01-01

    Purpose. Tendon structures have been studied for decades, but over the last decade, methodological development and renewed interest for metabolic, circulatory and tissue protein turnover in tendon tissue has resulted in a rising amount of investigations. Method. This paper will detail the various...... modern investigative techniques available to study tendons. Results. There are a variety of investigative methods available to study the correlations between mechanics and biology in tendons. Conclusion. The available methodologies not only allow for potential insight into physiological...... and pathophysiological mechanisms in tendon tissue, but also, to some extent, allow for more elaborate studies of the intact human tendon. Read More: http://informahealthcare.com/doi/full/10.1080/09638280701785403...

  18. Green Fluorescent Protein as a protein localization and topological reporter in mycobacteria.

    Science.gov (United States)

    Belardinelli, Juan Manuel; Jackson, Mary

    2017-07-01

    The cell envelope-associated proteins of Mycobacterium species play critical functions in the physiology and pathogenicity of these microorganisms. Because the determination of their subcellular localization and transmembrane topology is often critical to the understanding of their function, we investigated whether the Green Fluorescent Protein (GFP) could be used as a reporter to probe protein localization and map the topology of inner membrane proteins directly in intact mycobacterial cells. To this end, two GFP-based mycobacterial reporter plasmids were engineered and their functionality validated using a variety of membrane-associated, exported and cytosolic proteins. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Evaluation of bottlenecks in the late stages of protein secretion in Bacillus subtilis

    NARCIS (Netherlands)

    Bolhuis, A; Tjalsma, H; Smith, H.E; Meima, R.; Venema, G; Bron, S; van Dijl, J.M

    Despite a high capacity for secretion of homologous proteins, the secretion of heterologous proteins by Bacillus subtilis is frequently inefficient. In the present studies, we have investigated and compared bottlenecks in the secretion of four heterologous proteins: Bacillus lichenifomis

  20. Protein digestion in ruminants

    African Journals Online (AJOL)

    digestibility, or the contribution of endogenous protein to the indigestible feed .... endogenous protein fractions. Alternatively, Stern & Satter (1984) suggested a method whereby the increased protein outflow to the small intestine, resulting from the incremental addition of ..... definition of the various protein fractions. Finally ...

  1. The Protein Model Portal

    OpenAIRE

    Arnold, Konstantin; Kiefer, Florian; Kopp, J?rgen; Battey, James N. D.; Podvinec, Michael; Westbrook, John D.; Berman, Helen M.; Bordoli, Lorenza; Schwede, Torsten

    2008-01-01

    Structural Genomics has been successful in determining the structures of many unique proteins in a high throughput manner. Still, the number of known protein sequences is much larger than the number of experimentally solved protein structures. Homology (or comparative) modeling methods make use of experimental protein structures to build models for evolutionary related proteins. Thereby, experimental structure determination efforts and homology modeling complement each other in the exploratio...

  2. Photoswitchable cyan fluorescent protein for protein tracking.

    Science.gov (United States)

    Chudakov, Dmitriy M; Verkhusha, Vladislav V; Staroverov, Dmitry B; Souslova, Ekaterina A; Lukyanov, Sergey; Lukyanov, Konstantin A

    2004-11-01

    In recent years diverse photolabeling techniques using green fluorescent protein (GFP)-like proteins have been reported, including photoactivatable PA-GFP, photoactivatable protein Kaede, the DsRed 'greening' technique and kindling fluorescent proteins. So far, only PA-GFP, which is monomeric and gives 100-fold fluorescence contrast, could be applied for protein tracking. Here we describe a dual-color monomeric protein, photoswitchable cyan fluorescent protein (PS-CFP). PS-CFP is capable of efficient photoconversion from cyan to green, changing both its excitation and emission spectra in response to 405-nm light irradiation. Complete photoactivation of PS-CFP results in a 1,500-fold increase in the green-to-cyan fluorescence ratio, making it the highest-contrast monomeric photoactivatable fluorescent protein described to date. We used PS-CFP as a photoswitchable tag to study trafficking of human dopamine transporter in living cells. At moderate excitation intensities, PS-CFP can be used as a pH-stable cyan label for protein tagging and fluorescence resonance energy transfer applications.

  3. Protein- protein interaction detection system using fluorescent protein microdomains

    Science.gov (United States)

    Waldo, Geoffrey S.; Cabantous, Stephanie

    2010-02-23

    The invention provides a protein labeling and interaction detection system based on engineered fragments of fluorescent and chromophoric proteins that require fused interacting polypeptides to drive the association of the fragments, and further are soluble and stable, and do not change the solubility of polypeptides to which they are fused. In one embodiment, a test protein X is fused to a sixteen amino acid fragment of GFP (.beta.-strand 10, amino acids 198-214), engineered to not perturb fusion protein solubility. A second test protein Y is fused to a sixteen amino acid fragment of GFP (.beta.-strand 11, amino acids 215-230), engineered to not perturb fusion protein solubility. When X and Y interact, they bring the GFP strands into proximity, and are detected by complementation with a third GFP fragment consisting of GFP amino acids 1-198 (strands 1-9). When GFP strands 10 and 11 are held together by interaction of protein X and Y, they spontaneous association with GFP strands 1-9, resulting in structural complementation, folding, and concomitant GFP fluorescence.

  4. Potential disruption of protein-protein interactions by graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Mei [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Kang, Hongsuk; Luan, Binquan [Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Yang, Zaixing [Institute of Quantitative Biology and Medicine, SRMP and RAD-X, and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123 (China); Zhou, Ruhong, E-mail: ruhong@us.ibm.com [Department of Physics, Institute of Quantitative Biology, Zhejiang University, Hangzhou 310027 (China); Computational Biological Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598 (United States); Department of Chemistry, Columbia University, New York, New York 10027 (United States)

    2016-06-14

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  5. Potential disruption of protein-protein interactions by graphene oxide

    International Nuclear Information System (INIS)

    Feng, Mei; Kang, Hongsuk; Luan, Binquan; Yang, Zaixing; Zhou, Ruhong

    2016-01-01

    Graphene oxide (GO) is a promising novel nanomaterial with a wide range of potential biomedical applications due to its many intriguing properties. However, very little research has been conducted to study its possible adverse effects on protein-protein interactions (and thus subsequent toxicity to human). Here, the potential cytotoxicity of GO is investigated at molecular level using large-scale, all-atom molecular dynamics simulations to explore the interaction mechanism between a protein dimer and a GO nanosheet oxidized at different levels. Our theoretical results reveal that GO nanosheet could intercalate between the two monomers of HIV-1 integrase dimer, disrupting the protein-protein interactions and eventually lead to dimer disassociation as graphene does [B. Luan et al., ACS Nano 9(1), 663 (2015)], albeit its insertion process is slower when compared with graphene due to the additional steric and attractive interactions. This study helps to better understand the toxicity of GO to cell functions which could shed light on how to improve its biocompatibility and biosafety for its wide potential biomedical applications.

  6. Relationship between protein stabilization and protein rigidification induced by mannosylglycerate.

    Science.gov (United States)

    Pais, Tiago M; Lamosa, Pedro; Garcia-Moreno, Bertrand; Turner, David L; Santos, Helena

    2009-11-27

    Understanding protein stabilization by small organic compounds is a topic of great practical importance. The effect of mannosylglycerate, a charged compatible solute typical of thermophilic microorganisms, on a variant of staphylococcal nuclease was investigated using several NMR spectroscopy methods. No structural changes were apparent from the chemical shifts of amide protons. Measurements of (15)N relaxation and model-free analysis, water-amide saturation transfer (phase-modulated CLEAN chemical exchange), and hydrogen/deuterium exchange rates provided a detailed picture of the effects of mannosylglycerate on the backbone dynamics and time-averaged structure of this protein. The widest movements of the protein backbone were significantly constrained in the presence of mannosylglycerate, as indicated by the average 5-fold decrease of the hydrogen/deuterium exchange rates, but the effect on the millisecond timescale was small. At high frequencies, internal motions of staphylococcal nuclease were progressively restricted with increasing concentrations of mannosylglycerate or reduced temperature, while the opposite effect was observed with urea (a destabilizing solute). The order parameters showed a strong correlation with the changes in the T(m) values induced by different solutes, determined by differential scanning calorimetry. These data show that mannosylglycerate caused a generalised reduction of backbone motions and demonstrate a correlation between protein stabilization and protein rigidification.

  7. Applying ion-molecule reactions to studies of gas-phase protein structure

    Energy Technology Data Exchange (ETDEWEB)

    Ogorzalek Loo, R.R.; Loo, J.A.; Smith, R.D.

    1992-06-01

    Whether solution phase differences in protein higher order structure persist in the gas phase, is examined by means of proton transfer reactions on ions generated by electrospray ionization of different solution conformations. Ion-molecule reactions were carried out in the atmosphere-vacuum interface of a quadrupole mass spectrometer with a Y-shaped capillary inlet-reactor. An amine (dimethyl-, trimethyl-, or diethyl-) were delivered to one inlet arm. Reactivities of bovine cytochrome c ions sprayed from denatured and native solutions were determined; the ions generated shifted to about the same charge states. Addition of equal amounts of amine to ions generated from different solution conformations of bovine ubiquitin also yielded similar final charge states; however, the average charge state increased with temperature. Myoglobin and apomyoglobin also yielded similar final charge states. The results suggest that for the non-disulfide linked proteins, either there are not significant differences in gas phase higher order structure, or proton transfer reactions are not sensitive enough to detect higher order structural differences arising from noncovalent interactions. 2 refs, 2 figs. (DLC)

  8. Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.

    Science.gov (United States)

    Gaines, J C; Acebes, S; Virrueta, A; Butler, M; Regan, L; O'Hern, C S

    2018-05-01

    We compare side chain prediction and packing of core and non-core regions of soluble proteins, protein-protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high-resolution crystal structures of these 3 protein classes. We show that the solvent-inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein-protein interfaces and in the membrane-exposed regions of transmembrane proteins can be predicted by the hard-sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent-inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within 30°) up to a relative solvent accessibility, rSASA≲0.3, for all 3 protein classes. Our results show that ≈40% of the interface regions in protein complexes are "core", that is, densely packed with side chain conformations that can be accurately predicted using the hard-sphere model. We propose packing fraction as a metric that can be used to distinguish real protein-protein interactions from designed, non-binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins. © 2018 Wiley Periodicals, Inc.

  9. Interactions between whey proteins and kaolinite surfaces

    International Nuclear Information System (INIS)

    Barral, S.; Villa-Garcia, M.A.; Rendueles, M.; Diaz, M.

    2008-01-01

    The nature of the interactions between whey proteins and kaolinite surfaces was investigated by adsorption-desorption experiments at room temperature, performed at the isoelectric point (IEP) of the proteins and at pH 7. It was found that kaolinite is a strong adsorbent for proteins, reaching the maximum adsorption capacity at the IEP of each protein. At pH 7.0, the retention capacity decreased considerably. The adsorption isotherms showed typical Langmuir characteristics. X-ray diffraction data for the protein-kaolinite complexes showed that protein molecules were not intercalated in the mineral structure, but immobilized at the external surfaces and the edges of the kaolinite. Fourier transform IR results indicate the absence of hydrogen bonding between kaolinite surfaces and the polypeptide chain. The adsorption patterns appear to be related to electrostatic interactions, although steric effects should be also considered

  10. Measurement of glutathione-protein mixed disulfides

    International Nuclear Information System (INIS)

    Livesey, J.C.; Reed, D.J.

    1984-01-01

    The development of a sensitive and highly specific assay for the presence of mixed disulfides between protein thiol groups and endogenous thiols has been undertaken. Previous investigations on the concentrations of glutathione (GSH), glutathione disulfide (GSSG) and protein glutathione mixed disulfides (ProSSG) have been of limited usefulness because of the poor specificity of the assays used. Our assay for these forms of glutathione is based on high performance liquid chromatography (HPLC) and is an extension of an earlier method. After perchloric acid precipitation, the protein sample is washed with an organic solvent to fully denature the protein. Up to a 10-fold increase in GSH released from fetal bovine serum (FBS) protein has been found when the protein precipitate is washed with ethanol rather than ether, as earlier suggested. Similar effects have been observed with an as yet unidentified thiol which elutes in the chromatography system with a retention volume similar to cysteine

  11. Hydration shells exchange charge with their protein

    DEFF Research Database (Denmark)

    Abitan, Haim; Lindgård, Per-Anker; Nielsen, Bjørn Gilbert

    2010-01-01

    . In our experiments, the amplitude of an ultrasonic pressure wave is gradually increased (0–20 atm) while we simultaneously measure the Raman spectra from the hydrated protein (β-lactoglobulin and lysozyme). We detected two types of spectral changes: first, up to 70% increase in the intensity......Investigation of the interaction between a protein and its hydration shells is an experimental and theoretical challenge. Here, we used ultrasonic pressure waves in aqueous solutions of a protein to explore the conformational states of the protein and its interaction with its hydration shells...... the presence of an ultrasonic pressure, a protein and its hydration shells are in thermodynamic and charge equilibrium, i.e. a protein and its hydration shells exchange charges. The ultrasonic wave disrupts these equilibria which are regained within 30–45 min after the ultrasonic pressure is shut off....

  12. Adhesion protein protocols [Methods in molecular biology, v. 96

    National Research Council Canada - National Science Library

    Dejana, Elisabetta; Corada, Monica

    1999-01-01

    "An international corps of expert investigators describe their optimized techniques for both the identification of new cell adhesion proteins and for the characterization of novel adhesive structures...

  13. IGSF9 Family Proteins

    DEFF Research Database (Denmark)

    Hansen, Maria; Walmod, Peter Schledermann

    2013-01-01

    The Drosophila protein Turtle and the vertebrate proteins immunoglobulin superfamily (IgSF), member 9 (IGSF9/Dasm1) and IGSF9B are members of an evolutionarily ancient protein family. A bioinformatics analysis of the protein family revealed that invertebrates contain only a single IGSF9 family gene......, whereas vertebrates contain two to four genes. In cnidarians, the gene appears to encode a secreted protein, but transmembrane isoforms of the protein have also evolved, and in many species, alternative splicing facilitates the expression of both transmembrane and secreted isoforms. In most species......, the longest isoforms of the proteins have the same general organization as the neural cell adhesion molecule family of cell adhesion molecule proteins, and like this family of proteins, IGSF9 family members are expressed in the nervous system. A review of the literature revealed that Drosophila Turtle...

  14. Prediction of Protein-Protein Interactions Related to Protein Complexes Based on Protein Interaction Networks

    Directory of Open Access Journals (Sweden)

    Peng Liu

    2015-01-01

    Full Text Available A method for predicting protein-protein interactions based on detected protein complexes is proposed to repair deficient interactions derived from high-throughput biological experiments. Protein complexes are pruned and decomposed into small parts based on the adaptive k-cores method to predict protein-protein interactions associated with the complexes. The proposed method is adaptive to protein complexes with different structure, number, and size of nodes in a protein-protein interaction network. Based on different complex sets detected by various algorithms, we can obtain different prediction sets of protein-protein interactions. The reliability of the predicted interaction sets is proved by using estimations with statistical tests and direct confirmation of the biological data. In comparison with the approaches which predict the interactions based on the cliques, the overlap of the predictions is small. Similarly, the overlaps among the predicted sets of interactions derived from various complex sets are also small. Thus, every predicted set of interactions may complement and improve the quality of the original network data. Meanwhile, the predictions from the proposed method replenish protein-protein interactions associated with protein complexes using only the network topology.

  15. Personalizing Protein Nourishment

    Science.gov (United States)

    DALLAS, DAVID C.; SANCTUARY, MEGAN R.; QU, YUNYAO; KHAJAVI, SHABNAM HAGHIGHAT; VAN ZANDT, ALEXANDRIA E.; DYANDRA, MELISSA; FRESE, STEVEN A.; BARILE, DANIELA; GERMAN, J. BRUCE

    2016-01-01

    Proteins are not equally digestible—their proteolytic susceptibility varies by their source and processing method. Incomplete digestion increases colonic microbial protein fermentation (putrefaction), which produces toxic metabolites that can induce inflammation in vitro and have been associated with inflammation in vivo. Individual humans differ in protein digestive capacity based on phenotypes, particularly disease states. To avoid putrefaction-induced intestinal inflammation, protein sources and processing methods must be tailored to the consumer’s digestive capacity. This review explores how food processing techniques alter protein digestibility and examines how physiological conditions alter digestive capacity. Possible solutions to improving digestive function or matching low digestive capacity with more digestible protein sources are explored. Beyond the ileal digestibility measurements of protein digestibility, less invasive, quicker and cheaper techniques for monitoring the extent of protein digestion and fermentation are needed to personalize protein nourishment. Biomarkers of protein digestive capacity and efficiency can be identified with the toolsets of peptidomics, metabolomics, microbial sequencing and multiplexed protein analysis of fecal and urine samples. By monitoring individual protein digestive function, the protein component of diets can be tailored via protein source and processing selection to match individual needs to minimize colonic putrefaction and, thus, optimize gut health. PMID:26713355

  16. SYMPOSIUM ON PLANT PROTEIN PHOSPHORYLATION

    Energy Technology Data Exchange (ETDEWEB)

    JOHN C WALKER

    2011-11-01

    Protein phosphorylation and dephosphorylation play key roles in many aspects of plant biology, including control of cell division, pathways of carbon and nitrogen metabolism, pattern formation, hormonal responses, and abiotic and biotic responses to environmental signals. A Symposium on Plant Protein Phosphorylation was hosted on the Columbia campus of the University of Missouri from May 26-28, 2010. The symposium provided an interdisciplinary venue at which scholars studying protein modification, as it relates to a broad range of biological questions and using a variety of plant species, presented their research. It also provided a forum where current international challenges in studies related to protein phosphorylation could be examined. The symposium also stimulated research collaborations through interactions and networking among those in the research community and engaged students and early career investigators in studying issues in plant biology from an interdisciplinary perspective. The proposed symposium, which drew 165 researchers from 13 countries and 21 States, facilitated a rapid dissemination of acquired knowledge and technical expertise regarding protein phosphorylation in plants to a broad range of plant biologists worldwide.

  17. Graphene Nanopores for Protein Sequencing

    Science.gov (United States)

    Wilson, James; Sloman, Leila; He, Zhiren

    2016-01-01

    An inexpensive, reliable method for protein sequencing is essential to unraveling the biological mechanisms governing cellular behavior and disease. Current protein sequencing methods suffer from limitations associated with the size of proteins that can be sequenced, the time, and the cost of the sequencing procedures. Here, we report the results of all-atom molecular dynamics simulations that investigated the feasibility of using graphene nanopores for protein sequencing. We focus our study on the biologically significant phenylalanine-glycine repeat peptides (FG-nups)—parts of the nuclear pore transport machinery. Surprisingly, we found FG-nups to behave similarly to single stranded DNA: the peptides adhere to graphene and exhibit step-wise translocation when subject to a transmembrane bias or a hydrostatic pressure gradient. Reducing the peptide’s charge density or increasing the peptide’s hydrophobicity was found to decrease the translocation speed. Yet, unidirectional and stepwise translocation driven by a transmembrane bias was observed even when the ratio of charged to hydrophobic amino acids was as low as 1:8. The nanopore transport of the peptides was found to produce stepwise modulations of the nanopore ionic current correlated with the type of amino acids present in the nanopore, suggesting that protein sequencing by measuring ionic current blockades may be possible. PMID:27746710

  18. Effector proteins of rust fungi.

    Science.gov (United States)

    Petre, Benjamin; Joly, David L; Duplessis, Sébastien

    2014-01-01

    Rust fungi include many species that are devastating crop pathogens. To develop resistant plants, a better understanding of rust virulence factors, or effector proteins, is needed. Thus far, only six rust effector proteins have been described: AvrP123, AvrP4, AvrL567, AvrM, RTP1, and PGTAUSPE-10-1. Although some are well established model proteins used to investigate mechanisms of immune receptor activation (avirulence activities) or entry into plant cells, how they work inside host tissues to promote fungal growth remains unknown. The genome sequences of four rust fungi (two Melampsoraceae and two Pucciniaceae) have been analyzed so far. Genome-wide analyses of these species, as well as transcriptomics performed on a broader range of rust fungi, revealed hundreds of small secreted proteins considered as rust candidate secreted effector proteins (CSEPs). The rust community now needs high-throughput approaches (effectoromics) to accelerate effector discovery/characterization and to better understand how they function in planta. However, this task is challenging due to the non-amenability of rust pathosystems (obligate biotrophs infecting crop plants) to traditional molecular genetic approaches mainly due to difficulties in culturing these species in vitro. The use of heterologous approaches should be promoted in the future.

  19. Fluorescence Studies of Protein Crystal Nucleation

    Science.gov (United States)

    Pusey, Marc; Sumida, John

    2000-01-01

    We have postulated that, in the case of tetragonal chicken egg white lysozyme, crystal growth occurs by the addition of pre-critical nuclei sized n-mers that form in the bulk solution, and that the n-mer growth units were multiples of the tetrameric 4(sub 3) helical structure. These have the strongest intermolecular bonds in the crystal and are therefore likely to be the first species formed. High resolution AFM studies provide strong supporting evidence for this model, but the data also suggest that the actual species in solution may not be identical in structure to that found in the crystal. We are using fluorescence resonance energy transfer (FRET) to study the initial solution phase self-assembly process, using covalent fluorescent derivatives which crystallize in the characteristic P4(sub 3)2(sub 1)2(sub 1) space group. FRET studies are being carried out between the cascade blue (CB-lys, donor, Ex(sub max) 366 nm, Em 420 nm) and lucifer yellow (LY-lys, acceptor, Ex(sub max) 430 nm, Em 528 nm) asp101 derivatives. The estimated R(sub 0) for this probe pair, the distance where 50% of the donor energy is transferred to the acceptor, is approx. 1.2 nm, compared to 2.2 nm between the side chain carboxyls of adjacent asp101's in the crystalline 4(sub 3) helix. The short donor lifetime of 2.80 ns (chi(sup 2) = 0.644), coupled with the large average distances between the molecules (greater than or equal to 50 nm) in solution, ensure that any energy transfer observed is not due to random diffusive interactions. Lifetime data show that CB-lys has a single lifetime when it is the only species in solution. Similarly, LY-lys also exhibits a single lifetime of 4.63 ns (chi(sup 2) = 0.42) when alone in solution. Addition of LY-lys to CB-lys results in the appearance of a third lifetime component of 0.348ns for the CB-lys. The fractional intensities of the different species present can be used to estimate the distribution of monomer and n-mers in solution. The self

  20. Evolvability of thermophilic proteins from archaea and bacteria.

    Science.gov (United States)

    Takano, Kazufumi; Aoi, Atsushi; Koga, Yuichi; Kanaya, Shigenori

    2013-07-16

    Proteins from thermophiles possess high thermostability. The stabilization mechanisms differ between archaeal and bacterial proteins, whereby archaeal proteins are mainly stabilized via hydrophobic interactions and bacterial proteins by ion pairs. High stability is an important factor in promoting protein evolution, but the precise means by which different stabilization mechanisms affect the evolution process remain unclear. In this study, we investigated a random mutational drift of esterases from thermophilic archaea and bacteria at high temperatures. Our results indicate that mutations in archaeal proteins lead to improved function with no loss of stability, while mutant bacterial proteins are largely destabilized with decreased activity at high temperatures. On the basis of these findings, we suggest that archaeal proteins possess higher "evolvability" than bacterial proteins under temperature selection and are additionally able to evolve into eukaryotic proteins.

  1. Functionalization of protein crystals with metal ions, complexes and nanoparticles.

    Science.gov (United States)

    Abe, Satoshi; Maity, Basudev; Ueno, Takafumi

    2018-04-01

    Self-assembled proteins have specific functions in biology. With inspiration provided by natural protein systems, several artificial protein assemblies have been constructed via site-specific mutations or metal coordination, which have important applications in catalysis, material and bio-supramolecular chemistry. Similar to natural protein assemblies, protein crystals have been recognized as protein assemblies formed of densely-packed monomeric proteins. Protein crystals can be functionalized with metal ions, metal complexes or nanoparticles via soaking, co-crystallization, creating new metal binding sites by site-specific mutations. The field of protein crystal engineering with metal coordination is relatively new and has gained considerable attention for developing solid biomaterials as well as structural investigations of enzymatic reactions, growth of nanoparticles and catalysis. This review highlights recent and significant research on functionalization of protein crystals with metal coordination and future prospects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  2. Identification and characterization of the surface proteins of Clostridium difficile

    Energy Technology Data Exchange (ETDEWEB)

    Dailey, D.C.

    1988-01-01

    Several clostridial proteins were detected on the clostridial cell surface by sensitive radioiodination techniques. Two major proteins and six minor proteins comprised the radioiodinated proteins on the clostridial cell surface. Cellular fractionation of surface radiolabeled C. difficile determined that the radioiodinated proteins were found in the cell wall fraction of C. difficile and surprisingly were also present in the clostridial membrane. Furthermore, an interesting phenomenon of disulfide-crosslinking of the cell surface proteins of C. difficile was observed. Disulfide-linked protein complexes were found in both the membrane and cell wall fractions. In addition, the cell surface proteins of C. difficile were found to be released into the culture medium. In attempts to further characterize the clostridial proteins recombinant DNA techniques were employed. In addition, the role of the clostridial cell surface proteins in the interactions of C. difficile with human PMNs was also investigated.

  3. Efficient protein production method for NMR using soluble protein tags with cold shock expression vector

    International Nuclear Information System (INIS)

    Hayashi, Kokoro; Kojima, Chojiro

    2010-01-01

    The E. coli protein expression system is one of the most useful methods employed for NMR sample preparation. However, the production of some recombinant proteins in E. coli is often hampered by difficulties such as low expression level and low solubility. To address these problems, a modified cold-shock expression system containing a glutathione S-transferase (GST) tag, the pCold-GST system, was investigated. The pCold-GST system successfully expressed 9 out of 10 proteins that otherwise could not be expressed using a conventional E. coli expression system. Here, we applied the pCold-GST system to 84 proteins and 78 proteins were successfully expressed in the soluble fraction. Three other cold-shock expression systems containing a maltose binding protein tag (pCold-MBP), protein G B1 domain tag (pCold-GB1) or thioredoxin tag (pCold-Trx) were also developed to improve the yield. Additionally, we show that a C-terminal proline tag, which is invisible in 1 H- 15 N HSQC spectra, inhibits protein degradation and increases the final yield of unstable proteins. The purified proteins were amenable to NMR analyses. These data suggest that pCold expression systems combined with soluble protein tags can be utilized to improve the expression and purification of various proteins for NMR analysis.

  4. Relationship between Molecular Structure Characteristics of Feed Proteins and Protein In vitro Digestibility and Solubility

    OpenAIRE

    Bai, Mingmei; Qin, Guixin; Sun, Zewei; Long, Guohui

    2015-01-01

    The nutritional value of feed proteins and their utilization by livestock are related not only to the chemical composition but also to the structure of feed proteins, but few studies thus far have investigated the relationship between the structure of feed proteins and their solubility as well as digestibility in monogastric animals. To address this question we analyzed soybean meal, fish meal, corn distiller’s dried grains with solubles, corn gluten meal, and feather meal by Fourier transfor...

  5. Engineering Globular Protein Vesicles through Tunable Self-Assembly of Recombinant Fusion Proteins.

    Science.gov (United States)

    Jang, Yeongseon; Choi, Won Tae; Heller, William T; Ke, Zunlong; Wright, Elizabeth R; Champion, Julie A

    2017-09-01

    Vesicles assembled from folded, globular proteins have potential for functions different from traditional lipid or polymeric vesicles. However, they also present challenges in understanding the assembly process and controlling vesicle properties. From detailed investigation of the assembly behavior of recombinant fusion proteins, this work reports a simple strategy to engineer protein vesicles containing functional, globular domains. This is achieved through tunable self-assembly of recombinant globular fusion proteins containing leucine zippers and elastin-like polypeptides. The fusion proteins form complexes in solution via high affinity binding of the zippers, and transition through dynamic coacervates to stable hollow vesicles upon warming. The thermal driving force, which can be tuned by protein concentration or temperature, controls both vesicle size and whether vesicles are single or bi-layered. These results provide critical information to engineer globular protein vesicles via self-assembly with desired size and membrane structure. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. Protein Crystal Recombinant Human Insulin

    Science.gov (United States)

    1994-01-01

    The comparison of protein crystal, Recombiant Human Insulin; space-grown (left) and earth-grown (right). On STS-60, Spacehab II indicated that space-grown crystals are larger and of greater optical clarity than their earth-grown counterparts. Recombiant Human Insulin facilitates the incorporation of glucose into cells. In diabetics, there is either a decrease in or complete lack of insulin, thereby leading to several harmful complications. Principal Investigator is Larry DeLucas.

  7. Polymer Directed Protein Assemblies

    Directory of Open Access Journals (Sweden)

    Patrick van Rijn

    2013-05-01

    Full Text Available Protein aggregation and protein self-assembly is an important occurrence in natural systems, and is in some form or other dictated by biopolymers. Very obvious influences of biopolymers on protein assemblies are, e.g., virus particles. Viruses are a multi-protein assembly of which the morphology is dictated by poly-nucleotides namely RNA or DNA. This “biopolymer” directs the proteins and imposes limitations on the structure like the length or diameter of the particle. Not only do these bionanoparticles use polymer-directed self-assembly, also processes like amyloid formation are in a way a result of directed protein assembly by partial unfolded/misfolded biopolymers namely, polypeptides. The combination of proteins and synthetic polymers, inspired by the natural processes, are therefore regarded as a highly promising area of research. Directed protein assembly is versatile with respect to the possible interactions which brings together the protein and polymer, e.g., electrostatic, v.d. Waals forces or covalent conjugation, and possible combinations are numerous due to the large amounts of different polymers and proteins available. The protein-polymer interacting behavior and overall morphology is envisioned to aid in clarifying protein-protein interactions and are thought to entail some interesting new functions and properties which will ultimately lead to novel bio-hybrid materials.

  8. Quantitative Protein And Fat Metabolism In West African Dwarf ...

    African Journals Online (AJOL)

    Quantitative Protein And Fat Metabolism In West African Dwarf Sheep Fed Margaritaria Discoidea As Supplement. ... Animal Research International ... Protein and energy utilization and quantitative retention of protein, fat and energy was investigated with twelve castrated Djallonke sheep averaging (20.0 ± 2.2kg BW) in ...

  9. Power Law Behavior of Structural Properties of Protein Gels

    NARCIS (Netherlands)

    Verheul, Marleen; Roefs, Sebastianus P.F.M.; Mellema, J.; Kruif, Kees G.

    1998-01-01

    Whey proteins are globular, heat-sensitive proteins. The gel structure, the formation of this structure, and the rheological properties of particulate whey protein isolate (WPI) gels have been investigated. On increasing the NaCl concentration, the permeability of the WPI gels increased, indicating

  10. Other Sources of Animal Protein in Ogun State, Nigeria | Taiwo ...

    African Journals Online (AJOL)

    Inadequate animal protein intake is widely orchestrated among Nigerians especially Ogun State indigenes. This led to investigating other sources of animal protein in the rural and suburban areas of the state that could bridge inadequate supply from the conventional sources of animal protein. Structured questionnaires ...

  11. Nonlinear deterministic structures and the randomness of protein sequences

    CERN Document Server

    Huang Yan Zhao

    2003-01-01

    To clarify the randomness of protein sequences, we make a detailed analysis of a set of typical protein sequences representing each structural classes by using nonlinear prediction method. No deterministic structures are found in these protein sequences and this implies that they behave as random sequences. We also give an explanation to the controversial results obtained in previous investigations.

  12. Interaction between Protein, Phytate, and Microbial Phytase. In Vitro Studies

    NARCIS (Netherlands)

    Kies, A.K.; Jonge, de L.H.; Kemme, P.A.; Jongbloed, A.W.

    2006-01-01

    The interaction between protein and phytate was investigated in vitro using proteins extracted from five common feedstuffs and from casein. The appearance of naturally present soluble protein-phytate complexes in the feedstuffs, the formation of complexes at different pHs, and the degradation of

  13. Digestibility of Protein in Common Carp ( Cyprinus carpio ) Fed ...

    African Journals Online (AJOL)

    The digestibility of dietary protein by carp, Cyprinus carpio fed for 10 weeks on different levels of chicken gut and duckweed incorporated into the diets was investigated. Growth, food conversion efficiency, protein efficiency ratio and apparent net protein utilization all improved with increase in the level of chicken gut in diet.

  14. Directed Supramolecular Surface Assembly of SNAP-tag Fusion Proteins

    NARCIS (Netherlands)

    Uhlenheuer, D.A.; Wasserberg, D.; Haase, C.; Nguyen, Hoang D.; Schenkel, J.H.; Huskens, Jurriaan; Ravoo, B.J.; Jonkheijm, Pascal; Brunsveld, Luc

    2012-01-01

    Supramolecular assembly of proteins on surfaces and vesicles was investigated by site-selective incorporation of a supramolecular guest element on proteins. Fluorescent proteins were site-selectively labeled with bisadamantane by SNAP-tag technology. The assembly of the bisadamantane functionalized

  15. Effect of Nutrient Formulations on Permeation of Proteins and Lipids ...

    African Journals Online (AJOL)

    Purpose: To investigate the effect of nutrient formulations on the permeation of proteins and lipids through porcine intestine in vitro. Method: In vitro permeation studies of proteins and lipids of two peptide-based formulations, composed of various compounds and sources of hydrolyzed protein was carried out, and compared ...

  16. Immobilization of ferrocene-modified SNAP-fusion proteins

    NARCIS (Netherlands)

    Wasserberg, D.; Uhlenheuer, D.; Neirynck, P.; Neirynck, Pauline; Cabanas Danés, Jordi; Schenkel, J.H.; Ravoo, B.J.; An, Q.; Huskens, Jurriaan; Milroy, L.G.; Brunsveld, Luc; Jonkheijm, Pascal

    2013-01-01

    The supramolecular assembly of proteins on surfaces has been investigated via the site-selective incorporation of a supramolecular moiety on proteins. To this end, fluorescent proteins have been site-selectively labeled with ferrocenes, as supramolecular guest moieties, via SNAP-tag technology. The

  17. Evaluation of yeast single cell protein (SCP) diets on growth ...

    African Journals Online (AJOL)

    Jane

    An investigation was carried out on the possibility of replacing fishmeal with graded levels of yeast single cell protein (SCP; 10, 20, 30, 40 and 50%) in isonitrogenous feed formulations (30% protein) in the diet of Oreochromis niloticus fingerlings for a period of 12 weeks. The control diet had fishmeal as the primary protein ...

  18. Multiple-Localization and Hub Proteins

    Science.gov (United States)

    Ota, Motonori; Gonja, Hideki; Koike, Ryotaro; Fukuchi, Satoshi

    2016-01-01

    Protein-protein interactions are fundamental for all biological phenomena, and protein-protein interaction networks provide a global view of the interactions. The hub proteins, with many interaction partners, play vital roles in the networks. We investigated the subcellular localizations of proteins in the human network, and found that the ones localized in multiple subcellular compartments, especially the nucleus/cytoplasm proteins (NCP), the cytoplasm/cell membrane proteins (CMP), and the nucleus/cytoplasm/cell membrane proteins (NCMP), tend to be hubs. Examinations of keywords suggested that among NCP, those related to post-translational modifications and transcription functions are the major contributors to the large number of interactions. These types of proteins are characterized by a multi-domain architecture and intrinsic disorder. A survey of the typical hub proteins with prominent numbers of interaction partners in the type revealed that most are either transcription factors or co-regulators involved in signaling pathways. They translocate from the cytoplasm to the nucleus, triggered by the phosphorylation and/or ubiquitination of intrinsically disordered regions. Among CMP and NCMP, the contributors to the numerous interactions are related to either kinase or ubiquitin ligase activity. Many of them reside on the cytoplasmic side of the cell membrane, and act as the upstream regulators of signaling pathways. Overall, these hub proteins function to transfer external signals to the nucleus, through the cell membrane and the cytoplasm. Our analysis suggests that multiple-localization is a crucial concept to characterize groups of hub proteins and their biological functions in cellular information processing. PMID:27285823

  19. Protein-peptide interactions in mixtures of whey peptides and whey proteins

    NARCIS (Netherlands)

    Creusot, N.; Gruppen, H.

    2007-01-01

    The effects of several conditions on the amounts and compositions of aggregates formed in mixtures of whey protein hydrolysate, made with Bacillus licheniformis protease, and whey protein isolate were investigated using response surface methodology. Next, the peptides present in the aggregates were

  20. A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling

    DEFF Research Database (Denmark)

    Blagoev, B.; Kratchmarova, I.; Ong, S.E.

    2003-01-01

    Mass spectrometry-based proteomics can reveal protein-protein interactions on a large scale, but it has been difficult to separate background binding from functionally important interactions and still preserve weak binders. To investigate the epidermal growth factor receptor (EGFR) pathway, we em...

  1. Using Superfolder Green Fluorescent Protein for Periplasmic Protein Localization Studies ▿

    OpenAIRE

    Dinh, Thuy; Bernhardt, Thomas G.

    2011-01-01

    Studies investigating the subcellular localization of periplasmic proteins have been hampered by problems with the export of green fluorescent protein (GFP). Here we show that a superfolding variant of GFP (sfGFP) is fluorescent following Sec-mediated transport and works best when the cotranslational branch of the pathway is employed.

  2. Structural dynamics of green fluorescent protein alone and fused with a single chain Fv protein

    NARCIS (Netherlands)

    Hink, M.A.; Griep, R.A.; Borst, J.W.; Hoek, van A.; Eppink, M.H.M.; Schots, A.; Visser, A.J.W.G.

    2000-01-01

    Structural information on intracellular fusions of the green fluorescent protein (GFP) of the jellyfish Aequorea victoria with endogenous proteins is required as they are increasingly used in cell biology and biochemistry. We have investigated the dynamic properties of GFP alone and fused to a

  3. Protein Data Bank (PDB)

    Data.gov (United States)

    U.S. Department of Health & Human Services — The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and...

  4. Protein electrophoresis - urine

    Science.gov (United States)

    ... medlineplus.gov/ency/article/003589.htm Urine protein electrophoresis test To use the sharing features on this page, please enable JavaScript. The urine protein electrophoresis (UPEP) test is used to estimate how much ...

  5. Protein electrophoresis - serum

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003540.htm Protein electrophoresis - serum To use the sharing features on ... JavaScript. This lab test measures the types of protein in the fluid (serum) part of a blood ...

  6. Impact of protein pre-treatment conditions on the iron encapsulation efficiency of whey protein cold-set gel particles

    NARCIS (Netherlands)

    Martin, A.H.; Jong, G.A.H. de

    2012-01-01

    This paper investigates the possibility for iron fortification of food using protein gel particles in which iron is entrapped using cold-set gelation. The aim is to optimize the iron encapsulation efficiency of whey protein by giving the whey protein different heat treatment prior to gelation with

  7. In vivo characterization of protein-protein interactions in the AP1 system with fluorescence correlation spectroscopy (FCS).

    NARCIS (Netherlands)

    N. Baudendistel (Nina); T.A. Knoch (Tobias); G. Müller (Gabriele); M. Wachsmuth (Malte); T. Weidemann (Thomas); W. Waldeck (Waldemar); J. Langowski (Jörg)

    2002-01-01

    textabstractThe aim of these studies is the quantitative investigation of protein-protein interactions in the AP1 system in vivo. First results of FCS measurements show an exchange in the nucleus of the proteins Fos-CFP and Jun-YFP in the stably mono-transfected HeLa-Cells. This is also shown by

  8. Extracting Tenebrio molitor protein while preventing browning: effect of pH and NaCl on protein yield

    NARCIS (Netherlands)

    Yi, L.; Boekel, van T.; Lakemond, C.M.M.

    2017-01-01

    The potential of insects as an alternative protein source for food applications was investigated by studying the effect of pH and NaCl on extraction yield of water-soluble proteins from Tenebrio molitor, while preventing browning due to polyphenol oxidation. Minimum protein solubility (29.6%) was at

  9. CSF total protein

    Science.gov (United States)

    CSF total protein is a test to determine the amount of protein in your spinal fluid, also called cerebrospinal fluid (CSF). ... The normal protein range varies from lab to lab, but is typically about 15 to 60 milligrams per deciliter (mg/dL) ...

  10. Segmental isotopic labeling by asparaginyl endopeptidase-mediated protein ligation.

    Science.gov (United States)

    Mikula, Kornelia M; Krumwiede, Luisa; Plückthun, Andreas; Iwaï, Hideo

    2018-03-13

    Segmental isotopic labeling can facilitate NMR studies of large proteins, multi-domain proteins, and proteins with repetitive sequences by alleviating NMR signal overlaps. Segmental isotopic labeling also allows us to investigate an individual domain in the context of a full-length protein by NMR. Several established methods are available for segmental isotopic labeling such as intein-mediated ligation, but each has specific requirements and limitations. Here, we report an enzymatic approach using bacterially produced asparagine endopeptidase from Oldenlandia affinis for segmental isotopic labeling of a protein with repetitive sequences, a designed armadillo repeat protein, by overcoming some of the shortcomings of enzymatic ligation for segmental isotopic labeling.

  11. In vitro binding of germanium to proteins of rice shoots

    International Nuclear Information System (INIS)

    Matsumoto, Hideaki; Takahashi, Eiichi

    1976-01-01

    The possibility of in vitro binding between proteins of rice shoots and germanium (Ge) was investigated. The proteins in mixtures of aqueous extracts of rice shoots and radioactive germanium ( 68 GeO 2 ) were fractionated. The binding of radioactivity to the proteins was observed even after 5 successive fractionation steps from the original mixtures. At the final fractionation step using polyacrylamide gel electrophoresis, a constant proportionality between protein concentration and associated radioactivity was found in most samples although not all. These results indicate that the binding of 68 Ge to proteins is not due to the simple adsorption by proteins. (auth.)

  12. Detergent-mediated protein aggregation.

    Science.gov (United States)

    Neale, Chris; Ghanei, Hamed; Holyoake, John; Bishop, Russell E; Privé, Gilbert G; Pomès, Régis

    2013-04-01

    Because detergents are commonly used to solvate membrane proteins for structural evaluation, much attention has been devoted to assessing the conformational bias imparted by detergent micelles in comparison to the native environment of the lipid bilayer. Here, we conduct six 500-ns simulations of a system with >600,000 atoms to investigate the spontaneous self assembly of dodecylphosphocholine detergent around multiple molecules of the integral membrane protein PagP. This detergent formed equatorial micelles in which acyl chains surround the protein's hydrophobic belt, confirming existing models of the detergent solvation of membrane proteins. In addition, unexpectedly, the extracellular and periplasmic apical surfaces of PagP interacted with the headgroups of detergents in other micelles 85 and 60% of the time, respectively, forming complexes that were stable for hundreds of nanoseconds. In some cases, an apical surface of one molecule of PagP interacted with an equatorial micelle surrounding another molecule of PagP. In other cases, the apical surfaces of two molecules of PagP simultaneously bound a neat detergent micelle. In these ways, detergents mediated the non-specific aggregation of folded PagP. These simulation results are consistent with dynamic light scattering experiments, which show that, at detergent concentrations ≥600 mM, PagP induces the formation of large scattering species that are likely to contain many copies of the PagP protein. Together, these simulation and experimental results point to a potentially generic mechanism of detergent-mediated protein aggregation. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  13. The protein-protein interaction-mediated inactivation of PTEN.

    Science.gov (United States)

    De Melo, J; He, L; Tang, D

    2014-01-01

    PTEN (Phosphatase and Tensin homologue deleted on chromosome 10, 10q23.3) is the dominant phosphatase responsible for the dephosphorylation of the 3-position phosphate from the inositol ring of phosphatidylinositol 3,4,5 triphosphate (PIP3), and thereby directly antagonizes the actions mediated by Phosphatidylinositol-3 Kinase (PI3K). PI3K functions in numerous pathways and cellular processes, including tumourigenesis. Therefore, mechanisms regulating PTEN function, either positively or negatively are of great interest not only to oncogenesis but also to other aspects of human health. Since its discovery in 1997, PTEN has been one of the most-heavily studied tumour suppressors and has been the subject of numerous reviews. Most investigations and reviews center on PTEN's function and its regulation. While the regulation of PTEN function via genetic and/or epigenetic mechanisms has been extensively studied, the impact of protein-protein interaction on PTEN function remains less clear. Recent research has revealed that PTEN can be specifically inhibited by its interaction with other proteins, which are collectively termed PTEN-negative regulators (PTENNRs). This review will summarize our current understanding on the protein network that influences PTEN function with a specific focus on PTEN-NRs.

  14. Telomere-binding proteins of Arabidopsis thaliana.

    Science.gov (United States)

    Zentgraf, U

    1995-02-01

    The nucleoprotein structure of Arabidopsis thaliana telomeres was investigated. A protein specifically binding to telomeric sequences was characterized by gel mobility shift assays with synthetic oligonucleotides consisting of four 7 bp telomeric repeats of Arabidopsis (TTTAGGG) and crude nuclear protein extracts of Arabidopsis leaves. These DNA-protein binding studies revealed that the binding affinity of this telomere-binding protein to the G-rich single-strand as well as to the double-stranded telomeric DNA is much higher than to the C-rich single-strand. The molecular mass of the protein was identified by SDS-PAGE to be 67 kDa. The isoelectric points were determined to be 5.0, 4.85 and 4.7, respectively, indicating that either one protein with different modifications or three slightly different proteins have been isolated. An RNA component, possibly serving as a template for reverse transcription of a plant telomerase, does not mediate the DNA-protein contact because the DNA-protein interactions were not RNAse-sensitive.

  15. Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

    Science.gov (United States)

    Merabet, Samir; Litim-Mecheri, Isma; Karlsson, Daniel; Dixit, Richa; Saadaoui, Mehdi; Monier, Bruno; Brun, Christine; Thor, Stefan; Vijayraghavan, K; Perrin, Laurent; Pradel, Jacques; Graba, Yacine

    2011-10-01

    Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA), we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

  16. Insights into Hox protein function from a large scale combinatorial analysis of protein domains.

    Directory of Open Access Journals (Sweden)

    Samir Merabet

    2011-10-01

    Full Text Available Protein function is encoded within protein sequence and protein domains. However, how protein domains cooperate within a protein to modulate overall activity and how this impacts functional diversification at the molecular and organism levels remains largely unaddressed. Focusing on three domains of the central class Drosophila Hox transcription factor AbdominalA (AbdA, we used combinatorial domain mutations and most known AbdA developmental functions as biological readouts to investigate how protein domains collectively shape protein activity. The results uncover redundancy, interactivity, and multifunctionality of protein domains as salient features underlying overall AbdA protein activity, providing means to apprehend functional diversity and accounting for the robustness of Hox-controlled developmental programs. Importantly, the results highlight context-dependency in protein domain usage and interaction, allowing major modifications in domains to be tolerated without general functional loss. The non-pleoitropic effect of domain mutation suggests that protein modification may contribute more broadly to molecular changes underlying morphological diversification during evolution, so far thought to rely largely on modification in gene cis-regulatory sequences.

  17. Determination of the protein quality of cooked Canadian pulses

    OpenAIRE

    Nosworthy, Matthew G.; Neufeld, Jason; Frohlich, Peter; Young, Gina; Malcolmson, Linda; House, James D.

    2017-01-01

    Abstract A study to determine the protein digestibility?corrected amino acid score and protein efficiency ratio of nine different cooked Canadian pulse classes was conducted in support of the establishment of protein quality claims in Canada and the United States. Split green and yellow pea, whole green lentil, split red lentil, Kabuli chickpea, navy bean, pinto bean, light red kidney bean, and black bean were investigated. Protein digestibility?corrected amino acid score (PDCAAS) and the pro...

  18. Protein sequence databases.

    Science.gov (United States)

    Apweiler, Rolf; Bairoch, Amos; Wu, Cathy H

    2004-02-01

    A variety of protein sequence databases exist, ranging from simple sequence repositories, which store data with little or no manual intervention in the creation of the records, to expertly curated universal databases that cover all species and in which the original sequence data are enhanced by the manual addition of further information in each sequence record. As the focus of researchers moves from the genome to the proteins encoded by it, these databases will play an even more important role as central comprehensive resources of protein information. Several the leading protein sequence databases are discussed here, with special emphasis on the databases now provided by the Universal Protein Knowledgebase (UniProt) consortium.

  19. Protein hydration and dynamics

    International Nuclear Information System (INIS)

    Nakagawa, Hiroshi; Kataoka, Mikio

    2015-01-01

    Inelastic neutron scattering can measure the protein thermal fluctuations under the physi